Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002352.1 Hibiscus syriacus cultivar Beakdansim tig00004797_pilon, 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: 2012169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1483638 original size:23 final size:23
Alignment explanation
Indices: 1483583--1483638 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1483573 GTCACTTAGT
*
1483583 AAAA-TTAAATTATTAACTTCCA
1 AAAATTTAAATTAATAACTTCCA
**
1483605 AAAATAGAAATTAATAA-TTCCA
1 AAAATTTAAATTAATAACTTCCA
1483627 AAACATTTAAAT
1 AAA-ATTTAAAT
1483639 CATTTTAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAATTTAAATTAATAACTTCCA
Found at i:1486123 original size:298 final size:298
Alignment explanation
Indices: 1485581--1486167 Score: 919
Period size: 298 Copynumber: 2.0 Consensus size: 298
1485571 CACAAATTCC
* *
1485581 TAGTCGATCAGATTTATATATAAACCTCACTCTCTATGTATAATTAGTCGATTGATTTTTTGAAC
1 TAGTCAATCAGATTTACATATAAACCTCACTCTCTATGTATAATTAGTCGATTGATTTTTTGAAC
* *
1485646 AAGATCCTCGAACAAAATGAGTAATCTTTCTATGAATATGCATTTAAACAAAATATTTTCAAATA
66 AAGATCCTCAAACAAAATGAGTAATCTTTCTATGAATATACATTTAAACAAAATATTTTCAAATA
* ** *
1485711 TTTAGCAGATCATCAAAGAAATATGATGATGGAGTTATATAACGTTAACGACTTTTCTTTTACAT
131 TTTAGCAGATCACCAAAGAAATATGATGACAGAGTTATATAACGTTAACGACTTTTCTCTTACAT
** * *
1485776 AATAGAATTATGAATTCCTGAGAAACTTAGATATACTGGTCAAATTTTATCGAATTAAGACAAAT
196 AATAGAATTATGAATTCCCAAGAAACTTAGAGATACTGATCAAATTTTATCGAATTAAGACAAAT
1485841 TTTGAAACCTCTAATTTATGCACATTCCTATGTATAAT
261 TTTGAAACCTCTAATTTATGCACATTCCTATGTATAAT
* * *
1485879 TAGTCAATCAGATTTCCATATAAACCTCACTCTTTATGTATAATTAGTCTATTGA-TTTTTGCAA
1 TAGTCAATCAGATTTACATATAAACCTCACTCTCTATGTATAATTAGTCGATTGATTTTTTG-AA
* *
1485943 CAAGATCCTCAAACAAAATTAGTAATCTTTCTA-GCAATATACATTTAAGCAAAATATTTTCAAA
65 CAAGATCCTCAAACAAAATGAGTAATCTTTCTATG-AATATACATTTAAACAAAATATTTTCAAA
* * *
1486007 TATTTAGCAGATCACCAAATAAATATGATGACAGAGTTATATAATGTTAATGACTTTTCTCTTAC
129 TATTTAGCAGATCACCAAAGAAATATGATGACAGAGTTATATAACGTTAACGACTTTTCTCTTAC
* *
1486072 ATAATATAATTATGAATTCCCAAGAAAC-TACGAGATACTGATCAAATTTTATCGAATTGAGACA
194 ATAATAGAATTATGAATTCCCAAGAAACTTA-GAGATACTGATCAAATTTTATCGAATTAAGACA
*
1486136 AATTTTGAAACCTCTTATTTATGCACATTCCT
258 AATTTTGAAACCTCTAATTTATGCACATTCCT
1486168 CCAACATGTT
Statistics
Matches: 263, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
297 9 0.03
298 254 0.97
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (298 bp):
TAGTCAATCAGATTTACATATAAACCTCACTCTCTATGTATAATTAGTCGATTGATTTTTTGAAC
AAGATCCTCAAACAAAATGAGTAATCTTTCTATGAATATACATTTAAACAAAATATTTTCAAATA
TTTAGCAGATCACCAAAGAAATATGATGACAGAGTTATATAACGTTAACGACTTTTCTCTTACAT
AATAGAATTATGAATTCCCAAGAAACTTAGAGATACTGATCAAATTTTATCGAATTAAGACAAAT
TTTGAAACCTCTAATTTATGCACATTCCTATGTATAAT
Found at i:1488819 original size:66 final size:65
Alignment explanation
Indices: 1488712--1488863 Score: 250
Period size: 66 Copynumber: 2.3 Consensus size: 65
1488702 CCTATAATGA
1488712 CTTTGGGTGTCACAAAGCATCGGAGCCTACGCTCTACTAGTCTAGTCTTCAGGAGTACTTGGGAT
1 CTTTGGG-GTCACAAAGCATCGGAGCCTACGCTCTACTAGTCTAGTCTTCAGGAGTACTT-GGAT
1488777 GC
64 GC
* * * *
1488779 CTTTGGGGTCACAAAGCATCGGAGCCTACGTTCTAGTAGTCTAGTTTTCATGAGTACTTGGATGC
1 CTTTGGGGTCACAAAGCATCGGAGCCTACGCTCTACTAGTCTAGTCTTCAGGAGTACTTGGATGC
1488844 CTTTGGGGTCACAAAGCATC
1 CTTTGGGGTCACAAAGCATC
1488864 AAAGTTTACA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
65 26 0.32
66 48 0.59
67 7 0.09
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (65 bp):
CTTTGGGGTCACAAAGCATCGGAGCCTACGCTCTACTAGTCTAGTCTTCAGGAGTACTTGGATGC
Found at i:1490556 original size:20 final size:20
Alignment explanation
Indices: 1490523--1490572 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1490513 ATCCCACCAA
**
1490523 TATCGATACCGAGCATCTAG
1 TATCGATATTGAGCATCTAG
* *
1490543 TATCGATATTGAGCTTTTAG
1 TATCGATATTGAGCATCTAG
*
1490563 AATCGATATT
1 TATCGATATT
1490573 AAAACCCTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (20 bp):
TATCGATATTGAGCATCTAG
Found at i:1497508 original size:17 final size:19
Alignment explanation
Indices: 1497486--1497524 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1497476 AAGAATATAC
*
1497486 AAAATAAGT-CATAAA-TT
1 AAAATAAATACATAAAGTT
1497503 AAAATAAATACATAAAGTT
1 AAAATAAATACATAAAGTT
1497522 AAA
1 AAA
1497525 TACAAGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAATAAATACATAAAGTT
Found at i:1498881 original size:21 final size:21
Alignment explanation
Indices: 1498855--1498903 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
1498845 AGAATGATTT
1498855 ATCCTTTTTCACAGGGGA-CTG
1 ATCCTTTTTCACAGGGGATC-G
1498876 ATCCTTTTTCACAGGGGATCG
1 ATCCTTTTTCACAGGGGATCG
1498897 ATCCTTT
1 ATCCTTT
1498904 GTAAAACAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.37
Consensus pattern (21 bp):
ATCCTTTTTCACAGGGGATCG
Found at i:1507317 original size:59 final size:59
Alignment explanation
Indices: 1507235--1507411 Score: 263
Period size: 56 Copynumber: 3.1 Consensus size: 59
1507225 CTAACTCGAG
* * *
1507235 TATGACACATAAGGTCGTGCCCACCATCTGTACTAGTTATACTTAAGTGCAATCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
* *
1507294 TATGACACATAAGGTCGTTCCCACCATATGCACTA---ATACTTTAGTGCAATCCCGAG
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
* *
1507350 TATGACACATAAGGTCATGCACACCATATGCACTAGTTATACTTTAGTGCAAT-CCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
1507408 TATG
1 TATG
1507412 CAACCTGATG
Statistics
Matches: 106, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
56 51 0.48
58 8 0.08
59 47 0.44
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
Found at i:1507356 original size:56 final size:57
Alignment explanation
Indices: 1507231--1507404 Score: 242
Period size: 59 Copynumber: 3.0 Consensus size: 57
1507221 AGTGCTAACT
* * *
1507231 CGAGTATGACACATAAGGTCGTGCCCACCATCTGTACTAGTTATACTTAAGTGCAATCC
1 CGAGTATGACACATAAGGTCGTGCCCACCATATGCACTA--TATACTTTAGTGCAATCC
* *
1507290 CGAATATGACACATAAGGTCGTTCCCACCATATGCACTA-ATACTTTAGTGCAATCC
1 CGAGTATGACACATAAGGTCGTGCCCACCATATGCACTATATACTTTAGTGCAATCC
* *
1507346 CGAGTATGACACATAAGGTCATGCACACCATATGCACTAGTTATACTTTAGTGCAATCC
1 CGAGTATGACACATAAGGTCGTGCCCACCATATGCACTA--TATACTTTAGTGCAATCC
1507405 GAATATGCAA
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
56 51 0.50
59 52 0.50
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (57 bp):
CGAGTATGACACATAAGGTCGTGCCCACCATATGCACTATATACTTTAGTGCAATCC
Found at i:1510555 original size:14 final size:14
Alignment explanation
Indices: 1510536--1510566 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1510526 AAAGTTAGGA
1510536 TGTCTTACTGATAT
1 TGTCTTACTGATAT
1510550 TGTCTTACTGATAT
1 TGTCTTACTGATAT
1510564 TGT
1 TGT
1510567 TGGTTGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (14 bp):
TGTCTTACTGATAT
Found at i:1511158 original size:41 final size:41
Alignment explanation
Indices: 1511101--1511181 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
1511091 CCAACGGTAC
1511101 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAT
1 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAT
* *
1511142 TGAACATTGATACACGAATGTACCAAATCTGAATTGATAA
1 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
1511182 GTACTCACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (41 bp):
TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAT
Found at i:1511308 original size:18 final size:17
Alignment explanation
Indices: 1511291--1511351 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
1511281 AACAACTGTA
*
1511291 AAATATCTGATCTTTGT
1 AAATATCTGATATTTGT
* *
1511308 AATTATTTGATATTTGT
1 AAATATCTGATATTTGT
**
1511325 AAATCATCTGATAACTGT
1 AAAT-ATCTGATATTTGT
1511343 AAATCATCT
1 AAAT-ATCT
1511352 AATAACTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 17 0.47
18 19 0.53
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (17 bp):
AAATATCTGATATTTGT
Found at i:1511356 original size:18 final size:18
Alignment explanation
Indices: 1511322--1511364 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1511312 ATTTGATATT
*
1511322 TGTAAATCATCTGATAAC
1 TGTAAATCATCTAATAAC
1511340 TGTAAATCATCTAATAAC
1 TGTAAATCATCTAATAAC
*
1511358 TATAAAT
1 TGTAAAT
1511365 ATTTAGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (18 bp):
