Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 34 of 64
Found at i:5329694 original size:3 final size:3
Alignment explanation
Indices: 5329686--5329953 Score: 190
Period size: 3 Copynumber: 94.0 Consensus size: 3
5329676 TTTTTAATAC
* * * * *
5329686 TAT TAT TAT TTT TTT TGT TAT TAG TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5329734 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
5329782 TAT TAT CA- TAG TA- TAG TA- TAC TAT GTCA- TAG TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -T-AT TAT TAT TAT TAT TAT
* * * *
5329823 TA- TAC TAT TAC TA- TAT TA- TGT TA- TAT TAT TAG TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
5329865 CA- TAT T-G TAT TAT TAT TA- TAT TAT TAA TA- GAT GAT GAT GAT GAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
5329909 GAT GAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5329954 CATCTTTATT
Statistics
Matches: 226, Mismatches: 21, Indels: 36
0.80 0.07 0.13
Matches are distributed among these distances:
2 26 0.12
3 198 0.88
4 1 0.00
5 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:5329863 original size:26 final size:26
Alignment explanation
Indices: 5329731--5329888 Score: 97
Period size: 26 Copynumber: 5.8 Consensus size: 26
5329721 TTATTATTAT
* *
5329731 TATTATTATTATTATTATTATTATTATTA
1 TATTA-TATTATTACTA-TATTA-TATCA
*
5329760 TTATTATTATTATTATTATTATTATTATCA
1 -TATTA-TATTATTACTA-TATTA-TATCA
* * * *
5329790 TAGTATAGTA-TACTATGTCATAGT-A
1 TATTATATTATTACTATATTATA-TCA
* *
5329815 TATTATATTA-TACTATTACTATATTA
1 TATTATATTATTACTA-TATTATATCA
* *
5329841 TGTTATATTATTAGTATATTATATCA
1 TATTATATTATTACTATATTATATCA
* *
5329867 TATTGTATTATTATTATATTAT
1 TATTATATTATTACTATATTAT
5329889 TAATAGATGA
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
25 17 0.16
26 45 0.42
27 8 0.08
28 4 0.04
29 4 0.04
30 28 0.26
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (26 bp):
TATTATATTATTACTATATTATATCA
Found at i:5335917 original size:156 final size:155
Alignment explanation
Indices: 5335622--5335931 Score: 428
Period size: 156 Copynumber: 2.0 Consensus size: 155
5335612 ACTACCAACA
* *
5335622 TAATAGGTGTAGGTGGCATAGCCAAAAGTGAAAAATGTTATACCTAAGAGACCTTGGAGAAAGCA
1 TAATAGGTGTAGGTGGCATAACCAAAAGTGAAAAATGTTATACCTAAGAGACCTTAGAGAAAGCA
* * *
5335687 AAGATAAATAAGAGGATAGAGAAATATACTAAACTTGAATTGATCTCAAAGAAAGACATCCCAAA
66 AAGATAAATAAGAGGATAGAGAAACAGACTAAACCTGAATTGATCTCAAAGAAAGACATCCCAAA
* *
5335752 GTCTGTGCTAGAAAAAAAAAGCTTGC
131 GCCTATGCTAG-AAAAAAAAGCTTGC
* * *
5335778 TAATAGGTGTTGGTGGCATAACCAAAAGTGGAAGAA-GTTATACCTAGGAGACCTTAGAGAAAGC
1 TAATAGGTGTAGGTGGCATAACCAAAAGT-GAAAAATGTTATACCTAAGAGACCTTAGAGAAAGC
* * * *
5335842 AAAGA-AAGATAAGGGGATAGAGAAACAGACTGAACCTGAATTGATC-CTAAAGAAAGATATCCT
65 AAAGATAA-ATAAGAGGATAGAGAAACAGACTAAACCTGAATTGATCTC-AAAGAAAGACATCCC
*
5335905 AAAGCCTATGCTAGAAAAAGAAGCTTG
128 AAAGCCTATGCTAGAAAAAAAAGCTTG
5335932 TGAGTTTTTA
Statistics
Matches: 136, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
155 15 0.11
156 116 0.85
157 5 0.04
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (155 bp):
TAATAGGTGTAGGTGGCATAACCAAAAGTGAAAAATGTTATACCTAAGAGACCTTAGAGAAAGCA
AAGATAAATAAGAGGATAGAGAAACAGACTAAACCTGAATTGATCTCAAAGAAAGACATCCCAAA
GCCTATGCTAGAAAAAAAAGCTTGC
Found at i:5337983 original size:20 final size:20
Alignment explanation
Indices: 5337958--5338006 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5337948 CTATATAGAG
5337958 AGCCTTTTGCTATAAGGTTA
1 AGCCTTTTGCTATAAGGTTA
5337978 AGCCTTTTGCTATAAGGTTA
1 AGCCTTTTGCTATAAGGTTA
*
5337998 TGCCTTTTG
1 AGCCTTTTG
5338007 GATTGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (20 bp):
AGCCTTTTGCTATAAGGTTA
Found at i:5342358 original size:3 final size:3
Alignment explanation
Indices: 5342350--5342530 Score: 99
Period size: 3 Copynumber: 61.0 Consensus size: 3
5342340 TTTTTAGTAC
* *
5342350 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAG TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * ** * *
5342396 TATT TAT TAC TAT TAT TAT TGT TAAT TAT TAT TGC TAG TAT T-G TAT
1 TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
5342442 TAT TAT TGT ATAG TA- TAC TA- TAT CAT TCT ATAT TA- TAT TA- TAC
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * *
5342485 TAT TAC TA- TAT TA- TGT TA- TAT TAT TAG TAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
5342528 TAT
1 TAT
5342531 CATCATCATC
Statistics
Matches: 136, Mismatches: 28, Indels: 28
0.71 0.15 0.15
Matches are distributed among these distances:
2 14 0.10
3 108 0.79
4 14 0.10
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:5343386 original size:14 final size:12
Alignment explanation
Indices: 5343371--5343443 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 12
5343361 TTTTTCTTAT
5343371 TTTTATTTTTTGA
1 TTTTATTTTTT-A
5343384 TTTTATTTTTATAA
1 TTTTATTTTT-T-A
5343398 TTTTATTTTTTTA
1 TTTTA-TTTTTTA
* *
5343411 GTTT-CTTTTTA
1 TTTTATTTTTTA
* *
5343422 TTTTATTTATCA
1 TTTTATTTTTTA
5343434 TTATTATTTT
1 TT-TTATTTT
5343444 ACTAATTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
11 9 0.19
12 6 0.12
13 20 0.42
14 8 0.17
15 5 0.10
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:5343401 original size:27 final size:27
Alignment explanation
Indices: 5343371--5343422 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5343361 TTTTTCTTAT
*
5343371 TTTTATTTTTTGATTTTATTTTTATAA
1 TTTTATTTTTTGAGTTTATTTTTATAA
* *
5343398 TTTTATTTTTTTAGTTTCTTTTTAT
1 TTTTATTTTTTGAGTTTATTTTTAT
5343423 TTTATTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTTATTTTTTGAGTTTATTTTTATAA
Found at i:5343405 original size:19 final size:19
Alignment explanation
Indices: 5343367--5343406 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5343357 ATGTTTTTTC
*
5343367 TTATTTTTATTTTTTGATT
1 TTATTTTTATATTTTGATT
5343386 TTATTTTTATAATTTT-ATT
1 TTATTTTTAT-ATTTTGATT
5343405 TT
1 TT
5343407 TTTAGTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (19 bp):
TTATTTTTATATTTTGATT
Found at i:5344741 original size:58 final size:58
Alignment explanation
Indices: 5344673--5345175 Score: 483
Period size: 58 Copynumber: 8.6 Consensus size: 58
5344663 TTTTGTACAG
* *
5344673 GAAAATTTGATACTTTCAACTTTTCCCAAAAAATATTCTTTTG-AAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCCAAAAAATATT-TTTTGAAAACTTTAATTTCAA
* * *
5344731 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATTCA-TTTTTGAAAAC-TTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCC-CAAAAAAT-ATTTTTTGAAAACTTTAATTTCAA
* * * * *
5344789 GGAAAATTGATACTTGCAAATTTTTCCCCAAAAATATTTTTTGCGAAAAGC-TTATTTTCAA
1 GAAAAATTGATACTTTC-AACTTTTCCCAAAAAATATTTTTT--GAAAA-CTTTAATTTCAA
* * *
5344850 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTGTTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCC-AAAAA-A--TAT-TTTTTGAAAACTTTAATTTCAA
*** * *
5344913 GAAAAATTGATACTTTCAACTTTTCCTC-AAAAAT-CCCTTTCAAAA-TTT-ATCTTTAA
1 GAAAAATTGATACTTTCAACTTTTCC-CAAAAAATATTTTTTGAAAACTTTAAT-TTCAA
* *
5344969 GGAAAATTAATACTTTCAACTTTTTCCC--AAAATATTTTTTGAAAACTTTAATTTCAA
1 GAAAAATTGATACTTTCAAC-TTTTCCCAAAAAATATTTTTTGAAAACTTTAATTTCAA
* *
5345026 AAAAAATTGATACTTTCAACTTTTCTCC-AAAAATATTTTTTGGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTC-CCAAAAAATATTTTTT-GAAAACTTTAATTTCAA
* * ** * *
5345085 GGAAAATTAATACTTTCAACTTTTCCTCAAAAAACCTTTTTTGAAAA-TTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCC-CAAAAAATATTTTTTGAAAACTTTAATTTCAA
*
5345143 -AGAAAATTGATACTTTCAACTTTTCCCCAAAAA
1 GA-AAAATTGATACTTTCAACTTTTCCCAAAAAA
5345176 CCTTTTTTTT
Statistics
Matches: 373, Mismatches: 46, Indels: 53
0.79 0.10 0.11
Matches are distributed among these distances:
55 7 0.02
56 37 0.10
57 46 0.12
58 109 0.29
59 65 0.17
60 26 0.07
61 31 0.08
62 6 0.02
63 38 0.10
64 3 0.01
65 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTGAAAACTTTAATTTCAA
Found at i:5345236 original size:30 final size:28
Alignment explanation
Indices: 5345202--5345284 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 28
5345192 TTTATTTAAA
* *
5345202 GAAAATAGAATAATAAAACAAAATAAAAGT
1 GAAAATAAAAAAAT-AAA-AAAATAAAAGT
5345232 GAAAATAAAAAAATAAAAAAAT-AAA--
1 GAAAATAAAAAAATAAAAAAATAAAAGT
5345257 GAAAAGTAAAACAAA-AATAAAAATAAAA
1 GAAAA-TAAAA-AAATAA-AAAAATAAAA
5345285 TAAAGGTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
25 5 0.11
26 7 0.15
27 12 0.26
28 8 0.17
29 3 0.06
30 12 0.26
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.13
Consensus pattern (28 bp):
GAAAATAAAAAAATAAAAAAATAAAAGT
Found at i:5345243 original size:7 final size:8
Alignment explanation
Indices: 5345233--5345284 Score: 61
Period size: 8 Copynumber: 6.1 Consensus size: 8
5345223 AATAAAAGTG
5345233 AAAATAAA
1 AAAATAAA
5345241 AAAATAAA
1 AAAATAAA
5345249 AAAATAAA
1 AAAATAAA
5345257 GAAAAGTAAA
1 -AAAA-TAAA
5345267 ACAAA-AATA
1 A-AAATAA-A
5345276 AAAATAAA
1 AAAATAAA
5345284 A
1 A
5345285 TAAAGGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 23 0.59
9 9 0.23
10 7 0.18
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:5345295 original size:11 final size:11
Alignment explanation
Indices: 5345203--5345288 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 11
5345193 TTATTTAAAG
5345203 AAAATAGAATAAT
1 AAAATA-AA-AAT
*
5345216 AAAA-CAAAAT
1 AAAATAAAAAT
*
5345226 AAAAGTGAAAAT
1 AAAA-TAAAAAT
*
5345238 AAAA-AAATAAA
1 AAAATAAA-AAT
*
5345249 AAAATAAAGA-
1 AAAATAAAAAT
*
5345259 AAAGTAAAACA-
1 AAAATAAAA-AT
5345270 AAAATAAAAAT
1 AAAATAAAAAT
5345281 AAAATAAA
1 AAAATAAA
5345289 GGTAAAAGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
10 17 0.29
11 26 0.44
12 12 0.20
13 4 0.07
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:5345328 original size:4 final size:4
Alignment explanation
Indices: 5345321--5345358 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
5345311 CTAATCTAAT
*
