Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 8 of 18
Found at i:3241895 original size:33 final size:33
Alignment explanation
Indices: 3241845--3241929 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
3241835 AAATAAATTA
*
3241845 AAAT-AAAATATATAATATAAAAAA-TATATTAAAG
1 AAATGAAAATA-A-AATATAAAAAATTATAAT-AAG
* * *
3241879 AAATGAAAATAAAATATATAAGATTATAATAAT
1 AAATGAAAATAAAATATAAAAAATTATAATAAG
3241912 AAATGAAAATAAAATATA
1 AAATGAAAATAAAATATA
3241930 TGTCATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
33 29 0.64
34 10 0.22
35 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (33 bp):
AAATGAAAATAAAATATAAAAAATTATAATAAG
Found at i:3241996 original size:23 final size:23
Alignment explanation
Indices: 3241962--3242058 Score: 87
Period size: 21 Copynumber: 4.2 Consensus size: 23
3241952 ATGTGATATT
3241962 ATATAAA-A-ATTAATAATAAAA
1 ATATAAATATATTAATAATAAAA
* *
3241983 ATATAAATATATTAAAAAT-CAA
1 ATATAAATATATTAATAATAAAA
3242005 ATATAAAATATTATAATAATAAATAAAA
1 ATAT-AAATA-TAT--TAAT-AATAAAA
*
3242033 ATA-AAATATATT-ATATTAAAA
1 ATATAAATATATTAATAATAAAA
3242054 ATATA
1 ATATA
3242059 TTTAAGAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
21 16 0.26
22 10 0.16
23 14 0.23
24 3 0.05
25 3 0.05
26 8 0.13
27 3 0.05
28 5 0.08
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAAATATATTAATAATAAAA
Found at i:3242009 original size:22 final size:23
Alignment explanation
Indices: 3241962--3242035 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 23
3241952 ATGTGATATT
3241962 ATATAAA-A-ATTAATAATAA-AA
1 ATATAAATATATT-ATAATAATAA
3241983 ATATAAATATATTA-AA-AATCAA
1 ATATAAATATATTATAATAAT-AA
3242005 ATATAAA-ATATTATAATAATAA
1 ATATAAATATATTATAATAATAA
*
3242027 ATAAAAATA
1 ATATAAATA
3242036 AAATATATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
20 2 0.04
21 15 0.33
22 21 0.47
23 7 0.16
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (23 bp):
ATATAAATATATTATAATAATAA
Found at i:3242025 original size:113 final size:113
Alignment explanation
Indices: 3241884--3242111 Score: 354
Period size: 113 Copynumber: 2.0 Consensus size: 113
3241874 TAAAGAAATG
* *
3241884 AAAATAAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGT-CATTAAAAATATATT
1 AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATAT-TACATTAAAAATATATT
*
3241948 TAA-AATGTGATATTATATAAAAATTAATAAT-AAAAATATAAATATATTA
65 TAAGAA-ATGATATTATAT-AAAATTAATAATAAAAAATATAAATATATTA
* * *
3241997 AAAATCAAATATAAAATATTATAATAATAAATAAAAATAAAATATATTATATTAAAAATATATTT
1 AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATTACATTAAAAATATATTT
3242062 AAGAAATGATATTATATAAAATTAATAATAAAAAATATAAATATATTA
66 AAGAAATGATATTATATAAAATTAATAATAAAAAATATAAATATATTA
3242110 AA
1 AA
3242112 CTTATATTTT
Statistics
Matches: 106, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
112 13 0.12
113 91 0.86
114 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (113 bp):
AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATTACATTAAAAATATATTT
AAGAAATGATATTATATAAAATTAATAATAAAAAATATAAATATATTA
Found at i:3242043 original size:28 final size:27
Alignment explanation
Indices: 3241976--3242056 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 27
3241966 AAAAATTAAT
3241976 AATAAAAATAT-AAATA-TAT--TAAA
1 AATAAAAATATAAAATATTATAATAAA
*
3241999 AAT-CAAATATAAAATATTATAATAATA
1 AATAAAAATATAAAATATTATAATAA-A
*
3242026 AATAAAAATA-AAATATATTATATTAAA
1 AATAAAAATATAAA-ATATTATAATAAA
3242053 AATA
1 AATA
3242057 TATTTAAGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 6 0.12
23 8 0.17
24 3 0.06
26 3 0.06
27 12 0.25
28 16 0.33
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (27 bp):
AATAAAAATATAAAATATTATAATAAA
Found at i:3242278 original size:15 final size:15
Alignment explanation
Indices: 3242256--3242299 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
3242246 TGTTATTTTC
3242256 CCTGTAATCACATTA
1 CCTGTAATCACATTA
*
3242271 CTTGTAATCACATTA
1 CCTGTAATCACATTA
3242286 CCTGTAATCACATT
1 CCTGTAATCACATT
3242300 GCATCGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (15 bp):
CCTGTAATCACATTA
Found at i:3242491 original size:23 final size:22
Alignment explanation
Indices: 3242467--3242509 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3242457 CATGTTCTCT
3242467 TTTGAAACTTAATAAAATTCAC
1 TTTGAAACTTAATAAAATTCAC
* *
3242489 TTTGATATTTAATAAAATTCA
1 TTTGAAACTTAATAAAATTCA
3242510 ATATCTGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (22 bp):
TTTGAAACTTAATAAAATTCAC
Found at i:3243369 original size:21 final size:21
Alignment explanation
Indices: 3243322--3243369 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3243312 TAAAAGTTTC
3243322 AAAA-AAATTAATTAAGTTCA
1 AAAATAAATTAATTAAGTTCA
*
3243342 AAGATAAATTAATTAAG-TCTA
1 AAAATAAATTAATTAAGTTC-A
3243363 AAAATAA
1 AAAATAA
3243370 CACAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (21 bp):
AAAATAAATTAATTAAGTTCA
Found at i:3244077 original size:22 final size:22
Alignment explanation
Indices: 3244036--3244077 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3244026 TCAGTTCGAC
* *
3244036 TATAAAATATTAAATCTTTACT
1 TATAAAATATGAAATATTTACT
*
3244058 TATAAAATATGAATTATTTA
1 TATAAAATATGAAATATTTA
3244078 TGCATAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
TATAAAATATGAAATATTTACT
Found at i:3250218 original size:30 final size:28
Alignment explanation
Indices: 3250183--3250249 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
3250173 CGTGACAAAA
*
3250183 ATAAAAAAATAATTTTATTTTTAATTAATT
1 ATAAAAAAATAA-TTTAATTTT-ATTAATT
* **
3250213 TTAAAATTATAATTTAATTTTATTAATT
1 ATAAAAAAATAATTTAATTTTATTAATT
*
3250241 AAAAAAAAA
1 ATAAAAAAA
3250250 AAAAAAAAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
28 12 0.41
29 8 0.28
30 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAAAAAAATAATTTAATTTTATTAATT
Found at i:3250246 original size:28 final size:28
Alignment explanation
Indices: 3250184--3250247 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 28
3250174 GTGACAAAAA
*
3250184 TAAAAAAATAATTTTATTTTTAATTAATTT
1 TAAAAAAATAATTTTAATTTTAATTAA--T
**
3250214 TAAAATTATAA-TTTAATTTT-ATTAAT
1 TAAAAAAATAATTTTAATTTTAATTAAT
3250240 TAAAAAAA
1 TAAAAAAA
3250248 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 7 0.24
28 5 0.17
29 8 0.28
30 9 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAAAAAATAATTTTAATTTTAATTAAT
Found at i:3252549 original size:14 final size:13
Alignment explanation
Indices: 3252530--3252569 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
3252520 ATATCTAGAG
*
3252530 TTTTTTTTAAAGT
1 TTTTTTTTAAAAT
3252543 TTTTTTTTAAAATT
1 TTTTTTTTAAAA-T
3252557 TTATTTTTTAAAA
1 TT-TTTTTTAAAA
3252570 AAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 3 0.12
15 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTTTTTTAAAAT
Found at i:3252563 original size:16 final size:16
Alignment explanation
Indices: 3252544--3252590 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3252534 TTTTAAAGTT
3252544 TTTTTTTAAAATTTTA
1 TTTTTTTAAAATTTTA
* **
3252560 TTTTTTAAAAAAATTA
1 TTTTTTTAAAATTTTA
3252576 -TTTTTTAAAACTTTT
1 TTTTTTTAAAA-TTTT
3252591 CAAAAATCCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTTAAAATTTTA
Found at i:3257379 original size:107 final size:106
Alignment explanation
Indices: 3257260--3257737 Score: 419
Period size: 108 Copynumber: 4.5 Consensus size: 106
3257250 TCTCTCAGAC
* * * * * * **
3257260 CTTT-TTTTTCAAGACTTAAACTGGAGTTTCAGGTTATAATTTTAAATTATAGATGCAATTATTG
1 CTTTCTTTTTCAAGATTTAAACTGGAGTTTCATGTTATAATTTCAAGTTACAAATTTAATTATTG
* *
3257324 AAATATTTTTTATTTTTAGGTAAATATGCATAAATGTCTCAT
66 AAATAATTTTTATTTTTAGGTAAATATGCAT-AATTTCTCAT
* * * * *
3257366 CTTTCTTTTTCAAGATTTAAACCCGAAATTTCATGTTATAATTTCACGTTACAAATTTAATTCTT
1 CTTTCTTTTTCAAGATTTAAA-CTGGAGTTTCATGTTATAATTTCAAGTTACAAATTTAATTATT
* * *
3257431 GAAATAATTTTTATTTTTTAGATAAA-AGTGCGTAATTTCTTAT
65 GAAATAATTTTTA-TTTTTAGGTAAATA-TGCATAATTTCTCAT
* * * * * *
3257474 CATTCCTTTTCAAGATTTAAACTCGAGATTTTATATTATAATCTCAAGTTACAAATTTAATTATT
1 CTTTCTTTTTCAAGATTTAAACTGGAG-TTTCATGTTATAATTTCAAGTTACAAATTTAATTATT
*
3257539 AAAATAATTTTTATTTTTAGGTAAATATGCATAATTTCTCAT
65 GAAATAATTTTTATTTTTAGGTAAATATGCATAATTTCTCAT
* ** * * * * ** *
3257581 CATTCCATTTCTAA-CTTTAAACTCGAGATTTTATG-TACAATAACAAGTTACAAA-TTAATTAC
1 CTTTCTTTTTC-AAGATTTAAACTGGAG-TTTCATGTTATAATTTCAAGTTACAAATTTAATTAT
* ** *
3257643 TGAAATAATATTTATTTTTTAGGTAAATATGCATAATTTCAAAC
64 TGAAATAATTTTTA-TTTTTAGGTAAATATGCATAATTTCTCAT
* * * * * *
3257687 CATTC-CTTTCTGAGACTTAAACTCGAGATTTTATGTTATAATTTCAAGTTA
1 CTTTCTTTTTC-AAGATTTAAACTGGAG-TTTCATGTTATAATTTCAAGTTA
3257738 TAGATTAATT
Statistics
Matches: 310, Mismatches: 52, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
105 25 0.08
106 70 0.23
107 82 0.26
108 118 0.38
109 15 0.05
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (106 bp):
CTTTCTTTTTCAAGATTTAAACTGGAGTTTCATGTTATAATTTCAAGTTACAAATTTAATTATTG
AAATAATTTTTATTTTTAGGTAAATATGCATAATTTCTCAT
Found at i:3257404 original size:108 final size:107
Alignment explanation
Indices: 3257316--3257737 Score: 422
Period size: 108 Copynumber: 3.9 Consensus size: 107
3257306 TTATAGATGC
* *
3257316 AATTATTGAAATATTTTTTATTTTTAGGTAAATATGCATAAATGTCTCATCTTTCTTTTTCAAGA
1 AATTATTGAAATAATTTTTATTTTTAGGTAAATATGCAT-AATTTCTCATCTTTCTTTTTCAAGA
*
3257381 TTTAAACCCGAAATTTCATGTTATAATTTCACGTTACAAATTT
65 TTTAAACCCGAAATTTCATGTTATAATTTCAAGTTACAAATTT
* * * * * *
3257424 AATTCTTGAAATAATTTTTATTTTTTAGATAAA-AGTGCGTAATTTCTTATCATTCCTTTTCAAG
1 AATTATTGAAATAATTTTTA-TTTTTAGGTAAATA-TGCATAATTTCTCATCTTTCTTTTTCAAG
* * * * *
3257488 ATTTAAACTCGAGATTTTATATTATAATCTCAAGTTACAAATTT
64 ATTTAAACCCGAAATTTCATGTTATAATTTCAAGTTACAAATTT
* * ** *
3257532 AATTATTAAAATAATTTTTATTTTTAGGTAAATATGCATAATTTCTCATCATTCCATTTCTAA-C
1 AATTATTGAAATAATTTTTATTTTTAGGTAAATATGCATAATTTCTCATCTTTCTTTTTC-AAGA
* * * * **
3257596 TTTAAACTCGAGATTTTATG-TACAATAACAAGTTACAAA-TT
65 TTTAAACCCGAAATTTCATGTTATAATTTCAAGTTACAAATTT
* * ** * * * *
3257637 AATTACTGAAATAATATTTATTTTTTAGGTAAATATGCATAATTTCAAACCATTC-CTTTCTGAG