TGTAAATCATCTAATAAC
Found at i:1514324 original size:22 final size:20
Alignment explanation
Indices: 1514297--1514346 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1514287 GGCTTTCAAA
*
1514297 AAATTTTAGAGTTTTTTAAAAT
1 AAATTTTA-ACTTTTTT-AAAT
*
1514319 ATATTTTTAACTTTTTTAAAT
1 A-AATTTTAACTTTTTTAAAT
1514340 AAATTTT
1 AAATTTT
1514347 TTTAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.21
21 5 0.21
22 8 0.33
23 6 0.25
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
AAATTTTAACTTTTTTAAAT
Found at i:1514348 original size:23 final size:22
Alignment explanation
Indices: 1514308--1514351 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1514298 AATTTTAGAG
*
1514308 TTTTTTAAAATATATTTTTAAC
1 TTTTTTAAAAAATATTTTTAAC
*
1514330 TTTTTTAAATAAATTTTTTTAA
1 TTTTTTAAA-AAATATTTTTAA
1514352 AATTATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTTAAAAAATATTTTTAAC
Found at i:1515785 original size:20 final size:20
Alignment explanation
Indices: 1515746--1515785 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1515736 TAACTAAAAG
* *
1515746 TAAAATTTAATAATACTATA
1 TAAAACTTAATAATAATATA
*
1515766 TAAAACTTAATATTAATATA
1 TAAAACTTAATAATAATATA
1515786 AATTAACAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAACTTAATAATAATATA
Found at i:1515918 original size:43 final size:43
Alignment explanation
Indices: 1515855--1516019 Score: 213
Period size: 43 Copynumber: 3.8 Consensus size: 43
1515845 AATTTCAAAC
* *
1515855 TAACAATCCACAAATACACCAAACTAGCATATTAAAACTAAAG
1 TAACAATCCACAAATTCACCAAACTAACATATTAAAACTAAAG
* *
1515898 TAACAATCCTCAAATTCACCAAACTAACATATTAAAACTAAAC
1 TAACAATCCACAAATTCACCAAACTAACATATTAAAACTAAAG
* * * * * *
1515941 TAATAGTCCACAAATTCACTAAACCAACATATTAAAACCAATG
1 TAACAATCCACAAATTCACCAAACTAACATATTAAAACTAAAG
* * *
1515984 TAACAATCCACAAATGCATCAAACTATCATATTAAA
1 TAACAATCCACAAATTCACCAAACTAACATATTAAA
1516020 GGCATTCTTG
Statistics
Matches: 103, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 103 1.00
ACGTcount: A:0.51, C:0.24, G:0.03, T:0.22
Consensus pattern (43 bp):
TAACAATCCACAAATTCACCAAACTAACATATTAAAACTAAAG
Found at i:1520004 original size:23 final size:25
Alignment explanation
Indices: 1519968--1520023 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
1519958 ATATAATATA
*
1519968 TATATGATGAATGTTATGA-TACATG
1 TATATGATGAATG-TATAACTACATG
1519993 TATAT-AT-AATGTATAACTACATG
1 TATATGATGAATGTATAACTACATG
*
1520016 TATCTGAT
1 TATATGAT
1520024 CTATTGATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 14 0.52
24 4 0.15
25 5 0.19
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (25 bp):
TATATGATGAATGTATAACTACATG
Found at i:1520198 original size:2 final size:2
Alignment explanation
Indices: 1520191--1520221 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1520181 CCATTATACT
1520191 TA 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 TA T
1520222 GAAAGTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1521838 original size:41 final size:41
Alignment explanation
Indices: 1521793--1521870 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1521783 GTGGAGAAAG
* *
1521793 CCTCATTTTCTGTGATCTTGATCCAAGGGTAATCATTAGTT
1 CCTCAATTTCTGGGATCTTGATCCAAGGGTAATCATTAGTT
*
1521834 CCTCAATTTCTGGGATCTTGATCCAAGGGTGATCATT
1 CCTCAATTTCTGGGATCTTGATCCAAGGGTAATCATT
1521871 TATTTGGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (41 bp):
CCTCAATTTCTGGGATCTTGATCCAAGGGTAATCATTAGTT
Found at i:1522484 original size:26 final size:26
Alignment explanation
Indices: 1522433--1522486 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1522423 ATATAATTTT
**
1522433 ATTTTAAGTAGATAAGTATTTTTAAA
1 ATTTTAAGTAGATAAGTATTAATAAA
*
1522459 ATTTTAAGATAGAT-ATTATTAATAAA
1 ATTTTAAG-TAGATAAGTATTAATAAA
1522485 AT
1 AT
1522487 AAATAATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.44
Consensus pattern (26 bp):
ATTTTAAGTAGATAAGTATTAATAAA
Found at i:1522794 original size:10 final size:10
Alignment explanation
Indices: 1522779--1522817 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1522769 AACAAACACA
1522779 ATAAATGAAC
1 ATAAATGAAC
1522789 ATAAATGAAC
1 ATAAATGAAC
* *
1522799 GTAAACGAAC
1 ATAAATGAAC
1522809 ATAAATGAA
1 ATAAATGAA
1522818 AATATGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:1522808 original size:20 final size:20
Alignment explanation
Indices: 1522780--1522817 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1522770 ACAAACACAA
*
1522780 TAAATGAACATAAATGAACG
1 TAAACGAACATAAATGAACG
1522800 TAAACGAACATAAATGAA
1 TAAACGAACATAAATGAA
1522818 AATATGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (20 bp):
TAAACGAACATAAATGAACG
Found at i:1527157 original size:51 final size:51
Alignment explanation
Indices: 1527070--1527181 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 51
1527060 TAATTAGGTG
* * * * *
1527070 TCGATACTCGGGGGCTATATCGATGAGTACCGATACTACAAGAGACAAGTA
1 TCGATACTCTGGGGCCATATCAATAAGTACCAATACTACAAGAGACAAGTA
*
1527121 TCGATACTCTGGGGCCATATCAATAAGTATCAATACTACAAGAGACAAGTA
1 TCGATACTCTGGGGCCATATCAATAAGTACCAATACTACAAGAGACAAGTA
1527172 TCGATACTCT
1 TCGATACTCT
1527182 AGGTAGGGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (51 bp):
TCGATACTCTGGGGCCATATCAATAAGTACCAATACTACAAGAGACAAGTA
Found at i:1529626 original size:19 final size:19
Alignment explanation
Indices: 1529602--1529651 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1529592 TATGGGGTGT
*
1529602 ATCGATTCACTCCCTATGC
1 ATCGATACACTCCCTATGC
1529621 ATCGATACACTCCCTATGC
1 ATCGATACACTCCCTATGC
*
1529640 ATCGATGCACTC
1 ATCGATACACTC
1529652 ATTGCATTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.28
Consensus pattern (19 bp):
ATCGATACACTCCCTATGC
Found at i:1532510 original size:2 final size:2
Alignment explanation
Indices: 1532503--1532556 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
1532493 ATTGATATTC
1532503 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1532544 AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT
1532557 TAACATATTC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1532834 original size:21 final size:21
Alignment explanation
Indices: 1532810--1532849 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1532800 ATAGAATTTG
1532810 TCCCGAAGGACCACGTAGATA
1 TCCCGAAGGACCACGTAGATA
*
1532831 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCACGTAGA
1532850 CCCTCGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.28, T:0.12
Consensus pattern (21 bp):
TCCCGAAGGACCACGTAGATA
Found at i:1532977 original size:15 final size:13
Alignment explanation
Indices: 1532931--1532977 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1532921 CATTACACAT
1532931 TCACATA-TTCATA
1 TCACATAGTTC-TA
*
1532944 TCACATAGTTCTT
1 TCACATAGTTCTA
1532957 TCACATAGCTCTCTA
1 TCACATAG-T-TCTA
1532972 TCACAT
1 TCACAT
1532978 TTCATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 16 0.55
14 4 0.14
15 9 0.31
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (13 bp):
TCACATAGTTCTA
Found at i:1537584 original size:14 final size:16
Alignment explanation
Indices: 1537565--1537601 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1537555 ATTATCTTGA
*
1537565 TAATTAT-ATGAGTG-
1 TAATTATAATAAGTGT
1537579 TAATTATAATAAGTGT
1 TAATTATAATAAGTGT
1537595 TAATTAT
1 TAATTAT
1537602 TTTTTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 6 0.30
16 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (16 bp):
TAATTATAATAAGTGT
Found at i:1558908 original size:30 final size:30
Alignment explanation
Indices: 1558874--1558933 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1558864 ACTCTTCACG
1558874 AAACATTCACATCATTTTGCCAATGAGTGC
1 AAACATTCACATCATTTTGCCAATGAGTGC
*
1558904 AAACATTCGCATCATTTTGCCAATGAGTGC
1 AAACATTCACATCATTTTGCCAATGAGTGC
1558934 TTGCATCTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (30 bp):
AAACATTCACATCATTTTGCCAATGAGTGC
Found at i:1559594 original size:20 final size:19
Alignment explanation
Indices: 1559565--1559604 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1559555 GATGTAGGAG
1559565 TCTTTTTCTTTTCTTTTTT
1 TCTTTTTCTTTTCTTTTTT
*
1559584 TCTTCTTTCTTTTGTTTTTT
1 TCTT-TTTCTTTTCTTTTTT
1559604 T
1 T
1559605 ATTGCAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (19 bp):