5345321 AATA AATA AATA AATA AATA AACA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
5345359 ACCTAGAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:5345641 original size:15 final size:16
Alignment explanation
Indices: 5345616--5345645 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5345606 AACCTCCTCC
5345616 CTCTCTCTCTTCCTTT
1 CTCTCTCTCTTCCTTT
5345632 CTCT-TCTCTTCCTT
1 CTCTCTCTCTTCCTT
5345646 CTTTCTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (16 bp):
CTCTCTCTCTTCCTTT
Found at i:5345893 original size:14 final size:13
Alignment explanation
Indices: 5345866--5345907 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
5345856 AAAATTTTTC
5345866 AAAAATTTCCAAA
1 AAAAATTTCCAAA
**
5345879 AAAAATTTCGTAA
1 AAAAATTTCCAAA
*
5345892 AAAAATCTCCAAA
1 AAAAATTTCCAAA
5345905 AAA
1 AAA
5345908 CAAAATTCCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.21
Consensus pattern (13 bp):
AAAAATTTCCAAA
Found at i:5346245 original size:21 final size:21
Alignment explanation
Indices: 5346209--5346269 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
5346199 AATATTAATG
5346209 AAAATAAATAA-A-ATAAATC
1 AAAATAAATAACAGATAAATC
*
5346228 AAAA-AAATTAACAGATAAATT
1 AAAATAAA-TAACAGATAAATC
5346249 AAAATTAAATAACAGATAAAT
1 AAAA-TAAATAACAGATAAAT
5346270 TATAACATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 3 0.08
19 7 0.19
20 1 0.03
21 10 0.28
22 12 0.33
23 3 0.08
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAAATAACAGATAAATC
Found at i:5346247 original size:12 final size:12
Alignment explanation
Indices: 5346232--5346271 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
5346222 TAAATCAAAA
5346232 AAATTAACAGAT
1 AAATTAACAGAT
5346244 AAATTAA-A-ATT
1 AAATTAACAGA-T
5346255 AAA-TAACAGAT
1 AAATTAACAGAT
5346266 AAATTA
1 AAATTA
5346272 TAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (12 bp):
AAATTAACAGAT
Found at i:5346258 original size:32 final size:31
Alignment explanation
Indices: 5346177--5346260 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
5346167 ATAAATCAAA
*
5346177 AAAATATAA-AAAATTAAATAAAAATATTAATG
1 AAAATA-AATAAAATTAAATAAAAAAATTAA-G
5346209 AAAATAAATAAAA-TAAATCAAAAAAATTAA-
1 AAAATAAATAAAATTAAAT-AAAAAAATTAAG
* *
5346239 CAGATAAATTAAAATTAAATAA
1 AAAATAAA-TAAAATTAAATAA
5346261 CAGATAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
30 6 0.13
31 14 0.31
32 25 0.56
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (31 bp):
AAAATAAATAAAATTAAATAAAAAAATTAAG
Found at i:5346264 original size:22 final size:20
Alignment explanation
Indices: 5346186--5346271 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 20
5346176 AAAAATATAA
* *
5346186 AAAATTAAATAAAAATATTAATG
1 AAAA-TAAATAAAGATA--AATT
*
5346209 AAAATAAATAAA-ATAAATC
1 AAAATAAATAAAGATAAATT
5346228 AAAA-AAATTAACAGATAAATT
1 AAAATAAA-TAA-AGATAAATT
5346249 AAAATTAAATAACAGATAAATT
1 AAAA-TAAATAA-AGATAAATT
5346271 A
1 A
5346272 TAACATATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.05
19 10 0.18
20 1 0.02
21 13 0.23
22 22 0.39
23 7 0.12
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATAAATAAAGATAAATT
Found at i:5346404 original size:3 final size:3
Alignment explanation
Indices: 5346392--5346426 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
5346382 AAAAATATAT
5346392 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5346427 AAATGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:5346410 original size:9 final size:8
Alignment explanation
Indices: 5346374--5346426 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
5346364 ATAAGATAAA
*
5346374 AATAAAAG
1 AATAAAAT
5346382 AA-AAATAT
1 AATAAA-AT
5346390 ATATAAAAT
1 A-ATAAAAT
5346399 AATAATAAT
1 AATAA-AAT
5346408 AATAATAAT
1 AATAA-AAT
5346417 AATAAAAT
1 AATAAAAT
5346425 AA
1 AA
5346427 AAATGTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 3 0.08
8 13 0.32
9 21 0.52
10 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (8 bp):
AATAAAAT
Found at i:5346820 original size:83 final size:83
Alignment explanation
Indices: 5346625--5346961 Score: 426
Period size: 83 Copynumber: 4.1 Consensus size: 83
5346615 CTGATCAAAA
* *** * * ** * ** *
5346625 CTCCTCTAAGCAGAGGCTGAACGAC-TTTGAAAAAATAAATGGCTTTTCTAATCAGAGGTTCAAC
1 CTCCTCTAAACAGAGGCACCACGACTTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
5346689 GACTTTGAAAAAATAAATTA
65 GACTTTG-AAAAATAAATTG
5346709 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
5346774 ACTTTGAAAAATATATTG
66 ACTTTGAAAAATAAATTG
* * * *
5346792 CTCCTCTAAACAGAGGCAACATGACTTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCACG
1 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
5346857 ACTTTGAAAAGTAAATTG
66 ACTTTGAAAAATAAATTG
* * *
5346875 CTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTTTAAACAAAGGTACCACG
1 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
* *
5346939 ACTTTGAAAAGTAAATTA
66 ACTTTGAAAAATAAATTG
5346957 CTCCT
1 CTCCT
5346962 TGACAATCAT
Statistics
Matches: 224, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
82 56 0.25
83 110 0.49
84 54 0.24
85 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (83 bp):
CTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAATAAATTG
Found at i:5346962 original size:41 final size:41
Alignment explanation
Indices: 5346625--5346961 Score: 422
Period size: 41 Copynumber: 8.1 Consensus size: 41
5346615 CTGATCAAAA
* *** * *
5346625 CTCCTCTAAGCAGAGGCTGAACGACTTTGAAAAAATAAATGG
1 CTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTG
** * ** * * *
5346667 CTTTTCTAATCAGAGGTTCAACGACTTTGAAAAAATAAATTA
1 CTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTG
5346709 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTG
* *
5346751 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAATATATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
* * *
5346792 CTCCTCTAAACAGAGGCAACATGACTTTTGGAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTG
*
5346834 CTCCTCTAAATAGAGGCACCACGACTTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
5346875 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
* * * *
5346916 CTCCTTTAAACAAAGGTACCACGACTTTGAAAAGTAAATTA
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
5346957 CTCCT
1 CTCCT
5346962 TGACAATCAT
Statistics
Matches: 262, Mismatches: 31, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
41 134 0.51
42 124 0.47
43 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (41 bp):
CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
Found at i:5347983 original size:23 final size:21
Alignment explanation
Indices: 5347963--5348031 Score: 86
Period size: 23 Copynumber: 3.1 Consensus size: 21
5347953 TCCTTTTTCA
5347963 TTCACTTTTTTTTTTT-TTTTT
1 TTCA-TTTTTTTTTTTATTTTT
5347984 TTCATTTTTCATTTTTTATTTTT
1 TTCATTTTT--TTTTTTATTTTT
5348007 TTCATTTTTATTTTTTTATTTTT
1 TTCA-TTTT-TTTTTTTATTTTT
5348030 TT
1 TT
5348032 TCAAGCATAG
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.12
21 4 0.09
22 6 0.14
23 23 0.53
24 4 0.09
25 1 0.02
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (21 bp):
TTCATTTTTTTTTTTATTTTT
Found at i:5358613 original size:58 final size:59
Alignment explanation
Indices: 5358368--5358760 Score: 430
Period size: 58 Copynumber: 6.7 Consensus size: 59
5358358 TTTTGTCCAG
* ** *
5358368 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAATATTTTTTTGTGGAAAGCTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCCC-AAAAATCTTTTTTT-T-GAAAATTTATTTTTAA
* * ** *
5358430 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATC---CGTTTGAAAATTTATCTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
* **
5358486 GAAAAATTGATACTTTCAACTTTTCCCC-AAAA--TATTTTTTGAAAACTTTAATTTCGAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTGAAAA-TTT-ATTTTTAA
*
5358544 G-AAAATTGATACTTTCAACTTTTCCTC-AAAATCTTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
* * * * **
5358601 GGAAAATTGATACTTTCAACTTTTTCCCAAAAA--TATTTTTTGAAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTG-AAAA-TTTATTTTTAA
* * *
5358660 GAAAAATTTATACTTTCAACTTTTCCTCAAAAAAC-TTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
* *
5358718 GAAAAATTGATACTTTTAACTTTTCCCCAAAAACCTTTTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTT
5358761 TTAGATTTTA
Statistics
Matches: 279, Mismatches: 38, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.01
56 46 0.16
57 48 0.17
58 78 0.28
59 64 0.23
60 7 0.03
61 6 0.02
62 26 0.09
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
Found at i:5358702 original size:117 final size:115
Alignment explanation
Indices: 5358368--5358750 Score: 540
Period size: 117 Copynumber: 3.3 Consensus size: 115
5358358 TTTTGTCCAG
* * * *
5358368 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAATATTTTTTTGTGGAAAGC-TTATTTTCAAGG
1 GAAAAATTGATACTTTCAACTTTTCCCC-AAAAATA--TTTTT-T-GAAAACTTTAATTTCGAGA
*** *
5358432 AAAATTGATACTTTCAACTTTTCCTCAAAAA-TCCGTTTGAAAATTTATCTTTAA
61 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAA
5358486 GAAAAATTGATACTTTCAACTTTTCCCC-AAAATATTTTTTGAAAACTTTAATTTCGA-AGAAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGAGA-AAAA
*
5358549 TTGATACTTTCAACTTTTCCTCAAAATCTTTTTTTTGAAAATTTATTTTTAA
65 TTGATACTTTCAACTTTTCCTCAAAAAC-TTTTTTTGAAAATTTATTTTTAA
* *
5358601 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAAACTTTAATTTCGAGAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTG-AAAACTTTAATTTCGAGAAAAA
*
5358666 TTTATACTTTCAACTTTTCCTCAAAAAACTTTTTTTGAAAATTTATTTTTAA
65 TTGATACTTTCAACTTTTCCTC-AAAAACTTTTTTTGAAAATTTATTTTTAA
*
5358718 GAAAAATTGATACTTTTAACTTTTCCCCAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAA
5358751 CCTTTTTTTT
Statistics
Matches: 241, Mismatches: 16, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
112 5 0.02
113 39 0.16
114 5 0.02
115 45 0.19
116 19 0.08
117 94 0.39
118 34 0.14