1 AATTATTGAAATAATTTTTA-TTTTTAGGTAAATATGCATAATTTCTCATCTTTCTTTTTC-AAG
* * * *
3257701 ACTTAAACTCGAGATTTTATGTTATAATTTCAAGTTA
64 ATTTAAACCCGAAATTTCATGTTATAATTTCAAGTTA
3257738 TAGATTAATT
Statistics
Matches: 269, Mismatches: 38, Indels: 15
0.84 0.12 0.05
Matches are distributed among these distances:
105 25 0.09
106 66 0.25
107 65 0.24
108 98 0.36
109 15 0.06
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (107 bp):
AATTATTGAAATAATTTTTATTTTTAGGTAAATATGCATAATTTCTCATCTTTCTTTTTCAAGAT
TTAAACCCGAAATTTCATGTTATAATTTCAAGTTACAAATTT
Found at i:3257709 original size:213 final size:216
Alignment explanation
Indices: 3257316--3257737 Score: 543
Period size: 213 Copynumber: 2.0 Consensus size: 216
3257306 TTATAGATGC
* * * **
3257316 AATTATTGAAATATTTTTTATTTTTAGGTAAATATGCATAAATGTCTCATCTTTCTTTTTCAAGA
1 AATTATTAAAATAATTTTTATTTTTAGGTAAATATGCATAAATGTCTCATCATTCCATTTCAAGA
* ** * *
3257381 TTTAAACCCGAAATTTCATGTTATAATTTCACGTTACAAATTTAATTCTTGAAATAATTTTTATT
66 TTTAAACCCGAAATTTCATGTTACAATAACAAGTTACAAATTTAATTCTTGAAATAATATTTATT
* ** * *
3257446 TTTTAGATAAAAGTGCGTAATTTCTTATCATTCCTTTTCAAGATTTAAACTCGAGATTTTATATT
131 TTTTAGATAAAAGTGCATAATTTCAAACCATTCCTTTTCAAGACTTAAACTCGAGATTTTATATT
3257511 ATAATCTCAAGTTACAAATTT
196 ATAATCTCAAGTTACAAATTT
*
3257532 AATTATTAAAATAATTTTTATTTTTAGGTAAATATGCAT-AATTTCTCATCATTCCATTTCTAA-
1 AATTATTAAAATAATTTTTATTTTTAGGTAAATATGCATAAATGTCTCATCATTCCATTTC-AAG
* * * *
3257595 CTTTAAACTCGAGATTTTATG-TACAATAACAAGTTACAAA-TTAATTAC-TGAAATAATATTTA
65 ATTTAAACCCGAAATTTCATGTTACAATAACAAGTTACAAATTTAATT-CTTGAAATAATATTTA
* *
3257657 TTTTTTAGGTAAATA-TGCATAATTTCAAACCATTCC-TTTCTGAGACTTAAACTCGAGATTTTA
129 TTTTTTAGATAAA-AGTGCATAATTTCAAACCATTCCTTTTC-AAGACTTAAACTCGAGATTTTA
* *
3257720 TGTTATAATTTCAAGTTA
192 TATTATAATCTCAAGTTA
3257738 TAGATTAATT
Statistics
Matches: 178, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
212 4 0.02
213 84 0.47
214 17 0.10
215 34 0.19
216 39 0.22
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (216 bp):
AATTATTAAAATAATTTTTATTTTTAGGTAAATATGCATAAATGTCTCATCATTCCATTTCAAGA
TTTAAACCCGAAATTTCATGTTACAATAACAAGTTACAAATTTAATTCTTGAAATAATATTTATT
TTTTAGATAAAAGTGCATAATTTCAAACCATTCCTTTTCAAGACTTAAACTCGAGATTTTATATT
ATAATCTCAAGTTACAAATTT
Found at i:3273698 original size:50 final size:49
Alignment explanation
Indices: 3273623--3273724 Score: 186
Period size: 50 Copynumber: 2.1 Consensus size: 49
3273613 CTTACCTCTT
3273623 AACCTCCTATTTATACTAAATTATAGTACTTTCTTAAAAGTAGTTAGGAG
1 AACCTCCTATTTATACTAAATTATAGTACTTT-TTAAAAGTAGTTAGGAG
*
3273673 AACCTCCTATTTATACTAAATTATAGTACTTTTTTAAAGTAGTTAGGAG
1 AACCTCCTATTTATACTAAATTATAGTACTTTTTAAAAGTAGTTAGGAG
3273722 AAC
1 AAC
3273725 ATGTTTAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 19 0.37
50 32 0.63
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (49 bp):
AACCTCCTATTTATACTAAATTATAGTACTTTTTAAAAGTAGTTAGGAG
Found at i:3275704 original size:16 final size:15
Alignment explanation
Indices: 3275683--3275712 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3275673 CTCATATGTC
3275683 TGTAAAATCAAGAAGA
1 TGTAAAATC-AGAAGA
3275699 TGTAAAATCAGAAG
1 TGTAAAATCAGAAG
3275713 CCAGTATGAA
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:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (15 bp):
TGTAAAATCAGAAGA
Found at i:3286583 original size:3 final size:3
Alignment explanation
Indices: 3286575--3286617 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3286565 TCAAACGATG
3286575 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3286618 ATGTCTACGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3289205 original size:2 final size:2
Alignment explanation
Indices: 3289198--3289227 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3289188 ATAAAACGTG
3289198 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3289228 GCATAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3294831 original size:33 final size:34
Alignment explanation
Indices: 3294789--3294852 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
3294779 TGTTTTGTTT
3294789 TGGATTTCTTGTCTTTTTGTAGTT-AACAAAATA
1 TGGATTTCTTGTCTTTTTGTAGTTAAACAAAATA
*
3294822 TGGATTTCTTGTCTTTTTGTTGTTAAACAAA
1 TGGATTTCTTGTCTTTTTGTAGTTAAACAAA
3294853 GTAACAAACG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 23 0.79
34 6 0.21
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (34 bp):
TGGATTTCTTGTCTTTTTGTAGTTAAACAAAATA
Found at i:3298721 original size:15 final size:17
Alignment explanation
Indices: 3298688--3298722 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3298678 AACTATTGAA
3298688 TGAAAACAGAAAGAAAT
1 TGAAAACAGAAAGAAAT
3298705 TGAAAACA-AAA-AAAT
1 TGAAAACAGAAAGAAAT
3298720 TGA
1 TGA
3298723 GCCAAGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.66, C:0.06, G:0.14, T:0.14
Consensus pattern (17 bp):
TGAAAACAGAAAGAAAT
Found at i:3305029 original size:15 final size:15
Alignment explanation
Indices: 3305009--3305056 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
3304999 ATTTCTCTTT
3305009 AAAAGAGTTCCCTCC
1 AAAAGAGTTCCCTCC
*
3305024 AAAAGAGTTTCCTCC
1 AAAAGAGTTCCCTCC
* *
3305039 AAAATAATTCCCTCC
1 AAAAGAGTTCCCTCC
3305054 AAA
1 AAA
3305057 CATTTTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.40, C:0.29, G:0.08, T:0.23
Consensus pattern (15 bp):
AAAAGAGTTCCCTCC
Found at i:3308044 original size:87 final size:88
Alignment explanation
Indices: 3307883--3308045 Score: 267
Period size: 87 Copynumber: 1.8 Consensus size: 88
3307873 GGATAAATAC
*
3307883 AATGTTGCAAGCATCAATTACAAACTACAATTTATAAACCCAAACAAATAATCTAATTACAAACT
1 AATGTTGCAAGCATCAATTACAAACTACAAATTATAAACCC--ACAAATAATCTAATTACAAACT
3307948 ACAATTTATAAAATATTGCAAACAT
64 ACAATTTATAAAATATTGCAAACAT
*
3307973 AATGTTGCAAGCATCAATTACAAACTACAAAATTATAAA-CC-CAAATAATCTTATTACAAACTA
1 AATGTTGCAAGCATCAATTACAAACTAC-AAATTATAAACCCACAAATAATCTAATTACAAACTA
3308036 CAATTTATAA
65 CAATTTATAA
3308046 TTATAAACCT
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
87 31 0.44
90 30 0.43
91 9 0.13
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.28
Consensus pattern (88 bp):
AATGTTGCAAGCATCAATTACAAACTACAAATTATAAACCCACAAATAATCTAATTACAAACTAC
AATTTATAAAATATTGCAAACAT
Found at i:3314252 original size:23 final size:24
Alignment explanation
Indices: 3314226--3314285 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
3314216 TTTATAAAAA
3314226 TTTAAATAAATTTT-TATTTTTAT
1 TTTAAATAAATTTTATATTTTTAT
3314249 TTT-AATAAAATTTTTATATTTTTAT
1 TTTAAAT-AAA-TTTTATATTTTTAT
3314274 TTTAAATTAAAT
1 TTTAAA-TAAAT
3314286 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 3 0.09
23 6 0.19
24 4 0.12
25 13 0.41
26 5 0.16
27 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTAAATAAATTTTATATTTTTAT
Found at i:3314290 original size:30 final size:31
Alignment explanation
Indices: 3314235--3314296 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3314225 ATTTAAATAA
* * *
3314235 ATTTTTATTTTTATTTTAATAAAATTTTTAT
1 ATTTTTATTTTAAATTAAATAAAATTTTTAT
3314266 ATTTTTATTTTAAATTAAAT-AAATTTTTAT
1 ATTTTTATTTTAAATTAAATAAAATTTTTAT
3314296 A
1 A
3314297 ATTAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
ATTTTTATTTTAAATTAAATAAAATTTTTAT
Found at i:3336737 original size:15 final size:15
Alignment explanation
Indices: 3336717--3336745 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3336707 ATTGTACATC
3336717 AAAAATATTATTTAA
1 AAAAATATTATTTAA
3336732 AAAAATATTATTTA
1 AAAAATATTATTTA
3336746 GATAAGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAATATTATTTAA
Found at i:3337022 original size:27 final size:27
Alignment explanation
Indices: 3336981--3337037 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3336971 TGTAACAAAC
* * *
3336981 TATATAATAATTATTTTATTTTATTTT
1 TATAAAATAACTATTTTATTCTATTTT
3337008 TATAAAATAACTATTTTATTCTATTTT
1 TATAAAATAACTATTTTATTCTATTTT
3337035 TAT
1 TAT
3337038 CTATTTCGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (27 bp):
TATAAAATAACTATTTTATTCTATTTT
Found at i:3337347 original size:30 final size:29
Alignment explanation
Indices: 3337313--3337381 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
3337303 CTACAAATAG
3337313 AAAATAAAAATAAAAAAGTATAAAGAAATT
1 AAAATAAAAATAAAAAA-TATAAAGAAATT
* * * *
3337343 AAAATTAAAATTAAAATATATTAATAAATT
1 AAAA-TAAAAATAAAAAATATAAAGAAATT
3337373 AATAATAAA
1 AA-AATAAA
3337382 TTATTGATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAATAAAAATAAAAAATATAAAGAAATT
Found at i:3342102 original size:2 final size:2
Alignment explanation
Indices: 3342095--3342129 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3342085 GCAGGGCTAC
* *
3342095 AT AT AT AT AT AT AT AT AC AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3342130 AGCATATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3344729 original size:23 final size:23
Alignment explanation
Indices: 3344703--3344748 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3344693 AATATCATTA
3344703 AAAAAATAAAATTAATTT-TAATT
1 AAAAAATAAAATT-ATTTATAATT
**
3344726 AAAATTTAAAATTATTTATAATT
1 AAAAAATAAAATTATTTATAATT
3344749 GTAGTAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAAATAAAATTATTTATAATT
Found at i:3351390 original size:23 final size:23
Alignment explanation
Indices: 3351347--3351391 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3351337 TATACTCTCA
*
3351347 ATTTCTCTCTCTCGCGTTTTTAG
1 ATTTCTCTCTCTCGCGCTTTTAG
*
3351370 ATTTCTCTTTC-CTGCGCTTTTA
1 ATTTCTCTCTCTC-GCGCTTTTA
3351392 AGATACCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.09, C:0.27, G:0.11, T:0.53
Consensus pattern (23 bp):
ATTTCTCTCTCTCGCGCTTTTAG
Found at i:3351812 original size:29 final size:29
Alignment explanation
Indices: 3351763--3351835 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
3351753 TATTAAAGTG
* *
3351763 TAATAA-AATA-TTTTTAAATATGGCGTA
1 TAATAATAATATTTTTTAAATATGACCTA
* *
3351790 TAATAATAATATTTTTTCAATATGACCTG
1 TAATAATAATATTTTTTAAATATGACCTA
*
3351819 TAATAATAATTTTTTTT
1 TAATAATAATATTTTTT
