Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008935.1 Hibiscus syriacus cultivar Beakdansim tig00112253_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: 1775090
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:530714 original size:123 final size:126
Alignment explanation
Indices: 530419--530781 Score: 509
Period size: 123 Copynumber: 2.9 Consensus size: 126
530409 TATCTATTTA
* * *
530419 AAAAT-TTTCTTAATCGTTGATAACATATATACACCCTATAGACACAATTATTCGAACTCGAAAT
1 AAAATCTTTCTTAATCGTTGATAACATATACACACCCTGTAGACACAATTATTCGAACACGAAAT
530483 CTCTAAAAATAACAACACTTCTCTTTACCATTGAGATCATTCAATAGATTAGTATATATTC
66 CTCTAAAAATAACAACACTTCTCTTTACCATTGAGATCATTCAATAGATTAGTATATATTC
* * * * *
530544 AAAATCTTTCTTAATCGTTGATAACGTACACACACCCTGTAAACACAATTATTCGAGCACAAAAT
1 AAAATCTTTCTTAATCGTTGATAACATATACACACCCTGTAGACACAATTATTCGAACACGAAAT
* *
530609 CTCTAAATATAACAACACTTCTCTTTACCATTGAGA-C-TT-AATAGATTAGTATCTATTC
66 CTCTAAAAATAACAACACTTCTCTTTACCATTGAGATCATTCAATAGATTAGTATATATTC
* * ** *
530667 ATAATCTTTCTTAATCGGTGATAACATATACACACATTGTAGACACAATTATTCGAACCCGAAAT
1 AAAATCTTTCTTAATCGTTGATAACATATACACACCCTGTAGACACAATTATTCGAACACGAAAT
* * * * * *
530732 CTCTAGAGATAACAACACTTCTCTTTATCATCGAGATCACTCTATAGATT
66 CTCTAAAAATAACAACACTTCTCTTTACCATTGAGATCATTCAATAGATT
530782 CATGTTACTA
Statistics
Matches: 208, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
123 105 0.50
124 3 0.01
125 7 0.03
126 93 0.45
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (126 bp):
AAAATCTTTCTTAATCGTTGATAACATATACACACCCTGTAGACACAATTATTCGAACACGAAAT
CTCTAAAAATAACAACACTTCTCTTTACCATTGAGATCATTCAATAGATTAGTATATATTC
Found at i:538326 original size:21 final size:22
Alignment explanation
Indices: 538302--538355 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
538292 CCCTTGCTAG
538302 GTATCGATACATC-TTCAATGT
1 GTATCGATACATCTTTCAATGT
* * *
538323 GTATCAATACCCTCTTTGAATGT
1 GTATCGATA-CATCTTTCAATGT
538346 GTATCGATAC
1 GTATCGATAC
538356 CCCTAGATGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 8 0.30
22 4 0.15
23 15 0.56
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (22 bp):
GTATCGATACATCTTTCAATGT
Found at i:540308 original size:13 final size:13
Alignment explanation
Indices: 540279--540313 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
540269 TGAGAGTAAT
*
540279 TTTTCAAAATTGA
1 TTTTCAAAAATGA
540292 -TTTCAAAAATGA
1 TTTTCAAAAATGA
540304 TTTTCAAAAA
1 TTTTCAAAAA
540314 GAAAATCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:540626 original size:25 final size:25
Alignment explanation
Indices: 540587--540652 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
540577 AACCTTAATC
540587 GAGCCAAAAA-AAGTTTTATATAAG
1 GAGCCAAAAACAAGTTTTATATAAG
540611 GAGCCAAAAACAAGTTTTATATAAG
1 GAGCCAAAAACAAGTTTTATATAAG
540636 GAGCCAAAAACAAGTTT
1 GAGCCAAAAACAAGTTT
540653 CGAATGAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 10 0.24
25 31 0.76
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (25 bp):
GAGCCAAAAACAAGTTTTATATAAG
Found at i:543134 original size:18 final size:18
Alignment explanation
Indices: 543087--543136 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
543077 GCGGAAGCAT
* *
543087 AAGATGCCGATGTTGATA
1 AAGATGACGATTTTGATA
543105 AAGATGACGATTTTGATA
1 AAGATGACGATTTTGATA
* *
543123 AATATGATGATTTT
1 AAGATGACGATTTT
543137 TTTTGCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (18 bp):
AAGATGACGATTTTGATA
Found at i:546513 original size:31 final size:28
Alignment explanation
Indices: 546478--546553 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 28
546468 AGATAAAATT
*
546478 TGTTTCAAGAGAAATTGATTCAAACATTTTG
1 TGTTTCAAGAGAAATT--TTCAAA-ATTTTA
*
546509 TGTTTCAAGGGAAACGTTTTCAAAATTTTA
1 TGTTTCAAGAGAAA--TTTTCAAAATTTTA
546539 TGTTTCAAGAGAAAT
1 TGTTTCAAGAGAAAT
546554 CGTCTCAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 1 0.03
30 18 0.45
31 19 0.47
33 2 0.05
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (28 bp):