TCTTTTTCTTTTCTTTTTT
Found at i:1559601 original size:19 final size:19
Alignment explanation
Indices: 1559565--1559603 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1559555 GATGTAGGAG
*
1559565 TCTTTTTCTTTTCTTTTTT
1 TCTTTTTCTTTTCGTTTTT
1559584 TCTTCTTTCTTTT-GTTTTT
1 TCTT-TTTCTTTTCGTTTTT
1559603 T
1 T
1559604 TATTGCAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (19 bp):
TCTTTTTCTTTTCGTTTTT
Found at i:1567506 original size:27 final size:28
Alignment explanation
Indices: 1567464--1567551 Score: 160
Period size: 28 Copynumber: 3.2 Consensus size: 28
1567454 CAAATTCAAC
1567464 CTTGCCATGCATTTTTTTTCTTTCATCT
1 CTTGCCATGCATTTTTTTTCTTTCATCT
1567492 CTTGCCATGCATTTTTTTTCTTTCATCT
1 CTTGCCATGCATTTTTTTTCTTTCATCT
*
1567520 CTTGCCATTCA-TTTTTTTCTTTCATCT
1 CTTGCCATGCATTTTTTTTCTTTCATCT
1567547 CTTGC
1 CTTGC
1567552 TTACTTCAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 21 0.36
28 38 0.64
ACGTcount: A:0.10, C:0.26, G:0.07, T:0.57
Consensus pattern (28 bp):
CTTGCCATGCATTTTTTTTCTTTCATCT
Found at i:1567806 original size:25 final size:25
Alignment explanation
Indices: 1567776--1567834 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
1567766 TATGCATAAA
1567776 TAAAACAAATTTTCATACTCGTATT
1 TAAAACAAATTTTCATACTCGTATT
1567801 TAAAACAAATTTTCATACTCGTATT
1 TAAAACAAATTTTCATACTCGTATT
1567826 TAAAACAAA
1 TAAAACAAA
1567835 ATACAATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (25 bp):
TAAAACAAATTTTCATACTCGTATT
Found at i:1568417 original size:12 final size:11
Alignment explanation
Indices: 1568396--1568441 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
1568386 AGATATTAGA
*
1568396 AATCAAAACAG
1 AATCAGAACAG
1568407 ATATCAGAACAG
1 A-ATCAGAACAG
1568419 AATCCAGAACAG
1 AAT-CAGAACAG
1568431 AAATCAGAACA
1 -AATCAGAACA
1568442 AAATTCAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 3 0.10
12 25 0.81
13 3 0.10
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.11
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:1568420 original size:24 final size:25
Alignment explanation
Indices: 1568393--1568445 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1568383 CGGAGATATT
*
1568393 AGAAAT-CAAAACAGATATCAGAAC
1 AGAAATCCAAAACAGAAATCAGAAC
*
1568417 AG-AATCCAGAACAGAAATCAGAAC
1 AGAAATCCAAAACAGAAATCAGAAC
1568441 A-AAAT
1 AGAAAT
1568446 TCAGGTCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.58, C:0.17, G:0.13, T:0.11
Consensus pattern (25 bp):
AGAAATCCAAAACAGAAATCAGAAC
Found at i:1573834 original size:10 final size:11
Alignment explanation
Indices: 1573808--1573841 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1573798 TATTCATATT
1573808 AAAAAAACTAA
1 AAAAAAACTAA
*
1573819 AAAAAAACAAA
1 AAAAAAACTAA
1573830 TAAAAAAACTAA
1 -AAAAAAACTAA
1573842 CGATCAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAAAAACTAA
Found at i:1574915 original size:28 final size:29
Alignment explanation
Indices: 1574849--1574922 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
1574839 AAAAGTTTGA
*
1574849 ACACATATTTATAAAAAACGATATAATTTAG
1 ACACTTATTTAT-AAAAAC-ATATAATTTAG
* *
1574880 GCACTTATTTATAAAAA-ATATAATTTAT
1 ACACTTATTTATAAAAACATATAATTTAG
*
1574908 ACATTTATTTTATAA
1 ACACTTA-TTTATAA
1574923 TTAAGCCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 15 0.41
29 7 0.19
30 5 0.14
31 10 0.27
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (29 bp):
ACACTTATTTATAAAAACATATAATTTAG
Found at i:1575049 original size:11 final size:10
Alignment explanation
Indices: 1575025--1575068 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1575015 AGCGTGTCAC
*
1575025 AATTTATAAT
1 AATTTAAAAT
1575035 AATTTAAATAT
1 AATTTAAA-AT
*
1575046 AATTAAAAAT
1 AATTTAAAAT
*
1575056 ATTTTAAAAT
1 AATTTAAAAT
1575066 AAT
1 AAT
1575069 ACAAACGATC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:1580044 original size:20 final size:20
Alignment explanation
Indices: 1580019--1580060 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1580009 TGTATTTGTT
*
1580019 TACTTTTTTCTTCATGTAGC
1 TACTTTTTTCTTAATGTAGC
*
1580039 TACTTTTTTGTTAATGTAGC
1 TACTTTTTTCTTAATGTAGC
1580059 TA
1 TA
1580061 TCATAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.55
Consensus pattern (20 bp):
TACTTTTTTCTTAATGTAGC
Found at i:1590364 original size:24 final size:23
Alignment explanation
Indices: 1590320--1590365 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1590310 TAATTTTTTT
*
1590320 ATTTTAAAAAACACAATATTATA
1 ATTTTAAAAAACACAAAATTATA
*
1590343 ATTTTAAAAAACTCAAAAATTAT
1 ATTTTAAAAAACAC-AAAATTAT
1590366 TTCCTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTTTAAAAAACACAAAATTATA
Found at i:1590718 original size:21 final size:21
Alignment explanation
Indices: 1590693--1590732 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1590683 TTTGATTTTT
1590693 TATTTTT-TTTTGAAAAAAACA
1 TATTTTTATTTT-AAAAAAACA
1590714 TATTTTTATTTTAAAAAAA
1 TATTTTTATTTTAAAAAAA
1590733 TAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
TATTTTTATTTTAAAAAAACA
Found at i:1591612 original size:28 final size:28
Alignment explanation
Indices: 1591569--1591623 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1591559 AACTTAAACC
* * *
1591569 TAAACTCCAAATTCTACATCAAAATAAT
1 TAAACTCCAAACTCTAAACCAAAATAAT
*
1591597 TAAACTCTAAACTCTAAACCAAAATAA
1 TAAACTCCAAACTCTAAACCAAAATAA
1591624 CAACATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAACTCCAAACTCTAAACCAAAATAAT
Found at i:1591647 original size:24 final size:24
Alignment explanation
Indices: 1591620--1591673 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1591610 CTAAACCAAA
1591620 ATAACAACATAAAAATCCCAATTC
1 ATAACAACATAAAAATCCCAATTC
1591644 ATAACAACATAAAAATCCCAATTC
1 ATAACAACATAAAAATCCCAATTC
1591668 ATAACA
1 ATAACA
1591674 CCCAAATCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (24 bp):
ATAACAACATAAAAATCCCAATTC
Found at i:1591680 original size:21 final size:21
Alignment explanation
Indices: 1591632--1591697 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1591622 AACAACATAA
**
1591632 AAATCCCAATTCATAACAACATAA
1 AAATCCCAATTCATAAC-AC--CC
1591656 AAATCCCAATTCATAACACCC
1 AAATCCCAATTCATAACACCC
* * *
1591677 AAATCCTAAATCGTAACACCC
1 AAATCCCAATTCATAACACCC
1591698 GTCCCACAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.49
23 2 0.05
24 17 0.46
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.20
Consensus pattern (21 bp):
AAATCCCAATTCATAACACCC
Found at i:1596166 original size:15 final size:17
Alignment explanation
Indices: 1596129--1596178 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
1596119 TAACCATTAA
* * *
1596129 ATTACTTTTATTAAATA
1 ATTAATTTTATTAGATT
1596146 ATTAA-TTTATT-GATT
1 ATTAATTTTATTAGATT
1596161 ATTAATTTTATTAGATT
1 ATTAATTTTATTAGATT
1596178 A
1 A
1596179 AAAATTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 7 0.25
16 12 0.43
17 9 0.32
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (17 bp):
ATTAATTTTATTAGATT
Found at i:1596271 original size:2 final size:2
Alignment explanation
Indices: 1596264--1596322 Score: 61
Period size: 2 Copynumber: 30.5 Consensus size: 2
1596254 TTTAATTTTA
* * *
1596264 AT AT AT AT AT AT AT AT AT GT AT AT GT AT GT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1596305 AT -T AT ACT AT AT -T AT AT A
1 AT AT AT A-T AT AT AT AT AT A
1596323 GGCTAGGATC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1597835 original size:24 final size:23
Alignment explanation
Indices: 1597790--1597841 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
1597780 ATGTATCCAT
1597790 TATACTTATAATATTATATATAA
1 TATACTTATAATATTATATATAA
*
1597813 TATACTTATGTATATTATGTATATAA
1 TATACTTAT-AATATTA--TATATAA
1597839 TAT
1 TAT
1597842 TATAGACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 9 0.36
24 6 0.24
26 10 0.40
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (23 bp):
TATACTTATAATATTATATATAA
Found at i:1597890 original size:17 final size:17
Alignment explanation
Indices: 1597806--1597900 Score: 70
Period size: 17 Copynumber: 5.6 Consensus size: 17
1597796 TATAATATTA
* *
1597806 TATATAATATACTTATG
1 TATATTATATACATATG
*
1597823 TATATTATGT--ATAT-
1 TATATTATATACATATG
* * *
1597837 AATATTATAGACATAAG