3351836 TTTCAATATG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.15
28 4 0.10
29 29 0.74
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (29 bp):
TAATAATAATATTTTTTAAATATGACCTA
Found at i:3351981 original size:45 final size:45
Alignment explanation
Indices: 3351876--3351990 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 45
3351866 GGCTTGTCAC
* * * ** *
3351876 ATATTTTTGTACATGAAATATAACAACCTAATTATGATGTGTTAT
1 ATATTTTTGTACATGGAATGTAATAACCTAACCATGATGTGTAAT
* * **
3351921 ATGTTTTTGTGCATGGTGTGTAATAACCTAACCATGATGTGTAAT
1 ATATTTTTGTACATGGAATGTAATAACCTAACCATGATGTGTAAT
*
3351966 ATATTTTTGTACATGGCATGTAATA
1 ATATTTTTGTACATGGAATGTAATA
3351991 TATTTTTGTA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (45 bp):
ATATTTTTGTACATGGAATGTAATAACCTAACCATGATGTGTAAT
Found at i:3351987 original size:24 final size:24
Alignment explanation
Indices: 3351960--3352012 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
3351950 AACCATGATG
*
3351960 TGTAATATATTTTTGTACATGGCA
1 TGTAATATATTTTTGTACATGACA
3351984 TGTAATATATTTTTGTACATGACA
1 TGTAATATATTTTTGTACATGACA
3352008 TGTAA
1 TGTAA
3352013 CAATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (24 bp):
TGTAATATATTTTTGTACATGACA
Found at i:3352084 original size:45 final size:45
Alignment explanation
Indices: 3351986--3352087 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
3351976 ACATGGCATG
* * * *
3351986 TAATATATTTTTGTACATGACATGTAACAATTTAACTATAGCGTG
1 TAATATATTTTTATACATGACATGTAACAATCTAACCATAGCGTA
* * *
3352031 TCACATATTTTTATACATGACATGTAACAATCTAACCAT-GATGTA
1 TAATATATTTTTATACATGACATGTAACAATCTAACCATAG-CGTA
3352076 TAATATATTTTT
1 TAATATATTTTT
3352088 GTATATGATA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (45 bp):
TAATATATTTTTATACATGACATGTAACAATCTAACCATAGCGTA
Found at i:3371457 original size:2 final size:2
Alignment explanation
Indices: 3371446--3371482 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3371436 TTCTTCTTCT
3371446 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3371483 CTGTTTCCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3376294 original size:7 final size:7
Alignment explanation
Indices: 3376282--3376309 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3376272 AATGGAGGGC
3376282 GCAGCAA
1 GCAGCAA
3376289 GCAGCAA
1 GCAGCAA
3376296 GCAGCAA
1 GCAGCAA
3376303 GCAGCAA
1 GCAGCAA
3376310 CGCCCTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.29, T:0.00
Consensus pattern (7 bp):
GCAGCAA
Found at i:3376537 original size:23 final size:23
Alignment explanation
Indices: 3376492--3376541 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3376482 TTTTTTATCA
**
3376492 TTATTTTTTAAAATTATTAAATT
1 TTATTTTTTAAAAAAATTAAATT
3376515 TTATTTTTTAAAAAAAATT-AATT
1 TTATTTTTT-AAAAAAATTAAATT
3376538 TTAT
1 TTAT
3376542 GTAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATTTTTTAAAAAAATTAAATT
Found at i:3377419 original size:27 final size:27
Alignment explanation
Indices: 3377356--3377412 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
3377346 TATAAAATGT
* *
3377356 TATAAATATATATAATTGTATAAATAT
1 TATATATATATATAATTGTATAAATAA
*
3377383 TATATATATATATAATT-TATACATAA
1 TATATATATATATAATTGTATAAATAA
3377409 -ATAT
1 TATAT
3377413 TACTATAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 7 0.26
27 16 0.59
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATATATATATATAATTGTATAAATAA
Found at i:3377789 original size:221 final size:207
Alignment explanation
Indices: 3377375--3377837 Score: 486
Period size: 208 Copynumber: 2.2 Consensus size: 207
3377365 ATATAATTGT
* * *
3377375 ATAA-ATATTATATATATATATAATTTATACATAAATATTACTATAACTTATAATAAATTTTATT
1 ATAATATATTATATATAT-T-TAATTTATTCATAAGTATTACTATAACTTATAATAAACTTTATT
** *
3377439 TATATGGTTACACTTAATAATTTTATTAATTATCACTTTAGTTTTTATAACATATTGTTTACTTA
64 TATATAATTACACTTAATAATTTTATTAATTATCACTTTAATTTTTATAACATATTGTTTACTTA
* * *
3377504 TTATTTATACAAACTTTAATATAAAACATTATGATATATAAGTTGTATCATTAATTTCATATATA
129 TTATTTATACAAACTTTAATATAAAACATTATAACATATAAATTGTATCATTAATTTCATATATA
*
3377569 TATATATA-TAATAA
194 TA-ATAAAGTAATAA
* * *
3377583 AGTAATATATTATATATATTTAATTTATTCATAAGTATTATTGTAACTTATAATAGACTTTATTT
1 A-TAATATATTATATATATTTAATTTATTCATAAGTATTACTATAACTTATAATAAACTTTATTT
* * *
3377648 ATATAATTATACTTAATAATTTTATTAGTTTTCA-TCTTAATTTTTATAACATATTGTTTNNNNN
65 ATATAATTACACTTAATAATTTTATTAATTATCACT-TTAATTTTTATAACATATTGTTT-----
**** * * *
3377712 NNNNNATTATTTATACAAATTTTGATATTAAAATTAAAATATTATAACATATAAATTGTTTCATT
124 -ACTTATTATTTATACAAACTTT-A-A-T---A-TAAAACATTATAACATATAAATTGTATCATT
*
3377777 AATTTCATATATATAATAAAGTAATAT
181 AATTTCATATATATAATAAAGTAATAA
* *
3377804 ATTATATA-TACATATATTTAATTTATAT-ATAAGT
1 ATAATATATTATATATATTTAATTTAT-TCATAAGT
3377838 TGTGTATTTT
Statistics
Matches: 211, Mismatches: 26, Indels: 25
0.81 0.10 0.10
Matches are distributed among these distances:
207 1 0.00
208 91 0.43
209 4 0.02
210 13 0.06
214 17 0.08
215 1 0.00
216 1 0.00
217 1 0.00
219 23 0.11
220 12 0.06
221 47 0.22
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.48
Consensus pattern (207 bp):
ATAATATATTATATATATTTAATTTATTCATAAGTATTACTATAACTTATAATAAACTTTATTTA
TATAATTACACTTAATAATTTTATTAATTATCACTTTAATTTTTATAACATATTGTTTACTTATT
ATTTATACAAACTTTAATATAAAACATTATAACATATAAATTGTATCATTAATTTCATATATATA
ATAAAGTAATAA
Found at i:3378201 original size:30 final size:29
Alignment explanation
Indices: 3378167--3378249 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 29
3378157 ATTATAAGAG
3378167 TTTATTTAATTCAAAATAAAAATATAAAAA
1 TTTATTTAATT-AAAATAAAAATATAAAAA
*
3378197 TTTATTTATATTAAAATATAAATATAAAAA
1 TTTATTTA-ATTAAAATAAAAATATAAAAA
* * *
3378227 TTTAATAAAATAAAATAAAAATA
1 TTTATTTAATTAAAATAAAAATA
3378250 ATTTATTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
29 13 0.28
30 31 0.66
31 3 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (29 bp):
TTTATTTAATTAAAATAAAAATATAAAAA
Found at i:3378235 original size:24 final size:24
Alignment explanation
Indices: 3378190--3378254 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
3378180 AAATAAAAAT
*
3378190 ATAAAAATTTATTTATATTAAAATATAA
1 ATAAAAA-TAATTTA-A-TAAAATA-AA
*
3378218 ATATAAA-AATTTAATAAAATAAA
1 ATAAAAATAATTTAATAAAATAAA
3378241 ATAAAAATAATTTA
1 ATAAAAATAATTTA
3378255 TTTAACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 8 0.24
24 13 0.39
25 1 0.03
26 5 0.15
28 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAAAATAATTTAATAAAATAAA
Found at i:3382491 original size:28 final size:29
Alignment explanation
Indices: 3382460--3382535 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
3382450 TTTTTTAAAA
*
3382460 ATTTAAATAAATATTTAT-TTTTTATTAT
1 ATTTAAATAAATTTTTATATTTTTATTAT
* * *
3382488 ATTTAATTAAGTTTTTATATTTTTATTTT
1 ATTTAAATAAATTTTTATATTTTTATTAT
*
3382517 ATATTATATAAATTTTTAT
1 AT-TTAAATAAATTTTTAT
3382536 GATTAACAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 15 0.38
29 11 0.28
30 13 0.33
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (29 bp):
ATTTAAATAAATTTTTATATTTTTATTAT
Found at i:3382671 original size:20 final size:20
Alignment explanation
Indices: 3382635--3382672 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3382625 GTGAATGATG
*
3382635 ACATGATTTATTGATGTGGT
1 ACATGATTGATTGATGTGGT
3382655 ACATGATATGATT-ATGTG
1 ACATGAT-TGATTGATGTG
3382673 ATTTTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (20 bp):
ACATGATTGATTGATGTGGT
Found at i:3385905 original size:2 final size:2
Alignment explanation
Indices: 3385898--3385927 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3385888 TTGAATTTAA
*
3385898 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3385928 TATTGATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3388347 original size:22 final size:22
Alignment explanation
Indices: 3388323--3388371 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
3388313 AATTTATATT
*
3388323 TTTTTAT-TTTACTTTTTAAAA
1 TTTTTATCTTTAATTTTTAAAA
3388344 -TTTTATCTTTAATTTTTAAAA
1 TTTTTATCTTTAATTTTTAAAA
*
3388365 ATTTTAT
1 TTTTTAT
3388372 AATTTCATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 13 0.52
22 6 0.24
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTATCTTTAATTTTTAAAA
Found at i:3388354 original size:21 final size:21
Alignment explanation
Indices: 3388324--3388371 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
3388314 ATTTATATTT
*
3388324 TTTTATTTTACTTTTT-AAAA
1 TTTTATTTTAATTTTTAAAAA
3388344 TTTTATCTTTAATTTTTAAAAA
1 TTTTAT-TTTAATTTTTAAAAA
3388366 TTTTAT
1 TTTTAT
3388372 AATTTCATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 9 0.36
22 10 0.40
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTTTAATTTTTAAAAA
Found at i:3388397 original size:30 final size:30
Alignment explanation
Indices: 3388363--3388419 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3388353 TAATTTTTAA
*
3388363 AAATTTTATAATTTCATCTCTTCAAATATC
1 AAATTTTATAATTTCATCTCCTCAAATATC
* *
3388393 AAATTTTTTATTTTCATCTCCTCAAAT
1 AAATTTTATAATTTCATCTCCTCAAAT
3388420 TTAAAATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (30 bp):
AAATTTTATAATTTCATCTCCTCAAATATC
Found at i:3399069 original size:23 final size:23
Alignment explanation
Indices: 3399033--3399077 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3399023 TTTTATATTT
3399033 TTAAATTTCTACTAATA-TTTTCG
1 TTAAATTTCTACT-ATACTTTTCG
3399056 TTAAATTT-TGACTATACTTTTC
1 TTAAATTTCT-ACTATACTTTTC
3399078 TAGCACATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (23 bp):
TTAAATTTCTACTATACTTTTCG
Found at i:3400174 original size:19 final size:17
Alignment explanation
Indices: 3400150--3400192 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3400140 TGCTAATAGG
3400150 AAAATAATTTATTGAAAGA
1 AAAATAATTTATT-AAA-A
3400169 AAAAT-ATTTATTAAAA
1 AAAATAATTTATTAAAA
*
3400185 AAATTAAT
1 AAAATAAT
3400193 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.23
17 5 0.23
18 7 0.32
19 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
AAAATAATTTATTAAAA
Found at i:3416933 original size:2 final size:2