TGTTTCAAGAGAAATTTTCAAAATTTTA
Found at i:546604 original size:36 final size:36
Alignment explanation
Indices: 546556--546624 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
546546 AGAGAAATCG
*
546556 TCTCAAGGGAGACAAAATTT-TTTCCAAAGGAAACTA
1 TCTCAAGAGAGACAAAATTTATTT-CAAAGGAAACTA
*
546592 TCTCAAGAGAGACAAAATTTATTTCAAGGGAAA
1 TCTCAAGAGAGACAAAATTTATTTCAAAGGAAA
546625 TGTTTTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTTATTTCAAAGGAAACTA
Found at i:547022 original size:107 final size:107
Alignment explanation
Indices: 546831--547625 Score: 1306
Period size: 107 Copynumber: 7.4 Consensus size: 107
546821 TATTGTTCCA
* * * *
546831 AGTCTAATATCCTCCGCCGTGAAGTTGAAATTGGCTCT-AGAACT-GGGAATTTGTTTGTTGACA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AACTGGGGAAATTGTTTGTTGACA
*
546894 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
*
546937 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
* * * * *
547002 CCAGTCGTCCCTTCTCTGTGATGTTGAACTTGTATTGTCTTG
66 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
* * *
547044 AGTCCAATATTCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
*
547109 CCAGCCGTCCCTTCGATGTGAAGTTGAACTTGTGTTGTCTCG
66 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
547151 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
* * *
547216 CCAACCGTCCCTTCGCTATGAAGTTGAACTTGTATTGTCTCG
66 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
* *
547258 AGTCCAATATCATTCGCTGTGAAGTTAAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
*
547323 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCA
66 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
* *
547365 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
* *
547430 CCAGCCATCCCTTCGCTGTGAAGTTGAACTTATGTTGTCTCG
66 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
*
547472 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTTGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
* * *
547537 CCAACCGTCCCTTCACTGTGAAGTTGAACTTGTGTTGTCTCA
66 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
547579 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
547626 AAGCCCCTTC
Statistics
Matches: 637, Mismatches: 50, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
106 38 0.06
107 599 0.94
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (107 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
Found at i:548113 original size:32 final size:32
Alignment explanation
Indices: 548077--548151 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
548067 TTTGCATTAG
** * *
548077 GATGTTGAATCCCCAACGATGCCCCAATATTC
1 GATGTTGAATCCAAAAAGATGCCCCAAAATTC
* *
548109 GATGTTGAATCTAAAAAGATGCCCCAAAATTT
1 GATGTTGAATCCAAAAAGATGCCCCAAAATTC
548141 GATGTTGAATC
1 GATGTTGAATC
548152 TTCAAAGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCCAAAAAGATGCCCCAAAATTC
Found at i:548152 original size:32 final size:32
Alignment explanation
Indices: 548094--548163 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
548084 AATCCCCAAC
*
548094 GATGCCCCAATATTCGATGTTGAATCTAAAAA
1 GATGCCCCAAAATTCGATGTTGAATCTAAAAA
* **
548126 GATGCCCCAAAATTTGATGTTGAATCTTCAAA
1 GATGCCCCAAAATTCGATGTTGAATCTAAAAA
548158 GATGCC
1 GATGCC
548164 ATCATTGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (32 bp):
GATGCCCCAAAATTCGATGTTGAATCTAAAAA
Found at i:549287 original size:16 final size:15
Alignment explanation
Indices: 549226--549284 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
549216 TTTTCTTCAC
549226 TTTTTC-CTTTATTTT
1 TTTTTCTCTTT-TTTT
*
549241 TGTTTCTCTTTTTTT
1 TTTTTCTCTTTTTTT
*
549256 TTCTTT-TCTCTTTGTT
1 TT-TTTCTCT-TTTTTT
549272 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
549285 GTTCTGATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 19 0.53
16 17 0.47
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTCTCTTTTTTT
Found at i:550523 original size:7 final size:7