1 TATATTATATACATATG
* *
1597854 TACATTATATATATGCATG
1 TATATTATATACAT--ATG
1597873 TATATTATATACATATG
1 TATATTATATACATATG
1597890 TATACTTATAT
1 TATA-TTATAT
1597901 TTATATATAT
Statistics
Matches: 58, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
14 7 0.12
15 3 0.05
16 3 0.05
17 25 0.43
18 6 0.10
19 14 0.24
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.45
Consensus pattern (17 bp):
TATATTATATACATATG
Found at i:1597900 original size:18 final size:18
Alignment explanation
Indices: 1597870--1597917 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1597860 ATATATATGC
1597870 ATGTATA-TTATATACAT
1 ATGTATACTTATATACAT
**
1597887 ATGTATACTTATATTTAT
1 ATGTATACTTATATACAT
*
1597905 ATATATACTTATA
1 ATGTATACTTATA
1597918 CTTTTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (18 bp):
ATGTATACTTATATACAT
Found at i:1597917 original size:24 final size:24
Alignment explanation
Indices: 1597873--1597955 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
1597863 TATATGCATG
1597873 TATA-TTATATACATATGTATACT
1 TATATTTATATACATATGTATACT
*
1597896 TATATTTATATATATACT-TATACT
1 TATATTTATATACATA-TGTATACT
* * * *
1597920 TTTATATATATGCATAAGTATA-T
1 TATATTTATATACATATGTATACT
*
1597943 ATATATATATATA
1 -TATATTTATATA
1597956 TAAGTTTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
23 5 0.10
24 42 0.88
25 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (24 bp):
TATATTTATATACATATGTATACT
Found at i:1597925 original size:18 final size:18
Alignment explanation
Indices: 1597885--1597929 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1597875 TATTATATAC
*
1597885 ATATGTATACTTATATTT
1 ATATATATACTTATATTT
1597903 ATATATATACTTATACTTT
1 ATATATATACTTATA-TTT
1597922 -TATATATA
1 ATATATATA
1597930 TGCATAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (18 bp):
ATATATATACTTATATTT
Found at i:1598096 original size:14 final size:13
Alignment explanation
Indices: 1598079--1598129 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
1598069 TACATAAGTG
1598079 TATATAAGTATATA
1 TATATAA-TATATA
1598093 TATATAA-ATATA
1 TATATAATATATA
*
1598105 AATATAA-ATATA
1 TATATAATATATA
*
1598117 TACATACATATAT
1 TATATA-ATATAT
1598130 GTACATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 20 0.62
13 1 0.03
14 11 0.34
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (13 bp):
TATATAATATATA
Found at i:1598103 original size:12 final size:12
Alignment explanation
Indices: 1598088--1598129 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1598078 GTATATAAGT
1598088 ATATATATATAA
1 ATATATATATAA
*
1598100 ATATAAATATAA
1 ATATATATATAA
* *
1598112 ATATATACATAC
1 ATATATATATAA
1598124 ATATAT
1 ATATAT
1598130 GTACATATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATATATATAA
Found at i:1598510 original size:14 final size:14
Alignment explanation
Indices: 1598487--1598525 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
1598477 TAAATAAATT
1598487 AATT-ATTTAATAA
1 AATTAATTTAATAA
1598500 AATTAATTTAATAA
1 AATTAATTTAATAA
1598514 AATTAATTTAAT
1 AATTAATTTAAT
1598526 GATTATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTAATTTAATAA
Found at i:1598544 original size:13 final size:13
Alignment explanation
Indices: 1598521--1598564 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1598511 TAAAATTAAT
*
1598521 TTAATGATTATAA
1 TTAAAGATTATAA
**
1598534 TTAAATTTTATAA
1 TTAAAGATTATAA
1598547 TATAAAGATTATAA
1 T-TAAAGATTATAA
1598561 TTAA
1 TTAA
1598565 TATAGAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (13 bp):
TTAAAGATTATAA
Found at i:1598791 original size:16 final size:16
Alignment explanation
Indices: 1598747--1598798 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1598737 GTAAATCAGA
*
1598747 TCAGTTCAATTACAAG
1 TCAGATCAATTACAAG
*
1598763 TCAGATCATTTACAAG
1 TCAGATCAATTACAAG
* *
1598779 TTTAG-TCAATTACATG
1 -TCAGATCAATTACAAG
1598795 TCAG
1 TCAG
1598799 GTTCATAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (16 bp):
TCAGATCAATTACAAG
Found at i:1598821 original size:15 final size:16
Alignment explanation
Indices: 1598798--1598831 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1598788 TTACATGTCA
1598798 GGTTCATAACA-GTCG
1 GGTTCATAACAGGTCG
*
1598813 GGTTGATAACAGGTCG
1 GGTTCATAACAGGTCG
1598829 GGT
1 GGT
1598832 AATACCAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (16 bp):
GGTTCATAACAGGTCG
Found at i:1607246 original size:32 final size:32
Alignment explanation
Indices: 1607210--1607283 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
1607200 AACCGATCAT
*
1607210 ATATTGACTCGATCC-TAAATCTGACCAATCTA
1 ATATTGACTCGATCCGAAAAT-TGACCAATCTA
* *
1607242 ATATTAACAT-GATCCGAAAATTGACCGATCTA
1 ATATTGAC-TCGATCCGAAAATTGACCAATCTA
1607274 ATATTGACTC
1 ATATTGACTC
1607284 AAACTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 1 0.03
32 29 0.83
33 5 0.14
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (32 bp):
ATATTGACTCGATCCGAAAATTGACCAATCTA
Found at i:1609110 original size:60 final size:59
Alignment explanation
Indices: 1608957--1609117 Score: 162
Period size: 60 Copynumber: 2.7 Consensus size: 59
1608947 ATCCTCAAAT
* * * * * * *
1608957 TATGATCTTTATTTTAAATTAGTCCCTAAACTTTTAAATATTTCAATTTCATCTCTAAAC
1 TATGA-CTTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAATCTCATCCCTAAAA
* * * *
1609017 TTTGACTATCATTCTAAGTTAGTCGGC-ATACTTTTGAACATTTCAATCTCATCCCTAAAA
1 TATGACT-TCATTCTAAATTAGTC-CCTAAACTTTTGAACATTTCAATCTCATCCCTAAAA
*
1609077 TATGACCTTCATTCTAAACTAGTCCCTAAACTTTTTGAACA
1 TATGA-CTTCATTCTAAATTAGTCCCTAAAC-TTTTGAACA
1609118 GACAGTTTTC
Statistics
Matches: 80, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
59 3 0.04
60 65 0.81
61 12 0.15
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (59 bp):
TATGACTTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAATCTCATCCCTAAAA
Found at i:1609323 original size:31 final size:30
Alignment explanation
Indices: 1609288--1609385 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 30
1609278 GGGGACCAAT
1609288 TTAGAATGACAGTCATAGTTTGGGAATAAAA
1 TTAGAATGA-AGTCATAGTTTGGGAATAAAA
* * * * *
1609319 TTAGAAT--ATTCAAAAGTTTACGGAGT-AAT
1 TTAGAATGAAGTC-ATAGTTT-GGGAATAAAA
*
1609348 TTAGAATGAGGGTCATAGTTTGGGAATAAAA
1 TTAGAATGA-AGTCATAGTTTGGGAATAAAA
*
1609379 TTGGAAT
1 TTAGAAT
1609386 ATTCAAAAGT
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
28 3 0.06
29 15 0.31
30 8 0.16
31 21 0.43
32 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (30 bp):
TTAGAATGAAGTCATAGTTTGGGAATAAAA
Found at i:1609351 original size:29 final size:29
Alignment explanation
Indices: 1609319--1609414 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
1609309 GGGAATAAAA
*
1609319 TTAGAATATTCAAAAGTTTACGGAGTAAT
1 TTAGAATATTCAAAAGTTTAAGGAGTAAT
* * * * *
1609348 TTAGAATGAGGGTC-ATAGTTT-GGGAATAAAA
1 TTAGAAT-A--TTCAAAAGTTTAAGGAGT-AAT
*
1609379 TTGGAATATTCAAAAGTTTAAGGAGTAAT
1 TTAGAATATTCAAAAGTTTAAGGAGTAAT
1609408 TTAGAAT
1 TTAGAAT
1609415 GAGGGTCATA
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
28 2 0.04
29 21 0.43
30 10 0.20
31 14 0.29
32 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (29 bp):
TTAGAATATTCAAAAGTTTAAGGAGTAAT
Found at i:1609428 original size:31 final size:31
Alignment explanation
Indices: 1609333--1609433 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
1609323 AATATTCAAA
*
1609333 AGTTTACGGAGTAATTTAGAATGAGGGTCAT
1 AGTTTAAGGAGTAATTTAGAATGAGGGTCAT
* * * * * *
1609364 AGTTT-GGGAATAAAATTGGAAT-A--TTCAAA
1 AGTTTAAGGAGT-AATTTAGAATGAGGGTC-AT
1609393 AGTTTAAGGAGTAATTTAGAATGAGGGTCAT
1 AGTTTAAGGAGTAATTTAGAATGAGGGTCAT
*
1609424 AGTTTGAGGA
1 AGTTTAAGGA
1609434 TGAAATTGGA
Statistics
Matches: 51, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
28 2 0.04
29 14 0.27
30 10 0.20
31 23 0.45
32 2 0.04
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (31 bp):
AGTTTAAGGAGTAATTTAGAATGAGGGTCAT
Found at i:1609488 original size:60 final size:60
Alignment explanation
Indices: 1609285--1609470 Score: 277
Period size: 60 Copynumber: 3.1 Consensus size: 60
1609275 TTTGGGGACC
** * *
1609285 AATTTAGAATGACAGTCATAGTTTGGGAATAAAATTAGAATATTCAAAAGTTTACGGAGT
1 AATTTAGAATGAGGGTCATAGTTTGGGAATAAAATTGGAATATTCAAAAGTTTAAGGAGT
