Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1584166 original size:73 final size:68
Alignment explanation
Indices: 1584016--1584179 Score: 165
Period size: 69 Copynumber: 2.3 Consensus size: 68
1584006 ATATAATATA
* *
1584016 AAATATGA-TAAAAATAAAATAAATATTATTATTATAAATATATTAAAATTTATATAATAAAAAA
1 AAATAT-ATTAAAAATAAAATAAATAATATTATTATAAATATATTAAAATATATATAATAAAAAA
*
1584080 TTAT
65 TAAT
*
1584084 TAATATATTAAAATATATAAATAAATAATATTA-TAT-AATATTATTAAAATATATATATATAAT
1 AAATATATTAAAA-ATA-AAATAAATAATATTATTATAAATA-TATTAAAATATATATA-ATAA-
1584147 ATAACATAAAT
61 A-AA-AT-AAT
**
1584158 AAAT-TATTAAATTTAAAATAAA
1 AAATATATTAAAAATAAAATAAA
1584180 CTTCGGATAC
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
67 1 0.01
68 14 0.17
69 21 0.26
70 18 0.22
71 8 0.10
72 4 0.05
73 9 0.11
74 5 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (68 bp):
AAATATATTAAAAATAAAATAAATAATATTATTATAAATATATTAAAATATATATAATAAAAAAT
AAT
Found at i:1584724 original size:25 final size:25
Alignment explanation
Indices: 1584662--1584724 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1584652 TTATAATTTT
*
1584662 ATTTAAAATATTTTATATTAATATAA
1 ATTTAAAATA-TTCATATTAATATAA
** *
1584688 ATTTAATCTATTCGTATT-ATATAA
1 ATTTAAAATATTCATATTAATATAA
1584712 ATTTTAAAATATT
1 A-TTTAAAATATT
1584725 TATAGATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 7 0.23
25 15 0.50
26 8 0.27
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (25 bp):
ATTTAAAATATTCATATTAATATAA
Found at i:1585020 original size:33 final size:33
Alignment explanation
Indices: 1584982--1585047 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1584972 TAGGCAATTG
* * *
1584982 GTCCCAAAAGGACGTCAATAGCTCAATTGTAAA
1 GTCCCAAAAGGACATCAATAGCTAAATTCTAAA
1585015 GTCCCAAAAGGACATCAATAGCTAAATTCTAAA
1 GTCCCAAAAGGACATCAATAGCTAAATTCTAAA
1585048 CCCTCTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (33 bp):
GTCCCAAAAGGACATCAATAGCTAAATTCTAAA
Found at i:1585727 original size:2 final size:2
Alignment explanation
Indices: 1585716--1585748 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1585706 TCAAAAATGG
*
1585716 AT AT AT -T AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1585749 TAGAATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1586044 original size:13 final size:13
Alignment explanation
Indices: 1586018--1586052 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1586008 AAATATCATC
1586018 TAAACAAGTTTTTA
1 TAAACAA-TTTTTA
1586032 TAAACAATTTTTA
1 TAAACAATTTTTA
*
1586045 TAATCAAT
1 TAAACAAT
1586053 ATTATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (13 bp):
TAAACAATTTTTA
Found at i:1591049 original size:22 final size:22
Alignment explanation
Indices: 1591021--1591064 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1591011 TAAAGTTGAG
1591021 ATTTTATTATATTAATGTTTTA
1 ATTTTATTATATTAATGTTTTA
*
1591043 ATTTTATTATTTTAATGTTTTA
1 ATTTTATTATATTAATGTTTTA
1591065 TATGAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
ATTTTATTATATTAATGTTTTA
Found at i:1592152 original size:33 final size:33
Alignment explanation
Indices: 1592108--1592170 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1592098 ATGTAATGAA
* * * *
1592108 ATATAATTTTAAAATTTATATATAATTAATTAT
1 ATATAAATTTAAAAATTATAAATAAATAATTAT
1592141 ATATAAATTTAAAAATTATAAATAAATAAT
1 ATATAAATTTAAAAATTATAAATAAATAAT
1592171 ATTTAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATAAATTTAAAAATTATAAATAAATAATTAT
Found at i:1592159 original size:19 final size:19
Alignment explanation
Indices: 1592108--1592167 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
1592098 ATGTAATGAA
* *
1592108 ATATAATTTTAAAATTTAT
1 ATATAAATTTAAAAATTAT
1592127 ATAT-AA-TT---AATTAT
1 ATATAAATTTAAAAATTAT
1592141 ATATAAATTTAAAAATTAT
1 ATATAAATTTAAAAATTAT
*
1592160 AAATAAAT
1 ATATAAAT
1592168 AATATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 9 0.27
15 2 0.06
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATAAATTTAAAAATTAT
Found at i:1592184 original size:21 final size:20
Alignment explanation
Indices: 1592154--1592195 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1592144 TAAATTTAAA
*
1592154 AATTATAAATAAATAATATTT
1 AATTAAAAATAAA-AATATTT
*
1592175 AATTAAAAATAAAATTATTT
1 AATTAAAAATAAAAATATTT
1592195 A
1 A
1592196 TATATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTAAAAATAAAAATATTT
Found at i:1593134 original size:2 final size:2
Alignment explanation
Indices: 1593124--1593167 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1593114 AGAGAGAGAT
* * *
1593124 TA TA AA TA TA TA TA CA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1593166 TA
1 TA
1593168 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1593172 original size:2 final size:2
Alignment explanation
Indices: 1593167--1593200 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1593157 ATATATATAT
*
1593167 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1593201 GTGGGGGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1603297 original size:40 final size:42
Alignment explanation
Indices: 1603253--1603337 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 42
1603243 CCAAATCAGT
1603253 GCTCCATG-T-TTTTTATTCAAAGTTTAACGGAAGTTGGTGC
1 GCTCCATGTTCTTTTTATTCAAAGTTTAACGGAAGTTGGTGC
*
1603293 GCTCCATGTTTCACTTTTTATTCAAAGTTTAATGGAAGTTGGTGC
1 GCTCCATG-TT--CTTTTTATTCAAAGTTTAACGGAAGTTGGTGC
1603338 ATATAAATTC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
40 8 0.21
42 1 0.03
45 30 0.77
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.41
Consensus pattern (42 bp):
GCTCCATGTTCTTTTTATTCAAAGTTTAACGGAAGTTGGTGC
Found at i:1609102 original size:123 final size:125
Alignment explanation
Indices: 1608879--1609123 Score: 377
Period size: 123 Copynumber: 2.0 Consensus size: 125
1608869 TAGGTGATCA
*
1608879 AAACATTGTAGTGAACAATAGTTGGCCAATATTGATAGGATCAAAATTACAGTAAAAGGAAAATA
1 AAACATTGTAGTGAACAATAGTTAGCCAATATTGATAGGATCAAAA-TACAG-AAAAGGAAAATA
* * *
1608944 TAAAGCATTAAAATTCTAAAATTCACACAACATAAATAGTTGAGGTGCTCAAATGGACGAAT
64 TAAAGCAGTAAAATTCTAAAATTCACAAAACATAAATAGTTGAGATGCTCAAATGGACGAAT
* * **
1609006 AAACATTGTAGTGAACAGTAGTTAGCCAATATTGATAGGATCAAAA-CCA-CCAAGGAAAATATA
1 AAACATTGTAGTGAACAATAGTTAGCCAATATTGATAGGATCAAAATACAGAAAAGGAAAATATA
*
1609069 AAGCAGTAAAATTCTAAAATTCACAAAACATAAATAGTTGAGATGGTCAAATGGA
66 AAGCAGTAAAATTCTAAAATTCACAAAACATAAATAGTTGAGATGCTCAAATGGA
1609124 AGAAGACAAG
Statistics
Matches: 109, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
123 63 0.58
125 2 0.02
127 44 0.40
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (125 bp):
AAACATTGTAGTGAACAATAGTTAGCCAATATTGATAGGATCAAAATACAGAAAAGGAAAATATA
AAGCAGTAAAATTCTAAAATTCACAAAACATAAATAGTTGAGATGCTCAAATGGACGAAT
Found at i:1609241 original size:14 final size:14
Alignment explanation
Indices: 1609218--1609248 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1609208 AGTCTGCTTC
*
1609218 AAAAAGAAAAATCA
1 AAAAACAAAAATCA
1609232 AAAAACAAAAATCA
1 AAAAACAAAAATCA
1609246 AAA
1 AAA
1609249 TAATACCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.81, C:0.10, G:0.03, T:0.06
Consensus pattern (14 bp):
AAAAACAAAAATCA
Found at i:1612729 original size:2 final size:2
Alignment explanation
Indices: 1612722--1612808 Score: 67
Period size: 2 Copynumber: 45.0 Consensus size: 2
1612712 CGTGTCCTGC
* *
1612722 AT AT AT AT AT AT AT AT AT GT AT GA- AT -T AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
* * * *