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (115 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAAAT
TGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAA
Found at i:5358786 original size:5 final size:5
Alignment explanation
Indices: 5358778--5358873 Score: 58
Period size: 5 Copynumber: 18.6 Consensus size: 5
5358768 TTATTTAAAG
*
5358778 AAAAT AAAAT --AAC AAAAT AAAAT AAAAAGT GAAAAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAA-T -AAAAT AAAAT AAAAT
* *
5358823 AAAA- AAAAT AAAGA- AAAGT AAAAACA AAAAT AAAAAT AAAAT AAAGAT
1 AAAAT AAAAT AAA-AT AAAAT -AAAA-T AAAAT -AAAAT AAAAT AAA-AT
5358871 AAA
1 AAA
5358874 GAAATATTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 23
0.71 0.07 0.23
Matches are distributed among these distances:
3 2 0.03
4 8 0.11
5 34 0.47
6 23 0.32
7 5 0.07
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:5358796 original size:13 final size:12
Alignment explanation
Indices: 5358778--5358867 Score: 76
Period size: 13 Copynumber: 7.1 Consensus size: 12
5358768 TTATTTAAAG
5358778 AAAATAAAATAA
1 AAAATAAAATAA
5358790 CAAAATAAAATAA
1 -AAAATAAAATAA
*
5358803 AAAGTGAAAATAAAA
1 AAAAT-AAAAT--AA
*
5358818 AAAATAAAAAAA
1 AAAATAAAATAA
*
5358830 ATAAAGAAAAGTAA
1 A-AAATAAAA-TAA
5358844 AAACA-AAAAT-A
1 AAA-ATAAAATAA
5358855 AAAATAAAATAA
1 AAAATAAAATAA
5358867 A
1 A
5358868 GATAAAGAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.02
11 9 0.14
12 10 0.16
13 30 0.47
14 8 0.12
15 6 0.09
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:5358801 original size:18 final size:18
Alignment explanation
Indices: 5358778--5358866 Score: 56
Period size: 18 Copynumber: 4.7 Consensus size: 18
5358768 TTATTTAAAG
5358778 AAAATAAAATAACAAAAT
1 AAAATAAAATAACAAAAT
**
5358796 AAAATAAAA-AGTGAAAAT
1 AAAATAAAATA-ACAAAAT
*
5358814 AAAA-AAAATAAAAAAAAT
1 AAAATAAAAT-AACAAAAT
* *
5358832 AAAGAAAAGTAAAAACAAAAAT
1 AAA-ATAA--AATAAC-AAAAT
5358854 AAAAATAAAATAA
1 -AAAATAAAATAA
5358867 AGATAAAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
17 5 0.09
18 26 0.48
19 2 0.04
20 6 0.11
21 2 0.04
22 10 0.19
23 3 0.06
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (18 bp):
AAAATAAAATAACAAAAT
Found at i:5358839 original size:22 final size:22
Alignment explanation
Indices: 5358814--5358856 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5358804 AAGTGAAAAT
5358814 AAAA-AAAATAAAAAAAATAAAG
1 AAAAGAAAA-AAAAAAAATAAAG
* *
5358836 AAAAGTAAAAACAAAAATAAA
1 AAAAGAAAAAAAAAAAATAAA
5358857 AATAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.84, C:0.02, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAGAAAAAAAAAAAATAAAG
Found at i:5358852 original size:34 final size:33
Alignment explanation
Indices: 5358802--5358874 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
5358792 AAATAAAATA
* *
5358802 AAAAGTGAAAATAAAAAAAATAAAAAAAATAAAG
1 AAAAGTAAAAACAAAAAAAA-AAAAAAAATAAAG
* *
5358836 AAAAGTAAAAACAAAAATAAAAATAAAATAAAG
1 AAAAGTAAAAACAAAAAAAAAAAAAAAATAAAG
5358869 ATAAAG
1 A-AAAG
5358875 AAATATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 13 0.38
34 21 0.62
ACGTcount: A:0.78, C:0.01, G:0.08, T:0.12
Consensus pattern (33 bp):
AAAAGTAAAAACAAAAAAAAAAAAAAAATAAAG
Found at i:5359809 original size:12 final size:12
Alignment explanation
Indices: 5359789--5359833 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
5359779 TCAGATAAAT
*
5359789 CAAAAAAATTAA
1 CAAATAAATTAA
5359801 CAAATAAATTAA
1 CAAATAAATTAA
*
5359813 -AATTAAA-TAA
1 CAAATAAATTAA
5359823 CAAATAAATTA
1 CAAATAAATTA
5359834 TAACATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 3 0.11
11 12 0.43
12 13 0.46
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
CAAATAAATTAA
Found at i:5359880 original size:3 final size:3
Alignment explanation
Indices: 5359872--5360003 Score: 56
Period size: 3 Copynumber: 42.3 Consensus size: 3
5359862 ATTAACAGAA
* * *
5359872 AAT AAT AAT AAT AAT AAT AAT AAT AAG GAT -AT ATAT ATT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT
* * * *
5359918 AGT AGT AAT GAAT AAAT AAAT ACAT AA- GAT AAA AAT AAT ATAT ATAT
1 AAT AAT AAT -AAT -AAT -AAT A-AT AAT AAT AAT AAT AAT A-AT A-AT
* * * *
5359965 ATAT AAA AAC AAT AAT AAA AAT AA- AAT AA- AAT AAA AAT A
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5360004 TAAAATACAA
Statistics
Matches: 101, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
2 7 0.07
3 64 0.63
4 30 0.30
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5360378 original size:44 final size:43
Alignment explanation
Indices: 5360193--5360390 Score: 184
Period size: 44 Copynumber: 4.5 Consensus size: 43
5360183 CGTTATGACA
* *
5360193 AAAGGCTTAACAACTTTTGAAAAACATAAAAGACTTCTCTCAAC
1 AAAGGCTTAACAACTTTTGAAAAATATAAAAGAC-TCTCTAAAC
* * * * * * *
5360237 AGAGGTTTAACAACATTTAAAAAATATAAGAGGCTCTTTTAAAC
1 AAAGGCTTAACAACTTTTGAAAAATATAAAAGACTC-TCTAAAC
* ** *
5360281 AAAGTCCAAACAATTTTTGAAAAATATAAAA-AGCTCCTCTAAAC
1 AAAGGCTTAACAACTTTTGAAAAATATAAAAGA-CT-CTCTAAAC
* * *
5360325 AGAA-ACTTAACAACTTTTGAAAAATATAAAAGACTCATCTCAAT
1 A-AAGGCTTAACAACTTTTGAAAAATATAAAAGACTC-TCTAAAC
5360369 AAAGGCTTAACAACTTTTGAAA
1 AAAGGCTTAACAACTTTTGAAA
5360391 TGAATTAAAA
Statistics
Matches: 120, Mismatches: 27, Indels: 14
0.75 0.17 0.09
Matches are distributed among these distances:
43 5 0.04
44 111 0.93
45 4 0.03
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (43 bp):
AAAGGCTTAACAACTTTTGAAAAATATAAAAGACTCTCTAAAC
Found at i:5360381 original size:88 final size:88
Alignment explanation
Indices: 5360193--5360390 Score: 218
Period size: 88 Copynumber: 2.2 Consensus size: 88
5360183 CGTTATGACA
* * ***
5360193 AAAGGCTTAACAACTTTTGAAAAACATAAAAGACTTCTCTCAACAGAGGTTTAACAACATTTAAA
1 AAAGGCTTAACAACTTTTGAAAAACATAAAAGACTCCTCTAAACAGAAACTTAACAACATTTAAA
* * * *
5360258 AAATATAAGAGGCTCTTTTAAAC
66 AAATATAAAAGACTCATCTAAAC
* ** * * * *
5360281 AAAGTCCAAACAATTTTTGAAAAATATAAAA-AGCTCCTCTAAACAGAAACTTAACAACTTTTGA
1 AAAGGCTTAACAACTTTTGAAAAACATAAAAGA-CTCCTCTAAACAGAAACTTAACAACATTTAA
* *
5360345 AAAATATAAAAGACTCATCTCAAT
65 AAAATATAAAAGACTCATCTAAAC
5360369 AAAGGCTTAACAACTTTTGAAA
1 AAAGGCTTAACAACTTTTGAAA
5360391 TGAATTAAAA
Statistics
Matches: 87, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
87 1 0.01
88 86 0.99
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (88 bp):
AAAGGCTTAACAACTTTTGAAAAACATAAAAGACTCCTCTAAACAGAAACTTAACAACATTTAAA
AAATATAAAAGACTCATCTAAAC
Found at i:5361294 original size:22 final size:22
Alignment explanation
Indices: 5361240--5361288 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
5361230 ATGCATGGAG
5361240 GTCTTACAAATCATGCTCAAAA
1 GTCTTACAAATCATGCTCAAAA
*
5361262 GTCTTACAAATCATGCTCGAAA
1 GTCTTACAAATCATGCTCAAAA
5361284 GTCTT
1 GTCTT
5361289 GAAAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (22 bp):
GTCTTACAAATCATGCTCAAAA
Found at i:5361342 original size:21 final size:22
Alignment explanation
Indices: 5361237--5361363 Score: 73
Period size: 22 Copynumber: 5.8 Consensus size: 22
5361227 GTTATGCATG
*
5361237 GAGGTCTTACAAATCATG-CTCA
1 GAGGTCTTACAAATTATGTCT-A
* * * *
5361259 AAAGTCTTACAAATCATG-CTC
1 GAGGTCTTACAAATTATGTCTA
* ** *
5361280 GAAAGTCTTGA-AAATTATACCCA
1 G-AGGTCTT-ACAAATTATGTCTA
* * *
5361303 GAGGTCCTATAAATCATGTCTA
1 GAGGTCTTACAAATTATGTCTA
* *
5361325 GTGGTCTT-GAAATTATGTCTA
1 GAGGTCTTACAAATTATGTCTA
5361346 GAGGTCTTACAAATTATG
1 GAGGTCTTACAAATTATG
5361364 CATGGAGGTT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
21 19 0.24
22 58 0.73
23 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (22 bp):
GAGGTCTTACAAATTATGTCTA
Found at i:5361398 original size:65 final size:65
Alignment explanation
Indices: 5361329--5361452 Score: 164
Period size: 65 Copynumber: 1.9 Consensus size: 65
5361319 TGTCTAGTGG
*
5361329 TCTTGAA-ATTATGTCTAGAGGTCTT-ACAAATTATGCATGGAGGTTTTG-AGAATTATGCCCAA
1 TCTTGAAGATTAT-TCTAGAAGTCTTGA-AAATTATGCATGGAGGTTTTGAAG-ATTATGCCCAA
5361391 AGA
63 AGA
* * *
5361394 TCTTGAAGGTTATTCTTGAAGTCTTGAAAATTATGCTTGGAGGTTTTGAAGATTATGCC
1 TCTTGAAGATTATTCTAGAAGTCTTGAAAATTATGCATGGAGGTTTTGAAGATTATGCC
5361453 TGTAGGTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
65 45 0.87
66 7 0.13
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (65 bp):
TCTTGAAGATTATTCTAGAAGTCTTGAAAATTATGCATGGAGGTTTTGAAGATTATGCCCAAAGA
Found at i:5361525 original size:22 final size:22
Alignment explanation
Indices: 5361284--5361534 Score: 85
Period size: 22 Copynumber: 11.5 Consensus size: 22
5361274 ATGCTCGAAA
* * *
5361284 GTCTTGAAAATTATACCCAGAG
1 GTCTTAAAAATTATGCCTAGAG
* * * * *
5361306 GTCCTATAAATCATGTCTAGTG
1 GTCTTAAAAATTATGCCTAGAG
* *
5361328 GTCTT-GAAATTATGTCTAGAG
1 GTCTTAAAAATTATGCCTAGAG
* * *
5361349 GTCTTACAAATTATGCATGGAG
1 GTCTTAAAAATTATGCCTAGAG
* * * * *
5361371 GTTTTGAGAATTATGCCCAAAG
1 GTCTTAAAAATTATGCCTAGAG
* * ** * * *
5361393 ATCTTGAAGGTTAT-TCTTGAA
1 GTCTTAAAAATTATGCCTAGAG
* * *
5361414 GTCTTGAAAATTATGCTTGGAG
1 GTCTTAAAAATTATGCCTAGAG
* * *
5361436 GTTTTGAAGATTATGCCT-GTAG
1 GTCTTAAAAATTATGCCTAG-AG
* * * *
5361458 GTCTTAGAAATCATGTCTAAAG
1 GTCTTAAAAATTATGCCTAGAG
* ** * * * *
5361480 GTCATAAGGATCATACCCAAAG
1 GTCTTAAAAATTATGCCTAGAG
5361502 GTCTTAAAAATTATGCCTAGAG
1 GTCTTAAAAATTATGCCTAGAG
*
5361524 GTCTTACAAAT
1 GTCTTAAAAAT
5361535 CATTTCTTAG
Statistics
Matches: 159, Mismatches: 66, Indels: 8
0.68 0.28 0.03
Matches are distributed among these distances:
21 32 0.20
22 127 0.80
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (22 bp):
GTCTTAAAAATTATGCCTAGAG
Found at i:5363005 original size:22 final size:23
Alignment explanation
Indices: 5362980--5363027 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
5362970 CTTTCCACAT
5362980 TTTCCA-TTTTTCTTTTTTTTTC
1 TTTCCATTTTTTCTTTTTTTTTC
*
5363002 TTT-CATTTTTTCTTTTTTTTTT
1 TTTCCATTTTTTCTTTTTTTTTC
5363024 TTTC
1 TTTC