1609345 AATTTAGAATGAGGGTCATAGTTTGGGAATAAAATTGGAATATTCAAAAGTTTAAGGAGT
1 AATTTAGAATGAGGGTCATAGTTTGGGAATAAAATTGGAATATTCAAAAGTTTAAGGAGT
* **
1609405 AATTTAGAATGAGGGTCATAGTTTGAGG-ATGAAATTGGAATATTTTAAAGTTTAAGGA-T
1 AATTTAGAATGAGGGTCATAGTTTG-GGAATAAAATTGGAATATTCAAAAGTTTAAGGAGT
1609464 CAATTTA
1 -AATTTA
1609471 AAATAAAGGA
Statistics
Matches: 117, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
59 1 0.01
60 114 0.97
61 2 0.02
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (60 bp):
AATTTAGAATGAGGGTCATAGTTTGGGAATAAAATTGGAATATTCAAAAGTTTAAGGAGT
Found at i:1610290 original size:23 final size:22
Alignment explanation
Indices: 1610234--1610290 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
1610224 TCAGAAACTT
*
1610234 AAATATAATAATACCAAAAATAA
1 AAATAT-ATATTACCAAAAATAA
* *
1610257 AAAT-TAAATTACTAAAAACTAA
1 AAATATATATTACCAAAAA-TAA
1610279 AAATATATATTA
1 AAATATATATTA
1610291 TTTTGTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 10 0.36
22 8 0.29
23 10 0.36
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATATATATTACCAAAAATAA
Found at i:1610629 original size:14 final size:16
Alignment explanation
Indices: 1610610--1610641 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1610600 TAAACAAATG
1610610 TAATTTTT-A-ATTTT
1 TAATTTTTGAGATTTT
1610624 TAATTTTTGAGATTTT
1 TAATTTTTGAGATTTT
1610640 TA
1 TA
1610642 TAATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TAATTTTTGAGATTTT
Found at i:1610845 original size:23 final size:23
Alignment explanation
Indices: 1610809--1610852 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1610799 TAAAAAAGTC
1610809 GTAATATACATTTTTAATTTTTTA
1 GTAATATACATTTTT-ATTTTTTA
*
1610833 GTAATTTA-ATTTTTATTTTT
1 GTAATATACATTTTTATTTTT
1610853 GGTATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
GTAATATACATTTTTATTTTTTA
Found at i:1612279 original size:6 final size:6
Alignment explanation
Indices: 1612268--1612316 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
1612258 GACACGTATT
* * * *
1612268 ACCACG ACCACG ACAACG ACTACG ACAACG ACCACG ACAACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1612316 A
1 A
1612317 GACGAGACGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.41, C:0.41, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:1612292 original size:12 final size:12
Alignment explanation
Indices: 1612271--1612316 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
1612261 ACGTATTACC
1612271 ACGACCACGACA
1 ACGACCACGACA
*
1612283 ACGACTACGACA
1 ACGACCACGACA
1612295 ACGACCACGACA
1 ACGACCACGACA
1612307 ACGACCACGA
1 ACGACCACGA
1612317 GACGAGACGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.41, C:0.39, G:0.17, T:0.02
Consensus pattern (12 bp):
ACGACCACGACA
Found at i:1612828 original size:6 final size:6
Alignment explanation
Indices: 1612812--1612853 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
1612802 TCTCGTCTCG
1612812 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
1612854 TCTTCGACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1619627 original size:42 final size:43
Alignment explanation
Indices: 1619442--1619773 Score: 460
Period size: 43 Copynumber: 7.8 Consensus size: 43
1619432 AACAAAAAAT
* * * * *
1619442 GCCGCAAAAGGTCGAGATATTTAGCGACATTTTTGGAACAAAT
1 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
*
1619485 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATCAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
1619528 GCCGCAAAAGGTCGAGATTTATAGCAGCGTTTTTGGAAAAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
*
1619571 GCCACAAAAGGTCGAGATCTATAGCGGCG-TTTTGGAACAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
1619613 GCCGCTAAAA-GTCGAGATCTATAGCGGCG-TTTTGGAACAAAC
1 GCCGC-AAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
1619655 GCCGCTAAAA-GTCGAGATTTATAGCAGCGTTTTTGGAACAAAT
1 GCCGC-AAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
*
1619698 GCCACAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
*
1619740 GCCACAAAAGGTCGAGAAT-TATAGCGGCGTTTTT
1 GCCGCAAAAGGTCGAG-ATCTATAGCGGCGTTTTT
1619774 CTATACAAAC
Statistics
Matches: 262, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
42 118 0.45
43 142 0.54
44 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (43 bp):
GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
Found at i:1619702 original size:127 final size:127
Alignment explanation
Indices: 1619435--1619772 Score: 504
Period size: 127 Copynumber: 2.6 Consensus size: 127
1619425 GTTTGATAAC
* * * * * *
1619435 AAAAAATGCCGCAAAAGGTCGAGATATTTAGCGACATTTTTGGAACAAATGCCGCAAAAGGTCGA
1 AAAAAATGCCACAAAAGGTCGAGATCTATAGCGGC-GTTTTGGAACAAACGCCGCAAAAGGTCGA
*
1619500 GATCTATAGCGGCGTTTTTGGATCAAACGCCGCAAAAGGTCGAGATTTATAGCAGCGTTTTTGG
65 GATCTATAGCGGCG-TTTTGGAACAAACGCCGCAAAAGGTCGAGATTTATAGCAGCGTTTTTGG
*
1619564 AAAAAACGCCACAAAAGGTCGAGATCTATAGCGGCGTTTTGGAACAAACGCCGCTAAAA-GTCGA
1 AAAAAATGCCACAAAAGGTCGAGATCTATAGCGGCGTTTTGGAACAAACGCCGC-AAAAGGTCGA
1619628 GATCTATAGCGGCGTTTTGGAACAAACGCCGCTAAAA-GTCGAGATTTATAGCAGCGTTTTTGG
65 GATCTATAGCGGCGTTTTGGAACAAACGCCGC-AAAAGGTCGAGATTTATAGCAGCGTTTTTGG
* *
1619691 AACAAATGCCACAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGTCGA
1 AAAAAATGCCACAAAAGGTCGAGATCTATAGCGGCG-TTTTGGAACAAACGCCGCAAAAGGTCGA
1619755 GAAT-TATAGCGGCGTTTT
65 G-ATCTATAGCGGCGTTTT
1619773 TCTATACAAA
Statistics
Matches: 193, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
126 19 0.10
127 98 0.51
128 42 0.22
129 34 0.18
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (127 bp):
AAAAAATGCCACAAAAGGTCGAGATCTATAGCGGCGTTTTGGAACAAACGCCGCAAAAGGTCGAG
ATCTATAGCGGCGTTTTGGAACAAACGCCGCAAAAGGTCGAGATTTATAGCAGCGTTTTTGG
Found at i:1619932 original size:21 final size:21
Alignment explanation
Indices: 1619908--1619968 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
1619898 TAATTAAGAC
1619908 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
1619929 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
*
1619950 AGAAACTTGAAATCCATAA
1 ACAAACTTGAAATCCATAA
1619969 TAATAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.20
Consensus pattern (21 bp):
ACAAACTTGAAATCCATAACA
Found at i:1623315 original size:21 final size:21
Alignment explanation
Indices: 1623291--1623330 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1623281 TTTTAAATAA
1623291 ATAAAATAAAATATTATATAT
1 ATAAAATAAAATATTATATAT
* * *
1623312 ATAAATTTAAATGTTATAT
1 ATAAAATAAAATATTATAT
1623331 TTTTAGATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
ATAAAATAAAATATTATATAT
Found at i:1623905 original size:42 final size:43
Alignment explanation
Indices: 1623799--1623913 Score: 139
Period size: 42 Copynumber: 2.7 Consensus size: 43
1623789 AATGGTTAAA
* * **
1623799 CGCCAATAAAGTACTAGGTTTTAGCGGCG--TTTGTCTAAAAT
1 CGCCACTAAAGTATTAGGTTTTAGCGGCGTTTTTGAATAAAAT
* *
1623840 CGTCACTAAAGTATGA-GTATTTAGCGGCGTTTTTGAATAAAAT
1 CGCCACTAAAGTATTAGGT-TTTAGCGGCGTTTTTGAATAAAAT
1623883 -GCCACTAAAGTATTAGGTTTTAGCGGCGTTT
1 CGCCACTAAAGTATTAGGTTTTAGCGGCGTTT
1623914 ATTTAAAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
40 2 0.03
41 22 0.35
42 26 0.42
43 12 0.19
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (43 bp):
CGCCACTAAAGTATTAGGTTTTAGCGGCGTTTTTGAATAAAAT
Found at i:1624068 original size:164 final size:164
Alignment explanation
Indices: 1623820--1624254 Score: 581
Period size: 164 Copynumber: 2.6 Consensus size: 164
1623810 TACTAGGTTT
* * **
1623820 TAGCGGCGTTTGTCTAAAATCGTCACTAAAGTATGAGTATTTAGCGGCGTTTTTGAATAAAATGC
1 TAGCGGCGTTTGTTTAAAA-CGCCACTAAAGTACAAGTATTTAGCGGCGTTTTTGAATAAAATGC
* *
1623885 CACTAAAGTATTAGGTTTTAGCGGCGTTTATTTAAAAACGCAACGATATATATACCCTATTGCGG
65 CACTAAAGTACTAGGTTTTAGCGGCGTTTATTTAAAAACGCAACAATATATATACCCTATTGCGG
1623950 CGTTTGTTTAAAAACGCCACTAAAGAACGATTCTA
130 CGTTTGTTTAAAAACGCCACTAAAGAACGATTCTA
*
1623985 TAGCGGCGTTTGTTTACAAACGCCACTAAAGTACAAGT-TTTAGCGGCGTTTTTGCATAAAATGC
1 TAGCGGCGTTTGTTTA-AAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTTTGAATAAAATGC
* * * * * *
1624049 CTCTAAAGCACTAGGTTTTAGCGGCGTTTATCTAAAAATGCCACAATATATGTACCCTATTGCGG
65 CACTAAAGTACTAGGTTTTAGCGGCGTTTATTTAAAAACGCAACAATATATATACCCTATTGCGG
1624114 CGTTTGTTTAAAAACGCCACTAAAGAACGATTCTA
130 CGTTTGTTTAAAAACGCCACTAAAGAACGATTCTA
* * * * * *