1612763 A- AT AA AA AA AT TT AT GA- AT -T 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
1612803 AT AT AT
1 AT AT AT
1612809 GTATTTATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
1 5 0.07
2 64 0.90
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1617536 original size:2 final size:2
Alignment explanation
Indices: 1617529--1617568 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1617519 TCCGCAAGTC
1617529 AT AT AT AT 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
1617569 CTTTACTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1618151 original size:2 final size:2
Alignment explanation
Indices: 1618144--1618185 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1618134 CCTGAAATAG
* *
1618144 TA TA TA TA TA AA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1618186 ATACTTTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1618267 original size:76 final size:76
Alignment explanation
Indices: 1618174--1618322 Score: 289
Period size: 76 Copynumber: 2.0 Consensus size: 76
1618164 TATATATATA
1618174 TATATATATATAATACTTTGACTCCACCGACCCCAAAATATAAATATAATTTACAATGAAGGCCA
1 TATATATATATAATACTTTGACTCCACCGACCCCAAAATATAAATATAATTTACAATGAAGGCCA
1618239 ACATATATTGT
66 ACATATATTGT
1618250 TATATATATATAATACTTTGACTCCACCGACCCCAAAATATAAATATAATTTACAATGAAGGCCA
1 TATATATATATAATACTTTGACTCCACCGACCCCAAAATATAAATATAATTTACAATGAAGGCCA
*
1618315 ATATATAT
66 ACATATAT
1618323 GTTGTTTTTC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (76 bp):
TATATATATATAATACTTTGACTCCACCGACCCCAAAATATAAATATAATTTACAATGAAGGCCA
ACATATATTGT
Found at i:1618653 original size:15 final size:16
Alignment explanation
Indices: 1618635--1618668 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1618625 TATATTTATT
1618635 AAATATT-TTATTTTA
1 AAATATTATTATTTTA
*
1618650 AAATATTATTTTTTTA
1 AAATATTATTATTTTA
1618666 AAA
1 AAA
1618669 AATATGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATATTATTATTTTA
Found at i:1619550 original size:12 final size:12
Alignment explanation
Indices: 1619529--1619573 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1619519 ATTTTGCTCA
1619529 ATTA-TTTAATT
1 ATTATTTTAATT
1619540 ATTATTTTAATT
1 ATTATTTTAATT
* *
1619552 TTTATATTTAAAT
1 ATTAT-TTTAATT
1619565 ATTATTTTA
1 ATTATTTTA
1619574 TTAAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 4 0.14
12 15 0.52
13 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTATTTTAATT
Found at i:1619577 original size:28 final size:28
Alignment explanation
Indices: 1619537--1619622 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
1619527 CAATTATTTA
1619537 ATTATTATT-TTAATTTTTATATTTAAAT
1 ATTATTATTATTAATTTTTATA-TTAAAT
* *
1619565 ATTATT-TTATTAA-ATTTA-ATAAAAT
1 ATTATTATTATTAATTTTTATATTAAAT
1619590 ATATATTAATTA-TAATTTTT-TA-TAAAT
1 AT-TATT-ATTATTAATTTTTATATTAAAT
1619617 ATTATT
1 ATTATT
1619623 TTAATAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
25 7 0.15
26 9 0.19
27 15 0.31
28 17 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTATTATTATTAATTTTTATATTAAAT
Found at i:1619626 original size:28 final size:27
Alignment explanation
Indices: 1619539--1619631 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 27
1619529 ATTATTTAAT
*
1619539 TATTATTTTAATT---TTTATATTTAAA
1 TATTATTTTAATTAAATTTA-ATATAAA
1619564 TATTATTTT-ATTAAATTTAATA-AAA
1 TATTATTTTAATTAAATTTAATATAAA
* **
1619589 TA-TATATTAATTATAATTTTTTATAAA
1 TATTATTTTAATTA-AATTTAATATAAA
1619616 TATTATTTTAA-TAAAT
1 TATTATTTTAATTAAAT
1619632 ACCACTAAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
24 8 0.14
25 18 0.32
26 12 0.21
27 11 0.20
28 7 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTATTTTAATTAAATTTAATATAAA
Found at i:1619819 original size:20 final size:22
Alignment explanation
Indices: 1619768--1619822 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
1619758 TGGTTATATG
*
1619768 AATATATATGATAAAAATAATTA
1 AATATAAAT-ATAAAAATAATTA
1619791 AATATAAATATAAAAA-AA-TA
1 AATATAAATATAAAAATAATTA
1619811 AAT-TAAAATATA
1 AATAT-AAATATA
1619823 TATAGCATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 12 0.40
21 2 0.07
22 7 0.23
23 8 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AATATAAATATAAAAATAATTA
Found at i:1621415 original size:2 final size:2
Alignment explanation
Indices: 1621408--1621449 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1621398 ACTTAAGCTA
1621408 AT AT AT AT AT 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
1621450 TCTTACAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1623203 original size:34 final size:34
Alignment explanation
Indices: 1623160--1623229 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1623150 TACTTGGACA
1623160 ATATTAAGGAGAATCATCAGCAAATTATTTATTT
1 ATATTAAGGAGAATCATCAGCAAATTATTTATTT
1623194 ATATTAAGGAGAATCATCAGCAAATTATTTATTT
1 ATATTAAGGAGAATCATCAGCAAATTATTTATTT
1623228 AT
1 AT
1623230 TTATTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (34 bp):
ATATTAAGGAGAATCATCAGCAAATTATTTATTT
Found at i:1629862 original size:15 final size:15
Alignment explanation
Indices: 1629824--1629910 Score: 75
Period size: 15 Copynumber: 5.7 Consensus size: 15
1629814 ACTCTTGGGT
* *
1629824 TTTAAGTTTTTTTCA
1 TTTAAATTTTTTTAA
*
1629839 TCTTGAATTTTTTTAA
1 T-TTAAATTTTTTTAA
**
1629855 TTTAAATTTTTAAAA
1 TTTAAATTTTTTTAA
* *
1629870 TTTAAAATATTTTAAA
1 TTT-AAATTTTTTTAA
*
1629886 TTTAAATTATTTTAA
1 TTTAAATTTTTTTAA
*
1629901 TTTGAATTTT
1 TTTAAATTTT
1629911 ATCAAATTTA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
15 32 0.56
16 25 0.44
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTAAATTTTTTTAA
Found at i:1630939 original size:72 final size:72
Alignment explanation
Indices: 1630828--1630962 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
1630818 CTTCTGCAAC
* * *
1630828 AAAGTTATTTTTCATTAAACATAAAAATTTTGATGATAATAATA-TTCTATAAACCAAAGATAAA
1 AAAGATATTTTTCATTAAACACAAAAATTTTGATAATAATAATACTT-TATAAACCAAAGATAAA
1630892 CTTCAAAA
65 CTTCAAAA
* * * *
1630900 AAAGATATTTTTCATTAAATACATAAATTTTGGTAATAATTATACTTTATAAACCAAAGATAA
1 AAAGATATTTTTCATTAAACACAAAAATTTTGATAATAATAATACTTTATAAACCAAAGATAA
1630963 CCATATAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 53 0.96
73 2 0.04
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (72 bp):
AAAGATATTTTTCATTAAACACAAAAATTTTGATAATAATAATACTTTATAAACCAAAGATAAAC
TTCAAAA
Found at i:1632710 original size:2 final size:2
Alignment explanation
Indices: 1632705--1632740 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1632695 TTTGTTAACA
1632705 AT AT 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
1632741 TTGTTTACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1635437 original size:3 final size:3
Alignment explanation
Indices: 1635429--1635474 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1635419 AACCAATCAT
1635429 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1635475 GATGTGATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1637543 original size:16 final size:16
Alignment explanation
Indices: 1637519--1637549 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1637509 TGCATATTTT
1637519 TATTAATTATTTATTA
1 TATTAATTATTTATTA
*
1637535 TATTTATTATTTATT
1 TATTAATTATTTATT
1637550 TAAAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTAATTATTTATTA
Found at i:1641235 original size:13 final size:13
Alignment explanation
Indices: 1641217--1641241 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1641207 AGCCCAAACG