Alignment explanation
Indices: 3416926--3416951 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3416916 TAATTTATGT
3416926 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3416952 AAGCTTGAGG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3422507 original size:2 final size:2
Alignment explanation
Indices: 3422500--3422525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3422490 TTATCAAAAC
3422500 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
3422526 ACGCCTCACC
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:3426477 original size:11 final size:11
Alignment explanation
Indices: 3426458--3426487 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3426448 TGTGGCATAT
3426458 ACATCATCATC
1 ACATCATCATC
*
3426469 ACATTATCATC
1 ACATCATCATC
3426480 ACATCATC
1 ACATCATC
3426488 CACTGTTGCC
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:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (11 bp):
ACATCATCATC
Found at i:3427893 original size:12 final size:12
Alignment explanation
Indices: 3427876--3427901 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3427866 ATACACACAC
3427876 GTGTGTGTATGT
1 GTGTGTGTATGT
3427888 GTGTGTGTATGT
1 GTGTGTGTATGT
3427900 GT
1 GT
3427902 ACATATACGT
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:0.08, C:0.00, G:0.42, T:0.50
Consensus pattern (12 bp):
GTGTGTGTATGT
Found at i:3433109 original size:40 final size:41
Alignment explanation
Indices: 3433059--3433135 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
3433049 TGAAAGACAG
3433059 CAATCGTGGCAAGGTTAG-AAACCCCACTAAAGTGAATCAC
1 CAATCGTGGCAAGGTTAGAAAACCCCACTAAAGTGAATCAC
*
3433099 CAATCTTGGCAAGGTTAGAAAACCCCACTAAAGTGAA
1 CAATCGTGGCAAGGTTAGAAAACCCCACTAAAGTGAA
3433136 AAATAGCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 17 0.49
41 18 0.51
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
CAATCGTGGCAAGGTTAGAAAACCCCACTAAAGTGAATCAC
Found at i:3440914 original size:23 final size:22
Alignment explanation
Indices: 3440876--3440934 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
3440866 TTTTTATTTA
3440876 TTTA-TTATATATTTTTAAAAAGT
1 TTTATTTATATA-TTTT-AAAAGT
*
3440899 TTTATTTATATATTTTAAAATT
1 TTTATTTATATATTTTAAAAGT
3440921 TTTATTTATTATAT
1 TTTATTTA-TATAT
3440935 ATATATCGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 13 0.39
23 13 0.39
24 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTATTTATATATTTTAAAAGT
Found at i:3441078 original size:20 final size:21
Alignment explanation
Indices: 3441055--3441100 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 21
3441045 TTTTTCCACC
*
3441055 TCTTTTTCTCTCTT-TCTTTT
1 TCTTTTTCTCTATTGTCTTTT
3441075 TC--TTTCTCTATTGTCTTTT
1 TCTTTTTCTCTATTGTCTTTT
*
3441094 TTTTTTT
1 TCTTTTT
3441101 TCGTTTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.43
19 7 0.33
20 2 0.10
21 3 0.14
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (21 bp):
TCTTTTTCTCTATTGTCTTTT
Found at i:3441082 original size:18 final size:19
Alignment explanation
Indices: 3441059--3441094 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3441049 TCCACCTCTT
*
3441059 TTTCTCTCTT-TCTTTTTC
1 TTTCTCTATTGTCTTTTTC
3441077 TTTCTCTATTGTCTTTTT
1 TTTCTCTATTGTCTTTTT
3441095 TTTTTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTCTCTATTGTCTTTTTC
Found at i:3441290 original size:16 final size:17
Alignment explanation
Indices: 3441260--3441296 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3441250 TATCTTTTTT
3441260 TATTTATATTATTTAAC
1 TATTTATATTATTTAAC
*
3441277 TATTTATA-TATTTAAT
1 TATTTATATTATTTAAC
3441293 TATT
1 TATT
3441297 CTATGACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTATATTATTTAAC
Found at i:3444573 original size:27 final size:27
Alignment explanation
Indices: 3444523--3444596 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
3444513 ATATATAAGT
3444523 ATTATTTTGATG-AAATAAAACCATGC
1 ATTATTTTGATGAAAATAAAACCATGC
* **
3444549 ATTATTTTGATGAAAATAAAGCCATTT
1 ATTATTTTGATGAAAATAAAACCATGC
*
3444576 ATTATTTTGATGAAAAAAAAA
1 ATTATTTTGATGAAAATAAAA
3444597 TGCTAATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 12 0.29
27 30 0.71
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (27 bp):
ATTATTTTGATGAAAATAAAACCATGC
Found at i:3446159 original size:108 final size:108
Alignment explanation
Indices: 3446034--3446243 Score: 341
Period size: 108 Copynumber: 1.9 Consensus size: 108
3446024 TATAAGCAAT
*
3446034 TTTGAGTAAATTTAAATAAAAGGTAAATTGGGTAAGAATTGAATAATTTCAAAAGAA-AGTGTAT
1 TTTGAGTAAATTTAAATAAAAGGTAAATTGAGTAAGAATTGAATAATTTCAAAAGAATA-TGTAT
*
3446098 TTATAAATTGTGAAAGTTGTAACTAAATCAATATATTTTGCTAG
65 TTATAAATTGTGAAAGTTGTAACTAAATCAACATATTTTGCTAG
* *
3446142 TTTGAGTAAATTTAAATAAAAGGTAAATTGAGTAAGAGTTGAATAATTTTAAAAGAATATGTATT
1 TTTGAGTAAATTTAAATAAAAGGTAAATTGAGTAAGAATTGAATAATTTCAAAAGAATATGTATT
* * *
3446207 TGTAAGTTGTGAAAGTTGTAACTAAATCGACATATTT
66 TATAAATTGTGAAAGTTGTAACTAAATCAACATATTT
3446244 AGTCATTTTA
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 93 0.99
109 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAGGTAAATTGAGTAAGAATTGAATAATTTCAAAAGAATATGTATT
TATAAATTGTGAAAGTTGTAACTAAATCAACATATTTTGCTAG
Found at i:3447575 original size:31 final size:29
Alignment explanation
Indices: 3447537--3447660 Score: 100
Period size: 31 Copynumber: 4.2 Consensus size: 29
3447527 ATAATATTAT
3447537 AATTAAAATAAATATATAATATAAGAATAAA
1 AATTAAAATAAATATATAATAT-AGAA-AAA
*
3447568 AATTAAAATAAA-ATA-AA-ATA-TAAAA
1 AATTAAAATAAATATATAATATAGAAAAA
**
3447593 AATT--AATATTTATATAATATAGATAAAACA
1 AATTAAAATAAATATATAATATAG--AAAA-A
3447623 AATTAAAATAAAATATATAATATA-AAAAA
1 AATTAAAAT-AAATATATAATATAGAAAAA
3447652 TATATTAAA
1 -A-ATTAAA
3447661 GAAATGAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
23 4 0.05
24 3 0.04
25 9 0.12
26 4 0.05
27 1 0.01
28 2 0.03
29 6 0.08
30 13 0.17
31 18 0.24
32 3 0.04
33 12 0.16
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (29 bp):
AATTAAAATAAATATATAATATAGAAAAA
Found at i:3447590 original size:24 final size:25
Alignment explanation
Indices: 3447541--3447998 Score: 86
Period size: 27 Copynumber: 17.0 Consensus size: 25
3447531 TATTATAATT
*
3447541 AAAA-TAAATATATAATATAAGA-ATA
1 AAAATTAAA-ATAAAATATAA-ATATA
3447566 AAAATTAAAATAAAATA-AAATATAA
1 AAAATTAAAATAAAATATAAATAT-A
* * *
3447591 AAAATTAATATTTATATAATATAGATAAA
1 AAAATTAA-A---ATAAAATATAAATATA
3447620 ACAAATTAAAATAAAATATATAATATA
1 A-AAATTAAAATAAAATATA-AATATA
* * * *
3447647 AAAAATATATTAAAGAAATGAAA-A-A
1 AAAATTAAAATAAA-ATAT-AAATATA
* *
3447672 ATATATATAAAATTATAATA-ATAA-ATA
1 A-AAAT-TAAAA-TAAAATATA-AATATA
*
3447699 AAAA-TAAAATATATGACAT-TAAAAAT-
1 AAAATTAAAATA-A--A-ATATAAATATA
* * ** *
3447725 ATATTTAAAATATGATAT-TATATA
1 AAAATTAAAATAAAATATAAATATA
3447749 AAAATTAATAATATAAATATAAATATATTA
1 AAAATTAA-AATA-AAATAT-AA-ATA-TA
*
3447779 AAAATAAAATATAAAATATTATAATA-A
1 AAAATTAAA-ATAAAATA-TA-AATATA
* * *
3447806 TAAATAAAAATAAAATATATGATATTA
1 AAAATTAAAATAAAATATA-AATA-TA
* * *
3447833 AAAATATATTTAA-GAAATGATATTATATA
1 AAAAT-TA--AAATAAAAT-ATA-AATATA
3447862 AAAATTAATAA-AAAATATAAATAGATTA
1 AAAATTAA-AATAAAATATAAAT--A-TA
*
3447890 AAAATAAAATATAAAATATTATAA-A-A
1 AAAATTAAA-ATAAAATA-TA-AATATA
* *
3447916 ATAAATAAAAATAAAATATATGATATTA
1 A-AAATTAAAATAAAATATA-AATAT-A
** *
3447944 AAAA-TATATTTAAAAATGATATTATATA
1 AAAATTA-AAAT-AAAAT-ATA-AATATA
3447972 AAAATTAATAATAAAAATATAAATATA
1 AAAATTAA-AAT-AAAATATAAATATA
3447999 TTAAACTTAT
Statistics
Matches: 325, Mismatches: 50, Indels: 114
0.66 0.10 0.23
Matches are distributed among these distances:
23 8 0.02
24 16 0.05
25 39 0.12
26 64 0.20
27 69 0.21
28 34 0.10
29 57 0.18
30 36 0.11
31 2 0.01
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (25 bp):
AAAATTAAAATAAAATATAAATATA
Found at i:3447651 original size:21 final size:21
Alignment explanation
Indices: 3447627--3447838 Score: 56
Period size: 21 Copynumber: 10.3 Consensus size: 21
3447617 AAAACAAATT
3447627 AAAATAAAATATATAATATAA
1 AAAATAAAATATATAATATAA
* * * *
3447648 AAAATATATTAAAGAA-ATGAA
1 AAAATAAAATATATAATAT-AA
* *
3447669 AAAAT-ATATATAAAATTATAATA
1 AAAATAAAATATATAA-TAT-A-A
* *
3447692 ATAAATAAAA-ATAAAATATATG
1 A-AAATAAAATATATAATATA-A
* * *
3447714 ACATTAAAA-ATAT-AT-T-T
1 AAAATAAAATATATAATATAA
**
3447731 AAAATATGATAT-TA-TATAA
1 AAAATAAAATATATAATATAA
*
3447750 AAATTAATAATATA-AATATAA
1 AAAATAA-AATATATAATATAA
* *
3447771 ATATATTAAAA-ATAAAATATAA
1 A-A-AATAAAATATATAATATAA
* *
3447793 AATATTATAATA-ATAA-AT-A
1 AA-AATAAAATATATAATATAA
* *
3447812 AAAATAAAATATATGATATTA
1 AAAATAAAATATATAATATAA
3447833 AAAATA
1 AAAATA
3447839 TATTTAAGAA
Statistics
Matches: 142, Mismatches: 29, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
17 7 0.05
18 10 0.07
19 12 0.08
20 18 0.13
21 55 0.39
22 18 0.13
23 10 0.07
24 10 0.07
25 2 0.01
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATAAAATATATAATATAA
Found at i:3447688 original size:12 final size:11
Alignment explanation
Indices: 3447647--3447933 Score: 79
Period size: 11 Copynumber: 26.1 Consensus size: 11
3447637 ATATAATATA
*
3447647 AAAAATATATT
1 AAAAATATAAT
*
3447658 AAAGAA-ATGA-
1 AAA-AATATAAT
3447668 AAAAATATATAT
1 AAAAATATA-AT
*
3447680 AAAATTATAAT
1 AAAAATATAAT
*
3447691 AATAAATAAAAAT
1 AA-AAAT-ATAAT
3447704 AAAATATATGACATT
1 AAAA-ATAT-A-A-T
*
3447719 AAAAATATATT
1 AAAAATATAAT
* *
3447730 TAAAATATGAT
1 AAAAATATAAT
*
3447741 ---ATTAT-AT
1 AAAAATATAAT
3447748 AAAAAT-TAAT
1 AAAAATATAAT
*
3447758 -AATATA-AAT
1 AAAAATATAAT
* *
3447767 ATAAATATATT
1 AAAAATATAAT
*
3447778 AAAAATAAAAT
1 AAAAATATAAT
*
3447789 ATAAAATATTAT
1 A-AAAATATAAT
*
3447801 AATAATA-AAT
1 AAAAATATAAT
3447811 AAAAATA-AA-
1 AAAAATATAAT
* * *
3447820 ATATATGATATT
1 AAAAAT-ATAAT
*
3447832 AAAAATATATTT
1 AAAAATATA-AT
3447844 AAGAAATGATATTAT
1 AA-AAAT-ATA--AT
3447859 ATAAAA-ATTAAT
1 A-AAAATA-TAAT
3447871 AAAAA-AT-AT
1 AAAAATATAAT
* *
3447880 --AAATAGATT
1 AAAAATATAAT
*
3447889 AAAAATAAAAT
1 AAAAATATAAT
*
3447900 ATAAAATATTAT
1 A-AAAATATAAT
3447912 AAAAATA-AAT
1 AAAAATATAAT