Alignment explanation
Indices: 550511--550558 Score: 87
Period size: 7 Copynumber: 6.7 Consensus size: 7
550501 TGAAATGTAG
550511 ATGCAAA
1 ATGCAAA
550518 ATGCAAA
1 ATGCAAA
550525 ATGCAAA
1 ATGCAAA
550532 ATGCAAA
1 ATGCAAA
550539 ATGCAAA
1 ATGCAAA
550546 ATGCAAAA
1 ATGC-AAA
550554 ATGCA
1 ATGCA
550559 TGAAATGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 33 0.82
8 7 0.17
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGCAAA
Found at i:559085 original size:42 final size:42
Alignment explanation
Indices: 559022--559111 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
559012 CATTCAACGT
*
559022 TCCAACAATTGAAAAAGATCAACCCTCTACCGCACTCACCGA
1 TCCAACAATTGAAAAAGATCAACCCACTACCGCACTCACCGA
* *
559064 TCCAACAATTGAAAAATATCAATCCACTACCGCACTCACCGA
1 TCCAACAATTGAAAAAGATCAACCCACTACCGCACTCACCGA
*
559106 ACCAAC
1 TCCAAC
559112 TGCTTCATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.17
Consensus pattern (42 bp):
TCCAACAATTGAAAAAGATCAACCCACTACCGCACTCACCGA
Found at i:560323 original size:11 final size:11
Alignment explanation
Indices: 560307--560337 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
560297 AATGAAAATG
560307 GTAAATAAACA
1 GTAAATAAACA
560318 GTAAATAAACA
1 GTAAATAAACA
*
560329 GAAAATAAA
1 GTAAATAAA
560338 ATAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (11 bp):
GTAAATAAACA
Found at i:564143 original size:20 final size:20
Alignment explanation
Indices: 564107--564151 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
564097 GATAAAAAGT
*
564107 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
*
564127 AAAAGTTAAGGAA-GAAAGAG
1 AAAAGTTAA-AAATGAAAGAG
564147 AAAAG
1 AAAAG
564152 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:575692 original size:85 final size:86
Alignment explanation
Indices: 575598--575805 Score: 312
Period size: 85 Copynumber: 2.4 Consensus size: 86
575588 TATGACATTG
575598 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAAAATAA-AAAATTAGGGGCCTCAATTA
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAAAATAAGAAAATTAGGGGCCTCAATTA
* *
575662 TAAAGGTAAAAAGTGATATCA
66 TAAAGATAAAAAGTGAGATCA
* * *
575683 AAAAAATTAGGGACCTCAATTATAAAGGTAGAAAGTGAGATTAAGAAAATTAGGGGCCTCAATTA
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAAAATAAGAAAATTAGGGGCCTCAATTA
* * *
575748 TAAAGATAGAGAGTGAGATTA
66 TAAAGATAAAAAGTGAGATCA
* *
575769 AGAAAATTA-GGGCCTCAATTATAAAGGTAAAAAGTGA
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGA
575806 TTGAAAAAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
85 67 0.60
86 44 0.40
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.23
Consensus pattern (86 bp):
AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAAAATAAGAAAATTAGGGGCCTCAATTA
TAAAGATAAAAAGTGAGATCA
Found at i:575701 original size:43 final size:43
Alignment explanation
Indices: 575598--575821 Score: 312
Period size: 43 Copynumber: 5.3 Consensus size: 43
575588 TATGACATTG
* *
575598 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAAAAT-
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTA
* * *
575640 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGATATCA
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTA
*
575683 AAAAAATTAGGGACCTCAATTATAAAGGTAGAAAGTGAGATTA
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTA
* * *
575726 AGAAAATTAGGGGCCTCAATTATAAAGATAGAGAGTGAGATTA
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTA
* *
575769 AGAAAATTA-GGGCCTCAATTATAAAGGTAAAAAGT--GATTGA
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATT-A
575810 AAAAAATTAGGG
1 AAAAAATTAGGG
575822 ACTTGTAGAA
Statistics
Matches: 163, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 4 0.02
41 9 0.06
42 63 0.39
43 87 0.53
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.23
Consensus pattern (43 bp):
AAAAAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTA
Found at i:575789 original size:21 final size:21