5363028 GTGTTTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTCCATTTTTTCTTTTTTTTTC
Found at i:5363008 original size:21 final size:22
Alignment explanation
Indices: 5362986--5363027 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5362976 ACATTTTCCA
5362986 TTTTTCTTTTTTTTTCTTTCAT
1 TTTTTCTTTTTTTTTCTTTCAT
*
5363008 TTTTTCTTTTTTTTTTTTTC
1 TTTTTCTTTTTTTTTCTTTC
5363028 GTGTTTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTCTTTTTTTTTCTTTCAT
Found at i:5363012 original size:12 final size:10
Alignment explanation
Indices: 5362986--5363026 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
5362976 ACATTTTCCA
5362986 TTTTTCTTTT
1 TTTTTCTTTT
5362996 TTTTTCTTTCAT
1 TTTTTCTTT--T
5363008 TTTTTCTTTT
1 TTTTTCTTTT
5363018 TTTTT-TTTT
1 TTTTTCTTTT
5363027 CGTGTTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.14
10 15 0.52
12 10 0.34
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:5368052 original size:21 final size:20
Alignment explanation
Indices: 5368015--5368053 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5368005 TCTTTTTTGA
* *
5368015 ATTTTTTTTATTGATTCTTG
1 ATTTTTTTAATTAATTCTTG
5368035 ATTTTTTCTAATTAATTCT
1 ATTTTTT-TAATTAATTCT
5368054 AATAGGATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (20 bp):
ATTTTTTTAATTAATTCTTG
Found at i:5369047 original size:24 final size:23
Alignment explanation
Indices: 5369010--5369055 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
5369000 AATAGCAATT
*
5369010 CTAAACAAGGCCTTAAATACAACG
1 CTAAACAAGACCTT-AATACAACG
* *
5369034 CTAAACTAGACCTTTATACAAC
1 CTAAACAAGACCTTAATACAAC
5369056 AAACCCTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (23 bp):
CTAAACAAGACCTTAATACAACG
Found at i:5372389 original size:160 final size:159
Alignment explanation
Indices: 5372158--5372745 Score: 419
Period size: 158 Copynumber: 3.7 Consensus size: 159
5372148 ATATTACGAC
* * * * ** *
5372158 GAGATCACATTTGTGAAAGGTAAAAACTCTTGCTTATTTTGTAATGTGATTCTGGTTGG-GTATT
1 GAGATCA-ATTTGTGAAAAGTAAAAACTATTGCATATTTTATTTTATGATTCTGG-TGGTGTATT
* * * * * ** *
5372222 ATGATTGTTGAT-AAAGTTGATTGTGTAGTAATTGAAAGCCTAGTCATTGT-AGAAAATTCAATA
64 GTGATTGTTGATGAAA-TAGATAGTGTAGTAATTAAAAGACTAAACATTATAAG-AAATTCAATA
*
5372285 TTGAA-CTAAATAATATTTTGTACGTATTGAGAT
127 TT-AATCTAAATAATATATTGTACGTATTGAGAT
* * *
5372318 GAGATCAATATTGTGAAAAGTAAAAATTATTGCGTATTTTATTTTATGATTTTGGTGGTGTATTG
1 GAGATCAAT-TTGTGAAAAGTAAAAACTATTGCATATTTTATTTTATGATTCTGGTGGTGTATTG
5372383 TGATTGTTGATGAAATAGATAGTGTAGTAATTAAAAGACTAAACATTATAAGAAATTCAATATTA
65 TGATTGTTGATGAAATAGATAGTGTAGTAATTAAAAGACTAAACATTATAAGAAATTCAATATTA
** * ***
5372448 ATCTATGTAGTATATTGTGTTTATTGAGAT
130 ATCTAAATAATATATTGTACGTATTGAGAT
* * * * *
5372478 GCA-AT-AACTTTGTG-AAAGTGAAAACTATGGCATAATTTATTTTATGATTCTAGTTGTGTATT
1 G-AGATCAA-TTTGTGAAAAGTAAAAACTATTGCATATTTTATTTTATGATTCTGGTGGTGTATT
* * * * * * **
5372540 GTGATTGTTGCTGAAGTA-AGTAGTATAGTAATTGAAAGTCTAAACATTGTAAGATGAA-T-GGT
64 GTGATTGTTGATGAAATAGA-TAGTGTAGTAATTAAAAGACTAAACATTATAAGA--AATTCAAT
* * * * *
5372602 ATTGAA-CTATATAGTATATTATGCTTATTGAGAT
126 ATT-AATCTAAATAATATATTGTACGTATTGAGAT
* * * * * *** ** * * * *
5372636 -ACAATGAATTTATG-AAGGTGAAAACTATTATGTATTTTGCTTTGTAATTCTGGTTGTGTATTA
1 GA-GATCAATTTGTGAAAAGTAAAAACTATTGCATATTTTATTTTATGATTCTGGTGGTGTATTG
* * * *
5372699 CGATTGTTGATGAATTAGATAGTGTAGTAATTGAAAGCCTAAACATT
65 TGATTGTTGATGAAATAGATAGTGTAGTAATTAAAAGACTAAACATT
5372746 GTAGGATGAA
Statistics
Matches: 352, Mismatches: 61, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
156 1 0.00
157 1 0.00
158 199 0.57
159 20 0.06
160 125 0.36
161 6 0.02
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (159 bp):
GAGATCAATTTGTGAAAAGTAAAAACTATTGCATATTTTATTTTATGATTCTGGTGGTGTATTGT
GATTGTTGATGAAATAGATAGTGTAGTAATTAAAAGACTAAACATTATAAGAAATTCAATATTAA
TCTAAATAATATATTGTACGTATTGAGAT
Found at i:5372746 original size:158 final size:158
Alignment explanation
Indices: 5372355--5372767 Score: 449
Period size: 158 Copynumber: 2.6 Consensus size: 158
5372345 TATTGCGTAT
* * * * *
5372355 TTTATTTTATGATTTTGGTGGTGTATTGTGATTGTTGATGAAATAGATAGTGTAGTAATTAAAAG
1 TTTACTTTATAATTCTGGTTGTGTATTGTGATTGTTGATGAAATAGATAGTGTAGTAATTGAAAG
* ** * * * *
5372420 ACTAAACATTATAAGA--AATTCAATATT-AATCTATGTAGTATATTGTGTTTATTGAGATGCAA
66 ACTAAACATTGTAAGATGAA-T-GGTATTGAA-CTATATAGTATATTATGCTTATTGAGATACAA
* *
5372482 TAACTTTGTGAAAGTGAAAACTATGGCATAA
128 TAACTTTATGAAAGTGAAAACTATGACATAA
* * * * * *
5372513 TTTATTTTATGATTCTAGTTGTGTATTGTGATTGTTGCTGAAGTA-AGTAGTATAGTAATTGAAA
1 TTTACTTTATAATTCTGGTTGTGTATTGTGATTGTTGATGAAATAGA-TAGTGTAGTAATTGAAA
*
5372577 GTCTAAACATTGTAAGATGAATGGTATTGAACTATATAGTATATTATGCTTATTGAGATACAATG
65 GACTAAACATTGTAAGATGAATGGTATTGAACTATATAGTATATTATGCTTATTGAGATACAAT-
* * ** *
5372642 AA-TTTATGAAGGTGAAAACTATTATGTAT
129 AACTTTATGAAAGTGAAAACTATGACATAA
* * ** *
5372671 TTTGCTTTGTAATTCTGGTTGTGTATTACGATTGTTGATGAATTAGATAGTGTAGTAATTGAAAG
1 TTTACTTTATAATTCTGGTTGTGTATTGTGATTGTTGATGAAATAGATAGTGTAGTAATTGAAAG
* *
5372736 CCTAAACATTGTAGGATGAATGGTATTGAACT
66 ACTAAACATTGTAAGATGAATGGTATTGAACT
5372768 GTGTTGGAAT
Statistics
Matches: 215, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
157 1 0.00
158 206 0.96
159 6 0.03
160 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (158 bp):
TTTACTTTATAATTCTGGTTGTGTATTGTGATTGTTGATGAAATAGATAGTGTAGTAATTGAAAG
ACTAAACATTGTAAGATGAATGGTATTGAACTATATAGTATATTATGCTTATTGAGATACAATAA
CTTTATGAAAGTGAAAACTATGACATAA
Found at i:5373266 original size:21 final size:21
Alignment explanation
Indices: 5373242--5373287 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5373232 TATTGAGGAC
* * *
5373242 TTTTGTAGATGTTATGGATAT
1 TTTTATAGAAGTTATGAATAT
5373263 TTTTATAGAAGTTATGAATAT
1 TTTTATAGAAGTTATGAATAT
5373284 TTTT
1 TTTT
5373288 TAATATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.54
Consensus pattern (21 bp):
TTTTATAGAAGTTATGAATAT
Found at i:5381314 original size:35 final size:36
Alignment explanation
Indices: 5381257--5381328 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 36
5381247 AATTTTAAAT
5381257 TGTGTTATATTCATATCATTTTTCATAT-ATTTTTA
1 TGTGTTATATTCATATCATTTTTCATATCATTTTTA
**
5381292 TGTGTTATATTCATAT-ATTTTTTTGTATCATTTTTA
1 TGTGTTATATTCATATCA-TTTTTCATATCATTTTTA
5381328 T
1 T
5381329 AAGAGTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 24 0.73
36 8 0.24
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (36 bp):
TGTGTTATATTCATATCATTTTTCATATCATTTTTA
Found at i:5381813 original size:26 final size:25
Alignment explanation
Indices: 5381765--5381823 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
5381755 AAAATTTTAC
*
5381765 AAAAAAATGAAATATTTACAAAAATT
1 AAAAAAATAAAATATTTAC-AAAATT
* **
5381791 AAAAAACTAAAATATTTTTAAAATT
1 AAAAAAATAAAATATTTACAAAATT
*
5381816 ACAAAAAT
1 AAAAAAAT
5381824 TTTAAAATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAAAATAAAATATTTACAAAATT
Found at i:5381896 original size:24 final size:23
Alignment explanation
Indices: 5381862--5381915 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
5381852 AAAAATCTCA
*
5381862 AAAAATTAAAAGTTTT-TGAAAAAT
1 AAAAATGAAAA-TTTTAT-AAAAAT
5381886 AAAAATGAAAATTTTAATAAAAAT
1 AAAAATGAAAATTTT-ATAAAAAT
5381910 AAAAAT
1 AAAAAT
5381916 TTTCTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 4 0.15
24 22 0.81
25 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (23 bp):
AAAAATGAAAATTTTATAAAAAT
Found at i:5381904 original size:18 final size:18
Alignment explanation
Indices: 5381883--5381918 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5381873 GTTTTTGAAA
*
5381883 AATAAAAATGAAAATTTT
1 AATAAAAATAAAAATTTT
5381901 AATAAAAATAAAAATTTT
1 AATAAAAATAAAAATTTT
5381919 CTTGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AATAAAAATAAAAATTTT
Found at i:5382342 original size:18 final size:17
Alignment explanation
Indices: 5382302--5382339 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5382292 TTTTTTTGAA
* *
5382302 TTTTAAGAAATTTTATT
1 TTTTAAAAAAATTTATT
5382319 TTTTAAAAAAATTTATT
1 TTTTAAAAAAATTTATT
5382336 TTTT
1 TTTT
5382340 TAATTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTAAAAAAATTTATT
Found at i:5382438 original size:17 final size:17
Alignment explanation
Indices: 5382376--5382438 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 17
5382366 GGATTTTTTA
*
5382376 TTAAAATTTTTTGATTT
1 TTAAAATTTTTTAATTT
* *
5382393 TGT-GAA-TTTTTAAGTT
1 T-TAAAATTTTTTAATTT
*
5382409 TTAATAATGTTTTAATTT
1 TTAA-AATTTTTTAATTT
5382427 TTAAAATTTTTT
1 TTAAAATTTTTT
5382439 TAATATTTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
15 1 0.03
16 9 0.26
17 12 0.34
18 13 0.37
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (17 bp):
TTAAAATTTTTTAATTT
Found at i:5382495 original size:18 final size:18
Alignment explanation
Indices: 5382455--5382495 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
5382445 TTCAGTTTGA
5382455 TTTTTATAATTTTTAAAT
1 TTTTTATAATTTTTAAAT
* *
5382473 ATTTTATATTTTTTAAAT
1 TTTTTATAATTTTTAAAT
5382491 TTTTT
1 TTTTT
5382496 TTAGAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATAATTTTTAAAT
Found at i:5382514 original size:20 final size:20
Alignment explanation
Indices: 5382491--5382531 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5382481 TTTTTTAAAT
*
5382491 TTTTTTTAGAAAATTTTTAA
1 TTTTTTAAGAAAATTTTTAA
**
5382511 TTTTTTAAGAATTTTTTTAA
1 TTTTTTAAGAAAATTTTTAA
5382531 T
1 T
5382532 GTTAATGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTTAAGAAAATTTTTAA
Found at i:5382514 original size:30 final size:33
Alignment explanation
Indices: 5382469--5382529 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
5382459 TATAATTTTT
*
5382469 AAATATTTTATATTTTTTAA-ATTTTTTTTAGA
1 AAATATTTTATATTTTTTAAGAATTTTTTTAGA
5382501 AAAT-TTTTA-ATTTTTTAAGAATTTTTTTA
1 AAATATTTTATATTTTTTAAGAATTTTTTTA
5382530 ATGTTAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.33