1624149 TGGCGGCGTTTTTTTTAAAAACGCCACTAAAGTACTTA-TCTTTAGCGGCGCTTGTCGAAT-AAA
1 TAGCGGCG-TTTGTTT-AAAACGCCACTAAAGTAC-AAGTATTTAGCGGCG-TTTTTGAATAAAA
* * * *
1624212 CGCCACTAAAGTACGA-GTTTTAGCGGCGTTTGTTGAAAAACGC
62 TGCCACTAAAGTACTAGGTTTTAGCGGCGTTTATTTAAAAACGC
1624255 CGTTAATGTT
Statistics
Matches: 237, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
164 124 0.52
165 77 0.32
166 30 0.13
167 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (164 bp):
TAGCGGCGTTTGTTTAAAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTTTGAATAAAATGCC
ACTAAAGTACTAGGTTTTAGCGGCGTTTATTTAAAAACGCAACAATATATATACCCTATTGCGGC
GTTTGTTTAAAAACGCCACTAAAGAACGATTCTA
Found at i:1624086 original size:123 final size:124
Alignment explanation
Indices: 1623946--1624255 Score: 305
Period size: 124 Copynumber: 2.5 Consensus size: 124
1623936 ATACCCTATT
* * *
1623946 GCGGCGTTTGTTTAAAAACGCCACTAAAGAACGATTCTATAGCGGCGTTTGTTTACAAACGCCAC
1 GCGGCGTTTGTCTAAAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTTTAAAAACGCCAC
* * *
1624011 TAAAGTACAAGTT-T-TAGCGGCGTTTTTGCAT-AAAATGCCTCTAAAGCAC-TAGGT-TTTA
66 TAAAGAACAA-TTCTATAGCGGCGTTTTT-CATAAAAACGCCACTAAAGCACTTA--TCTTTA
* * * ** *
1624069 GCGGCGTTTATCTAAAAATGCCAC-AATA-TATGTACCCTATTGCGGCGTTTGTTTAAAAACGCC
1 GCGGCGTTTGTCTAAAAACGCCACTAA-AGTACG-ATTCTATAGCGGCGTTTGTTTAAAAACGCC
* * ** *
1624132 ACTAAAGAACGATTCTATGGCGGCGTTTTTTTTAAAAACGCCACTAAAGTACTTATCTTTA
64 ACTAAAGAACAATTCTATAGCGGCGTTTTTCATAAAAACGCCACTAAAGCACTTATCTTTA
* * *
1624193 GCGGCGCTTGTCGAATAAACGCCACTAAAGTACGAGTT-T-TAGCGGCGTTTGTTGAAAAACGCC
1 GCGGCGTTTGTCTAA-AAACGCCACTAAAGTACGA-TTCTATAGCGGCGTTTGTTTAAAAACGCC
1624256 GTTAATGTTA
Statistics
Matches: 150, Mismatches: 26, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
122 6 0.04
123 61 0.41
124 65 0.43
125 13 0.09
126 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (124 bp):
GCGGCGTTTGTCTAAAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTTTAAAAACGCCAC
TAAAGAACAATTCTATAGCGGCGTTTTTCATAAAAACGCCACTAAAGCACTTATCTTTA
Found at i:1624197 original size:42 final size:40
Alignment explanation
Indices: 1623796--1624255 Score: 303
Period size: 41 Copynumber: 11.2 Consensus size: 40
1623786 GTTAATGGTT
* *
1623796 AAACGCCAATAAAGTACTAGGTTTTAGCGGCGTTTGTCTAA
1 AAACGCCACTAAAGTACTA-GTTTTAGCGGCGTTTGTTTAA
* * *
1623837 AATCGTCACTAAAGTA-TGAGTATTTAGCGGCGTTT-TTGAATA
1 AAACGCCACTAAAGTACT-AGT-TTTAGCGGCGTTTGTT-TA-A
* * *
1623879 AAATGCCACTAAAGTATTAGGTTTTAGCGGCGTTTATTTAA
1 AAACGCCACTAAAGTACTA-GTTTTAGCGGCGTTTGTTTAA
* ** *
1623920 AAACGCAACGATATATA-TAC-CCTATT-GCGGCGTTTGTTTAA
1 AAACGCCAC--TA-A-AGTACTAGTTTTAGCGGCGTTTGTTTAA
* * *
1623961 AAACGCCACTAAAGAACGA-TTCTATAGCGGCGTTTGTTTAC
1 AAACGCCACTAAAGTACTAGTT-T-TAGCGGCGTTTGTTTAA
* *
1624002 AAACGCCACTAAAGTACAAGTTTTAGCGGCGTTT-TTGCATA
1 AAACGCCACTAAAGTACTAGTTTTAGCGGCGTTTGTT-TA-A
* * * * *
1624043 AAATGCCTCTAAAGCACTAGGTTTTAGCGGCGTTTATCTAA
1 AAACGCCACTAAAGTACTA-GTTTTAGCGGCGTTTGTTTAA
* * ** *
1624084 AAATGCCACAATATATGTAC-CCTATT-GCGGCGTTTGTTTAA
1 AAACGCCAC--TA-AAGTACTAGTTTTAGCGGCGTTTGTTTAA
* * * *
1624125 AAACGCCACTAAAGAACGA-TTCTATGGCGGCGTTTTTTTTAA
1 AAACGCCACTAAAGTACTAGTT-T-TAGCGGCG-TTTGTTTAA
* **
1624167 AAACGCCACTAAAGTACTTA-TCTTTAGCGGCGCTTGTCGAA
1 AAACGCCACTAAAGTAC-TAGT-TTTAGCGGCGTTTGTTTAA
* *
1624208 TAAACGCCACTAAAGTACGAGTTTTAGCGGCGTTTGTTGAA
1 -AAACGCCACTAAAGTACTAGTTTTAGCGGCGTTTGTTTAA
1624249 AAACGCC
1 AAACGCC
1624256 GTTAATGTTA
Statistics
Matches: 331, Mismatches: 55, Indels: 67
0.73 0.12 0.15
Matches are distributed among these distances:
37 1 0.00
38 9 0.03
39 8 0.02
40 25 0.08
41 164 0.50
42 102 0.31
43 13 0.04
44 8 0.02
45 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACGCCACTAAAGTACTAGTTTTAGCGGCGTTTGTTTAA
Found at i:1624411 original size:11 final size:11
Alignment explanation
Indices: 1624395--1624430 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
1624385 CGATACCAGT
1624395 CTTTCGTCTAC
1 CTTTCGTCTAC
1624406 CTTTCGTCTAC
1 CTTTCGTCTAC
*
1624417 CTTCCGTCTAC
1 CTTTCGTCTAC
1624428 CTT
1 CTT
1624431 CAAGACCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.08, C:0.39, G:0.08, T:0.44
Consensus pattern (11 bp):
CTTTCGTCTAC
Found at i:1625628 original size:41 final size:41
Alignment explanation
Indices: 1625583--1625668 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
1625573 GCCTGGCCTG
* *
1625583 GCCTATTTAACTAAACAGGCCAGGCCCAGGCCTTTTTAAAA
1 GCCTATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAA
**
1625624 GCCTATTTAACTAAACAGGCCAGGCTTAGGCCTATTAAAAA
1 GCCTATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAA
1625665 GCCT
1 GCCT
1625669 TATAAGCCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (41 bp):
GCCTATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAA
Found at i:1625819 original size:17 final size:18
Alignment explanation
Indices: 1625797--1625836 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
1625787 TATTGTTAAA
1625797 CAGGCTTTTAAACAGG-C
1 CAGGCTTTTAAACAGGCC
1625814 CAGGCTTTTAAACAGGCC
1 CAGGCTTTTAAACAGGCC
1625832 CAGGC
1 CAGGC
1625837 CAGGCCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (18 bp):
CAGGCTTTTAAACAGGCC
Found at i:1627070 original size:60 final size:60
Alignment explanation
Indices: 1626997--1627117 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
1626987 ATGCAATACT
*
1626997 ATTCGCAACGCGAACTTTGACTATCGCAATGCGAATCTAGAAACTGATTTGCGATACCGG
1 ATTCGCAACGCGAACTTCGACTATCGCAATGCGAATCTAGAAACTGATTTGCGATACCGG
*
1627057 ATTCGTAACGCGAACTTCGACTATCGCAATGCGAATCTAGAAACTGATTTGCGATACCGG
1 ATTCGCAACGCGAACTTCGACTATCGCAATGCGAATCTAGAAACTGATTTGCGATACCGG
1627117 A
1 A
1627118 GATCGCGTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (60 bp):
ATTCGCAACGCGAACTTCGACTATCGCAATGCGAATCTAGAAACTGATTTGCGATACCGG
Found at i:1631844 original size:22 final size:22
Alignment explanation
Indices: 1631819--1631863 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1631809 GGCATGTGAA
*
1631819 ATTTATCCCGAAGGACCTCTGT
1 ATTTATCCCGAAGGACCTATGT
* *
1631841 ATTTGTCTCGAAGGACCTATGT
1 ATTTATCCCGAAGGACCTATGT
1631863 A
1 A
1631864 ATGTATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (22 bp):
ATTTATCCCGAAGGACCTATGT
Found at i:1636337 original size:17 final size:17
Alignment explanation
Indices: 1636308--1636354 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1636298 TAAGAGTTAT
* *
1636308 TTTAATAAATGAACTAG
1 TTTAATGAATGAACTAC
*
1636325 TTTGATGAATGAACTAC
1 TTTAATGAATGAACTAC
*
1636342 TTTAATTAATGAA
1 TTTAATGAATGAA
1636355 TTAATTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAC
Found at i:1636366 original size:17 final size:17
Alignment explanation
Indices: 1636308--1636367 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
1636298 TAAGAGTTAT
* *
1636308 TTTAATAAATGAACTAG
1 TTTAATTAATGAACTAA
* * *
1636325 TTTGATGAATGAACTAC
1 TTTAATTAATGAACTAA
*
1636342 TTTAATTAATGAATTAA
1 TTTAATTAATGAACTAA
*
1636359 TTTTATTAA
1 TTTAATTAA
1636368 ATGACTAGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (17 bp):
TTTAATTAATGAACTAA
Found at i:1641228 original size:2 final size:2
Alignment explanation
Indices: 1641221--1641269 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1641211 TTTAACGGAG
1641221 GA GA GA 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 GA GA GA
1641263 GA GA GA G
1 GA GA GA G
1641270 GGAAAAACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1642282 original size:2 final size:2
Alignment explanation
Indices: 1642242--1642270 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1642232 ATGAACAAAA
1642242 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1642271 TCAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1644201 original size:19 final size:20
Alignment explanation
Indices: 1644164--1644200 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1644154 TCATTCAATT
1644164 ATCATTTTAATTATATTTTG
1 ATCATTTTAATTATATTTTG
1644184 ATCA-TTTAATTAT-TTTT
1 ATCATTTTAATTATATTTT
1644201 TCAATATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
ATCATTTTAATTATATTTTG
Found at i:1649041 original size:21 final size:22
Alignment explanation
Indices: 1649009--1649049 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1648999 CATAGCCTTG
1649009 ATTTCTTCTTCCAACTGCTTCA