*
3447922 AAAAATAAAAT
1 AAAAATATAAT
3447933 A
1 A
3447934 TATGATATTA
Statistics
Matches: 205, Mismatches: 38, Indels: 66
0.66 0.12 0.21
Matches are distributed among these distances:
7 5 0.02
8 5 0.02
9 17 0.08
10 34 0.17
11 62 0.30
12 45 0.22
13 15 0.07
14 10 0.05
15 11 0.05
16 1 0.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AAAAATATAAT
Found at i:3447692 original size:11 final size:12
Alignment explanation
Indices: 3447630--3447992 Score: 87
Period size: 12 Copynumber: 29.9 Consensus size: 12
3447620 ACAAATTAAA
3447630 ATAAAATATATAAT
1 ATAAAA-ATAT-AT
3447644 ATAAAAA-ATAT
1 ATAAAAATATAT
*
3447655 ATTAAAGAA-AT-G
1 A-TAAA-AATATAT
3447667 A-AAAAATATAT
1 ATAAAAATATAT
*
3447678 ATAAAATTATA-
1 ATAAAAATATAT
* *
3447689 ATAATAAATAAAA
1 ATAA-AAATATAT
*
3447702 ATAAAATATATGAC
1 ATAAAA-ATAT-AT
3447716 ATTAAAAATATAT
1 A-TAAAAATATAT
*
3447729 TTAAAATATGATATT
1 ATAAAA-AT-ATA-T
*
3447744 ATATAAA-A-AT
1 ATAAAAATATAT
* *
3447754 -TAATAATATAA
1 ATAAAAATATAT
*
3447765 ATATAAATATAT
1 ATAAAAATATAT
*
3447777 -TAAAAATA-AA
1 ATAAAAATATAT
3447787 ATATAAAATATTAT
1 ATA-AAAATA-TAT
* *
3447801 AATAATAAATAAAA
1 -ATAA-AAATATAT
3447815 ATAAAATATATGAT
1 ATAAAA-ATAT-AT
3447829 ATTAAAAATATAT
1 A-TAAAAATATAT
*
3447842 TTAAGAAATGATATT
1 ATAA-AAAT-ATA-T
3447857 ATATAAAA-AT-T
1 ATA-AAAATATAT
3447868 A-ATAAAA-A-AT
1 ATA-AAAATATAT
*
3447878 AT--AAATAGAT
1 ATAAAAATATAT
*
3447888 -TAAAAATA-AA
1 ATAAAAATATAT
3447898 ATATAAAATAT-T
1 ATA-AAAATATAT
3447910 ATAAAAATA-A-
1 ATAAAAATATAT
3447920 ATAAAAATA-A-
1 ATAAAAATATAT
* *
3447930 A-ATATATGATAT
1 ATAAAAAT-ATAT
3447942 -TAAAAATATAT
1 ATAAAAATATAT
*
3447953 TTAAAAATGATATT
1 ATAAAAAT-ATA-T
3447967 ATATAAAA-ATTAAT
1 ATA-AAAATA-T-AT
3447981 AATAAAAATATA
1 -ATAAAAATATA
3447993 AATATATTAA
Statistics
Matches: 265, Mismatches: 33, Indels: 103
0.66 0.08 0.26
Matches are distributed among these distances:
8 3 0.01
9 12 0.05
10 32 0.12
11 39 0.15
12 67 0.25
13 35 0.13
14 38 0.14
15 38 0.14
16 1 0.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
ATAAAAATATAT
Found at i:3447706 original size:87 final size:86
Alignment explanation
Indices: 3447537--3447707 Score: 192
Period size: 87 Copynumber: 2.0 Consensus size: 86
3447527 ATAATATTAT
*
3447537 AATTAAAATAAATATATAATATAAGAATAAAAATTAAAATAAAATAAAATATAAAAAATTAATAT
1 AATTAAAATAAATATATAATATAAGAATAAAAATTAAAATAAAATAAAATATAAAAAATTAATAA
* * *
3447602 TTATATAATATAGATAAAACA
66 TAATATAATAAAAATAAAACA
*
3447623 AATTAAAATAAAATATATAATATAA-AA-AATATATTAAAGA-AATGAA-AAAATATATATAAAA
1 AATTAAAAT-AAATATATAATATAAGAATAA-AAATTAAA-ATAA--AATAAAATATA-A-AAAA
3447684 TT-ATAATAATA-AATAAAAATAAAA
59 TTAATAATAATATAATAAAAATAAAA
3447708 TATATGACAT
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
85 2 0.03
86 20 0.27
87 35 0.48
88 10 0.14
89 6 0.08
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (86 bp):
AATTAAAATAAATATATAATATAAGAATAAAAATTAAAATAAAATAAAATATAAAAAATTAATAA
TAATATAATAAAAATAAAACA
Found at i:3447722 original size:87 final size:87
Alignment explanation
Indices: 3447631--3447797 Score: 191
Period size: 87 Copynumber: 1.9 Consensus size: 87
3447621 CAAATTAAAA
* *
3447631 TAAAATATATAATATAAAAAAT-ATATTA-A-AGAAATGAAAAAATATATATA-AAATTATAATA
1 TAAAA-ATAT-ATATAAAAAATGATATTATATAAAAAT-AAAAAATATAAATATAAA-TATAATA
3447692 ATAAATAAAA-ATAAAATATATGACAT
62 A-AAATAAAATATAAAATATATGACAT
* * * * *
3447718 TAAAAATATATTTAAAATATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAA
1 TAAAAATATATATAAAAAATGATATTATATAAAAATAAAAAATATAAATATAAATATAATAAAAA
3447783 TAAAATATAAAATAT
66 TAAAATATAAAATAT
3447798 TATAATAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
85 9 0.13
86 18 0.26
87 33 0.49
88 8 0.12
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (87 bp):
TAAAAATATATATAAAAAATGATATTATATAAAAATAAAAAATATAAATATAAATATAATAAAAA
TAAAATATAAAATATATGACAT
Found at i:3447733 original size:27 final size:26
Alignment explanation
Indices: 3447668--3448003 Score: 177
Period size: 27 Copynumber: 12.1 Consensus size: 26
3447658 AAAGAAATGA
3447668 AAAAATATATATAAAAT-TATA-A-T
1 AAAAATATATATAAAATATATATATT
* * *
3447691 AATAAATAAAAATAAAATATATGACATT
1 AA-AAATATATATAAAATATAT-ATATT
*
3447719 AAAAATATATTTAAAATATGATATTATAT
1 AAAAATATATATAAAATAT-ATA-TAT-T
*
3447748 AAAAATTAATAATATAAATATAAATATATT
1 AAAAA-T-AT-ATATAAA-ATATATATATT
* *
3447778 AAAAATAAAATATAAAATAT-TATAAT
1 AAAAAT-ATATATAAAATATATATATT
* *
3447804 AATAAATAAAAATAAAATATATGATATT
1 AA-AAATATATATAAAATATAT-ATATT
*
3447832 AAAAATATATTTAAGAA-ATGATATTATAT
1 AAAAATATATATAA-AATAT-ATA-TAT-T
* *
3447861 AAAAAT-TAATAAAAAATATAAATAGATT
1 AAAAATAT-ATATAAAATAT--ATATATT
* **
3447889 AAAAATAAAATATAAAATAT-TATAAA
1 AAAAAT-ATATATAAAATATATATATT
* *
3447915 AATAAATAAAAATAAAATATATGATATT
1 AA-AAATATATATAAAATATAT-ATATT
*
3447943 AAAAATATATTTAAAA-ATGATATTATAT
1 AAAAATATATATAAAATAT-ATA-TAT-T
3447971 AAAAAT-TAATAATAAAAATATAAATATATT
1 AAAAATAT-AT-AT-AAAATAT--ATATATT
3448001 AAA
1 AAA
3448004 CTTATATTTT
Statistics
Matches: 245, Mismatches: 33, Indels: 63
0.72 0.10 0.18
Matches are distributed among these distances:
23 2 0.01
24 13 0.05
25 3 0.01
26 40 0.16
27 58 0.24
28 51 0.21
29 35 0.14
30 18 0.07
31 10 0.04
32 12 0.05
33 3 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAAATATATATAAAATATATATATT
Found at i:3447748 original size:72 final size:69
Alignment explanation
Indices: 3447622--3447773 Score: 173
Period size: 72 Copynumber: 2.2 Consensus size: 69
3447612 TAGATAAAAC
* *
3447622 AAATTAAAATAAAATATATAATATAAAAAATATATTAAAGAAATGAAAAAATATATATAAAATT-
1 AAATAAAAATAAAATATATAACATAAAAAATATATTAAAGAAATG--AAAATATATA-AAAATTA
3447686 ATAATAAT
63 ATAAT-AT
* * * * *
3447694 AAATAAAAATAAAATATATGACATTAAAAATATATTTAAA-ATATGATATTATATAAAAATTAAT
1 AAATAAAAATAAAATATATAACATAAAAAATATA-TTAAAGAAATGAAAATATATAAAAATTAAT
3447758 AATAT
65 AATAT
*
3447763 AAATATAAATA
1 AAATAAAAATA
3447774 TATTAAAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
69 18 0.26
70 13 0.19
72 34 0.49
73 5 0.07
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (69 bp):
AAATAAAAATAAAATATATAACATAAAAAATATATTAAAGAAATGAAAATATATAAAAATTAATA
ATAT
Found at i:3447769 original size:6 final size:6
Alignment explanation
Indices: 3447758--3447824 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
3447748 AAAAATTAAT
* *
3447758 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
3447808 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
3447825 TGATATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:3447812 original size:113 final size:111
Alignment explanation
Indices: 3447674--3448003 Score: 574
Period size: 111 Copynumber: 2.9 Consensus size: 111
3447664 ATGAAAAAAT
*
3447674 ATATATAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAAATAT
1 ATATA-AAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAA-AT
3447738 GATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAA
64 GATATTATATAAAAATTAATAATA-AAATATAAATATATTAAAAATAAA
3447787 ATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATG
1 ATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAA-AAATG
*
3447852 ATATTATATAAAAATTAATAA-AAAATATAAATAGATTAAAAATAAA
65 ATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAA
*
3447898 ATATAAAATATTATAAAAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAAATGA
1 ATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAAATGA
3447963 TATTATATAAAAATTAATAATAAAAATATAAATATATTAAA
66 TATTATATAAAAATTAATAAT-AAAATATAAATATATTAAA
3448004 CTTATATTTT
Statistics
Matches: 209, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
110 26 0.12
111 81 0.39
112 22 0.11
113 78 0.37
114 2 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (111 bp):
ATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAAATGA
TATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAA
Found at i:3447819 original size:33 final size:34
Alignment explanation
Indices: 3447777--3447935 Score: 103
Period size: 33 Copynumber: 4.4 Consensus size: 34
3447767 ATAAATATAT
3447777 TAAAAATAAAATATAAAATATTATAATAATA-AA
1 TAAAAATAAAATATAAAATATTATAATAATAGAA
** * *
3447810 TAAAAATAAAATATATGATATTA-AA-AATATATT
1 TAAAAATAAAATATAAAATATTATAATAATAGA-A
* *
3447843 TAAGAAATGATATTATATAAAA-ATTAATAAAAAATATAAATAGAT
1 TAA-AAAT-A-A-AATATAAAATATT-AT-----A-AT-AATAGAA
*
3447888 TAAAAATAAAATATAAAATATTATAAAAATA-AA
1 TAAAAATAAAATATAAAATATTATAATAATAGAA
3447921 TAAAAATAAAATATA
1 TAAAAATAAAATATA
3447936 TGATATTAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 34
0.69 0.07 0.24
Matches are distributed among these distances:
31 4 0.04
32 3 0.03
33 40 0.40
34 8 0.08
35 2 0.02
36 5 0.05
37 7 0.07
41 10 0.10
42 4 0.04
43 2 0.02
44 5 0.05
45 4 0.04
46 5 0.05
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (34 bp):
TAAAAATAAAATATAAAATATTATAATAATAGAA
Found at i:3447906 original size:23 final size:22
Alignment explanation
Indices: 3447743--3447929 Score: 85
Period size: 21 Copynumber: 8.5 Consensus size: 22
3447733 AATATGATAT
*
3447743 TATATAAA-AATTAATAATATAAA
1 TATA-AAATAATTAAAAATA-AAA
3447766 TAT-AAATATATTAAAAATAAAA
1 TATAAAATA-ATTAAAAATAAAA
3447788 TATAAAAT-ATTATAATAAT-AAA
1 TATAAAATAATTA-AA-AATAAAA
* **
3447810 TA-AAAAT-A--AAATATATGA
1 TATAAAATAATTAAAAATAAAA
* *
3447828 TATTAAAAATATATTTAAGAAATGATAT
1 TA-T-AAAATA-A-TTAA-AAAT-AAAA
*
3447856 TATATAAA-AATTAATAA-AAAA
1 TATA-AAATAATTAAAAATAAAA
3447877 TAT-AAATAGATTAAAAATAAAA
1 TATAAAATA-ATTAAAAATAAAA
*
3447899 TATAAAATATTATAAAAAT-AAA
1 TATAAAATAAT-TAAAAATAAAA
3447921 TA-AAAATAA
1 TATAAAATAA
3447930 AATATATGAT
Statistics
Matches: 129, Mismatches: 13, Indels: 46
0.69 0.07 0.24
Matches are distributed among these distances:
17 2 0.02
18 5 0.04
19 4 0.03
20 1 0.01
21 36 0.28
22 27 0.21
23 34 0.26
24 4 0.03
25 1 0.01
26 4 0.03
27 7 0.05
28 4 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
TATAAAATAATTAAAAATAAAA
Found at i:3447958 original size:33 final size:33
Alignment explanation
Indices: 3447880--3447960 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 33
3447870 TAAAAAATAT