31 14 0.52
32 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (33 bp):
AAATATTTTATATTTTTTAAGAATTTTTTTAGA
Found at i:5382982 original size:22 final size:25
Alignment explanation
Indices: 5382957--5383011 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
5382947 ATATTTTTTA
5382957 TTTTATT-AAA-TTT-ATATATAAT
1 TTTTATTAAAATTTTAATATATAAT
*
5382979 TTTTATTAAAATTTTAAATATATTAT
1 TTTTATTAAAATTTT-AATATATAAT
5383005 TTTTATT
1 TTTTATT
5383012 TTTTTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 7 0.25
23 3 0.11
24 3 0.11
26 15 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTATTAAAATTTTAATATATAAT
Found at i:5383031 original size:13 final size:13
Alignment explanation
Indices: 5382997--5383048 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
5382987 AAATTTTAAA
5382997 TATATTATT-T-T
1 TATATTATTATAT
* *
5383008 TATTTTTTTATAT
1 TATATTATTATAT
5383021 TATATTATTATAT
1 TATATTATTATAT
*
5383034 TATATT-TTAAAT
1 TATATTATTATAT
5383046 TAT
1 TAT
5383049 TAGCCCTACA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 7 0.21
12 9 0.26
13 18 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATATTATTATAT
Found at i:5383557 original size:10 final size:10
Alignment explanation
Indices: 5383517--5383559 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
5383507 GTGCTATGTA
5383517 TATTTT-ATT
1 TATTTTAATT
5383526 TATTTTAATT
1 TATTTTAATT
5383536 ATATTTTAATT
1 -TATTTTAATT
5383547 TATTATT-ATT
1 TATT-TTAATT
5383557 TAT
1 TAT
5383560 CTAAAAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 6 0.19
10 13 0.42
11 12 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTAATT
Found at i:5384299 original size:2 final size:2
Alignment explanation
Indices: 5384292--5384320 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5384282 GAAAGAATGT
5384292 TA 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 TA T
5384321 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5385055 original size:19 final size:19
Alignment explanation
Indices: 5385031--5385069 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5385021 TTTTTTTATG
* *
5385031 CTTTTTGTTTTTCTTTTTTA
1 CTTTTT-TTTATCTGTTTTA
5385051 CTTTTTTTTATCTGTTTTA
1 CTTTTTTTTATCTGTTTTA
5385070 ATATTTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.08, C:0.10, G:0.05, T:0.77
Consensus pattern (19 bp):
CTTTTTTTTATCTGTTTTA
Found at i:5385089 original size:21 final size:22
Alignment explanation
Indices: 5385065--5385106 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5385055 TTTTTATCTG
* *
5385065 TTTTAATATT-TAACAAATATT
1 TTTTAAAATTATAAAAAATATT
5385086 TTTTAAAATTATAAAAAATAT
1 TTTTAAAATTATAAAAAATAT
5385107 ACTTTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTAAAATTATAAAAAATATT
Found at i:5385172 original size:12 final size:12
Alignment explanation
Indices: 5385155--5385191 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5385145 TATACTAAAC
5385155 TTTCTTTTTTCT
1 TTTCTTTTTTCT
*
5385167 TTTCTTTTTTCC
1 TTTCTTTTTTCT
5385179 TTT-TTTTTTCT
1 TTTCTTTTTTCT
5385190 TT
1 TT
5385192 GTTAAGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:5385465 original size:21 final size:20
Alignment explanation
Indices: 5385439--5385484 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5385429 TTATTTTATA
*
5385439 AATATTTAAGAAATAATTTTT
1 AATATTTAACAAAT-ATTTTT
* *
5385460 AATATTTTACAAATTTTTTT
1 AATATTTAACAAATATTTTT
5385480 AATAT
1 AATAT
5385485 GAGTCCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
AATATTTAACAAATATTTTT
Found at i:5387401 original size:225 final size:225
Alignment explanation
Indices: 5387006--5387410 Score: 575
Period size: 225 Copynumber: 1.8 Consensus size: 225
5386996 TTCTTTTGTA
*
5387006 AAATATATTTAAAAACAAAAGATAATATAAGGATTATTGATAAAAAAAATTAAAGATATTAAATA
1 AAATATATTTAAAAACAAAAGATAATATAAGAATTATTGATAAAAAAAATTAAAGATATTAAATA
* * *
5387071 ATATTTTTTAAAAGTTGAGATAAATTTAAATACTCGTGTTAATTGCAAATAAATTAAAAAAGATA
66 ATATTTTTTAAAAGTTGAGATAAATTTAAATACTCATGATAATTCCAAATAAATTAAAAAAGATA
* * * * *
5387136 GTTACTTTAAAATTGATTTTAAATTGAGGTGAGGTGATGTATAGGAGAAACTTTCTTGAAATTAT
131 ATTACTTTAAAATTGATTTTAAATTGAGATGAGATGATGTACAAGAGAAACTTTCTTGAAATTAT
5387201 TATGGTATTTTATTTTTTTCATTTTTTTTG
196 TATGGTATTTTATTTTTTTCATTTTTTTTG
** * * * **
5387231 AAATATATTTAAAAATTGAAA-ATAATGTAAGAATTATTTATCAAAAGTATTAAAGATATTAAAT
1 AAATATATTTAAAAA-CAAAAGATAATATAAGAATTATTGATAAAAAAAATTAAAGATATTAAAT
* *
5387295 AATA-TTTTTAAAAGTTGTGATAAATTTAAATACTCATGATAATTCCACATAAATTGAAAAAA-A
65 AATATTTTTTAAAAGTTGAGATAAATTTAAATACTCATGATAATTCCAAATAAATT-AAAAAAGA
*
5387358 TAAATTACTTTAAAATT-AGTTTTAAATTGAGATTAGATGATGTACAAGAGAAA
129 T-AATTACTTTAAAATTGA-TTTTAAATTGAGATGAGATGATGTACAAGAGAAA
5387411 GCAATTTCAT
Statistics
Matches: 157, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
224 49 0.31
225 105 0.67
226 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (225 bp):
AAATATATTTAAAAACAAAAGATAATATAAGAATTATTGATAAAAAAAATTAAAGATATTAAATA
ATATTTTTTAAAAGTTGAGATAAATTTAAATACTCATGATAATTCCAAATAAATTAAAAAAGATA
ATTACTTTAAAATTGATTTTAAATTGAGATGAGATGATGTACAAGAGAAACTTTCTTGAAATTAT
TATGGTATTTTATTTTTTTCATTTTTTTTG
Found at i:5388134 original size:2 final size:2
Alignment explanation
Indices: 5388127--5388153 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5388117 TCCATTCTTT
5388127 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
5388154 TTAGTGAATA
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:5389926 original size:29 final size:30
Alignment explanation
Indices: 5389887--5389956 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
5389877 CTTTTTTTCA
* *
5389887 TTTTTTATTTTAACA-TTTT-CTCTTTTCTT
1 TTTTTTATTTT-ACATTTTTGCCCTTTTATT
*
5389916 TTTTTT-TTTTTCATTTTTGCCCTTTTATT
1 TTTTTTATTTTACATTTTTGCCCTTTTATT
5389945 TTTTTTATTTTA
1 TTTTTTATTTTA
5389957 GGTTTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.06
28 8 0.24
29 20 0.59
30 4 0.12
ACGTcount: A:0.11, C:0.11, G:0.01, T:0.76
Consensus pattern (30 bp):
TTTTTTATTTTACATTTTTGCCCTTTTATT
Found at i:5390244 original size:17 final size:17
Alignment explanation
Indices: 5390222--5390266 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
5390212 CTTTCCTACA
5390222 TTTTGTATTA-TTTATTT
1 TTTTGT-TTATTTTATTT
5390239 TTTTGTTTATTTTATTT
1 TTTTGTTTATTTTATTT
5390256 TATTT-TTTATT
1 T-TTTGTTTATT
5390267 AAATATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (17 bp):
TTTTGTTTATTTTATTT
Found at i:5391479 original size:19 final size:20
Alignment explanation
Indices: 5391433--5391479 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
5391423 ATTCATATAT
**
5391433 ATATATATATATTATTTTTT
1 ATATATATATATTATTTTAG
*
5391453 ACTCTATATAT-TTATTTTAG
1 A-TATATATATATTATTTTAG
5391473 ATATATA
1 ATATATA
5391480 ATTACAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.23
20 9 0.41
21 8 0.36
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
ATATATATATATTATTTTAG
Found at i:5393469 original size:67 final size:67
Alignment explanation
Indices: 5393387--5393523 Score: 193
Period size: 67 Copynumber: 2.0 Consensus size: 67
5393377 AAAAATGAAA
* ** * *
5393387 AAAGAAAAAATATGAAAAGCAAATAGTTGATTGTAATATTATACAGGTGAGACACTCAAATGAAT
1 AAAGAAAAAACATGAAAAAAAAATAGTTGATTGTAACATTATACAGATGAGACACTCAAATGAAT
*
5393452 TC
66 CC
* * *
5393454 AAAGAGAAAACATGAAAAAAAAATAGTTGATTGTAACATTATACATATGAGACACTCAAATTAAT
1 AAAGAAAAAACATGAAAAAAAAATAGTTGATTGTAACATTATACAGATGAGACACTCAAATGAAT
5393519 CC
66 CC
5393521 AAA
1 AAA
5393524 ATCAAGAAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (67 bp):
AAAGAAAAAACATGAAAAAAAAATAGTTGATTGTAACATTATACAGATGAGACACTCAAATGAAT
CC
Found at i:5393895 original size:16 final size:16
Alignment explanation
Indices: 5393857--5393902 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5393847 GAAACATGTG
* *
5393857 AAGAAAAGAAAGAGAAA
1 AAGAAATGAAA-AAAAA
*
5393874 ATGAAATGAAAAAAAA
1 AAGAAATGAAAAAAAA
5393890 AAGAAATGAAAAA
1 AAGAAATGAAAAA
5393903 TGATGACAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (16 bp):
AAGAAATGAAAAAAAA
Found at i:5395345 original size:38 final size:38
Alignment explanation
Indices: 5395255--5395353 Score: 130
Period size: 37 Copynumber: 2.6 Consensus size: 38
5395245 ACTTGTCAGC
* * *
5395255 CCTCGAATG-GGAAAAACTTTCCAAGATAAGATTTGAAT
1 CCTCAAATGAGGAAAAA-TTTTCAAAATAAGATTTGAAT
*
5395293 CTTCAAATGA-GAAAAATTTTCAAAATAAGATTTGAAT
1 CCTCAAATGAGGAAAAATTTTCAAAATAAGATTTGAAT
*
5395330 CCTCAAATGAGGAAAACTTTTCAA
1 CCTCAAATGAGGAAAAATTTTCAA
5395354 GTGAGATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 28 0.53
38 25 0.47
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.28
Consensus pattern (38 bp):
CCTCAAATGAGGAAAAATTTTCAAAATAAGATTTGAAT
Found at i:5395361 original size:37 final size:36
Alignment explanation
Indices: 5395267--5395407 Score: 129
Period size: 37 Copynumber: 3.7 Consensus size: 36
5395257 TCGAATGGGA
* *
5395267 AAAACTTTCCAAGATAAGATTTGAATCTTCAAATGAG
1 AAAACTTTTCAAG-TAAGATTTGAATCCTCAAATGAG
* *
5395304 AAAAATTTTCAAAATAAGATTTGAATCCTCAAATGAGG
1 AAAACTTTTC-AAGTAAGATTTGAATCCTCAAATGA-G
* * * * **
5395342 AAAACTTTTCAAGTGAGATTTTTAGTTCTTGAATGAG
1 AAAACTTTTCAAGTAAGA-TTTGAATCCTCAAATGAG
5395379 AAAACCTTTTTCAAGATAAGATTTGAATC
1 AAAA-C-TTTTCAAG-TAAGATTTGAATC
5395408 ATTGAATAGG
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
37 40 0.49
38 25 0.30
39 13 0.16
40 4 0.05
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (36 bp):
AAAACTTTTCAAGTAAGATTTGAATCCTCAAATGAG
Found at i:5395466 original size:77 final size:77
Alignment explanation
Indices: 5395298--5395471 Score: 180
Period size: 77 Copynumber: 2.3 Consensus size: 77
5395288 TGAATCTTCA
*
5395298 AATGAGAAAA-A-TTTTCAAAATAAGATTTGAATCCTCAAATGAGGAAAACTTTTCAAGTGAGAT
1 AATGAGAAAACATTTTTCAAAATAAGATTTGAATCATCAAATGAGGAAAACTTTTCAAGTGAGAT
**
5395361 TTTTAGTTCTTG
66 TTTTAACTCTTG
* * **