Alignment explanation
Indices: 575722--575789 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
575712 AGAAAGTGAG
575722 ATTAAGAAAATTAGGGGCCTCA
1 ATTAAGAAAATTA-GGGCCTCA
* * ** *
575744 ATTATA-AAGA-TAGAGAGTGA
1 ATTA-AGAAAATTAGGGCCTCA
575764 GATTAAGAAAATTAGGGCCTCA
1 -ATTAAGAAAATTAGGGCCTCA
575786 ATTA
1 ATTA
575790 TAAAGGTAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 9
0.63 0.20 0.18
Matches are distributed among these distances:
20 5 0.16
21 13 0.41
22 13 0.41
23 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (21 bp):
ATTAAGAAAATTAGGGCCTCA
Found at i:578157 original size:3 final size:3
Alignment explanation
Indices: 578149--578222 Score: 68
Period size: 3 Copynumber: 26.0 Consensus size: 3
578139 TTTGTTTTAT
* *
578149 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
578193 TTA TTA TTA -AA TAAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
578223 CAAACAGGCC
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 9 0.15
3 49 0.80
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:578175 original size:19 final size:19
Alignment explanation
Indices: 578148--578222 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
578138 ATTTGTTTTA
* *
578148 TTTATTATTATTATTTTGT
1 TTTATTATTATTATTATAT
*
578167 TTTAATATTATTATTATAT
1 TTTATTATTATTATTATAT
* *
578186 TATATTATTATTATTAAATAA
1 TTTATTATTATTATT--ATAT
*
578207 ATTATTATTATTATTA
1 TTTATTATTATTATTA
578223 CAAACAGGCC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 30 0.65
21 16 0.35
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTATTATTATTATTATAT
Found at i:578175 original size:22 final size:22
Alignment explanation
Indices: 578139--578201 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
578129 TTTTATTTCA
578139 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
*
578162 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
578184 ATTATATTATTATTATTA
1 TTTGTTTTATTATTATTA
578202 AATAAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 26 0.74
23 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:579545 original size:12 final size:11
Alignment explanation
Indices: 579528--579576 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
579518 TTAATTCCTT
579528 TTATTTTAATTA
1 TTATTTT-ATTA
* *
579540 TTATTTGCAATA
1 TTATTT-TATTA
579552 TTATTTTATTA
1 TTATTTTATTA
579563 TTATTCTTATTA
1 TTATT-TTATTA
579575 TT
1 TT
579577 TATATAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 8 0.26
12 23 0.74
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:579787 original size:20 final size:19
Alignment explanation
Indices: 579762--579803 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
579752 TTATTTTATA
579762 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
579782 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
579801 AAT
1 AAT
579804 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:588344 original size:76 final size:75
Alignment explanation
Indices: 588242--588387 Score: 184
Period size: 76 Copynumber: 1.9 Consensus size: 75
588232 GTGAATACCC
* * *
588242 TTTTCAATCAGAATCAGGAATATTGATGTATCCTGAATGTTTATATCAGCAAAATGCTGGGGCAT
1 TTTTCAATCAGAATCAAGAATATTGATGTATCCTGAACGTTCATATCAGC-AAATGCTGGGGCAT
588307 GCTGAAAGCCT
65 GCTGAAAGCCT
* * * ** * * *
588318 TTTTCAATCAGAATGAAGAATGTTGATGTCTTTTGAACGTTCGTATCAGCAATTGTTGGGGCATG
1 TTTTCAATCAGAATCAAGAATATTGATGTATCCTGAACGTTCATATCAGCAAATGCTGGGGCATG
588383 CTGAA
66 CTGAA
588388 GGCCCACATC
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
75 18 0.31
76 41 0.69
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (75 bp):
TTTTCAATCAGAATCAAGAATATTGATGTATCCTGAACGTTCATATCAGCAAATGCTGGGGCATG
CTGAAAGCCT
Found at i:589732 original size:22 final size:23
Alignment explanation
Indices: 589681--589736 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
589671 ATCTACACTC
* *
589681 TTCAAAGATGATAGATTCCCTTT
1 TTCAAAGATGACAAATTCCCTTT