1641217 GAAAAAGAAAAAT
1 GAAAAAGAAAAAT
1641230 GAAAAAGAAAAA
1 GAAAAAGAAAAA
1641242 AAAAAGGAGG
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:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
GAAAAAGAAAAAT
Found at i:1646807 original size:23 final size:22
Alignment explanation
Indices: 1646781--1646823 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1646771 AATTATTAAT
1646781 TAATAAATTTAAATATATTTTTA
1 TAATAAATTT-AATATATTTTTA
* *
1646804 TAATGAATTTATTATATTTT
1 TAATAAATTTAATATATTTT
1646824 GTTACTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TAATAAATTTAATATATTTTTA
Found at i:1648651 original size:37 final size:37
Alignment explanation
Indices: 1648609--1648680 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
1648599 CGGAAAATGG
*
1648609 CTATATAAACCCCATTTTGTTCACATAGCTTTATTGA
1 CTATATAAACCCCATTTTGGTCACATAGCTTTATTGA
* *
1648646 CTATATATACCCCATTTTGGTCATATAGCTTTATT
1 CTATATAAACCCCATTTTGGTCACATAGCTTTATT
1648681 AAGAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (37 bp):
CTATATAAACCCCATTTTGGTCACATAGCTTTATTGA
Found at i:1650150 original size:10 final size:10
Alignment explanation
Indices: 1650127--1650191 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
1650117 TTGACAGCAC
1650127 TTTT-ATAA-
1 TTTTAATAAT
1650135 TTTTAATAAT
1 TTTTAATAAT
*
1650145 TTTTAATATAA
1 TTTTAATA-AT
1650156 TTTT-ATAAT
1 TTTTAATAAT
*
1650165 TATTT-TTAA-
1 T-TTTAATAAT
*
1650174 TTTCAATAAT
1 TTTTAATAAT
1650184 TTTTAATA
1 TTTTAATA
1650192 TGATTTTATC
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 6 0.13
9 10 0.22
10 24 0.53
11 5 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:1650157 original size:12 final size:12
Alignment explanation
Indices: 1650140--1650198 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 12
1650130 TATAATTTTA
1650140 ATAATTTTTAAT
1 ATAATTTTTAAT
1650152 ATAATTTTATAAT
1 ATAATTTT-TAAT
1650165 -T-ATTTTTAATTT
1 ATAATTTTTAA--T
1650177 CAATAATTTTTAAT
1 --ATAATTTTTAAT
*
1650191 ATGATTTT
1 ATAATTTT
1650199 ATCACTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
10 3 0.08
11 5 0.13
12 17 0.44
13 4 0.10
14 1 0.03
15 1 0.03
16 8 0.21
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
ATAATTTTTAAT
Found at i:1650169 original size:23 final size:21
Alignment explanation
Indices: 1650130--1650199 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1650120 ACAGCACTTT
1650130 TATAATTTTAATAATTTTTAA
1 TATAATTTTAATAATTTTTAA
1650151 TATAATTTT-ATAATTATTT--
1 TATAATTTTAATAATT-TTTAA
*
1650170 T-TAATTTCAATAATTTTTAA
1 TATAATTTTAATAATTTTTAA
*
1650190 TATGATTTTA
1 TATAATTTTA
1650200 TCACTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
18 9 0.22
19 7 0.17
20 7 0.17
21 18 0.44
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (21 bp):
TATAATTTTAATAATTTTTAA
Found at i:1650690 original size:24 final size:24
Alignment explanation
Indices: 1650658--1650769 Score: 63
Period size: 25 Copynumber: 4.6 Consensus size: 24
1650648 ATTAGATGTG
*
1650658 AATTTTTAATTAATTTATAATTTT
1 AATTATTAATTAATTTATAATTTT
*
1650682 AATTATTAAATTTAATAT-TAATTTCT
1 AATTATT-AA-TTAATTTATAATTT-T
* * *
1650708 ATATGAATT-ATAAATTTTTAATTTT
1 A-AT-TATTAATTAATTTATAATTTT
*
1650733 -ATTA--AATTAAATTATTAATTTT
1 AATTATTAATTAATTTA-TAATTTT
* *
1650755 TATTATTAATAAATT
1 AATTATTAATTAATT
1650770 AAATTATTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 21
0.67 0.11 0.21
Matches are distributed among these distances:
21 6 0.09
22 8 0.12
23 6 0.09
24 6 0.09
25 20 0.30
26 15 0.23
27 2 0.03
28 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (24 bp):
AATTATTAATTAATTTATAATTTT
Found at i:1650749 original size:13 final size:13
Alignment explanation
Indices: 1650731--1650796 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
1650721 ATTTTTAATT
1650731 TTATTAAATTAAA
1 TTATTAAATTAAA
* *
1650744 TTATTAATTTTTATTA
1 TTATTAA--ATTA-AA
*
1650760 TTAATAAATTAAA
1 TTATTAAATTAAA
*
1650773 TTATTTAAATTAATT
1 TTA-TTAAATTAA-A
1650788 TTATTAAAT
1 TTATTAAAT
1650797 AATTATAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 11 0.27
14 17 0.41
15 6 0.15
16 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATTAAATTAAA
Found at i:1650752 original size:29 final size:29
Alignment explanation
Indices: 1650713--1650796 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
1650703 TTTCTATATG
*
1650713 AATTATAAATTTTTAATTTTATTAAATTA
1 AATTATTAATTTTTAATTTTATTAAATTA
*
1650742 AATTATTAATTTTT-ATTATTAATAAATTA
1 AATTATTAATTTTTAATT-TTATTAAATTA
*
1650771 AATTATTTAA--ATTAATTTTATTAAAT
1 AATTA-TTAATTTTTAATTTTATTAAAT
1650797 AATTATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 13 0.27
29 31 0.65
30 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
AATTATTAATTTTTAATTTTATTAAATTA
Found at i:1650759 original size:23 final size:23
Alignment explanation
Indices: 1650684--1650759 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1650674 ATAATTTTAA
*
1650684 TTATTAAATTTAA-TATTAATTT
1 TTATTAAATTAAATTATTAATTT
* * *
1650706 CTATATGAATTATAAATTTTTAA-TT
1 -T-TATTAAAT-TAAATTATTAATTT
1650731 TTATTAAATTAAATTATTAATTT
1 TTATTAAATTAAATTATTAATTT
1650754 TTATTA
1 TTATTA
1650760 TTAATAAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
22 10 0.24
23 15 0.36
24 7 0.17
25 5 0.12
26 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (23 bp):
TTATTAAATTAAATTATTAATTT
Found at i:1651846 original size:2 final size:2
Alignment explanation
Indices: 1651839--1651879 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1651829 TAACAATTTC
1651839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1651880 AAGATATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1652574 original size:18 final size:19
Alignment explanation
Indices: 1652542--1652587 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 19
1652532 ATTCAAATAC
1652542 TTATTCATTTAAAAATATTT
1 TTATT-ATTTAAAAATATTT
1652562 TTATTATTTAAAAATATTT
1 TTATTATTTAAAAATATTT
1652581 TATATTA
1 T-TATTA
1652588 ATATTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATTTAAAAATATTT
Found at i:1652639 original size:32 final size:32
Alignment explanation
Indices: 1652551--1652657 Score: 94
Period size: 32 Copynumber: 3.2 Consensus size: 32
1652541 CTTATTCATT
*
1652551 TAAAAATATTTTTATTATTTAAA-AATATTTTA
1 TAAAAATA-TTTTATTATTTAAATAATATTTAA
** *
1652583 TATTAATA-TTTATCTTTTATAAATAA-ATTTAA
1 TAAAAATATTTTAT-TATT-TAAATAATATTTAA
1652615 TAAAACATATTTTATTATTTAAATAATAATTTAAA
1 TAAAA-ATATTTTATTATTTAAATAAT-ATTT-AA
*
1652650 TATAAATA
1 TAAAAATA
1652658 AATTTACCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
30 5 0.08
31 3 0.05
32 25 0.42
33 8 0.14
34 12 0.20
35 6 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (32 bp):
TAAAAATATTTTATTATTTAAATAATATTTAA
Found at i:1655225 original size:22 final size:23
Alignment explanation
Indices: 1655197--1655245 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
1655187 TCTCTAGATC
*
1655197 TTGCAATCTACTTGATGC-TAAT
1 TTGCAATCTACTTGATGCGTAAG
1655219 TTGCAATCTACTTGATGCGTAAG
1 TTGCAATCTACTTGATGCGTAAG
1655242 TTGC
1 TTGC
1655246 TGAGTGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (23 bp):
TTGCAATCTACTTGATGCGTAAG
Found at i:1656117 original size:21 final size:21
Alignment explanation
Indices: 1656088--1656132 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1656078 GTAATTTGAG
**
1656088 TTAATATAATTTAAATTATTAT
1 TTAATATAATAAAAATTATT-T
1656110 TTAA-ATAATAAAAATTATTT
1 TTAATATAATAAAAATTATTT
1656130 TTA
1 TTA