3447880 AAATAGATTAAAAATAAAATATAAAATATTATAA
1 AAATA-ATTAAAAATAAAATATAAAATATTATAA
* **
3447914 AAATAAATAAAAATAAAATATATGATATTA-AA
1 AAATAATTAAAAATAAAATATAAAATATTATAA
*
3447946 AATATATTTAAAAAT
1 AA-ATAATTAAAAAT
3447961 GATATTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 4 0.10
33 32 0.78
34 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (33 bp):
AAATAATTAAAAATAAAATATAAAATATTATAA
Found at i:3448173 original size:15 final size:15
Alignment explanation
Indices: 3448153--3448206 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
3448143 TTTTCCCTGT
*
3448153 AATCACATTGCTTGC
1 AATCACATTACTTGC
3448168 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
3448183 AATCACATTACCTGT
1 AATCACATTACTTGC
3448198 AATCACATT
1 AATCACATT
3448207 GCATTGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:3448413 original size:26 final size:26
Alignment explanation
Indices: 3448336--3448427 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 26
3448326 AAGGGCGTTT
* * **
3448336 CAAGTGCATAACACTCAAGGATGTTC
1 CAAGTGCGTAACACTCAGGGACATTC
3448362 CTAAGTGCGTAACACAT-AGTGG-CATTC
1 C-AAGTGCGTAACAC-TCAG-GGACATTC
*
3448389 CAAGTGTGTAACACTCAGGGACATTCC
1 CAAGTGCGTAACACTCAGGGACATT-C
*
3448416 CAAGTGCATAAC
1 CAAGTGCGTAAC
3448428 TTATAAAGAC
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
25 3 0.06
26 19 0.36
27 28 0.53
28 3 0.06
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (26 bp):
CAAGTGCGTAACACTCAGGGACATTC
Found at i:3448421 original size:53 final size:53
Alignment explanation
Indices: 3448302--3448427 Score: 137
Period size: 53 Copynumber: 2.4 Consensus size: 53
3448292 TAATACCCAT
** * *
3448302 GACATTCCCAAGTGCATAATGCATAAGGGCGTTTCAAGTGCATAACACTCAAG
1 GACATTCCCAAGTGCATAACACATAAGGGCATTCCAAGTGCATAACACTCAAG
** * * ** *
3448355 GATGTTCCTAAGTGCGTAACACAT-AGTGGCATTCCAAGTGTGTAACACTCAGG
1 GACATTCCCAAGTGCATAACACATAAG-GGCATTCCAAGTGCATAACACTCAAG
3448408 GACATTCCCAAGTGCATAAC
1 GACATTCCCAAGTGCATAAC
3448428 TTATAAAGAC
Statistics
Matches: 57, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
52 2 0.04
53 55 0.96
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (53 bp):
GACATTCCCAAGTGCATAACACATAAGGGCATTCCAAGTGCATAACACTCAAG
Found at i:3448475 original size:26 final size:26
Alignment explanation
Indices: 3448439--3448507 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
3448429 TATAAAGACA
* *
3448439 TTCTAAATGCATAACGC-ATAGGAATG
1 TTCTAAGTGCATAACGCAAAAGG-ATG
*
3448465 TT-TCAAGTGCATAATGCAAAAGGATG
1 TTCT-AAGTGCATAACGCAAAAGGATG
3448491 TTCTAAGTGCATAACGC
1 TTCTAAGTGCATAACGC
3448508 TCAGAGATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 1 0.03
26 30 0.83
27 5 0.14
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (26 bp):
TTCTAAGTGCATAACGCAAAAGGATG
Found at i:3449461 original size:60 final size:60
Alignment explanation
Indices: 3449368--3449483 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
3449358 TCAACAAGCG
* * * * *
3449368 TTCCTTAACGTACTCTTCCATAACAAGCTCCCATGATT-ATGCTTAACATCTAATAAGTTA
1 TTCCTTAACATACTCTTCCATAACAAGCACCCATAATTGA-ACTTAACATCCAATAAGTTA
* *
3449428 TTCCTTAACATGCTCTTCCATTACAAGCACCCATAATTGAACTTAACATCCAATAA
1 TTCCTTAACATACTCTTCCATAACAAGCACCCATAATTGAACTTAACATCCAATAA
3449484 CTATTTTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 47 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.33
Consensus pattern (60 bp):
TTCCTTAACATACTCTTCCATAACAAGCACCCATAATTGAACTTAACATCCAATAAGTTA
Found at i:3450462 original size:20 final size:21
Alignment explanation
Indices: 3450427--3450465 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3450417 TCAGTAAAAA
*
3450427 TTCTCTTTTGCTGAACTTTTT
1 TTCTCTTTTACTGAACTTTTT
3450448 TTCTC-TTTACTGAACTTT
1 TTCTCTTTTACTGAACTTT
3450466 CTCTAGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.13, C:0.21, G:0.08, T:0.59
Consensus pattern (21 bp):
TTCTCTTTTACTGAACTTTTT
Found at i:3454376 original size:22 final size:21
Alignment explanation
Indices: 3454351--3454419 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
3454341 CTTCTGATAC
3454351 AAAATATTTTTAAATTATAATA
1 AAAATATTTTT-AATTATAATA
* * *
3454373 AAAATATGTTTGT-ATTTTGATG
1 AAAATAT-TTT-TAATTATAATA
*
3454395 AAAATATTATTTAATTATAGTA
1 AAAATATT-TTTAATTATAATA
3454417 AAA
1 AAA
3454420 GGTATTTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
21 2 0.06
22 30 0.83
23 3 0.08
24 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
AAAATATTTTTAATTATAATA
Found at i:3455718 original size:5 final size:5
Alignment explanation
Indices: 3455708--3455863 Score: 131
Period size: 5 Copynumber: 32.2 Consensus size: 5
3455698 AATTAGGGTA
*
3455708 TCAAT TCAAT T-AAT T-AAT TTAAT TCAAT TCAA- TCAAT TCAATT ATCAATT
1 TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAA-T -TCAA-T
3455758 ATCAAT T-AAT TCAA- TCAAT TCAATT ATCAAT T-AAT TCAA- TCAAT
1 -TCAAT TCAAT TCAAT TCAAT TCAA-T -TCAAT TCAAT TCAAT TCAAT
*
3455802 TCAATT ATCAAT TCCA- TCAA- TCAA- TCAA- TCAA- TCAAT T-AAT TCAAT
1 TCAA-T -TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT
3455848 TCAAT TCAAT TCAAT T
1 TCAAT TCAAT TCAAT T
3455864 ATCAATTATC
Statistics
Matches: 134, Mismatches: 3, Indels: 28
0.81 0.02 0.17
Matches are distributed among these distances:
4 51 0.38
5 58 0.43
6 6 0.04
7 19 0.14
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (5 bp):
TCAAT
Found at i:3455729 original size:9 final size:9
Alignment explanation
Indices: 3455708--3455863 Score: 120
Period size: 9 Copynumber: 18.1 Consensus size: 9
3455698 AATTAGGGTA
3455708 TCAATTCAAT
1 TCAATT-AAT
3455718 T-AATTAAT
1 TCAATTAAT
*
3455726 TTAATTCAAT
1 TCAATT-AAT
*
3455736 TCAATCAAT
1 TCAATTAAT
3455745 TCAATT-A-
1 TCAATTAAT
3455752 TCAATT-A-
1 TCAATTAAT
3455759 TCAATTAAT
1 TCAATTAAT
*
3455768 TCAATCAAT
1 TCAATTAAT
3455777 TCAATT-A-
1 TCAATTAAT
3455784 TCAATTAAT
1 TCAATTAAT
*
3455793 TCAATCAAT
1 TCAATTAAT
3455802 TCAATT-A-
1 TCAATTAAT
*
3455809 TCAATTCCA-
1 TCAATT-AAT
*
3455818 TCAATCAA-
1 TCAATTAAT
*
3455826 TCAATCAA-
1 TCAATTAAT
3455834 TCAATTAAT
1 TCAATTAAT
3455843 TCAATTCAAT
1 TCAATT-AAT
3455853 TCAATTCAAT
1 TCAATT-AAT
3455863 T
1 T
3455864 ATCAATTATC
Statistics
Matches: 126, Mismatches: 10, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
7 25 0.20
8 25 0.20
9 54 0.43
10 22 0.17
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (9 bp):
TCAATTAAT
Found at i:3455743 original size:32 final size:32
Alignment explanation
Indices: 3455707--3455862 Score: 136
Period size: 32 Copynumber: 5.1 Consensus size: 32
3455697 TAATTAGGGT
3455707 ATCAATTCAATTAATTAATTTAATTCAATTCA
1 ATCAATTCAATTAATTAATTTAATTCAATTCA
*
3455739 ATCAATTCAATT-ATCAATTATCAATT-AATTCA
1 ATCAATTCAATTAATTAATT-T-AATTCAATTCA
*
3455771 ATCAATTCAATT-ATCAA-TTAATTCAA-TCA
1 ATCAATTCAATTAATTAATTTAATTCAATTCA
* * *
3455800 ATTCAATT--ATCAATTCCA-TCAA-TCAA-TCA
1 A-TCAATTCAATTAATT-AATTTAATTCAATTCA
*
3455829 ATCAA-TCAATTAATTCAATTCAATTCAATTCA
1 ATCAATTCAATTAATT-AATTTAATTCAATTCA
3455861 AT
1 AT
3455863 TATCAATTAT
Statistics
Matches: 106, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
27 1 0.01
28 6 0.06
29 26 0.25
30 17 0.16
31 11 0.10
32 41 0.39
33 4 0.04
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (32 bp):
ATCAATTCAATTAATTAATTTAATTCAATTCA
Found at i:3455786 original size:25 final size:25
Alignment explanation
Indices: 3455713--3455858 Score: 162
Period size: 25 Copynumber: 6.0 Consensus size: 25
3455703 GGGTATCAAT
*
3455713 TCAATTAATT-AATTTAATTCAA-T-
1 TCAATTAATTCAA-TCAATTCAATTA
* *
3455736 TCAATCAATTCAAT-TA-TCAATTA
1 TCAATTAATTCAATCAATTCAATTA
3455759 TCAATTAATTCAATCAATTCAATTA
1 TCAATTAATTCAATCAATTCAATTA
3455784 TCAATTAATTCAATCAATTCAATTA
1 TCAATTAATTCAATCAATTCAATTA
* *
3455809 TCAATTCCA-TCAATCAA-TCAATCAA
1 TCAATT-AATTCAATCAATTCAAT-TA
3455834 TCAATTAATTCAATTCAATTCAATT
1 TCAATTAATTCAA-TCAATTCAATT
3455859 CAATTATCAA
Statistics
Matches: 105, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.04
22 2 0.02
23 23 0.22
24 9 0.09
25 57 0.54
26 5 0.05
27 5 0.05
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (25 bp):
TCAATTAATTCAATCAATTCAATTA
Found at i:3455826 original size:4 final size:4
Alignment explanation
Indices: 3455731--3455862 Score: 65
Period size: 4 Copynumber: 31.2 Consensus size: 4
3455721 TTAATTTAAT
* * *
3455731 TCAA TTCAA TCAA TTCAA T-TA TCAA T-TA TCAA TTAA TTCAA TCAA TTCAA
1 TCAA -TCAA TCAA -TCAA TCAA TCAA TCAA TCAA TCAA -TCAA TCAA -TCAA
* * * *
3455781 T-TA TCAA TTAA TTCAA TCAA TTCAA T-TA TCAA TTCCA TCAA TCAA TCAA
1 TCAA TCAA TCAA -TCAA TCAA -TCAA TCAA TCAA -TCAA TCAA TCAA TCAA
*
3455830 TCAA TCAA TTAA TTCAA TTCAA TTCAA TTCAA T
1 TCAA TCAA TCAA -TCAA -TCAA -TCAA -TCAA T
3455863 TATCAATTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 23
0.72 0.12 0.17
Matches are distributed among these distances:
3 8 0.08
4 49 0.49
5 43 0.43
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (4 bp):
TCAA
Found at i:3455875 original size:46 final size:48
Alignment explanation
Indices: 3455759--3455877 Score: 84
Period size: 46 Copynumber: 2.7 Consensus size: 48
3455749 TTATCAATTA
*
3455759 TCAATT-AATTCAA-TCAATTCAATTATCAATT-A--ATTCAATCAAT
1 TCAATTCAATTCAATTCAATTCAATTATCAATTCATCAATCAATCAAT
* * *
3455802 TCAATT--A-TCAATTCCA-TCAATCAATCAA-TCAATCAATTAATTCAAT
1 TCAATTCAATTCAATTCAATTCAAT-TATCAATTC-ATCAATCAA-TCAAT
3455848 TCAATTCAATTCAATT--A-TCAATTATCAATT
1 TCAATTCAATTCAATTCAATTCAATTATCAATT
3455878 ATGTAGCTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
41 10 0.17
42 9 0.15
43 7 0.12
45 4 0.07
46 16 0.27
47 7 0.12
48 1 0.02
49 6 0.10
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (48 bp):
TCAATTCAATTCAATTCAATTCAATTATCAATTCATCAATCAATCAAT
Found at i:3465841 original size:173 final size:173
Alignment explanation
Indices: 3465448--3465982 Score: 689
Period size: 173 Copynumber: 3.1 Consensus size: 173
3465438 CAGCAATGGA
* * * * * * * *
3465448 TCATTGAATTATGGACTTTGGGAATGCCTCTTCACCTAATCCTTGTTTACACGGAACATGTTCAA
1 TCATTGAAGTATTGACTTTGGAAATGCCTCTCCACCTAATCCTTGCTTACGCTGAACATTTTCAA