* *
589704 TTAAAAGATGACAAATTCTC-TT
1 TTCAAAGATGACAAATTCCCTTT
589726 TTCAAAGATGA
1 TTCAAAGATGA
589737 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (23 bp):
TTCAAAGATGACAAATTCCCTTT
Found at i:590341 original size:113 final size:113
Alignment explanation
Indices: 590172--590912 Score: 1110
Period size: 113 Copynumber: 6.6 Consensus size: 113
590162 ATTTCTAGAA
*
590172 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
590237 CAACTTTTCACTTGAATTTATCATTCGATGGATCAGTATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
590285 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
590350 CAACTTTTCGCTTGAATTCATCATTCGATGGATCA-CATTGCCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
590397 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
590462 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGTCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
*
590510 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
590575 TAACTTTTCGCTTGAATTTATCATTCGATGGACCAGCATTGCCAGGGC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
* *
590623 GAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGATAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * **
590688 CAACTTTTCGCTTGAATTTATCATTCGATAGACCAGCATTGCCAGGGG
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
* * *
590736 GAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAACTTG--
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * *
590799 ------TT-GCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG-A
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAG-GTC
* * *
590840 GAGTTCATAATGAGAAGAATTCATCTGAAG-AGGAAGAGGAAGTTCATAATTAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
590904 CAATCTTTT
66 CAA-CTTTT
590913 GCATGATTCT
Statistics
Matches: 581, Mismatches: 36, Indels: 23
0.91 0.06 0.04
Matches are distributed among these distances:
103 28 0.05
104 56 0.10
105 3 0.01
112 112 0.19
113 382 0.66
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
Found at i:590534 original size:225 final size:223
Alignment explanation
Indices: 590143--590912 Score: 1126
Period size: 225 Copynumber: 3.5 Consensus size: 223
590133 AGTTCAAATC
* * * **
590143 CATCATTCAATGGATCAACATTTCTAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 CATCATTCGATGGATC-ACATTGCCAGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
590208 GAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTCACTTGAATTTATCATTCGATGGATCAG
65 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATCAG
* * *
590273 TATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
130 CATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
590338 GAAGAACTTGTTCAACTTTTCGCTTGAATT
195 GAAGAACTTGTT-AACTTTTCGCTTGAATT
590368 CATCATTCGATGGATCACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 CATCATTCGATGGATCACATTGCCAGG-CGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
590433 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAG
65 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATCAG
*
590498 CATTGTCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
130 CATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
590563 GAAGAACTTGTTTAACTTTTCGCTTGAATT
195 GAAGAACTTG-TTAACTTTTCGCTTGAATT
* * *
590593 TATCATTCGATGGACCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCA-CATTGCCA-GGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
590658 AGAAGAAGTTCATAATGATAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATAGACCA
64 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATCA
** * *
590723 GCATTGCCAGGGGGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATG
129 GCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
*
590788 AGAAGAACTTG-------TT-GCTCGAATT
194 AGAAGAACTTGTTAACTTTTCGCTTGAATT
* * * * *
590810 CATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAATTCATCTGAAG-AGGA