5395373 AATGAGAAAACCTTTTTCAAGATAAGATTTGAATCATTGAAT-AGGAAAAACTTTT-AAGATGAG
1 AATGAGAAAACATTTTTCAAAATAAGATTTGAATCATCAAATGAGG-AAAACTTTTCAAG-TGAG
5395436 -TTTTTACACT-TTG
64 ATTTTTA-ACTCTTG
* *
5395449 GATGAGGAGAACATTTTTTCAAA
1 AATGA-GAAAACA-TTTTTCAAA
5395472 TTTTAAAGTT
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
75 10 0.12
76 19 0.23
77 44 0.54
78 8 0.10
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (77 bp):
AATGAGAAAACATTTTTCAAAATAAGATTTGAATCATCAAATGAGGAAAACTTTTCAAGTGAGAT
TTTTAACTCTTG
Found at i:5395852 original size:24 final size:23
Alignment explanation
Indices: 5395816--5395996 Score: 124
Period size: 24 Copynumber: 8.0 Consensus size: 23
5395806 ACAAATCTTT
*
5395816 AAATTTTAG-ATGTGAATCTCTA
1 AAATTTTTGAATGTGAATCTCTA
5395838 AGAATTTTTGAATGTGAATCT-T-
1 A-AATTTTTGAATGTGAATCTCTA
* * *
5395860 GAATTTTAG-ATGTGAATCTTTAA
1 AAATTTTTGAATGTGAATCTCT-A
* ** * *
5395883 AAAGTTTCAAATGAGAATCTTTGA
1 AAATTTTTGAATGTGAATCTCT-A
*
5395907 AATTTTTTG-ATGTGAATCTCTA
1 AAATTTTTGAATGTGAATCTCTA
* * * *
5395929 AACTTTTTTGAATGAGAATTTTTA
1 AA-ATTTTTGAATGTGAATCTCTA
*
5395953 AAATTTTTAGAATGTGAATCT-TT
1 AAATTTTT-GAATGTGAATCTCTA
*
5395976 AAA-TTTTGGATGTGAATCTCT
1 AAATTTTTGAATGTGAATCTCT
5395997 GAATTTTAAA
Statistics
Matches: 126, Mismatches: 23, Indels: 20
0.75 0.14 0.12
Matches are distributed among these distances:
20 10 0.08
21 19 0.15
22 9 0.07
23 39 0.31
24 49 0.39
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (23 bp):
AAATTTTTGAATGTGAATCTCTA
Found at i:5395872 original size:20 final size:21
Alignment explanation
Indices: 5395645--5396004 Score: 97
Period size: 21 Copynumber: 16.2 Consensus size: 21
5395635 ATATTTGATT
* * *
5395645 TTTTATATATGAATCTTTAAAA
1 TTTTAGATGTGAATC-TTAGAA
* *
5395667 TTTTGAAATGTGAATCTTTGAA
1 TTTT-AGATGTGAATCTTAGAA
*
5395689 TTTTAGATGTGAA-CTCTAAAA
1 TTTTAGATGTGAATCT-TAGAA
* * * *
5395710 TTTTCAAATGTAAATATTTGAA
1 TTTT-AGATGTGAATCTTAGAA
* *
5395732 TTTTAGATATGAATCTCTA-AT
1 TTTTAGATGTGAATCT-TAGAA
* * * *
5395753 TTTTAAATGAGGATCATT-GGA
1 TTTTAGATGTGAATC-TTAGAA
* * *
5395774 TTTTGGATGTGAAACTTTACAA
1 TTTTAGATGTGAATC-TTAGAA
* ****
5395796 TTTTTTGAAAACAAATCTTTA-AA
1 -TTTTAG-ATGTGAATC-TTAGAA
5395819 TTTTAGATGTGAATCTCTAAGAA
1 TTTTAGATGTGAATCT-T-AGAA
*
5395842 TTTTTGAATGTGAATCTT-GAA
1 TTTTAG-ATGTGAATCTTAGAA
*
5395863 TTTTAGATGTGAATCTTTAAAAA
1 TTTTAGATGTGAATC-TT-AGAA
* * * *
5395886 GTTTCAAATGAGAATCTTTGAAA
1 -TTTTAGATGTGAATCTTAG-AA
*
5395909 TTTTTTGATGTGAATCTCTA-AA
1 -TTTTAGATGTGAATCT-TAGAA
* * * *
5395931 CTTTTTTGAATGAGAATTTTTAAAA
1 --TTTTAG-ATGTGAA-TCTTAGAA
5395956 TTTTTAGAATGTGAATCTTTA-AA
1 -TTTTAG-ATGTGAATC-TTAGAA
*
5395979 TTTTGGATGTGAATCTCT-GAA
1 TTTTAGATGTGAATCT-TAGAA
5396000 TTTTA
1 TTTTA
5396005 AATATGAACT
Statistics
Matches: 247, Mismatches: 64, Indels: 55
0.67 0.17 0.15
Matches are distributed among these distances:
20 13 0.05
21 80 0.32
22 42 0.17
23 53 0.21
24 55 0.22
25 4 0.02
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (21 bp):
TTTTAGATGTGAATCTTAGAA
Found at i:5395922 original size:47 final size:46
Alignment explanation
Indices: 5395611--5396026 Score: 237
Period size: 45 Copynumber: 9.4 Consensus size: 46
5395601 CTCTTGGCAT
* * * ** * *
5395611 AATCTCT--AAATTTTTCTAATGTGAATATTTGATTTTTTATATATG
1 AATCTCTAAAAATTTTT-GAATGAGAATCTTTGAAATTTTAGATGTG
* *
5395656 AATCT-TTAAAA-TTTTGAAATGTGAATCTTTG-AATTTTAGATGTG
1 AATCTCTAAAAATTTTTG-AATGAGAATCTTTGAAATTTTAGATGTG
** * *
5395700 AA-CTCT-AAAATTTTCAAATGTA-AATATTTG-AATTTTAGATATG
1 AATCTCTAAAAATTTTTGAATG-AGAATCTTTGAAATTTTAGATGTG
* * * * *
5395743 AATCTCT---AATTTTTAAATGAGGATCATTG-GATTTTGGATGTG
1 AATCTCTAAAAATTTTTGAATGAGAATCTTTGAAATTTTAGATGTG
* * * * * *
5395785 AAACTTTACAATTTTTTGAA-AACAAATCTTT-AAATTTTAGATGTG
1 AATCTCTAAAAATTTTTGAATGA-GAATCTTTGAAATTTTAGATGTG
* *
5395830 AATCTCTAAGAATTTTTGAATGTGAATC-TTG-AATTTTAGATGTG
1 AATCTCTAAAAATTTTTGAATGAGAATCTTTGAAATTTTAGATGTG
* * ** *
5395874 AATCTTTAAAAAGTTTCAAATGAGAATCTTTGAAATTTTTTGATGTG
1 AATCTCTAAAAATTTTTGAATGAGAATCTTTGAAA-TTTTAGATGTG
** * *
5395921 AATCTCTAAACTTTTTTGAATGAGAATTTTTAAAATTTTTAGAATGTG
1 AATCTCTAAAAATTTTTGAATGAGAATCTTTGAAA-TTTTAG-ATGTG
* * * * * *
5395969 AATCT-T-TAAA-TTTTGGATGTGAATCTCTG-AATTTTAAATATG
1 AATCTCTAAAAATTTTTGAATGAGAATCTTTGAAATTTTAGATGTG
*
5396011 AA-CTGTAAAAATTTTT
1 AATCTCTAAAAATTTTT
5396027 CAAATGTAAA
Statistics
Matches: 286, Mismatches: 63, Indels: 45
0.73 0.16 0.11
Matches are distributed among these distances:
41 3 0.01
42 38 0.13
43 39 0.14
44 64 0.22
45 82 0.29
46 6 0.02
47 44 0.15
48 10 0.03
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (46 bp):
AATCTCTAAAAATTTTTGAATGAGAATCTTTGAAATTTTAGATGTG
Found at i:5396003 original size:91 final size:90
Alignment explanation
Indices: 5395644--5395978 Score: 219
Period size: 87 Copynumber: 3.7 Consensus size: 90
5395634 AATATTTGAT
* * * * * *
5395644 TTTTTATATATGAATCTTTAA-AA-TTTTGAAATGTGAATCTTTGAATTTTAGATGTGAA-CTCT
1 TTTTTAGATGTGAATCTCTAAGAATTTTTG-AATGAGAATC-TTAAATTTTAGATGTGAATCTTT
* * *
5395706 AAAATTTTCAAATGTA-AATATTTG-AA
64 AAAAGTTTCAAATG-AGAATCTCTGAAA
* * * ** * *
5395732 -TTTTAGATATGAATCTCT---AATTTTTAAATGAGGATCATTGGATTTTGGATGTGAAACTTTA
1 TTTTTAGATGTGAATCTCTAAGAATTTTTGAATGAGAATC-TTAAATTTTAGATGTGAATCTTTA
** * ** *
5395793 CAATTTTTTGAAAACA-AATCT-TTAAA
65 -AA-AGTTTCAAATGAGAATCTCTGAAA
* *
5395819 -TTTTAGATGTGAATCTCTAAGAATTTTTGAATGTGAATCTTGAATTTTAGATGTGAATCTTTAA
1 TTTTTAGATGTGAATCTCTAAGAATTTTTGAATGAGAATCTTAAATTTTAGATGTGAATCTTT-A
*
5395883 AAAGTTTCAAATGAGAATCTTTGAAA
65 AAAGTTTCAAATGAGAATCTCTGAAA
* * *
5395909 TTTTTTGATGTGAATCTCTAA-ACTTTTTTGAATGAGAATTTTTAAAATTTTTAGAATGTGAATC
1 TTTTTAGATGTGAATCTCTAAGA-ATTTTTGAATGAGAA-TCTT-AAA-TTTTAG-ATGTGAATC
5395973 TTTAAA
61 TTTAAA
5395979 TTTTGGATGT
Statistics
Matches: 197, Mismatches: 33, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
85 26 0.13
86 9 0.05
87 42 0.21
88 14 0.07
89 27 0.14
90 21 0.11
91 32 0.16
92 3 0.02
93 2 0.01
94 9 0.05
95 12 0.06
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (90 bp):
TTTTTAGATGTGAATCTCTAAGAATTTTTGAATGAGAATCTTAAATTTTAGATGTGAATCTTTAA
AAGTTTCAAATGAGAATCTCTGAAA
Found at i:5396060 original size:27 final size:27
Alignment explanation
Indices: 5396029--5396085 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
5396019 AAATTTTTCA
5396029 AATGTA-AATCTTGGAATTTTAAATATG
1 AATGTATAATCTT-GAATTTTAAATATG
* *
5396056 AATGTATACTCTTGAATTTTAAATGTG
1 AATGTATAATCTTGAATTTTAAATATG
5396083 AAT
1 AAT
5396086 CTTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (27 bp):
AATGTATAATCTTGAATTTTAAATATG
Found at i:5396094 original size:137 final size:137
Alignment explanation
Indices: 5395644--5396095 Score: 303
Period size: 136 Copynumber: 3.4 Consensus size: 137
5395634 AATATTTGAT
* * * * * *
5395644 TTTTTATATATGAATCTTTAAA-ATTTTGAAATGTGAATCTTTGAA-TTTTAGATGTGAA-CTCT
1 TTTTTAAATATGAATCTATAAACTTTTTTAAATGAGAATCTTTAAATTTTTAGATGTGAATCTCT
** * * * * * * *
5395706 AA-AATTTTCAAATGTAAATATTTGAATTTTAGATATGAATCTCT---AATTTTTAAATGAGGAT
66 AAGAATTTTTGAATGTGAAT-CTTGAATTTTAAATATGAATCTGTAAAAAGTTTCAAATGAGAAT
* *
5395767 CATTG-GA
130 CTTTGAAA
** * * * **
5395774 -TTTTGGATGTGAAACTTTACAA-TTTTTTGAAAACA-AATCTTTAAA-TTTTAGATGTGAATCT
1 TTTTTAAATATGAATCTATA-AACTTTTTT-AAATGAGAATCTTTAAATTTTTAGATGTGAATCT
* * *
5395835 CTAAGAATTTTTGAATGTGAATCTTGAATTTTAGATGTGAATCTTTAAAAAGTTTCAAATGAGAA
64 CTAAGAATTTTTGAATGTGAATCTTGAATTTTAAATATGAATCTGTAAAAAGTTTCAAATGAGAA
5395900 TCTTTGAAA
129 TCTTTGAAA
** * * * *
5395909 TTTTTTGATGTGAATCTCTAAACTTTTTTGAATGAGAATTTTTAAAATTTTTAGAATGTGAATCT
1 TTTTTAAATATGAATCTATAAACTTTTTTAAATGAGAATCTTT-AAATTTTTAG-ATGTGAATCT
* * *
5395974 -TTA-AA-TTTTGGATGTGAATCTCTGAATTTTAAATATGAA-CTGTAAAAATTTTTCAAATGTA
64 CTAAGAATTTTTGAATGTGAATCT-TGAATTTTAAATATGAATCTGTAAAAA-GTTTCAAATG-A
*
5396035 -AATC-TTGGAA
126 GAATCTTTGAAA
* ** *
5396045 -TTTTAAATATGAATGTATACTCTTGAATTTTAAATGTGAATCTTTAAATTT
1 TTTTTAAATATGAATCTATAAACTT---TTTTAAATGAGAATCTTTAAATTT
5396096 CTTTTGCAAA
Statistics
Matches: 257, Mismatches: 45, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
129 15 0.06
130 28 0.11
131 30 0.12
132 14 0.05
134 18 0.07
135 23 0.09
136 56 0.22
137 39 0.15
138 24 0.09
139 10 0.04
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (137 bp):
TTTTTAAATATGAATCTATAAACTTTTTTAAATGAGAATCTTTAAATTTTTAGATGTGAATCTCT
AAGAATTTTTGAATGTGAATCTTGAATTTTAAATATGAATCTGTAAAAAGTTTCAAATGAGAATC
TTTGAAA
Found at i:5396274 original size:18 final size:18
Alignment explanation
Indices: 5396222--5396316 Score: 67
Period size: 18 Copynumber: 5.3 Consensus size: 18
5396212 TCATGTGTAC
5396222 ATCTTTGAATTAT-TTGTGA
1 ATCTTTGAA--ATCTTGTGA
5396241 ATCTTT-ACAA--TTGTGA
1 ATCTTTGA-AATCTTGTGA
5396257 ATCTTTGAAATCTTGTGA
1 ATCTTTGAAATCTTGTGA
* *
5396275 ATTTTTTG-AATGCTTATGA
1 A-TCTTTGAAAT-CTTGTGA
*
5396294 ATCTTT-AAATTCTTATGA
1 ATCTTTGAAA-TCTTGTGA
5396312 ATCTT
1 ATCTT
5396317 CAAGTTCTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
16 14 0.22
17 2 0.03
18 29 0.45
19 20 0.31
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.49
Consensus pattern (18 bp):
ATCTTTGAAATCTTGTGA
Found at i:5396324 original size:18 final size:18
Alignment explanation
Indices: 5396287--5396325 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5396277 TTTTTGAATG
*
5396287 CTTATGAATCTTTAAATT
1 CTTATGAATCTTCAAATT
*
5396305 CTTATGAATCTTCAAGTT
1 CTTATGAATCTTCAAATT
5396323 CTT
1 CTT
5396326 TTGCAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (18 bp):
CTTATGAATCTTCAAATT
Found at i:5401591 original size:18 final size:18
Alignment explanation
Indices: 5401565--5401613 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
5401555 TATATCATAT
*
5401565 CATGTAATAATAATAAAC
1 CATGCAATAATAATAAAC
*
5401583 CATGCAATAAT-AT-AAT
1 CATGCAATAATAATAAAC
5401599 CATGCAATAA-AATAA
1 CATGCAATAATAATAA
5401614 TATATCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.52