* * * * *
3465513 CAATAATGTTATGAGATATTGTATAGAGATTTTTGTGATAGGAATTAGATGCAATACTATAAATA
66 CAATAATGTTATGAGATATTATATAGAGATTTTTGTGATAGG-A--AGATGTAGTATTACAAATA
* **** *
3465578 AATTAAAAAAATGT-CTCAGAGACAATAGAAAGAAAGACTGGAA-TAG
128 AATAAAAAAAATGTACT-AGAGGTGGTGGAAAGAAAGACT-GAAGTAG
* * *
3465624 TTATTGAAGTATTGACTTTAGAAATGCCTCACCACCTAATCCTTGCTTACGCTGAACATTTTCAA
1 TCATTGAAGTATTGACTTTGGAAATGCCTCTCCACCTAATCCTTGCTTACGCTGAACATTTTCAA
* *
3465689 CAATAATGTTATGAGATATTATACATAGATTTTTGTGATAGGAAGATGTAGTATTACAAATAAAT
66 CAATAATGTTATGAGATATTATATAGAGATTTTTGTGATAGGAAGATGTAGTATTACAAATAAAT
*
3465754 AAAAAAAATGTACTAGAGGTGGTGGAAAGGAAGACTGAAGTAG
131 AAAAAAAATGTACTAGAGGTGGTGGAAAGAAAGACTGAAGTAG
* * * *
3465797 TCATTGAAATATTGACTTTGGAAATGCAC-CTCCACCTAATCCTTGCTTATGTTGGACATTTTCA
1 TCATTGAAGTATTGACTTTGGAAATGC-CTCTCCACCTAATCCTTGCTTACGCTGAACATTTTCA
* *
3465861 ACAATAATGTTATGAGATATTTTATAGAGATTTTTGTGATAGGAAGATGTAGTATTGCAAATAAA
65 ACAATAATGTTATGAGATATTATATAGAGATTTTTGTGATAGGAAGATGTAGTATTACAAATAAA
* * *
3465926 TAAAAAAGATGTACTAGAGGTGGTGGAAAGAAAGATTGGAGTAG
130 TAAAAAAAATGTACTAGAGGTGGTGGAAAGAAAGACTGAAGTAG
3465970 TCATTGAAGTATT
1 TCATTGAAGTATT
3465983 AAGTGTTATG
Statistics
Matches: 315, Mismatches: 41, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
172 3 0.01
173 215 0.68
174 3 0.01
175 1 0.00
176 93 0.30
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.32
Consensus pattern (173 bp):
TCATTGAAGTATTGACTTTGGAAATGCCTCTCCACCTAATCCTTGCTTACGCTGAACATTTTCAA
CAATAATGTTATGAGATATTATATAGAGATTTTTGTGATAGGAAGATGTAGTATTACAAATAAAT
AAAAAAAATGTACTAGAGGTGGTGGAAAGAAAGACTGAAGTAG
Found at i:3466330 original size:22 final size:22
Alignment explanation
Indices: 3466299--3466342 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3466289 AATTCCTTCC
* *
3466299 TTTTTGTATAAAGCTTTTAGTT
1 TTTTTATATAAAGCCTTTAGTT
3466321 TTTTTATATAAAGCCTTTAGTT
1 TTTTTATATAAAGCCTTTAGTT
3466343 ACCAACCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (22 bp):
TTTTTATATAAAGCCTTTAGTT
Found at i:3468972 original size:55 final size:54
Alignment explanation
Indices: 3468888--3469111 Score: 207
Period size: 55 Copynumber: 4.1 Consensus size: 54
3468878 TTGAGTTCAA
* *
3468888 AAAAATTTAGTTGTTACGCGTCATGTTAAAAATTT-GTTTGTTACACACTATGTAG
1 AAAAATTTAGTTGTTACACGTCATATTAAAAATTTAG-TTGTTACACACTATGT-G
* * * * *
3468943 AAAAATGTAGTTGTTACACGTCATATTAAAGATTTAGTTGTTATACGCTATGTT
1 AAAAATTTAGTTGTTACACGTCATATTAAAAATTTAGTTGTTACACACTATGTG
* ** * * * *
3468997 AAAAATTTAGTTATTACAAATCATATTAAAAAATATAGTTATTACACACCATGTT
1 AAAAATTTAGTTGTTACACGTCATATT-AAAAATTTAGTTGTTACACACTATGTG
* * * * ** * *
3469052 AAAAATTTAATTATTACACGTTATGTTGAAAAATACAGTTGTTACACACCATGTT
1 AAAAATTTAGTTGTTACACGTCATATT-AAAAATTTAGTTGTTACACACTATGTG
3469107 AAAAA
1 AAAAA
3469112 AGTCATTACA
Statistics
Matches: 142, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
54 23 0.16
55 118 0.83
56 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (54 bp):
AAAAATTTAGTTGTTACACGTCATATTAAAAATTTAGTTGTTACACACTATGTG
Found at i:3469014 original size:82 final size:81
Alignment explanation
Indices: 3468888--3469112 Score: 215
Period size: 82 Copynumber: 2.7 Consensus size: 81
3468878 TTGAGTTCAA
*
3468888 AAAAATTTAGTTG-T-TACGCGTCATGTTAAAAATTT-GTTTGTTACACACTATGTAGAAAAATG
1 AAAAATTTAGTTGTTATACGC-T-ATGTTAAAAATTTAG-TTGTTACACACTATGTA-AAAAATA
* **
3468950 TAGTTGTTACACGTCATATT
62 TAGTTATTACACACCATATT
* * *
3468970 AAAGATTTAGTTGTTATACGCTATGTTAAAAATTTAGTTATTACAAATCATAT-TAAAAAATATA
1 AAAAATTTAGTTGTTATACGCTATGTTAAAAATTTAGTTGTTACACA-C-TATGTAAAAAATATA
*
3469034 GTTATTACACACCATGTT
64 GTTATTACACACCATATT
* * * * ** *
3469052 AAAAATTTAATTATTACACGTTATGTTGAAAAATACAGTTGTTACACACCATGTTAAAAAA
1 AAAAATTTAGTTGTTATACGCTATGTT-AAAAATTTAGTTGTTACACACTATG-TAAAAAA
3469113 GTCATTACAC
Statistics
Matches: 117, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
81 2 0.02
82 78 0.67
83 29 0.25
84 8 0.07
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (81 bp):
AAAAATTTAGTTGTTATACGCTATGTTAAAAATTTAGTTGTTACACACTATGTAAAAAATATAGT
TATTACACACCATATT
Found at i:3469035 original size:28 final size:27
Alignment explanation
Indices: 3468995--3469069 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
3468985 ATACGCTATG
*
3468995 TTAAAAATTTAGTTATTACAAATCATA
1 TTAAAAATTTAGTTATTACAAACCATA
* * *
3469022 TTAAAAAATATAGTTATTACACACCATG
1 TT-AAAAATTTAGTTATTACAAACCATA
*
3469050 TTAAAAATTTAATTATTACA
1 TTAAAAATTTAGTTATTACA
3469070 CGTTATGTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 18 0.44
28 23 0.56
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (27 bp):
TTAAAAATTTAGTTATTACAAACCATA
Found at i:3469105 original size:28 final size:27
Alignment explanation
Indices: 3468888--3469111 Score: 171
Period size: 27 Copynumber: 8.2 Consensus size: 27
3468878 TTGAGTTCAA
* **
3468888 AAAAATTTAGTTGTTACGCGTCATGTT
1 AAAAATTTAGTTGTTACACACCATGTT
* *
3468915 AAAAATTT-GTTTGTTACACACTATGTAG
1 AAAAATTTAG-TTGTTACACACCATGT-T
* ** *
3468943 AAAAATGTAGTTGTTACACGTCATATT
1 AAAAATTTAGTTGTTACACACCATGTT
* * * *
3468970 AAAGATTTAGTTGTTATACGCTATGTT
1 AAAAATTTAGTTGTTACACACCATGTT
* * * *
3468997 AAAAATTTAGTTATTACAAATCATATT
1 AAAAATTTAGTTGTTACACACCATGTT
* *
3469024 AAAAAATATAGTTATTACACACCATGTT
1 -AAAAATTTAGTTGTTACACACCATGTT
* * ***
3469052 AAAAATTTAATTATTACACGTTATGTT
1 AAAAATTTAGTTGTTACACACCATGTT
**
3469079 GAAAAATACAGTTGTTACACACCATGTT
1 -AAAAATTTAGTTGTTACACACCATGTT
3469107 AAAAA
1 AAAAA
3469112 AGTCATTACA
Statistics
Matches: 151, Mismatches: 41, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
26 1 0.01
27 87 0.58
28 62 0.41
29 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (27 bp):
AAAAATTTAGTTGTTACACACCATGTT
Found at i:3470107 original size:15 final size:15
Alignment explanation
Indices: 3470087--3470115 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3470077 GTTTAAAGAA
3470087 GGTCTTAAAGATCCC
1 GGTCTTAAAGATCCC
3470102 GGTCTTAAAGATCC
1 GGTCTTAAAGATCC
3470116 GTTTGGTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (15 bp):
GGTCTTAAAGATCCC
Found at i:3470934 original size:228 final size:228
Alignment explanation
Indices: 3470595--3471047 Score: 719
Period size: 228 Copynumber: 2.0 Consensus size: 228
3470585 AAGGCAACAG
* * *
3470595 CAAATTGGCTACAAGCTGTTAATGTGCTTCCTTCATTGTTGCAGTTAGATATGTCTGGCTGTGAA
1 CAAATTGGCTACAAGCTGTTAATATGCTTCCTTCATTGTTGCAATTAGATATGTCTGACTGTGAA
* * *
3470660 CTTTTTGACCTTCCTCAATCTCTTCTATTTGTAAATTTCTCGTCACTTCAGGCTCTTGACCTCTC
66 CTTTTTGACCTTCCTCAATCTCTTCCATTTGTAAATTCCACGTCACTTCAGGCTCTTGACCTCTC
* * *
3470725 ATATAATAAATTCAGCTCTTCAATACCTCAGTGGCTCTTTAATCTCACTAACCTCAAGCAACTTA
131 AGATAATAAATTCAGCTCTCCAATACCACAGTGGCTCTTTAATCTCACTAACCTCAAGCAACTTA
3470790 AGCTTGCTGGTTCTAACCTTACAGGTCCCACAA
196 AGCTTGCTGGTTCTAACCTTACAGGTCCCACAA
* * *
3470823 CAAATTGGCTACAAGCTGTTAATATGCTTCCTTCATTGTTGCAATTGGATTTGTCTTACTGTCG-
1 CAAATTGGCTACAAGCTGTTAATATGCTTCCTTCATTGTTGCAATTAGATATGTCTGACTGT-GA
* * *
3470887 ACTTTTTGACCTTCCTCAATCTTTTCCGTTTGTGAATTCCACGTCACTTCAGGCTCTTGACCTCT
65 ACTTTTTGACCTTCCTCAATCTCTTCCATTTGTAAATTCCACGTCACTTCAGGCTCTTGACCTCT
* * *
3470952 CAGATAATAGATTCAGCTCTCCAATACCACAGTGGCTCTTTAATCTCAGTAACCTCAGGCAACTT
130 CAGATAATAAATTCAGCTCTCCAATACCACAGTGGCTCTTTAATCTCACTAACCTCAAGCAACTT
*
3471017 AAGCTTGCTGGTTCTGACCTTACAGGTCCCA
195 AAGCTTGCTGGTTCTAACCTTACAGGTCCCA
3471048 TTCCCACATT
Statistics
Matches: 205, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
228 204 1.00
229 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (228 bp):
CAAATTGGCTACAAGCTGTTAATATGCTTCCTTCATTGTTGCAATTAGATATGTCTGACTGTGAA
CTTTTTGACCTTCCTCAATCTCTTCCATTTGTAAATTCCACGTCACTTCAGGCTCTTGACCTCTC
AGATAATAAATTCAGCTCTCCAATACCACAGTGGCTCTTTAATCTCACTAACCTCAAGCAACTTA
AGCTTGCTGGTTCTAACCTTACAGGTCCCACAA
Found at i:3478833 original size:4 final size:4
Alignment explanation
Indices: 3478824--3478849 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3478814 TTCAACCATG
3478824 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
3478850 TATATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:3483430 original size:3 final size:3
Alignment explanation
Indices: 3483422--3483446 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3483412 GCAGGGACTG
3483422 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3483447 CAAAAGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3503546 original size:21 final size:24
Alignment explanation
Indices: 3503521--3503574 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 24
3503511 CACCCCATGT
3503521 TTCTCTCTCTCTCT-G-CATT-TC
1 TTCTCTCTCTCTCTCGCCATTCTC
3503542 TTCTCTCTCTCTCTCGTCCATTCTC
1 TTCTCTCTCTCTCTCG-CCATTCTC
3503567 TTCTCTCT
1 TTCTCTCT
3503575 ACTCCGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.48
22 1 0.03
24 4 0.14
25 10 0.34
ACGTcount: A:0.04, C:0.41, G:0.04, T:0.52
Consensus pattern (24 bp):
TTCTCTCTCTCTCTCGCCATTCTC
Found at i:3503556 original size:25 final size:25
Alignment explanation
Indices: 3503522--3503574 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
3503512 ACCCCATGTT
*
3503522 TCTCTCTCTCTC-TGCATT-TCTTC
1 TCTCTCTCTCTCGTCCATTCTCTTC
3503545 TCTCTCTCTCTCGTCCATTCTCTTC
1 TCTCTCTCTCTCGTCCATTCTCTTC
3503570 TCTCT
1 TCTCT
3503575 ACTCCGACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 12 0.44
24 5 0.19
25 10 0.37
ACGTcount: A:0.04, C:0.42, G:0.04, T:0.51
Consensus pattern (25 bp):
TCTCTCTCTCTCGTCCATTCTCTTC
Found at i:3509358 original size:30 final size:30
Alignment explanation
Indices: 3509322--3509438 Score: 234
Period size: 30 Copynumber: 3.9 Consensus size: 30
3509312 TCTGGTTCAT
3509322 CCACGTCTACTATTGAGGTTGTCCTAGTAC
1 CCACGTCTACTATTGAGGTTGTCCTAGTAC
3509352 CCACGTCTACTATTGAGGTTGTCCTAGTAC
1 CCACGTCTACTATTGAGGTTGTCCTAGTAC
3509382 CCACGTCTACTATTGAGGTTGTCCTAGTAC
1 CCACGTCTACTATTGAGGTTGTCCTAGTAC
3509412 CCACGTCTACTATTGAGGTTGTCCTAG
1 CCACGTCTACTATTGAGGTTGTCCTAG
3509439 AACCAAACCA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (30 bp):
CCACGTCTACTATTGAGGTTGTCCTAGTAC
Found at i:3513673 original size:2 final size:2