1 CATCATTCGATGGATC-ACATTGCCAG-GCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
590874 AGAGGAAGTTCATAATTAGAAGAACTTGTTCAATCTTTT
64 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
590913 GCATGATTCT
Statistics
Matches: 502, Mismatches: 36, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
216 35 0.07
217 61 0.12
218 3 0.01
224 8 0.02
225 216 0.43
226 177 0.35
227 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (223 bp):
CATCATTCGATGGATCACATTGCCAGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATCAGC
ATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTAACTTTTCGCTTGAATT
Found at i:591207 original size:19 final size:20
Alignment explanation
Indices: 591180--591236 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
591170 ATTTGTTTTA
* *
591180 TTTATTATTATTATT-TTGT
1 TTTAATATTATTATTATTAT
*
591199 TTTAATATTAATATTATTAT
1 TTTAATATTATTATTATTAT
*
591219 ATT-ATATTATTATTATTA
1 TTTAATATTATTATTATTA
591237 AATAAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 27 0.84
20 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTAATATTATTATTATTAT
Found at i:591207 original size:22 final size:22
Alignment explanation
Indices: 591171--591236 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
591161 TTTTATTTCA
591171 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
* *
591194 TTTGTTTTAATATTAATATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
591216 TATATTATATTATTATTATTA
1 TTTGTTTTATTATTATTATTA
591237 AATAAATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 27 0.75
23 9 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:591232 original size:25 final size:25
Alignment explanation
Indices: 591185--591233 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
591175 TTTTATTTAT
* * *
591185 TATTATTATTTTGTTTTAATATTAA
1 TATTATTATATTATATTAATATTAA
*
591210 TATTATTATATTATATTATTATTA
1 TATTATTATATTATATTAATATTA
591234 TTAAATAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TATTATTATATTATATTAATATTAA
Found at i:591256 original size:3 final size:3
Alignment explanation
Indices: 591181--591236 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
591171 TTTGTTTTAT
* * *
591181 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA ATA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
591225 TTA TTA TTA TTA
1 TTA TTA TTA TTA
591237 AATAAATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 8 0.18
3 37 0.82
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:592822 original size:20 final size:19
Alignment explanation
Indices: 592782--592838 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
592772 AAATAAATAA
*
592782 ATATATT-ATTTTATAAATT
1 ATATATTAATTTT-TTAATT
592801 ATATATTAATTGTTTTAATT
1 ATATATTAATT-TTTTAATT
* *
592821 ATTTATTTATTTTTTAAT
1 ATATATTAATTTTTTAAT
592839 ATCAAAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.42
20 17 0.52
21 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATATATTAATTTTTTAATT
Found at i:597816 original size:20 final size:20
Alignment explanation
Indices: 597791--597841 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
597781 CAGGGTTGTA
*
597791 GTATCGATACCAGAAGCTCG
1 GTATCGAGACCAGAAGCTCG
597811 GTATCGAGACCAGAAGCTCG
1 GTATCGAGACCAGAAGCTCG
* *
597831 ATATCAAGACC
1 GTATCGAGACC
597842 TAATGACTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (20 bp):
GTATCGAGACCAGAAGCTCG
Found at i:598766 original size:20 final size:20
Alignment explanation
Indices: 598737--598787 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
598727 GTTATTTTTG
*
598737 GTATCGATACTCAGGGGTCA
1 GTATCGATACTCAAGGGTCA
* * *
598757 TTATCAATACTTAAGGGTCA
1 GTATCGATACTCAAGGGTCA
598777 GTATCGATACT
1 GTATCGATACT
598788 GCTGATATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (20 bp):
GTATCGATACTCAAGGGTCA
Found at i:605395 original size:16 final size:16
Alignment explanation
Indices: 605374--605407 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