1 ATTTCTTCTTCCAACTGCTTCA
*
1649031 ATTTC-TCTTCCATCTGCTT
1 ATTTCTTCTTCCAACTGCTT
1649050 GTTTAGCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.15, C:0.32, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTTCTTCTTCCAACTGCTTCA
Found at i:1649580 original size:31 final size:30
Alignment explanation
Indices: 1649543--1649640 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
1649533 AATGTAAATA
1649543 AAATAAAATGCAAACATGAAAAACGAAATGT
1 AAATAAAATGCAAACAT-AAAAACGAAATGT
* * *
1649574 AAATAAAATG-TAA-AT-AGAACGTAAAATAT
1 AAATAAAATGCAAACATAAAAACG--AAATGT
**
1649603 AAATAAAATGCAAACATAAAATGTGAAATGT
1 AAATAAAATGCAAACATAAAA-ACGAAATGT
1649634 AAATAAA
1 AAATAAA
1649641 TAAAATATAG
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
27 5 0.09
29 17 0.32
30 4 0.08
31 24 0.45
32 2 0.04
33 1 0.02
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.20
Consensus pattern (30 bp):
AAATAAAATGCAAACATAAAAACGAAATGT
Found at i:1649639 original size:18 final size:17
Alignment explanation
Indices: 1649628--1649689 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 17
1649618 ATAAAATGTG
1649628 AAATGTAAA--TAAATA
1 AAATGTAAATGTAAATA
* *
1649643 AAATATAGAATATAAATA
1 AAATGTA-AATGTAAATA
1649661 AAATGTGAAATGTAAATA
1 AAATGT-AAATGTAAATA
1649679 AAATGTAAATG
1 AAATGTAAATG
1649690 CATGTCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 6 0.15
16 2 0.05
17 5 0.12
18 26 0.65
19 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.27
Consensus pattern (17 bp):
AAATGTAAATGTAAATA
Found at i:1649645 original size:22 final size:22
Alignment explanation
Indices: 1649618--1649680 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
1649608 AAATGCAAAC
1649618 ATAAAATGTGAAATGTAAATAA
1 ATAAAATGTGAAATGTAAATAA
*
1649640 ATAAAA--T-ATA-G-AATATAA
1 ATAAAATGTGAAATGTAA-ATAA
1649658 ATAAAATGTGAAATGTAAATAA
1 ATAAAATGTGAAATGTAAATAA
1649680 A
1 A
1649681 ATGTAAATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 2 0.06
18 11 0.33
19 2 0.06
20 2 0.06
21 2 0.06
22 12 0.36
23 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (22 bp):
ATAAAATGTGAAATGTAAATAA
Found at i:1649651 original size:60 final size:59
Alignment explanation
Indices: 1649538--1649664 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 59
1649528 TATAAAATGT
**
1649538 AAATAAAATAAAATGCAAACATGAAAAACGAAATGTAAATAAAATGTAAATAGAACGTA
1 AAATAAAATAAAATGCAAACATGAAAAACGAAATGTAAATAAAATAAAAATAGAACGTA
**
1649597 AAATATAAATAAAATGCAAACAT-AAAATGTGAAATGTAAAT-AAATAAAATATAGAA--TA
1 AAATA-AAATAAAATGCAAACATGAAAA-ACGAAATGTAAATAAAATAAAA-ATAGAACGTA
1649655 TAAATAAAAT
1 -AAATAAAAT
1649665 GTGAAATGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
58 6 0.10
59 20 0.33
60 34 0.57
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.22
Consensus pattern (59 bp):
AAATAAAATAAAATGCAAACATGAAAAACGAAATGTAAATAAAATAAAAATAGAACGTA
Found at i:1652740 original size:22 final size:22
Alignment explanation
Indices: 1652715--1652756 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1652705 CAAAAAGGGG
1652715 GCAGAGTTTTGGTACAAAACGA
1 GCAGAGTTTTGGTACAAAACGA
1652737 GCAGAGTTTTGGTACAAAAC
1 GCAGAGTTTTGGTACAAAAC
1652757 ATGCAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (22 bp):
GCAGAGTTTTGGTACAAAACGA
Found at i:1652766 original size:22 final size:22
Alignment explanation
Indices: 1652719--1652767 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1652709 AAGGGGGCAG
*
1652719 AGTTTTGGTACAAAACGAGCAG
1 AGTTTTGGTACAAAACGAGCAA
1652741 AGTTTTGGTACAAAAC-ATGCAA
1 AGTTTTGGTACAAAACGA-GCAA
1652763 AGTTT
1 AGTTT
1652768 CAGTACTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTTTTGGTACAAAACGAGCAA
Found at i:1652773 original size:22 final size:22
Alignment explanation
Indices: 1652726--1652773 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1652716 CAGAGTTTTG
* **
1652726 GTACAAAACGAGCAGAGTTTTG
1 GTACAAAACGAGCAAAGTTTCA
1652748 GTACAAAAC-ATGCAAAGTTTCA
1 GTACAAAACGA-GCAAAGTTTCA
1652770 GTAC
1 GTAC
1652774 TACTAAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (22 bp):
GTACAAAACGAGCAAAGTTTCA
Found at i:1653230 original size:5 final size:5
Alignment explanation
Indices: 1653222--1653261 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1653212 AATGAAAACA
**
1653222 AAAAT AAAAT AAAAAT AAAAT ATGAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1653262 GGATCACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1656509 original size:18 final size:18
Alignment explanation
Indices: 1656482--1656527 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1656472 CACAAATGCC
*
1656482 TTCTTCTTACTAGAACCA
1 TTCTTTTTACTAGAACCA
* *
1656500 TTCTTTTTACTAGATCCC
1 TTCTTTTTACTAGAACCA
1656518 TTCTTCTTTA
1 TTCTT-TTTA
1656528 GGAGGGGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.20, C:0.26, G:0.04, T:0.50
Consensus pattern (18 bp):
TTCTTTTTACTAGAACCA
Found at i:1657383 original size:5 final size:5
Alignment explanation
Indices: 1657373--1657412 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1657363 AATGTAAACA
**
1657373 AAAAT AAAAT AAAAAT AAAAT ATGAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1657413 GGATCACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1660662 original size:18 final size:18
Alignment explanation
Indices: 1660635--1660680 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1660625 CACAAATGCC
*
1660635 TTCTTCTTACTAGATCCA
1 TTCTTTTTACTAGATCCA
*
1660653 TTCTTTTTACTAGATCCC
1 TTCTTTTTACTAGATCCA
1660671 TTCTTCTTTA
1 TTCTT-TTTA
1660681 GGAGGGGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.17, C:0.26, G:0.04, T:0.52
Consensus pattern (18 bp):
TTCTTTTTACTAGATCCA
Found at i:1661534 original size:5 final size:5
Alignment explanation
Indices: 1661526--1661565 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1661516 AATGAAAACA
**
1661526 AAAAT AAAAT AAAAAT AAAAT ATGAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1661566 GGATCACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1664784 original size:18 final size:18
Alignment explanation
Indices: 1664757--1664802 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
1664747 CACAAATGCC
*
1664757 TTCTTCTTACTAGATCCA
1 TTCTTTTTACTAGATCCA
1664775 TTCTTTTTACTAGATCCA
1 TTCTTTTTACTAGATCCA
1664793 TTCTTCTTTA
1 TTCTT-TTTA
1664803 GGAGGGGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (18 bp):
TTCTTTTTACTAGATCCA
Found at i:1665656 original size:5 final size:5
Alignment explanation
Indices: 1665648--1665687 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1665638 AATGAAAACA
**
1665648 AAAAT AAAAT AAAAAT AAAAT ATGAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1665688 GGATCACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1668937 original size:18 final size:18
Alignment explanation
Indices: 1668910--1668960 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
1668900 CACAAATGCC
*
1668910 TTCTTCTTACTAGATCCA
1 TTCTTTTTACTAGATCCA
1668928 TTCTTTTTACTAGATCCA
1 TTCTTTTTACTAGATCCA
1668946 TTCTTTTTACTAGAT
1 TTCTTTTTACTAGAT
1668961 GACATTCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.51
Consensus pattern (18 bp):
TTCTTTTTACTAGATCCA
Found at i:1681657 original size:15 final size:15
Alignment explanation
Indices: 1681637--1681666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1681627 TGAGACCTTA
*
1681637 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
1681652 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
1681667 TTCACCTAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.67, G:0.17, T:0.07
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:1702641 original size:14 final size:13
Alignment explanation
Indices: 1702610--1702634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1702600 TTCATTGAAA
1702610 AACCGAAAAACCG
1 AACCGAAAAACCG
1702623 AACCGAAAAACC
1 AACCGAAAAACC
1702635 CGTACCGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.32, G:0.12, T:0.00
Consensus pattern (13 bp):
AACCGAAAAACCG
Found at i:1712442 original size:170 final size:173
Alignment explanation
Indices: 1712136--1712467 Score: 535
Period size: 170 Copynumber: 1.9 Consensus size: 173
1712126 TTCAGATTTG
* * * *
1712136 CATAAAACTTTAACAATATCGTCCAATTAGAAATTTGATCATGTTTGTAATTCAATTTACTGACA