1656133 TTTAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATATAATAAAAATTATTT
Found at i:1658548 original size:15 final size:15
Alignment explanation
Indices: 1658518--1658547 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1658508 TTTTATTTTT
1658518 ATTATAAAAAATAAA
1 ATTATAAAAAATAAA
1658533 ATTA-AAAAAATAAA
1 ATTATAAAAAATAAA
1658547 A
1 A
1658548 AAACTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATTATAAAAAATAAA
Found at i:1660639 original size:16 final size:16
Alignment explanation
Indices: 1660594--1660642 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 16
1660584 TTTAATAATT
* *
1660594 TTAAT-TTTTTTATTA
1 TTAATATTTATTATAA
1660609 TTAATATTTA--A-AA
1 TTAATATTTATTATAA
1660622 TTAATATTTATTATAA
1 TTAATATTTATTATAA
1660638 TTAAT
1 TTAAT
1660643 TATAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 6 0.21
16 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATATTTATTATAA
Found at i:1660651 original size:25 final size:27
Alignment explanation
Indices: 1660602--1660677 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 27
1660592 TTTTAATTTT
* *
1660602 TTTATTAT-TA-ATATTTAAAATTAATA
1 TTTATTATATATATAATTATAA-TAATA
1660628 TTTATTATA-AT-TAATTATAATAATA
1 TTTATTATATATATAATTATAATAATA
*
1660653 TTTATTATATTTATAATTATAATAA
1 TTTATTATATATATAATTATAATAA
1660678 ATATAACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 14 0.33
26 17 0.40
27 12 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTATTATATATATAATTATAATAATA
Found at i:1661049 original size:30 final size:28
Alignment explanation
Indices: 1661015--1661089 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 28
1661005 ATATTAATAT
* *
1661015 AAAAATTATTTTTAATATTTTAAATA-ATTA
1 AAAAATTATTTATAA-A-TTT-AATAGATAA
1661045 AAAAA-TATTTATAAATTTAATAGATAA
1 AAAAATTATTTATAAATTTAATAGATAA
1661072 AAAAATTA-TTATCAAATT
1 AAAAATTATTTAT-AAATT
1661090 ACAATCTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 4 0.10
27 15 0.38
28 8 0.20
29 8 0.20
30 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
AAAAATTATTTATAAATTTAATAGATAA
Found at i:1661063 original size:27 final size:28
Alignment explanation
Indices: 1661009--1661077 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
1660999 ATATACATAT
* *
1661009 TAATATAAAAATTATTTTTAATATTTTAAA
1 TAAT-TAAAAAATATTTATAATATTTT-AA
1661039 TAATTAAAAAATATTTATAA-A-TTTAA
1 TAATTAAAAAATATTTATAATATTTTAA
*
1661065 TAGATAAAAAAAT
1 TA-ATTAAAAAAT
1661078 TATTATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 4 0.11
27 12 0.34
28 1 0.03
29 14 0.40
30 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
TAATTAAAAAATATTTATAATATTTTAA
Found at i:1661170 original size:26 final size:25
Alignment explanation
Indices: 1661141--1661191 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
1661131 CCATTTAAAT
*
1661141 TTTTTAAATTTTTTTTACTGATTTAA
1 TTTTTAAATTTATTTTA-TGATTTAA
* *
1661167 TTTTTTAATTTATTTTATTATTTAA
1 TTTTTAAATTTATTTTATGATTTAA
1661192 AAATATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTTAAATTTATTTTATGATTTAA
Found at i:1661612 original size:36 final size:35
Alignment explanation
Indices: 1661568--1661635 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 35
1661558 AATTTTATTA
*
1661568 TTATATTTATATGAATGATTTAAATTTATAATTTAT
1 TTATATTTATATGAAT-ATTAAAATTTATAATTTAT
* *
1661604 TTATATTTATATTAATATTAAAATTTTTAATT
1 TTATATTTATATGAATATTAAAATTTATAATT
1661636 AAATTTAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 14 0.48
36 15 0.52
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (35 bp):
TTATATTTATATGAATATTAAAATTTATAATTTAT
Found at i:1661827 original size:25 final size:24
Alignment explanation
Indices: 1661775--1661827 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
1661765 TAATTTTTCA
* *
1661775 TTTTACTTGAAAAATTTACTCACT
1 TTTTACTTGAAAAAATTACTCACC
1661799 TTTTACTTGAAAAAAATTA-TCCACC
1 TTTTACTTG-AAAAAATTACT-CACC
1661824 TTTT
1 TTTT
1661828 TTATTTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (24 bp):
TTTTACTTGAAAAAATTACTCACC
Found at i:1662572 original size:2 final size:2
Alignment explanation
Indices: 1662567--1662598 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1662557 AAAACCACAC
1662567 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
1662599 TTAGTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1662889 original size:18 final size:17
Alignment explanation
Indices: 1662857--1662890 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1662847 TATATATTTT
*
1662857 AAAATAGATTAAAAATA
1 AAAATAGAATAAAAATA
1662874 AAAATATGAATAAAAAT
1 AAAATA-GAATAAAAAT
1662891 TGATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAATAGAATAAAAATA
Found at i:1663255 original size:2 final size:2
Alignment explanation
Indices: 1663248--1663289 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1663238 ATAATTTTTA
* *
1663248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT 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
1663290 GTATCCTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1667458 original size:2 final size:2
Alignment explanation
Indices: 1667451--1667491 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1667441 CTAAGACCTT
1667451 TA TA TA TA TA 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 TA TA TA TA TA T
1667492 TTGGATGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1669010 original size:18 final size:18
Alignment explanation
Indices: 1668979--1669016 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1668969 ATACATATTA
1668979 TTTTATTAATTTTAAATT
1 TTTTATTAATTTTAAATT
1668997 TTTTAATTAA-TTTAAATT
1 TTTT-ATTAATTTTAAATT
1669015 TT
1 TT
1669017 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATTAATTTTAAATT
Found at i:1669570 original size:20 final size:20
Alignment explanation
Indices: 1669545--1669588 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1669535 TTAAAATACG
*
1669545 AAATAAAAATATTAATATA-T
1 AAAT-AAAATATTAACATATT
1669565 AAATAAAATATTAACATATT
1 AAATAAAATATTAACATATT
1669585 AAAT
1 AAAT
1669589 GATATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAAAATATTAACATATT
Found at i:1669572 original size:19 final size:19
Alignment explanation
Indices: 1669545--1669607 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
1669535 TTAAAATACG
1669545 AAATAAAAATATTAATATAT
1 AAAT-AAAATATTAATATAT
*
1669565 AAATAAAATATTAACATATT
1 AAATAAAATATTAATATA-T
* * * *
1669585 AAATGATATATAAATATAA
1 AAATAAAATATTAATATAT
1669604 AAAT
1 AAAT
1669608 TTTAAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAATAAAATATTAATATAT
Found at i:1671271 original size:2 final size:2
Alignment explanation
Indices: 1671259--1671294 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1671249 AAGTTCAATG
*
1671259 AT AT AT CT 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
1671295 GAAAATATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1671373 original size:2 final size:2
Alignment explanation
Indices: 1671366--1671408 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1671356 AAAGAAACAA
1671366 AT AT AT AT AT 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
1671408 A
1 A
1671409 GTTTGGTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1671899 original size:126 final size:126
Alignment explanation
Indices: 1671729--1671988 Score: 477
Period size: 127 Copynumber: 2.1 Consensus size: 126
1671719 ATTTAAATTT
*
1671729 TAATATTTGTAATTATTTTTTTATTTTAAGTTATAAAGTAATTGTTATTGTATTTATTTATCTA-