17 3 0.11
18 10 0.37
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (18 bp):
CATGCAATAATAATAAAC
Found at i:5401755 original size:18 final size:18
Alignment explanation
Indices: 5401712--5401757 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
5401702 AAATATATTG
*
5401712 ATAATCAAACGATTAAAT
1 ATAATCATACGATTAAAT
5401730 ATAATCATACGATTAAAT
1 ATAATCATACGATTAAAT
5401748 ATAATCATAC
1 ATAATCATAC
5401758 AATCATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAATCATACGATTAAAT
Found at i:5401794 original size:3 final size:3
Alignment explanation
Indices: 5401788--5401828 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
5401778 TAAAAAAAGA
5401788 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5401829 TAGGTGATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5401825 original size:94 final size:96
Alignment explanation
Indices: 5401727--5401920 Score: 284
Period size: 94 Copynumber: 2.0 Consensus size: 96
5401717 CAAACGATTA
* *
5401727 AATATAATCATACGATTAAATATAATCATACAATCATTCAAAATTAAATACTAAAAAAAG-AAAT
1 AATATAATCAGACGATTAAATATAATCATACAATCATGCAAAATTAAATACTAAAAAAAGAAAAT
5401791 AATAATAATA-ATAATAATAATAATAATAAT
66 AATAATAATATATAATAATAATAATAATAAT
* ** * *
5401821 AATATAATTAGGTGATTAAATATAGTCATACAATCATGCAAAATTAAATACTAACAAAAGAAAAT
1 AATATAATCAGACGATTAAATATAATCATACAATCATGCAAAATTAAATACTAAAAAAAGAAAAT
* *
5401886 AATAATAATATTATTATTATAATAATAATAAT
66 AATAATAATA-TATAATAATAATAATAATAAT
5401918 AAT
1 AAT
5401921 TAAATACTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 53 0.60
95 14 0.16
97 21 0.24
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (96 bp):
AATATAATCAGACGATTAAATATAATCATACAATCATGCAAAATTAAATACTAAAAAAAGAAAAT
AATAATAATATATAATAATAATAATAATAAT
Found at i:5401891 original size:3 final size:3
Alignment explanation
Indices: 5401883--5401948 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
5401873 AACAAAAGAA
* * * * *
5401883 AAT AAT AAT AAT -AT TAT TAT TAT AAT AAT AAT AAT AAT TA- AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5401929 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
5401949 CTTAAAAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 3 0.05
3 53 0.95
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:5401909 original size:20 final size:21
Alignment explanation
Indices: 5401884--5401943 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
5401874 ACAAAAGAAA
* *
5401884 ATAATAATAATATTATT-ATT
1 ATAATAATAATATAATTAAAT
5401904 ATAATAATAATAATAATTAAAT
1 ATAATAATAAT-ATAATTAAAT
5401926 ACTAATAATAATAATAAT
1 A-TAATAATAAT-ATAAT
5401944 AATAACTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 11 0.31
21 5 0.14
22 3 0.09
23 16 0.46
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATAATAATATAATTAAAT
Found at i:5401919 original size:26 final size:27
Alignment explanation
Indices: 5401883--5401947 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
5401873 AACAAAAGAA
* * *
5401883 AATAATAATAATATTATTA-TTATAAT
1 AATAATAATAATATAAATACTAATAAT
5401909 AATAATAATAAT-TAAATACTAATAAT
1 AATAATAATAATATAAATACTAATAAT
5401935 AATAATAATAATA
1 AATAATAATAATA
5401948 ACTTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.12
26 30 0.88
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
AATAATAATAATATAAATACTAATAAT
Found at i:5401984 original size:15 final size:13
Alignment explanation
Indices: 5401961--5401999 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
5401951 TAAAAAAGAG
*
5401961 AAAAGAAAAAATT
1 AAAATAAAAAATT
5401974 CAAAATCAAAAAATT
1 -AAAAT-AAAAAATT
5401989 AAAATAAAAAA
1 AAAATAAAAAA
5402000 ACAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:5402000 original size:15 final size:15
Alignment explanation
Indices: 5401966--5402012 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
5401956 AAGAGAAAAG
*
5401966 AAAAAATTCAAAATC
1 AAAAAATTCAAAATA
5401981 AAAAAATT-AAAATA
1 AAAAAATTCAAAATA
5401995 AAAAAA--CAAAA-A
1 AAAAAATTCAAAATA
5402007 AAAAAA
1 AAAAAA
5402013 AGAAAAACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 7 0.23
13 4 0.13
14 11 0.37
15 8 0.27
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAATTCAAAATA
Found at i:5402920 original size:21 final size:22
Alignment explanation
Indices: 5402895--5402945 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
5402885 ACTTTTTAAT
* *
5402895 AATAATAATAGTAAATAAAT-A
1 AATAAAAACAGTAAATAAATCA
*
5402916 AATAAAAACAGTAATTAAATCA
1 AATAAAAACAGTAAATAAATCA
*
5402938 AATTAAAA
1 AATAAAAA
5402946 TTAAAATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (22 bp):
AATAAAAACAGTAAATAAATCA
Found at i:5403520 original size:18 final size:18
Alignment explanation
Indices: 5403497--5403533 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5403487 CAAAGGTTAT
5403497 AGTTTCACAGAGATTCCA
1 AGTTTCACAGAGATTCCA
* *
5403515 AGTTTCATAGAGTTTCCA
1 AGTTTCACAGAGATTCCA
5403533 A
1 A
5403534 ATTTGTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (18 bp):
AGTTTCACAGAGATTCCA
Found at i:5403686 original size:52 final size:52
Alignment explanation
Indices: 5403615--5403714 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
5403605 GAGTTTTAAA
* *
5403615 TTTGAAAAAATTAGAAGATTCACAAAACTTTCATATTCACAAGAATTTTAGG
1 TTTGAAAAAATTAGAAGATTCAAAAAACTTTCAAATTCACAAGAATTTTAGG
* *
5403667 TTTGCAAAAAATTA-AAGATTCAAAAAACTTTTAAATTCATAAGAATTT
1 TTTG-AAAAAATTAGAAGATTCAAAAAACTTTCAAATTCACAAGAATTT
5403715 CAGATGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 34 0.79
53 9 0.21
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (52 bp):
TTTGAAAAAATTAGAAGATTCAAAAAACTTTCAAATTCACAAGAATTTTAGG
Found at i:5403752 original size:41 final size:41
Alignment explanation
Indices: 5403680--5403760 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
5403670 GCAAAAAATT
* * *
5403680 AAAGATTCAAAAAACTTTTAAATTCATAAGAATTTCAGATG
1 AAAGATTCAAAAAACTTTCAAATTCACAAGAACTTCAGATG
* *
5403721 AAAGATTCACAAAAAC-TTCATATTTACAAGAACTTCAGAT
1 AAAGATTCA-AAAAACTTTCAAATTCACAAGAACTTCAGAT
5403761 TTGCAAAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 28 0.82
42 6 0.18
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.30
Consensus pattern (41 bp):
AAAGATTCAAAAAACTTTCAAATTCACAAGAACTTCAGATG
Found at i:5403754 original size:17 final size:17
Alignment explanation
Indices: 5403723--5403768 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
5403713 TTCAGATGAA
*
5403723 AGATTCACAAAAACTTC
1 AGATTTACAAAAACTTC
* *
5403740 ATATTTACAAGAACTTC
1 AGATTTACAAAAACTTC
*
5403757 AGATTTGCAAAA
1 AGATTTACAAAA
5403769 GTTTCACAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (17 bp):
AGATTTACAAAAACTTC
Found at i:5403928 original size:30 final size:29
Alignment explanation
Indices: 5403863--5403931 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
5403853 GGGATTTACA
* *
5403863 TCAAAGATTTCAAGCTTTATAGGCAAAAT
1 TCAAAGATTTCAAGCTTTACAGCCAAAAT
*
5403892 TCAAAGATTTCAAGCTTTCACATCCAAAAGT
1 TCAAAGATTTCAAGCTTT-ACAGCCAAAA-T
5403923 T-AAAGATTT
1 TCAAAGATTT
5403932 TCATTCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 18 0.51
30 15 0.43
31 2 0.06
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (29 bp):
TCAAAGATTTCAAGCTTTACAGCCAAAAT
Found at i:5404061 original size:22 final size:23
Alignment explanation
Indices: 5403998--5404064 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
5403988 TAAAGATTTT
*
5403998 TATTCAAAAAACTTAGAGATTGA
1 TATTCAAAAAACTTAGAGATTCA
* * *
5404021 CA-T-AAAAAATTTCGAAGATTCA
1 TATTCAAAAAACTTAG-AGATTCA
5404043 TATTCAAAAAA-TTAGAGATTCA
1 TATTCAAAAAACTTAGAGATTCA
5404065 CATCTAAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
21 9 0.26
22 15 0.43
23 5 0.14
24 6 0.17
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.30
Consensus pattern (23 bp):
TATTCAAAAAACTTAGAGATTCA
Found at i:5405178 original size:18 final size:19
Alignment explanation
Indices: 5405155--5405194 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
5405145 TCAATTTAAA
*
5405155 TTTTTTTCTC-TTTTTTA-
1 TTTTTTTTTCATTTTTTAC
5405172 TTTTTTTTTCATTTTTTAC
1 TTTTTTTTTCATTTTTTAC
5405191 TTTT
1 TTTT
5405195 ATTGCACACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 7 0.35
19 4 0.20
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTCATTTTTTAC
Found at i:5410008 original size:18 final size:20
Alignment explanation
Indices: 5409971--5410018 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
5409961 TACCATGCAA
*
5409971 TAATAATATATTATATCATG
1 TAATAATATATTATACCATG
5409991 TAATAATA-A-TATACCATG
1 TAATAATATATTATACCATG
*
5410009 CAATAATATA
1 TAATAATATA
5410019 ATCATTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.60
19 2 0.08
20 8 0.32
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (20 bp):
TAATAATATATTATACCATG
Found at i:5410601 original size:11 final size:11
Alignment explanation
Indices: 5410585--5410609 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5410575 CTTCAAATAA
5410585 ACCTAGAATCC
1 ACCTAGAATCC
5410596 ACCTAGAATCC
1 ACCTAGAATCC
5410607 ACC
1 ACC
5410610 ATTCTGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.40, G:0.08, T:0.16
Consensus pattern (11 bp):
ACCTAGAATCC
Found at i:5411283 original size:16 final size:15
Alignment explanation
Indices: 5411254--5411288 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
5411244 ATAATAATAA
5411254 TAAATAAATAAAAAT
1 TAAATAAATAAAAAT
*
5411269 TAAATCAAATTAAAAT
1 TAAAT-AAATAAAAAT
5411285 TAAA
1 TAAA
5411289 ATGTAGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATAAATAAAAAT
Found at i:5420962 original size:2 final size:2
Alignment explanation
Indices: 5420955--5420979 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5420945 GAATACAAGG
5420955 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
5420980 TATATATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5424868 original size:15 final size:16