1 CATAAAACTTTAACAAAATCATACAATTAGAAATTTGATCATGTTTCTAATTCAATTTACTGACA
* *
1712201 GAGCATTTCATTTCCAAAATCTTCTACTTTTTATTAGTTAATTCACGGTCAGAGGTCTTTCATCA
66 GAACATTTCATTTCCAAAATCTTCTACTTTTTATTAGTTAATTCACGGTCAGAGGTCTTTCACCA
1712266 GCAACAGGAGGAACAATAAATAA-TTAAAAAATTAAAATAACT
131 GCAACAGGAGGAACAATAAATAATTTAAAAAATTAAAATAACT
* *
1712308 CATAAAA-TTTAATAAAATCATACAATTAGAAATTTGATCATG-TTCTAGTTCAATTTACTGACA
1 CATAAAACTTTAACAAAATCATACAATTAGAAATTTGATCATGTTTCTAATTCAATTTACTGACA
** * *
1712371 GAATGTTTCATTTCCGAAATCTTCTCCTTTTTATTAGTTAATTCACGGTCAGAGGTCTTTCACCA
66 GAACATTTCATTTCCAAAATCTTCTACTTTTTATTAGTTAATTCACGGTCAGAGGTCTTTCACCA
1712436 GCAACAGGAGGAACAATAAATAATTTAAAAAA
131 GCAACAGGAGGAACAATAAATAATTTAAAAAA
1712468 ATAAGCCCTA
Statistics
Matches: 147, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
170 101 0.69
171 39 0.27
172 7 0.05
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (173 bp):
CATAAAACTTTAACAAAATCATACAATTAGAAATTTGATCATGTTTCTAATTCAATTTACTGACA
GAACATTTCATTTCCAAAATCTTCTACTTTTTATTAGTTAATTCACGGTCAGAGGTCTTTCACCA
GCAACAGGAGGAACAATAAATAATTTAAAAAATTAAAATAACT
Found at i:1713664 original size:22 final size:20
Alignment explanation
Indices: 1713611--1713667 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
1713601 AACTGAAATG
*
1713611 AATAAAA-AAATAAAGAGAA
1 AATAAAATAAATAAACAGAA
*
1713630 AATAGAATAAAATAAACAGAGA
1 AATAAAAT-AAATAAACAGA-A
1713652 AATAAAGATAAATAAA
1 AATAAA-ATAAATAAA
1713668 TAAAATACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.19
21 10 0.32
22 13 0.42
23 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.14
Consensus pattern (20 bp):
AATAAAATAAATAAACAGAA
Found at i:1713842 original size:22 final size:21
Alignment explanation
Indices: 1713817--1713866 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1713807 TATATATAAT
1713817 ATATATAAATAGAAATAGAAAC
1 ATATATAAATAGAAATA-AAAC
* *
1713839 ATATCA-AAATATAAATAAAAT
1 ATAT-ATAAATAGAAATAAAAC
1713860 ATATATA
1 ATATATA
1713867 TATATATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 8 0.33
22 14 0.58
23 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (21 bp):
ATATATAAATAGAAATAAAAC
Found at i:1713897 original size:15 final size:14
Alignment explanation
Indices: 1713845--1713898 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
1713835 AAACATATCA
1713845 AAATATAAATAAAAT
1 AAATATAAAT-AAAT
* * *
1713860 ATATATATATATAT
1 AAATATAAATAAAT
1713874 AACATATAAATAAAT
1 AA-ATATAAATAAAT
1713889 AAATAATAAA
1 AAAT-ATAAA
1713899 ATAGTACGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 6 0.19
15 25 0.81
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATATAAATAAAT
Found at i:1715060 original size:8 final size:8
Alignment explanation
Indices: 1715039--1715087 Score: 57
Period size: 8 Copynumber: 6.0 Consensus size: 8
1715029 AAAAATTATA
1715039 ATTATAAT
1 ATTATAAT
1715047 -TTATAAT
1 ATTATAAT
1715054 ATTATAAT
1 ATTATAAT
1715062 A-TATATAT
1 ATTATA-AT
1715070 ATATATATAT
1 AT-TATA-AT
1715080 ATTATAAT
1 ATTATAAT
1715088 TTAGACGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
7 11 0.30
8 13 0.35
9 4 0.11
10 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
ATTATAAT
Found at i:1717244 original size:16 final size:16
Alignment explanation
Indices: 1717225--1717262 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1717215 CCCTAAACGT
*
1717225 TTTTTTCTCTTTTTTG
1 TTTTTTCTCTTTTTTC
*
1717241 TTTTTTCTTTTTTTTC
1 TTTTTTCTCTTTTTTC
1717257 TTTTTT
1 TTTTTT
1717263 TTTTCTTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:1717265 original size:10 final size:9
Alignment explanation
Indices: 1717224--1717264 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
1717214 ACCCTAAACG
1717224 TTTTTTTC-
1 TTTTTTTCT
*
1717232 TCTTTTT-T
1 TTTTTTTCT
*
1717240 GTTTTTTCT
1 TTTTTTTCT
1717249 TTTTTTTCT
1 TTTTTTTCT
1717258 TTTTTTT
1 TTTTTTT
1717265 TTCTTCGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 11 0.41
9 16 0.59
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1720637 original size:21 final size:21
Alignment explanation
Indices: 1720595--1720637 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1720585 TTTTTGGGCT
* * *
1720595 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1720616 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1720637 A
1 A
1720638 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1721367 original size:149 final size:150
Alignment explanation
Indices: 1721175--1721490 Score: 564
Period size: 150 Copynumber: 2.1 Consensus size: 150
1721165 GGGTAGAGGG
* *
1721175 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGAAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGAAACATGTGTGAAGTCTTGGAAAGACACA
*
1721239 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
1721304 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
* *
1721324 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGAAACATGTGTGAAGTCTTGGAAAGACACA
1721389 TACTTGATCCCTAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
1721454 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
1721474 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1721491 TGCATTTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
149 51 0.32
150 109 0.68
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGAAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:1721502 original size:23 final size:23
Alignment explanation
Indices: 1721458--1721502 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1721448 ATCATTATAT
*
1721458 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1721481 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1721503 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1727069 original size:19 final size:17
Alignment explanation
Indices: 1727045--1727079 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
1727035 TCCTCTCATT
1727045 TCTTCTTCCTTCTTCCTTA
1 TCTTCTT-C-TCTTCCTTA
1727064 TCTTCTTCTCTTCCTT
1 TCTTCTTCTCTTCCTT
1727080 CTCCAAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (17 bp):
TCTTCTTCTCTTCCTTA
Found at i:1728298 original size:23 final size:23
Alignment explanation
Indices: 1728254--1728298 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1728244 ATCATTATAT
*
1728254 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1728277 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1728299 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1736741 original size:25 final size:22
Alignment explanation
Indices: 1736698--1736797 Score: 69
Period size: 25 Copynumber: 4.2 Consensus size: 22
1736688 AACGTGTTAG
1736698 ATAAAAAATAAAAATAAATAAA
1 ATAAAAAATAAAAATAAATAAA
*
1736720 ATAAAGAAAGTAAAAATCAAATGAA
1 ATAAA-AAA-TAAAAAT-AAATAAA
* *
1736745 ATAAATAAA-AGGGAAATAAA-AAG
1 ATAAA-AAATA--AAAATAAATAAA
1736768 ATAAAAAAGTAAACAAAATAAATAAA
1 ATAAAAAA-T--A-AAAATAAATAAA
1736794 ATAA
1 ATAA
1736798 TATAGGATGA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
22 8 0.13
23 10 0.17
24 10 0.17
25 25 0.42
26 7 0.12
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (22 bp):
ATAAAAAATAAAAATAAATAAA
Found at i:1736792 original size:21 final size:21
Alignment explanation
Indices: 1736743--1736794 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
1736733 AAATCAAATG
* *
1736743 AAATAAAT-AAAAGGGAAATA
1 AAATAAATAAAAAAGGAAACA
* *
1736763 AAA-AGATAAAAAAGTAAACA
1 AAATAAATAAAAAAGGAAACA
1736783 AAATAAATAAAA
1 AAATAAATAAAA
1736795 TAATATAGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.12
20 15 0.60
21 7 0.28
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.13
Consensus pattern (21 bp):
AAATAAATAAAAAAGGAAACA
Found at i:1736988 original size:3 final size:3
Alignment explanation
Indices: 1736970--1737052 Score: 68
Period size: 3 Copynumber: 28.3 Consensus size: 3
1736960 ATATATATAT
* *
1736970 ATA ATA TATT ATA ATA ATA ATA ATA A-A ATA TACA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* *
1737016 A-A GACA A-A A-A ATG ATA A-A ATA ATA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1737053 ATAGTATAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
2 9 0.13
3 53 0.79
4 5 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Done.