1 TAATATTTGTAATTATTTTTTTATTTTAAGTTATAAAGTAATTGTTACTGTATTTATTTATCTAT
1671793 TTTTTAATTAATTTTATTTAAAAGTTGAGTAATTTATGTTATATTGAATTGAGTTTGAATA
66 TTTTTAATTAATTTTATTTAAAAGTTGAGTAATTTATGTTATATTGAATTGAGTTTGAATA
1671854 TAATATTTGTAATTATTTTTTTATTTTTAAGTTATAAAGTAATTGTTACTGTATTTATTTATCTA
1 TAATATTTGTAATTATTTTTTTA-TTTTAAGTTATAAAGTAATTGTTACTGTATTTATTTATCTA
*
1671919 TTTTTTAATTAATTTTATTTAAAATTTGAGTAATTTATGTTATATTGAATTGAGTTTGAATA
65 TTTTTTAATTAATTTTATTTAAAAGTTGAGTAATTTATGTTATATTGAATTGAGTTTGAATA
*
1671981 TAAGATTT
1 TAATATTT
1671989 AGTGATTAGA
Statistics
Matches: 130, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
125 23 0.18
126 40 0.31
127 67 0.52
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.56
Consensus pattern (126 bp):
TAATATTTGTAATTATTTTTTTATTTTAAGTTATAAAGTAATTGTTACTGTATTTATTTATCTAT
TTTTTAATTAATTTTATTTAAAAGTTGAGTAATTTATGTTATATTGAATTGAGTTTGAATA
Found at i:1672040 original size:127 final size:124
Alignment explanation
Indices: 1671783--1672012 Score: 280
Period size: 127 Copynumber: 1.8 Consensus size: 124
1671773 TTATTGTATT
1671783 TATTTATCTATTTTTAATTAATTTTATTTAAAAGTTGAGTAATTTATGTTATATTGAATTGAGTT
1 TATTTATCTATTTTTAATTAATTTTATTTAAAAGTTGAGTAATTTATGTTATATTGAATTGAGTT
* * ** ** * * ** **
1671848 TGAATATAATATTTGTAATTATTTTTTTATTTTTAAGTTATAAAGTAATTGTTACTGTATT
66 TGAATATAAGATTTGTAATTAATTGATTAGATTTAA--TATAAAGTAATTATTAATAAAAA
*
1671909 TATTTATCTATTTTTTAATTAATTTTATTTAAAATTTGAGTAATTTATGTTATATTGAATTGAGT
1 TATTTATCTA-TTTTTAATTAATTTTATTTAAAAGTTGAGTAATTTATGTTATATTGAATTGAGT
* *
1671974 TTGAATATAAGATTTAGTGATTAGATTGATTCGATTTAA
65 TTGAATATAAGATTT-GTAATTA-ATTGATTAGATTTAA
1672013 ATCATTATTT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
126 10 0.11
127 67 0.73
128 6 0.07
129 9 0.10
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (124 bp):
TATTTATCTATTTTTAATTAATTTTATTTAAAAGTTGAGTAATTTATGTTATATTGAATTGAGTT
TGAATATAAGATTTGTAATTAATTGATTAGATTTAATATAAAGTAATTATTAATAAAAA
Found at i:1672095 original size:19 final size:19
Alignment explanation
Indices: 1672069--1672142 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 19
1672059 AAGATATATA
*
1672069 AATATTTATATAA-AAATT
1 AATATTTAAATAATAAATT
1672087 AATATTTTAAATAATAAA-T
1 AATA-TTTAAATAATAAATT
*
1672106 AA-ATTTATA-AATCAAA-T
1 AATATTTAAATAAT-AAATT
*
1672123 AAAATTTAAATAA-AAATT
1 AATATTTAAATAATAAATT
1672141 AA
1 AA
1672143 AAAATTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
16 3 0.06
17 14 0.30
18 14 0.30
19 13 0.28
20 3 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATTTAAATAATAAATT
Found at i:1672143 original size:18 final size:17
Alignment explanation
Indices: 1672066--1672167 Score: 62
Period size: 19 Copynumber: 5.6 Consensus size: 17
1672056 TATAAGATAT
*
1672066 ATAAATATTTATATAAAA
1 ATAAA-ATTTAAATAAAA
*
1672084 ATTAATATTTTAAATAATAA
1 A-TAA-AATTTAAATAA-AA
* *
1672104 ATAAATTTATAAAT-CAA
1 ATAAAATT-TAAATAAAA
1672121 ATAAAATTTAAATAAAA
1 ATAAAATTTAAATAAAA
* * *
1672138 ATTAAAAAATTAAATTATA
1 A-T-AAAATTTAAATAAAA
*
1672157 ATATAATTTAA
1 ATAAAATTTAA
1672168 TTCATAAACA
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
16 5 0.07
17 19 0.28
18 7 0.10
19 32 0.48
20 4 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATTTAAATAAAA
Found at i:1672739 original size:7 final size:7
Alignment explanation
Indices: 1672727--1672757 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1672717 ATTATTTAAT
1672727 AAATTTA
1 AAATTTA
1672734 AAATTTA
1 AAATTTA
1672741 AAATTTA
1 AAATTTA
*
1672748 ATATTTA
1 AAATTTA
1672755 AAA
1 AAA
1672758 GTTTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:1673518 original size:24 final size:22
Alignment explanation
Indices: 1673491--1673560 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 22
1673481 ATTAAATAAA
1673491 TTAATTAATTAAAAATATTAAATT
1 TTAATT-ATTAAAAATA-TAAATT
1673515 TTAAATT-TT-AAAATAT--ATT
1 TT-AATTATTAAAAATATAAATT
1673534 TTAA-TATTAAAAATAATAAATAT
1 TTAATTATTAAAAAT-ATAAAT-T
1673557 TTAA
1 TTAA
1673561 AAATTTATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
17 1 0.03
18 4 0.10
19 10 0.26
20 2 0.05
21 1 0.03
22 8 0.21
23 7 0.18
24 2 0.05
25 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATTATTAAAAATATAAATT
Found at i:1674307 original size:29 final size:29
Alignment explanation
Indices: 1674248--1674304 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1674238 TTTAAATTTT
*
1674248 TATTTAAATTTAATTATAAAATATATAAA
1 TATTTAAATTTAATTATAAAAAATATAAA
* * *
1674277 TATTTTAATTTATTTTTAAAAAA-ATAAA
1 TATTTAAATTTAATTATAAAAAATATAAA
1674305 ATAAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TATTTAAATTTAATTATAAAAAATATAAA
Found at i:1674798 original size:20 final size:17
Alignment explanation
Indices: 1674773--1674812 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
1674763 CATCGTATCA
1674773 TTTCTTTCTTCTTCTTTTCT
1 TTTCTTTC-TCTT-TTTT-T
1674793 TTTCTTTCTCTTTTTTT
1 TTTCTTTCTCTTTTTTT
1674810 TTT
1 TTT
1674813 TAATATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 4 0.20
19 4 0.20
20 8 0.40
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTCTCTTTTTTT
Found at i:1674990 original size:29 final size:30
Alignment explanation
Indices: 1674931--1674990 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
1674921 CATCTCCCAG
*
1674931 TACTTCGCTTTTGTTTCCCTTTCATTATTT
1 TACTTCGCTTTTGTTTCCCTTTCACTATTT
* *
1674961 TACTTC-CTTTT-TTTCCACTTTGACTCTTT
1 TACTTCGCTTTTGTTTCC-CTTTCACTATTT
1674990 T
1 T
1674991 TTTTTTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 15 0.58
30 6 0.23
ACGTcount: A:0.10, C:0.25, G:0.05, T:0.60
Consensus pattern (30 bp):
TACTTCGCTTTTGTTTCCCTTTCACTATTT
Found at i:1680114 original size:19 final size:19
Alignment explanation
Indices: 1680071--1680116 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1680061 AAATTTATAA
* **
1680071 TAATAAAATAATATATTAT
1 TAATAAATTAATATAAAAT
1680090 TAATAAATTAATATAAAAT
1 TAATAAATTAATATAAAAT
*
1680109 TTATAAAT
1 TAATAAAT
1680117 ATTAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATAAATTAATATAAAAT
Found at i:1681113 original size:22 final size:23
Alignment explanation
Indices: 1681100--1681144 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1681090 TTTGATTTTT
1681100 ATTAA-AATTTATTTAGATATAA
1 ATTAATAATTTATTTAGATATAA
*
1681122 ATTAATAATTTATTTAAATATAA
1 ATTAATAATTTATTTAGATATAA
1681145 TAAAGTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAATAATTTATTTAGATATAA
Found at i:1688460 original size:22 final size:23
Alignment explanation
Indices: 1688419--1688464 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1688409 AGGTTTGTAT
1688419 AGTTTGTAGTTCTTTTTTGCTGG
1 AGTTTGTAGTTCTTTTTTGCTGG
1688442 AGTTTGTAGTTC-TTTTTGCTGG
1 AGTTTGTAGTTCTTTTTTGCTGG
1688464 A
1 A
1688465 TGAGTGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.11, C:0.09, G:0.26, T:0.54
Consensus pattern (23 bp):
AGTTTGTAGTTCTTTTTTGCTGG
Found at i:1701975 original size:31 final size:31
Alignment explanation
Indices: 1701940--1702014 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
1701930 AATAATTTTA
1701940 TATTTCAATTGATGAATGAAAGCAAGCACAT
1 TATTTCAATTGATGAATGAAAGCAAGCACAT
*
1701971 TATTTCAATTGATGAATGAAAGCAAGCACGT
1 TATTTCAATTGATGAATGAAAGCAAGCACAT
*
1702002 TATATCAATTGAT
1 TATTTCAATTGAT
1702015 AAAATCTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (31 bp):
TATTTCAATTGATGAATGAAAGCAAGCACAT
Found at i:1704024 original size:2 final size:2
Alignment explanation