605364 ATTTATGTAG
605374 TTTGAGCTACTTCGCT
1 TTTGAGCTACTTCGCT
605390 TTTGAGCTACTTCGCT
1 TTTGAGCTACTTCGCT
605406 TT
1 TT
605408 ACACCTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (16 bp):
TTTGAGCTACTTCGCT
Found at i:608187 original size:17 final size:17
Alignment explanation
Indices: 608139--608188 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
608129 TTCCTTTCAT
608139 TATATTGTATCTTTTAC
1 TATATTGTATCTTTTAC
** * * *
608156 TGCACTATATATTTTAC
1 TATATTGTATCTTTTAC
608173 TATATTGTATCTTTTA
1 TATATTGTATCTTTTA
608189 GTTTCATTTC
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (17 bp):
TATATTGTATCTTTTAC
Found at i:608511 original size:21 final size:21
Alignment explanation
Indices: 608460--608516 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
608450 CGTGAAACCC
*
608460 ATAATGCACATATAGTGTCAG
1 ATAATGCACATAAAGTGTCAG
*
608481 A-ACT-CACATAAAGT-TCTAG
1 ATAATGCACATAAAGTGTC-AG
*
608500 ATAATGCACATATAGTG
1 ATAATGCACATAAAGTG
608517 CATGACAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 4 0.14
21 10 0.36
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (21 bp):
ATAATGCACATAAAGTGTCAG
Found at i:610804 original size:18 final size:18
Alignment explanation
Indices: 610781--610816 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
610771 TTTGACCTTC
610781 TTTTATTA-GTCTCTGATG
1 TTTTATTACGT-TCTGATG
610799 TTTTATTACGTTCTGATG
1 TTTTATTACGTTCTGATG
610817 ATTCAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.56
Consensus pattern (18 bp):
TTTTATTACGTTCTGATG
Found at i:611726 original size:21 final size:20
Alignment explanation
Indices: 611661--611737 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 20
611651 ACAAATACCA
*
611661 ACACGAAGTACTCTCCAAGT
1 ACACAAAGTACTCTCCAAGT
*
611681 ACAC-AAGTACTCTTGACACAGT
1 ACACAAAGTACTC-T-CCA-AGT
611703 ACACAAAGTACTACTCCAAGT
1 ACACAAAGTACT-CTCCAAGT
611724 ACACAAAGTACTCT
1 ACACAAAGTACTCT
611738 TACAAAAATG
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
19 8 0.16
20 7 0.14
21 17 0.34
22 9 0.18
23 8 0.16
24 1 0.02
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.21
Consensus pattern (20 bp):
ACACAAAGTACTCTCCAAGT
Found at i:621308 original size:19 final size:20
Alignment explanation
Indices: 621284--621327 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
621274 GCTATTTTTG
*
621284 GTATCGATACTC-AAGGTTA
1 GTATCGATACTCAAAGGTCA
621303 GTATCGATACTCAAAGGTCA
1 GTATCGATACTCAAAGGTCA
621323 GTATC
1 GTATC
621328 AATAATGCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (20 bp):
GTATCGATACTCAAAGGTCA
Found at i:624751 original size:36 final size:36
Alignment explanation
Indices: 624704--624777 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
624694 GAGTCAGAGG
*
624704 ATGCAGCCTTAGAAACATCCTCAACAGAGGTTGGGA
1 ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
624740 ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
1 ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
624776 AT
1 AT
624778 ACCATCATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (36 bp):
ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
Found at i:624947 original size:18 final size:18
Alignment explanation
Indices: 624924--624959 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
624914 GAAATGTGCT
*
624924 AGAGTCCTAGTTAAGTTA
1 AGAGTCCTAGCTAAGTTA
624942 AGAGTCCTAGCTAAGTTA
1 AGAGTCCTAGCTAAGTTA
624960 GCCTTATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (18 bp):
AGAGTCCTAGCTAAGTTA
Found at i:627545 original size:116 final size:116
Alignment explanation
Indices: 627321--627538 Score: 409
Period size: 116 Copynumber: 1.9 Consensus size: 116
627311 GGTGGTCGTC
*
627321 TCCCGAGGTTAACACGATAGCTCCGAAAATCGTACACCCAAAGATCGGAGTGGACAACAATGGTA
1 TCCCGAGGTTAACACGATAGCTCCGAAAATCATACACCCAAAGATCGGAGTGGACAACAATGGTA
627386 CTACTATTCTCTTAGCACCGAAAAGAAAGCTTAGAAATCTTTAGGGTCATT
66 CTACTATTCTCTTAGCACCGAAAAGAAAGCTTAGAAATCTTTAGGGTCATT