Alignment explanation
Indices: 3513660--3513690 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3513650 TTTAGGGATT
*
3513660 TA TA TG 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 T
3513691 CAAAATCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3515738 original size:28 final size:27
Alignment explanation
Indices: 3515680--3515774 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 27
3515670 CTGTTGGTTG
3515680 AAAATATCCATCTACCACTTTTGGTGTTT
1 AAAATATCCAT-TA-CACTTTTGGTGTTT
3515709 AAAATATCCATTACTACTTTTGGT-TATT
1 AAAATATCCATTAC-ACTTTTGGTGT-TT
* *
3515737 AAAAGTATCCATT-CACTTTTGATGGTT
1 AAAA-TATCCATTACACTTTTGGTGTTT
3515764 AAAATTATCCA
1 AAAA-TATCCA
3515775 GGCACATATC
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
27 22 0.37
28 18 0.31
29 19 0.32
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (27 bp):
AAAATATCCATTACACTTTTGGTGTTT
Found at i:3520288 original size:20 final size:20
Alignment explanation
Indices: 3520259--3520310 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3520249 ATATGGGCTG
3520259 ACCCGGCCCAGCTC-AGCTCA
1 ACCCGGCCCAGCTCGA-CTCA
*
3520279 ACCCGACCCAGCTCGACTCA
1 ACCCGGCCCAGCTCGACTCA
*
3520299 GCCCGGCCCAGC
1 ACCCGGCCCAGC
3520311 CCTTGTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.19, C:0.52, G:0.21, T:0.08
Consensus pattern (20 bp):
ACCCGGCCCAGCTCGACTCA
Found at i:3520515 original size:40 final size:41
Alignment explanation
Indices: 3520434--3520517 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
3520424 GTTTATTTTT
* *
3520434 ATTTTTTTTAAAAAATTAATTTTTATAATTCTACTTGATAA
1 ATTTTTTTTAAAAAATTAATTTTTATAATTCTAATTCATAA
*
3520475 ATTTTTTATTAATAAAATT-A-TTTTATGATT-TAATTCATAA
1 ATTTTTT-TTAA-AAAATTAATTTTTATAATTCTAATTCATAA
3520515 ATT
1 ATT
3520518 GAATAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
40 11 0.29
41 16 0.42
42 5 0.13
43 6 0.16
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (41 bp):
ATTTTTTTTAAAAAATTAATTTTTATAATTCTAATTCATAA
Found at i:3528337 original size:23 final size:21
Alignment explanation
Indices: 3528284--3528338 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
3528274 AGGCTTTTTT
3528284 TAAAAAATAATAATAAAATTA
1 TAAAAAATAATAATAAAATTA
* **
3528305 TATAATAATAATTTTTAAAATTAA
1 TA-AAAAATAA-TAATAAAATT-A
3528329 TAAAAAATAA
1 TAAAAAATAA
3528339 ATTATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 7 0.26
23 15 0.56
24 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAATAATAATAAAATTA
Found at i:3557049 original size:69 final size:69
Alignment explanation
Indices: 3556930--3557070 Score: 228
Period size: 69 Copynumber: 2.0 Consensus size: 69
3556920 AAACTCTGTA
* *
3556930 ATGTCACTAAATAGTTTTATGTTATTGCAATAAATTTGGCCTACTTCTGTGACTTTTTCCATGTA
1 ATGTCACTAAATAGTTTTATGTTATTGCAATAAATTTGGCCTACTACTGTGACTTTTGCCATGTA
3556995 TGTG
66 TGTG
* * * *
3556999 ATGTGACTAAATAGTTTTATGTTATTGCCATAAATTTGGCCTTCTACTGTGACTTTTGCCTTGTA
1 ATGTCACTAAATAGTTTTATGTTATTGCAATAAATTTGGCCTACTACTGTGACTTTTGCCATGTA
3557064 TGTG
66 TGTG
3557068 ATG
1 ATG
3557071 GAGGCATTGG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (69 bp):
ATGTCACTAAATAGTTTTATGTTATTGCAATAAATTTGGCCTACTACTGTGACTTTTGCCATGTA
TGTG
Found at i:3561854 original size:104 final size:104
Alignment explanation
Indices: 3561674--3561880 Score: 405
Period size: 104 Copynumber: 2.0 Consensus size: 104
3561664 TTTTATTTCA
3561674 TAACATCTCTGTGCATCTTTCTTGTTGAATTTTATTTTGGCTTTGATAGTCTGACGATGTCCAAC
1 TAACATCTCTGTGCATCTTTCTTGTTGAATTTTATTTTGGCTTTGATAGTCTGACGATGTCCAAC
3561739 CATGTTTGTTATCTTTGATACAGCTTGATGAGATGCTTT
66 CATGTTTGTTATCTTTGATACAGCTTGATGAGATGCTTT
*
3561778 TAACATCTCTGTGCATCTTTCTTGTTGAATTTTATTTTGGCTTTGATAGTCTGACGATGTCCTAC
1 TAACATCTCTGTGCATCTTTCTTGTTGAATTTTATTTTGGCTTTGATAGTCTGACGATGTCCAAC
3561843 CATGTTTGTTATCTTTGATACAGCTTGATGAGATGCTT
66 CATGTTTGTTATCTTTGATACAGCTTGATGAGATGCTT
3561881 CAAAGGCAGG
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (104 bp):
TAACATCTCTGTGCATCTTTCTTGTTGAATTTTATTTTGGCTTTGATAGTCTGACGATGTCCAAC
CATGTTTGTTATCTTTGATACAGCTTGATGAGATGCTTT
Found at i:3571482 original size:80 final size:80
Alignment explanation
Indices: 3571349--3571597 Score: 272
Period size: 80 Copynumber: 3.1 Consensus size: 80
3571339 AGTAACGTTT
* * * *
3571349 TCATAAATCATT-ATCATGCTTAGCCTATAGTGTATATAACTATCTCAACACATACATTTCATGG
1 TCATAAATCATTCA-CATGCTTAGCCTATAGTGTACATGA-TATTTCAACACATACATCTCATGG
3571413 CATGCAT-TGCATAATC
64 CATGCATATGCATAATC
*
3571429 TCATAAATCATTCACATGCTTAGCCTATAGTGTACATGATATGTTCAACACATACAACTCATGGC
1 TCATAAATCATTCACATGCTTAGCCTATAGTGTACATGATAT-TTCAACACATACATCTCATGGC
* * *
3571494 ATGCATGTGAAAAATC
65 ATGCATATGCATAATC
* * * * * * * *
3571510 TCATAATTCATCCATATGCTTAGCCCATAGTTTACATGACATTCTTAACACATACATCTCATGAC
1 TCATAAATCATTCACATGCTTAGCCTATAGTGTACATGATATT-TCAACACATACATCTCATGGC
*
3571575 AT--ATATGTCATTATC
65 ATGCATATG-CATAATC
3571590 TCATAAAT
1 TCATAAAT
3571598 GGAATTCATG
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
79 7 0.05
80 72 0.50
81 64 0.45
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.34
Consensus pattern (80 bp):
TCATAAATCATTCACATGCTTAGCCTATAGTGTACATGATATTTCAACACATACATCTCATGGCA
TGCATATGCATAATC
Found at i:3571546 original size:81 final size:80
Alignment explanation
Indices: 3571349--3571572 Score: 256
Period size: 81 Copynumber: 2.8 Consensus size: 80
3571339 AGTAACGTTT
* * * * *
3571349 TCATAAATCAT-TATCATGCTTAGCCTATAGTGTATATAAC-TATCTCAACACATACATTTCATG
1 TCATAAATCATCCA-CATGCTTAGCCCATAGTGTACATGACAT-TCTCAACACATACATCTCATG
* *
3571412 GCATGCATTGCATAATC
64 GCATGCATTGAAAAATC
* * * *
3571429 TCATAAATCATTCACATGCTTAGCCTATAGTGTACATGATATGT-TCAACACATACAACTCATGG
1 TCATAAATCATCCACATGCTTAGCCCATAGTGTACATGACAT-TCTCAACACATACATCTCATGG
3571493 CATGCATGTGAAAAATC
65 CATGCAT-TGAAAAATC
* * * *
3571510 TCATAATTCATCCATATGCTTAGCCCATAGTTTACATGACATTCTTAACACATACATCTCATG
1 TCATAAATCATCCACATGCTTAGCCCATAGTGTACATGACATTCTCAACACATACATCTCATG
3571573 ACATATATGT
Statistics
Matches: 123, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
80 60 0.49
81 63 0.51
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (80 bp):
TCATAAATCATCCACATGCTTAGCCCATAGTGTACATGACATTCTCAACACATACATCTCATGGC
ATGCATTGAAAAATC
Found at i:3572807 original size:17 final size:16
Alignment explanation
Indices: 3572782--3572824 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3572772 AATTTGGATT
*
3572782 AAATAAAAATATAAAAA
1 AAATCAAAATAT-AAAA
*
3572799 AAATCAAAATCTAAAA
1 AAATCAAAATATAAAA
*
3572815 GAATCAAAAT
1 AAATCAAAAT
3572825 CAAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (16 bp):
AAATCAAAATATAAAA
Found at i:3572819 original size:16 final size:15
Alignment explanation
Indices: 3572795--3572829 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
3572785 TAAAAATATA
3572795 AAAAAAATCAAAATC
1 AAAAAAATCAAAATC
*
3572810 TAAAAGAATCAAAATC
1 -AAAAAAATCAAAATC
3572826 AAAA
1 AAAA
3572830 TTTTAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.14
Consensus pattern (15 bp):
AAAAAAATCAAAATC
Found at i:3574665 original size:28 final size:28
Alignment explanation
Indices: 3574634--3574703 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
3574624 AAGAAATGCG
3574634 TTTCCAACGGAATTCCGTTTCAAAAGAA
1 TTTCCAACGGAATTCCGTTTCAAAAGAA
3574662 TTTCCAACGGAATTCCGTTTCAAAAGAA
1 TTTCCAACGGAATTCCGTTTCAAAAGAA
3574690 TTTCCAACGGAATT
1 TTTCCAACGGAATT
3574704 TTCGTTGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (28 bp):
TTTCCAACGGAATTCCGTTTCAAAAGAA
Found at i:3574801 original size:26 final size:25
Alignment explanation
Indices: 3574769--3574838 Score: 122
Period size: 25 Copynumber: 2.7 Consensus size: 25
3574759 TTTTCAACAG
3574769 AATTTTTTGACAGAATTTTCTGTTGAA
1 AATTTTTT-AC-GAATTTTCTGTTGAA
3574796 AATTTTTTACGAATTTTCTGTTGAA
1 AATTTTTTACGAATTTTCTGTTGAA
3574821 AATTTTTTACGAATTTTC
1 AATTTTTTACGAATTTTC
3574839 AACGGAAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 33 0.77
26 2 0.05
27 8 0.19
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (25 bp):
AATTTTTTACGAATTTTCTGTTGAA
Found at i:3574846 original size:25 final size:25
Alignment explanation
Indices: 3574793--3574846 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
3574783 ATTTTCTGTT
****
3574793 GAAAATTTTTTACGAATTTTCTGTT
1 GAAAATTTTTTACGAATTTTCAACG
3574818 GAAAATTTTTTACGAATTTTCAACG
1 GAAAATTTTTTACGAATTTTCAACG
3574843 GAAA
1 GAAA
3574847 GTATTTTCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (25 bp):
GAAAATTTTTTACGAATTTTCAACG
Found at i:3579544 original size:2 final size:2
Alignment explanation
Indices: 3579537--3579573 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3579527 TAACTCTTTA
3579537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3579574 AGCAAACATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3582970 original size:40 final size:42
Alignment explanation
Indices: 3582925--3583002 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 42
3582915 TAAATTTTTA
*
3582925 TTTCTTGTAGTAAT-ACCTAGAACTATTA-AA-AATAATTATT
1 TTTCTTATAGTAATGA-CTAGAACTATTACAAGAATAATTATT
*
3582965 TTTCTTATAGTAATGAGTAGAACTATTACAAGAATAAT
1 TTTCTTATAGTAATGACTAGAACTATTACAAGAATAAT
3583003 AAAAATCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 24 0.73
41 3 0.09
42 6 0.18
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (42 bp):
TTTCTTATAGTAATGACTAGAACTATTACAAGAATAATTATT
Found at i:3587030 original size:18 final size:18
Alignment explanation
Indices: 3587009--3587045 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3586999 TAACAGTCAA
3587009 GGTAACCAATAATTCTTT
1 GGTAACCAATAATTCTTT
3587027 GGTAACCAATAATTCTTT
1 GGTAACCAATAATTCTTT
3587045 G
1 G
3587046 CTACTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (18 bp):
GGTAACCAATAATTCTTT
Found at i:3588808 original size:2 final size:2
Alignment explanation
Indices: 3588803--3588838 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3588793 GTGTGTGTGT
3588803 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3588839 AGTAAAGGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.