Indices: 1704017--1704056 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1704007 AGTAAAATCC
1704017 AT AT AT AT 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
1704057 TCTCAAATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1704595 original size:17 final size:19
Alignment explanation
Indices: 1704565--1704601 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1704555 AATTTTAATT
*
1704565 TATTTAATAGTTTATATTA
1 TATTTAATAGTTTACATTA
1704584 TATTT-ATA-TTTACATTA
1 TATTTAATAGTTTACATTA
1704601 T
1 T
1704602 TAATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TATTTAATAGTTTACATTA
Found at i:1706260 original size:2 final size:2
Alignment explanation
Indices: 1706253--1706300 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1706243 TAATTTTATT
* * * * *
1706253 TA TA TA TA TG TA TA TA TG CA CA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1706295 TA TA TA
1 TA TA TA
1706301 ATTTTCAACA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1708525 original size:3 final size:3
Alignment explanation
Indices: 1708513--1708549 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
1708503 TGTAATTACG
1708513 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1708550 GCTTTATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1712601 original size:25 final size:26
Alignment explanation
Indices: 1712573--1712629 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1712563 ATATTAATTC
*
1712573 TTTTACAA-AATTAATATTAAAATAT
1 TTTTACAATAATTAATATAAAAATAT
* *
1712598 TTTTATAATTAATTTATATAAAAATAT
1 TTTTACAA-TAATTAATATAAAAATAT
1712625 TTTTA
1 TTTTA
1712630 TTAATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 7 0.26
27 20 0.74
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTACAATAATTAATATAAAAATAT
Found at i:1712616 original size:27 final size:28
Alignment explanation
Indices: 1712581--1712637 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
1712571 TCTTTTACAA
*
1712581 AATTAATATTAAAATATTTTTA-TAATT
1 AATTAATATAAAAATATTTTTATTAATT
*
1712608 AATTTATATAAAAATATTTTTATTAATT
1 AATTAATATAAAAATATTTTTATTAATT
1712636 AA
1 AA
1712638 ATCATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTAATATAAAAATATTTTTATTAATT
Found at i:1712649 original size:15 final size:14
Alignment explanation
Indices: 1712629--1712668 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
1712619 AAATATTTTT
1712629 ATTAATTAAATCATA
1 ATTAATTAAATC-TA
1712644 ATTAATTTAAATCTA
1 ATTAA-TTAAATCTA
*
1712659 ATTAAATAAA
1 ATTAATTAAA
1712669 AATATTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 12 0.52
16 7 0.30
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTAATTAAATCTA
Found at i:1713282 original size:28 final size:29
Alignment explanation
Indices: 1713251--1713316 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
1713241 ATAAAAAAGA
1713251 TAAAATAATATTAATTTAAAT-TTA-AATT
1 TAAAATAATATTAA-TTAAATATTATAATT
**
1713279 TAAAATTAA-ATTAATTAAATATTATTTTT
1 TAAAA-TAATATTAATTAAATATTATAATT
1713308 TAAAATAAT
1 TAAAATAAT
1713317 TATACCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 6 0.19
28 16 0.50
29 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAAATAATATTAATTAAATATTATAATT
Found at i:1714439 original size:2 final size:2
Alignment explanation
Indices: 1714428--1714468 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1714418 TCTAATTCAT
1714428 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1714469 CCAAATACCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1714552 original size:4 final size:4
Alignment explanation
Indices: 1714543--1714571 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1714533 AATCCAGCTA
1714543 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
1714572 TGCCTTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1715720 original size:4 final size:4
Alignment explanation
Indices: 1715705--1715756 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
1715695 ATTATATAAA
* *
1715705 AATT AA-T AATT AATT AATT AATTT AATC AA-T AAAT AATT AAATT AATT
1 AATT AATT AATT AATT AATT AA-TT AATT AATT AATT AATT -AATT AATT
1715753 AATT
1 AATT
1715757 TATTTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
3 5 0.12
4 28 0.68
5 8 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (4 bp):
AATT
Found at i:1715730 original size:20 final size:20
Alignment explanation
Indices: 1715704--1715756 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1715694 TATTATATAA
*
1715704 AAATTAATAATTAATTAATT
1 AAATTAATAATTAAATAATT
*
1715724 AATTTAATCAA-TAAATAATT
1 AAATTAAT-AATTAAATAATT
1715744 AAATTAATTAATT
1 AAATTAA-TAATT
1715757 TATTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATTAATAATTAAATAATT
Found at i:1715756 original size:41 final size:40
Alignment explanation
Indices: 1715663--1715756 Score: 99
Period size: 37 Copynumber: 2.5 Consensus size: 40
1715653 AATATCGATT
* * * * *
1715663 TAATTAAA--AATTAAATATTTATTTAATTTAATATTATA
1 TAATTAAATTAATTAATTAATTAATTAATTTAATAATAAA
1715701 TAA--AAATTAA-TAATTAATTAATTAATTTAATCAATAAA
1 TAATTAAATTAATTAATTAATTAATTAATTTAAT-AATAAA
1715739 TAATTAAATTAATTAATT
1 TAATTAAATTAATTAATT
1715757 TATTTTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
36 3 0.07
37 18 0.40
38 12 0.27
40 7 0.16
41 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (40 bp):
TAATTAAATTAATTAATTAATTAATTAATTTAATAATAAA
Found at i:1717028 original size:37 final size:37
Alignment explanation
Indices: 1716987--1717093 Score: 110
Period size: 37 Copynumber: 3.2 Consensus size: 37
1716977 ATTTAATTCA
1716987 TTATAATAGTTATTTAATTATAAATTTATTTGATATT
1 TTATAATAGTTATTTAATTATAAATTTATTTGATATT
* * *
1717024 TTATAATA---ATATGATTATTAA---A-TT--TA--
1 TTATAATAGTTATTTAATTATAAATTTATTTGATATT
1717050 TTATAATAGTTATTTAATTATAAATTTATTTGATATT
1 TTATAATAGTTATTTAATTATAAATTTATTTGATATT
1717087 TTATAAT
1 TTATAAT
1717094 GATTATGATA
Statistics
Matches: 53, Mismatches: 6, Indels: 22
0.65 0.07 0.27
Matches are distributed among these distances:
26 8 0.15
28 2 0.04
29 10 0.19
30 2 0.04
31 1 0.02
32 1 0.02
33 2 0.04
34 10 0.19
35 2 0.04
37 15 0.28
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (37 bp):
TTATAATAGTTATTTAATTATAAATTTATTTGATATT
Found at i:1717085 original size:63 final size:64
Alignment explanation
Indices: 1716976--1717102 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 64
1716966 AGTTAAAACA
*
1716976 TATTTAATTCATTATAATAGTTATTTAATTATAAATTTATTTGATATTTTATAAT-AATATGAT
1 TATTAAATTCATTATAATAGTTATTTAATTATAAATTTATTTGATATTTTATAATGAATATGAT
* *
1717039 TATTAAATTTATTATAATAGTTATTTAATTATAAATTTATTTGATATTTTATAATGATTATGAT
1 TATTAAATTCATTATAATAGTTATTTAATTATAAATTTATTTGATATTTTATAATGAATATGAT
1717103 AAAATTTTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 53 0.88
64 7 0.12
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (64 bp):
TATTAAATTCATTATAATAGTTATTTAATTATAAATTTATTTGATATTTTATAATGAATATGAT
Found at i:1717266 original size:19 final size:19
Alignment explanation
Indices: 1717242--1717324 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 19
1717232 TAAATCAAAT
1717242 TATTATTATAATTATATTA
1 TATTATTATAATTATATTA
* *
1717261 TATTATTTTAATTATTATTT
1 TATTATTATAATTA-TATTA
* **
1717281 TATT-TTTTAAAAATAATTA
1 TATTATTATAATTAT-ATTA
* * * *
1717300 TTTTATTATAACTCTATTT
1 TATTATTATAATTATATTA
1717319 TATTAT
1 TATTAT
1717325 AAAAACTAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
18 1 0.02
19 34 0.69
20 14 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTATTATAATTATATTA
Found at i:1719504 original size:2 final size:2
Alignment explanation
Indices: 1719497--1719533 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1719487 AATAATAAGC
1719497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1719534 ATAATAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1719776 original size:14 final size:14
Alignment explanation
Indices: 1719739--1719788 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
1719729 CAATAAAAAA
*
1719739 ATATTTTTATTTTT
1 ATATTTTAATTTTT
* *
1719753 ATATTATTAAATTTG
1 ATATT-TTAATTTTT
1719768 ATATTTTAATTTTT
1 ATATTTTAATTTTT
1719782 ATATTTT
1 ATATTTT
1719789 TAAAATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
ATATTTTAATTTTT
Found at i:1724897 original size:23 final size:22
Alignment explanation
Indices: 1724849--1724897 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
1724839 ATTTTATTTT
***
1724849 AAATTTTTTTTATATATTTAAA
1 AAATTTTTTTTATATACACAAA
*
1724871 AAATTTTATTTTATATACACAAC
1 AAATTTT-TTTTATATACACAAA
1724894 AAAT
1 AAAT
1724898 ACGAGAACTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTTTTTTTATATACACAAA
Found at i:1729210 original size:4 final size:4
Alignment explanation
Indices: 1729193--1729236 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
1729183 TTTTCTCTCA
* *
1729193 ATGT ATGA ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1729237 CAGTATGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:1731458 original size:18 final size:18
Alignment explanation
Indices: 1731416--1731481 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
1731406 AAACAAAACC
* * *
1731416 TCATCAGATTCGTCCTCA
1 TCATCAGAATCATCTTCA
* *
1731434 TCCTCAGAATCATCTTCC
1 TCATCAGAATCATCTTCA
* *
1731452 TCATCAGAACCATTTTCA
1 TCATCAGAATCATCTTCA
*
1731470 TCCTCAGAATCA
1 TCATCAGAATCA
1731482 CTATCCTTGT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.32
Consensus pattern (18 bp):
TCATCAGAATCATCTTCA
Found at i:1732708 original size:3 final size:3
Alignment explanation
Indices: 1732700--1732731 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1732690 AAAGGAGCAA
1732700 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1732732 AAAACAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1734357 original size:12 final size:13
Alignment explanation
Indices: 1734323--1734371 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
1734313 GAAAACTTTA
*
1734323 ATTTTATTTATTC
1 ATTTTATTTATTT
1734336 A-TTTATTTATTT
1 ATTTTATTTATTT
1734348 ATTTTA-TTA-TT
1 ATTTTATTTATTT
1734359 ATTATTA-TTATTT
1 ATT-TTATTTATTT
1734372 GCTGATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.16
12 20 0.62
13 7 0.22
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:1743647 original size:22 final size:22
Alignment explanation
Indices: 1743601--1743650 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1743591 CATTGTAATA
*
1743601 AAATAAAATTTATCTAATTTAT
1 AAATAAAAATTATCTAATTTAT
1743623 AAATAAAAATT-T-TAATTTTACT
1 AAATAAAAATTATCTAA-TTTA-T
1743645 AAATAA
1 AAATAA
1743651 TTATATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 17 0.68
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAAAAATTATCTAATTTAT
Found at i:1745051 original size:26 final size:25
Alignment explanation
Indices: 1744999--1745054 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1744989 TATGAATTAT
**
1744999 TATTTAATATTAAAAATATTATTTA
1 TATTTAATATTAAAAATATTAAATA
1745024 TATTTAAT-TATAAAAATATATAAATA
1 TATTTAATAT-TAAAAATAT-TAAATA
1745050 TATTT
1 TATTT
1745055 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 17 0.63
26 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTTAATATTAAAAATATTAAATA
Found at i:1745759 original size:23 final size:21
Alignment explanation
Indices: 1745711--1745766 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
1745701 ATTTTTAATT
**
1745711 TATTTTTAAATTAATTCATAA
1 TATTTTTAAATTAATAAATAA
*
1745732 AATTTTTAAATTAAAATAAATAA
1 TATTTTTAAATT--AATAAATAA
1745755 TATTTTGTAAAT
1 TATTTT-TAAAT
1745767 AAATTTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 11 0.39
23 12 0.43
24 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TATTTTTAAATTAATAAATAA
Found at i:1746856 original size:21 final size:21
Alignment explanation
Indices: 1746830--1746874 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1746820 AGATCATTTC
1746830 ATATTCATATTCAAATATGCA
1 ATATTCATATTCAAATATGCA
1746851 ATATTCATATTCAAATATGCA
1 ATATTCATATTCAAATATGCA
1746872 ATA
1 ATA
1746875 GATACAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (21 bp):
ATATTCATATTCAAATATGCA
Found at i:1748335 original size:6 final size:6
Alignment explanation
Indices: 1748326--1748354 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1748316 ATCATCATCC
1748326 TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
1748355 CTCATCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCTCT
Found at i:1751107 original size:38 final size:38
Alignment explanation
Indices: 1751056--1751141 Score: 136
Period size: 38 Copynumber: 2.3 Consensus size: 38
1751046 AATGCCAAAT
*
1751056 ATGTGCATGTGCAGATTGGGTAAATTAGGAAAACCAAC
1 ATGTGCATGTGCAGATTGGGTAAATTACGAAAACCAAC
* **
1751094 ATGTGCATGTGCAGATTGGGTAATTTACGAAAATTAAC
1 ATGTGCATGTGCAGATTGGGTAAATTACGAAAACCAAC
1751132 ATGTGCATGT
1 ATGTGCATGT
1751142 TCATAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (38 bp):
ATGTGCATGTGCAGATTGGGTAAATTACGAAAACCAAC
Found at i:1756602 original size:16 final size:16
Alignment explanation
Indices: 1756571--1756601 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1756561 TAATTGACAC
1756571 CTGTCAAAATTCTTTT
1 CTGTCAAAATTCTTTT
1756587 CTGTCAAAATT-TTTT
1 CTGTCAAAATTCTTTT
1756602 TAGATATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (16 bp):
CTGTCAAAATTCTTTT
Found at i:1757212 original size:268 final size:267
Alignment explanation
Indices: 1756710--1757245 Score: 1000
Period size: 268 Copynumber: 2.0 Consensus size: 267
1756700 TCATGAAGAC
1756710 GATTCTACCATTACAATTCCAGCGAGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATAA
1 GATTCTACCATTACAATTCCAGCGAGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATAA
1756775 TCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTAAGTGGTGGAACCACGAGGAAGAGGTG
66 TCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTAAGTGGTGGAACCACGAGGAAGAGGTG
1756840 AAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGGT
131 AAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGGT
1756905 TTTTGGAGATTTTGTAATGCTGTGTTCTTCAAGCGTTCTTGGAGGCAATCTTACTTTCGTTTCTT
196 TTTTGGAGATTTTGTAATGCTGTGTTCTTCAAGCGTTCTTGGAGGCAATCTTACTTTCGTTTCTT
1756970 GGACAAT
261 GGACAAT
* *
1756977 GATTCTGCCATTACAGTTCCAGCGAGGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATA
1 GATTCTACCATTACAATTCCAGCGA-GGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATA
* *
1757042 ATCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTCAGTGGTGGAACCGCGAGGAAGAGGT
65 ATCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTAAGTGGTGGAACCACGAGGAAGAGGT
1757107 GAAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGG
130 GAAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGG
* * *
1757172 TTTTTGGGGATTTTGTAGTGCTGTGTTCTTCAAGCGTTCTTGGAGGCAGTCTTACTTTCGTTTCT
195 TTTTTGGAGATTTTGTAATGCTGTGTTCTTCAAGCGTTCTTGGAGGCAATCTTACTTTCGTTTCT
1757237 TGGACAAT
260 TGGACAAT
1757245 G
1 G
1757246 CAAAGAATTT
Statistics
Matches: 261, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
267 23 0.09