Alignment explanation
Indices: 5424843--5424875 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5424833 TATATTTTTA
*
5424843 TTTTATACGAATTAAT
1 TTTTATACGAATCAAT
5424859 TTTTAT-CGAATCAAT
1 TTTTATACGAATCAAT
5424874 TT
1 TT
5424876 AAATTGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTTATACGAATCAAT
Found at i:5431676 original size:50 final size:50
Alignment explanation
Indices: 5431598--5432009 Score: 238
Period size: 50 Copynumber: 8.3 Consensus size: 50
5431588 GAGGTTTCAC
* * * *
5431598 AACTCTTTGAAAATAAGTTGAAATGAAAACTTCTCTCATCAAAGGCTCTAC
1 AACT-TTTAAAAATAAATTGAAAAGAAAACTTCTCTCATCAAAGGCTCTAT
* * * * *
5431649 AACTTTTAAAAATGAATTGAAAAGAAAACTCCTCTAACCAAAGGCTCCAT
1 AACTTTTAAAAATAAATTGAAAAGAAAACTTCTCTCATCAAAGGCTCTAT
* * * * *
5431699 AATTTTTAAAAATAAATT---AAGAATAACTCCTTTCACCAGAGGCTCTAT
1 AACTTTTAAAAATAAATTGAAAAGAA-AACTTCTCTCATCAAAGGCTCTAT
* * * * *
5431747 AATTTTTAAAAATAATTTGAAATGAAAAC-TCTTCTCAT-AAAGACTCCAT
1 AACTTTTAAAAATAAATTGAAAAGAAAACTTC-TCTCATCAAAGGCTCTAT
* * * * * * * * * *
5431796 GACTATTTAAAAATGAATTAAAAAGAAGAA-TACTATAATTAGAGGATTTAT
1 AACT-TTTAAAAATAAATTGAAAAGAA-AACTTCTCTCATCAAAGGCTCTAT
* * * * *
5431847 AACTTTTAAAAATAAACTG-AGAGTAAAACCCTTTTTTCA-CTAGAA-ACTCTAT
1 AACTTTTAAAAATAAATTGAAAAG-AAAA--CTTCTCTCATC-A-AAGGCTCTAT
* * * *
5431899 AACTTTTGAAAATAAATTGAAATGAAAACTTCTCT-AACTAGAGGCTC-AT
1 AACTTTTAAAAATAAATTGAAAAGAAAACTTCTCTCATC-AAAGGCTCTAT
* * * * *
5431948 CAA-TTTTAAAAATTAATTGAAATGAAAACTTTTTTCATCAAAGGCTCTAA
1 -AACTTTTAAAAATAAATTGAAAAGAAAACTTCTCTCATCAAAGGCTCTAT
5431998 AAC-TTTAAAAAT
1 AACTTTTAAAAAT
5432010 CTTATCTTAA
Statistics
Matches: 273, Mismatches: 66, Indels: 46
0.71 0.17 0.12
Matches are distributed among these distances:
47 5 0.02
48 37 0.14
49 66 0.24
50 112 0.41
51 20 0.07
52 30 0.11
53 3 0.01
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (50 bp):
AACTTTTAAAAATAAATTGAAAAGAAAACTTCTCTCATCAAAGGCTCTAT
Found at i:5431809 original size:98 final size:98
Alignment explanation
Indices: 5431640--5431816 Score: 232
Period size: 98 Copynumber: 1.8 Consensus size: 98
5431630 CTCTCATCAA
* *
5431640 AGGCTCTACAACTTTTAAAAATGAATTGAAAAGAAAACTCCTCTAACCAAAGGCTCCATAATTTT
1 AGGCTCTACAACTTTTAAAAATGAATTGAAAAGAAAACTCCTCTAACCAAAGACTCCATAATATT
5431705 TAAAAATAAATTAAGAATAACTCCTTTCACCAG
66 TAAAAATAAATTAAGAATAACTCCTTTCACCAG
* * * * * * *
5431738 AGGCTCTATAATTTTTAAAAAT-AATTTGAAATGAAAACTCTTCTCA-TAAAGACTCCATGACTA
1 AGGCTCTACAACTTTTAAAAATGAA-TTGAAAAGAAAACTCCTCTAACCAAAGACTCCAT-AATA
*
5431801 TTTAAAAATGAATTAA
64 TTTAAAAATAAATTAA
5431817 AAAGAAGAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
97 12 0.18
98 55 0.82
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (98 bp):
AGGCTCTACAACTTTTAAAAATGAATTGAAAAGAAAACTCCTCTAACCAAAGACTCCATAATATT
TAAAAATAAATTAAGAATAACTCCTTTCACCAG
Found at i:5432050 original size:48 final size:49
Alignment explanation
Indices: 5431997--5432101 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
5431987 AAAGGCTCTA
*
5431997 AAACTTTAAAAATCTT-ATCTTA-AAATA-CTTATTAAAACAAAGGTT-TG
1 AAACTTTAAAAAT-TTCATCTTAGAAA-AGCTCATTAAAACAAAGGTTATG
* *
5432044 ACAACTTTAAAAATTTCGTCTTAGAAAAGCTCATTTAAACAAAGGTTATG
1 A-AACTTTAAAAATTTCATCTTAGAAAAGCTCATTAAAACAAAGGTTATG
5432094 AAACTTTA
1 AAACTTTA
5432102 TCTTGGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
47 3 0.06
48 18 0.36
49 26 0.52
50 3 0.06
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (49 bp):
AAACTTTAAAAATTTCATCTTAGAAAAGCTCATTAAAACAAAGGTTATG
Found at i:5432799 original size:24 final size:22
Alignment explanation
Indices: 5432772--5432819 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
5432762 ATGACTTCGG
*
5432772 ATATCACCACCAGAGAGAATTCAA
1 ATATCACCACCA-AGA-AATACAA
5432796 ATATCACCACCAAGAAATACAA
1 ATATCACCACCAAGAAATACAA
5432818 AT
1 AT
5432820 GTATTAGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
23 3 0.13
24 12 0.52
ACGTcount: A:0.50, C:0.25, G:0.08, T:0.17
Consensus pattern (22 bp):
ATATCACCACCAAGAAATACAA
Found at i:5439463 original size:18 final size:19
Alignment explanation
Indices: 5439440--5439475 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5439430 TGCACAATTT
5439440 ATTATT-TTTATTTTTTAA
1 ATTATTATTTATTTTTTAA
*
5439458 ATTATTATTTCTTTTTTA
1 ATTATTATTTATTTTTTA
5439476 TTTGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTATTATTTATTTTTTAA
Found at i:5440376 original size:14 final size:14
Alignment explanation
Indices: 5440357--5440386 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5440347 GTCCCATTTC
*
5440357 TTTTGTTTTTGTTT
1 TTTTGTTTTAGTTT
5440371 TTTTGTTTTAGTTT
1 TTTTGTTTTAGTTT
5440385 TT
1 TT
5440387 GGCATTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.83
Consensus pattern (14 bp):
TTTTGTTTTAGTTT
Found at i:5441774 original size:9 final size:9
Alignment explanation
Indices: 5441760--5441792 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5441750 TGGCCATTAA
5441760 ATAAAAAAT
1 ATAAAAAAT
5441769 AT-AAAAAT
1 ATAAAAAAT
*
5441777 ACAAAAAAT
1 ATAAAAAAT
5441786 ATAAAAA
1 ATAAAAA
5441793 TCATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:5442387 original size:16 final size:16
Alignment explanation
Indices: 5442366--5442401 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5442356 CCACAACAGT
*
5442366 GAAAAGAAAAGGAGGC
1 GAAAAGAAAAGAAGGC
5442382 GAAAAGAAAAGAAGGC
1 GAAAAGAAAAGAAGGC
5442398 -AAAA
1 GAAAA
5442402 AAGGCTGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.64, C:0.06, G:0.31, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAAGAAGGC
Found at i:5444222 original size:64 final size:63
Alignment explanation
Indices: 5444147--5444346 Score: 183
Period size: 64 Copynumber: 3.2 Consensus size: 63
5444137 GCTGAAAGTA
* * *
5444147 CCTTCAATAATCCAATCAATAAATTTTTATGAAGGATTATTGAAGGTAATTTTGATAAAAAATG
1 CCTTTAATAAT-CAATCAATAAATTTTTATGAAGGATTATTGAAGGCAATTTTGGTAAAAAATG
* * ** * ** ** *
5444211 CCTTTAGTAATCTATACAA-AAA-AGTTA-GAATGGATTCTTGAAGGCGTTTTTGGTGCAAAATA
1 CCTTTAATAATCAAT-CAATAAATTTTTATGAA-GGATTATTGAAGGCAATTTTGGTAAAAAATG
* *
5444273 CCTTTAATAATTCACTCAATAAATTTTTATG-AGAGATTATTGAAGGCAATTTTGGTTAAAAATG
1 CCTTTAATAA-TCAATCAATAAATTTTTATGAAG-GATTATTGAAGGCAATTTTGGTAAAAAATG
*
5444337 CCTTCAATAA
1 CCTTTAATAA
5444347 CATTTTGTTA
Statistics
Matches: 104, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
61 3 0.03
62 38 0.37
63 13 0.12
64 49 0.47
65 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (63 bp):
CCTTTAATAATCAATCAATAAATTTTTATGAAGGATTATTGAAGGCAATTTTGGTAAAAAATG
Found at i:5444504 original size:34 final size:36
Alignment explanation
Indices: 5444433--5444504 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
5444423 ATTATATATG
* *
5444433 TGAAGTTAGTTGTAGGTTTATGCCCAGAAAAACATT
1 TGAAGTCAGTTGTAGATTTATGCCCAGAAAAACATT
5444469 TGAAGTCAGTTGTA-ATTTATGCCCAG-AAAACATT
1 TGAAGTCAGTTGTAGATTTATGCCCAGAAAAACATT
5444503 TG
1 TG
5444505 GTTTATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 10 0.29
35 11 0.32
36 13 0.38
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (36 bp):
TGAAGTCAGTTGTAGATTTATGCCCAGAAAAACATT
Found at i:5447786 original size:30 final size:29
Alignment explanation
Indices: 5447752--5447810 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
5447742 CATTCAGCAT
5447752 CAAAACCAA-TATCATACAATACCATGTCAA
1 CAAAA-CAATTATCATACAATACCAT-TCAA
*
5447782 CAAAACAATTATCATGCAATACCATTCAA
1 CAAAACAATTATCATACAATACCATTCAA
5447811 GTTAAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.49, C:0.25, G:0.03, T:0.22
Consensus pattern (29 bp):
CAAAACAATTATCATACAATACCATTCAA
Found at i:5449060 original size:18 final size:18
Alignment explanation
Indices: 5449037--5449071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5449027 TATATATTTC
*
5449037 AAATATATTTTTATATAA
1 AAATATAGTTTTATATAA
*
5449055 AAATATGGTTTTATATA
1 AAATATAGTTTTATATA
5449072 TTTTAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
AAATATAGTTTTATATAA
Found at i:5450583 original size:21 final size:21
Alignment explanation
Indices: 5450559--5450601 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5450549 ATTGATTTGG
5450559 TTTTAAAGAGAGAGA-ATAAAT
1 TTTTAAAGAGAGA-ATATAAAT
*
5450580 TTTTAGAGAGAGAATATAAAT
1 TTTTAAAGAGAGAATATAAAT
5450601 T
1 T
5450602 GAGATGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTTAAAGAGAGAATATAAAT
Found at i:5451432 original size:31 final size:31
Alignment explanation
Indices: 5451397--5451455 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5451387 ATTATTAATG
* *
5451397 AATCAGATGATAACAACTCATTAATGAGATA
1 AATCAAATAATAACAACTCATTAATGAGATA
*
5451428 AATCAAATAATAACATCTCATTAATGAG
1 AATCAAATAATAACAACTCATTAATGAG
5451456 TAAGTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (31 bp):
AATCAAATAATAACAACTCATTAATGAGATA
Found at i:5452236 original size:2 final size:2
Alignment explanation
Indices: 5452231--5452259 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5452221 CTTATTTGGA
5452231 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 A
5452260 ATCTAACCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5457886 original size:31 final size:31
Alignment explanation
Indices: 5457767--5457886 Score: 127
Period size: 31 Copynumber: 3.8 Consensus size: 31
5457757 ATAAATCTAT
* *
5457767 TTTTTAAAATGATATGAAAATTTTTTACATAA
1 TTTTTAAAATGATAT-ATAATTTTTTACTTAA
** *
5457799 TATTTTAAAATGATAT-TAAGATTTTATTTAA
1 T-TTTTAAAATGATATATAATTTTTTACTTAA
*
5457830 TTTCTTAAACTGATATATACA-TTTTTACTTAA
1 TTT-TTAAAATGATATATA-ATTTTTTACTTAA
*
5457862 TTTTTAAAATGATATATCATTTTTT
1 TTTTTAAAATGATATATAATTTTTT
5457887 TAAAATTATT
Statistics
Matches: 73, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
30 3 0.04
31 40 0.55
32 15 0.21
33 15 0.21
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTTTAAAATGATATATAATTTTTTACTTAA
Done.