268 238 0.91
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (267 bp):
GATTCTACCATTACAATTCCAGCGAGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATAA
TCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTAAGTGGTGGAACCACGAGGAAGAGGTG
AAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGGT
TTTTGGAGATTTTGTAATGCTGTGTTCTTCAAGCGTTCTTGGAGGCAATCTTACTTTCGTTTCTT
GGACAAT
Found at i:1757492 original size:166 final size:166
Alignment explanation
Indices: 1757218--1757537 Score: 604
Period size: 166 Copynumber: 1.9 Consensus size: 166
1757208 TTCTTGGAGG
*
1757218 CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGGCTTTATGTTTCAATTGCTCTGCTGA
1 CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGACTTTATGTTTCAATTGCTCTGCTGA
*
1757283 AAGTAACGTTGGGGAATAAAATTAAAACTTATTTTTCATCAAATTGCAAAAGGTAAATTGCTTGA
66 AAGTAACGTTGGGGAATAAAATTAAAACTTATTTTTCATCAAATTGAAAAAGGTAAATTGCTTGA
*
1757348 CTGAATTTTACTTTTGTTTCCCCTTTTATTTTTCAT
131 CTGAATTTTACCTTTGTTTCCCCTTTTATTTTTCAT
1757384 CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGACTTTATGTTTCAATTGCTCTGCTGA
1 CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGACTTTATGTTTCAATTGCTCTGCTGA
*
1757449 AAGTAACGTTGGGGAATAGAATTAAAACTTATTTTTCATCAAATTGAAAAAGGTAAATTGCTTGA
66 AAGTAACGTTGGGGAATAAAATTAAAACTTATTTTTCATCAAATTGAAAAAGGTAAATTGCTTGA
1757514 CTGAATTTTACCTTTGTTTCCCCT
131 CTGAATTTTACCTTTGTTTCCCCT
1757538 ATTCTTTAAA
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 150 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (166 bp):
CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGACTTTATGTTTCAATTGCTCTGCTGA
AAGTAACGTTGGGGAATAAAATTAAAACTTATTTTTCATCAAATTGAAAAAGGTAAATTGCTTGA
CTGAATTTTACCTTTGTTTCCCCTTTTATTTTTCAT
Found at i:1759263 original size:25 final size:24
Alignment explanation
Indices: 1759235--1759281 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1759225 ATCAGAAGAA
*
1759235 AAGACAAAAAGATAAAGAAAAAGTT
1 AAGAAAAAAAGA-AAAGAAAAAGTT
*
1759260 AAGAAAAAAAGAAAAGGAAAAG
1 AAGAAAAAAAGAAAAGAAAAAG
1759282 ACAAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.06
Consensus pattern (24 bp):
AAGAAAAAAAGAAAAGAAAAAGTT
Found at i:1760732 original size:2 final size:2
Alignment explanation
Indices: 1760725--1760755 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1760715 ATCCATTATT
1760725 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
1760756 CCAAAAAAGA
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:1761448 original size:11 final size:12
Alignment explanation
Indices: 1761416--1761452 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1761406 CCAAATGAAT
1761416 AATC-AAATGCTA
1 AATCAAAATG-TA
1761428 AATCAAAATGTA
1 AATCAAAATGTA
1761440 AAT-AAAATGTA
1 AATCAAAATGTA
1761451 AA
1 AA
1761453 CTTGAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 9 0.38
13 5 0.21
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AATCAAAATGTA
Found at i:1761549 original size:19 final size:20
Alignment explanation
Indices: 1761522--1761582 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
1761512 TCAGTAACTC
*
1761522 AAAAGAAAAGAGAAA-AACA
1 AAAACAAAAGAGAAAGAACA
*
1761541 AAAACAAAAAAGAAAGAA-A
1 AAAACAAAAGAGAAAGAACA
1761560 AAAAC-AAAG-GAAAGAACA
1 AAAACAAAAGAGAAAGAACA
1761578 AAAAC
1 AAAAC
1761583 TAGGGAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.19
18 9 0.24
19 19 0.51
20 2 0.05
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAACAAAAGAGAAAGAACA
Found at i:1761561 original size:12 final size:12
Alignment explanation
Indices: 1761528--1761579 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1761518 ACTCAAAAGA
*
1761528 AAAGAGAAAAAC
1 AAAGAAAAAAAC
* *
1761540 AAAAACAAAAAAG
1 AAAGA-AAAAAAC
1761553 AAAGAAAAAAAC
1 AAAGAAAAAAAC
* *
1761565 AAAGGAAAGAAC
1 AAAGAAAAAAAC
1761577 AAA
1 AAA
1761580 AACTAGGGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAC
Found at i:1763998 original size:13 final size:13
Alignment explanation
Indices: 1763980--1764004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1763970 TCGGTTTTTG
1763980 TTTCATATATTTC
1 TTTCATATATTTC
1763993 TTTCATATATTT
1 TTTCATATATTT
1764005 ACAATATACT
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:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCATATATTTC
Found at i:1775515 original size:28 final size:27
Alignment explanation
Indices: 1775476--1775574 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 27
1775466 TTTATCATTT
* *
1775476 TATTTAATTAAATAGTATATTTTTATTA
1 TATTTAAATAAAT-TTATATTTTTATTA
* *
1775504 TATTTAAATAAATTTTTAATATTTATTTA
1 TATTTAAATAAATTTAT-ATTTTTA-TTA
* *
1775533 TATTAAAAT-AATTTTTAATTTTTAATTA
1 TATTTAAATAAATTTAT-ATTTTT-ATTA
*
1775561 TAATTAAATAAATT
1 TATTTAAATAAATT
1775575 CTTGACGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.03
28 41 0.69
29 16 0.27
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
TATTTAAATAAATTTATATTTTTATTA
Found at i:1775543 original size:29 final size:27
Alignment explanation
Indices: 1775497--1775574 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 27
1775487 ATAGTATATT
1775497 TTTATTATATTTAAATAAATTTTTAATA
1 TTTATTATA-TTAAATAAATTTTTAATA
*
1775525 TTTATTTATATTAAA-ATAATTTTTAATT
1 TTTA-TTATATTAAATA-AATTTTTAATA
1775553 TTTAATTATAATTAAATAAATT
1 TTT-ATTAT-ATTAAATAAATT
1775575 CTTGACGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
27 1 0.02
28 26 0.59
29 16 0.36
30 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATTATATTAAATAAATTTTTAATA
Found at i:1775848 original size:22 final size:22
Alignment explanation
Indices: 1775794--1775849 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1775784 AGTTATAATT
1775794 ATATAAAT-ATGAAATAAATAAA
1 ATATAAATAATG-AATAAATAAA
*
1775816 ATATTTAATAATG-ATAAATATAA
1 ATA-TAAATAATGAATAAATA-AA
1775839 ATATAAATAAT
1 ATATAAATAAT
1775850 AAAATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 17 0.59
23 9 0.31
24 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATAAATAATGAATAAATAAA
Found at i:1775898 original size:18 final size:18
Alignment explanation
Indices: 1775839--1775898 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
1775829 ATAAATATAA
1775839 ATATAAATAAT-AAAATTT
1 ATATAAAT-ATCAAAATTT
*
1775857 ATAT-AATA-C-GAA-TT
1 ATATAAATATCAAAATTT
1775871 AT-TAATATATCAAAATTT
1 ATATAA-ATATCAAAATTT
1775889 ATATAAATAT
1 ATATAAATAT
1775899 AAACAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 5 0.15
16 2 0.06
17 5 0.15
18 12 0.36
19 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATAAATATCAAAATTT
Found at i:1776719 original size:3 final size:3
Alignment explanation
Indices: 1776713--1776741 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1776703 TGTAAATTAT
1776713 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1776742 TATTGTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1778471 original size:2 final size:2
Alignment explanation
Indices: 1778464--1778496 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1778454 ACATAATGTG
1778464 TA 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 TA T
1778497 TAGCACATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1779954 original size:2 final size:2
Alignment explanation
Indices: 1779947--1779982 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1779937 GTAAGTAAAT
* *
1779947 GA GA GA GA AA GA GA GA GA AA 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
1779983 AGCGAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Done.