*
627437 TCCCGAGGTTAACACGATAGTTCCGAAAATCATACACCCAAAGATCGGAGTGGACAACAATGGTA
1 TCCCGAGGTTAACACGATAGCTCCGAAAATCATACACCCAAAGATCGGAGTGGACAACAATGGTA
*
627502 CTACTCTTCTCTTAGCACCGAAAAGAAAGCTTAGAAA
66 CTACTATTCTCTTAGCACCGAAAAGAAAGCTTAGAAA
627539 GTTTTAGAGG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 99 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (116 bp):
TCCCGAGGTTAACACGATAGCTCCGAAAATCATACACCCAAAGATCGGAGTGGACAACAATGGTA
CTACTATTCTCTTAGCACCGAAAAGAAAGCTTAGAAATCTTTAGGGTCATT
Found at i:633392 original size:21 final size:21
Alignment explanation
Indices: 633363--633407 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
633353 CCCATACCAA
*
633363 ACCAGACCCGACCCGCACCTG
1 ACCAAACCCGACCCGCACCTG
633384 ACCAAACCCGACCCGCACCTG
1 ACCAAACCCGACCCGCACCTG
633405 ACC
1 ACC
633408 CTAGCTCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.53, G:0.16, T:0.04
Consensus pattern (21 bp):
ACCAAACCCGACCCGCACCTG
Found at i:634466 original size:17 final size:16
Alignment explanation
Indices: 634424--634466 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
634414 TTCGATTACA
*
634424 TGTTTAATTTTGCATT
1 TGTTTAATTTAGCATT
*
634440 TATTTCAATTTAGTCATT
1 TGTTT-AATTTAG-CATT
634458 TGTTTAATT
1 TGTTTAATT
634467 CACATAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 8 0.36
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (16 bp):
TGTTTAATTTAGCATT
Found at i:634563 original size:28 final size:29
Alignment explanation
Indices: 634512--634578 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
634502 CTATAAATTT
*
634512 CAATTTAGTCCCTAATTCTAA-TTTATTG
1 CAATTTAGTTCCTAATTCTAATTTTATTG
* * * *
634540 CAATTTAGTTCCTATTTTTTATTTTATTT
1 CAATTTAGTTCCTAATTCTAATTTTATTG
*
634569 TAATTTAGTT
1 CAATTTAGTT
634579 TTCACTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.57
Consensus pattern (29 bp):
CAATTTAGTTCCTAATTCTAATTTTATTG
Found at i:639189 original size:22 final size:22
Alignment explanation
Indices: 639164--639208 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
639154 CATTATCATT
639164 TTACCTATTGAACATGCTGTCA
1 TTACCTATTGAACATGCTGTCA
639186 TTACCTATTGAACATGCTGTCA
1 TTACCTATTGAACATGCTGTCA
639208 T
1 T
639209 AAGTTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (22 bp):
TTACCTATTGAACATGCTGTCA
Found at i:641091 original size:9 final size:9
Alignment explanation
Indices: 641059--641118 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
641049 CTGCTGGAAA
641059 ACCGGTTTG
1 ACCGGTTTG
*
641068 ACCAGTTTTG
1 ACC-GGTTTG
641078 AACCGGTTTG
1 -ACCGGTTTG
*
641088 ACCGGTTCG
1 ACCGGTTTG
641097 AACCGGTTTG
1 -ACCGGTTTG
*
641107 ACCGGTCTG
1 ACCGGTTTG
641116 ACC
1 ACC
641119 CGACTCGTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 22 0.51
10 18 0.42
11 3 0.07
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:641101 original size:19 final size:19
Alignment explanation
Indices: 641058--641112 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
641048 GCTGCTGGAA
* *
641058 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
641078 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
641097 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
641113 CTGACCCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:648371 original size:9 final size:9
Alignment explanation
Indices: 648339--648398 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
648329 CTGCTGGAAA
648339 ACCGGTTTG
1 ACCGGTTTG
*
648348 ACCAGTTTTG
1 ACC-GGTTTG
648358 AACCGGTTTG
1 -ACCGGTTTG
*
648368 ACCGGTCTGG
1 ACCGGT-TTG
648378 ACCGGTTTG
1 ACCGGTTTG
*
648387 ACCGGTCTG
1 ACCGGTTTG
648396 ACC
1 ACC
648399 CGACCCGTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 22 0.51
10 18 0.42
11 3 0.07
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:648383 original size:19 final size:19
Alignment explanation
Indices: 648338--648396 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
648328 GCTGCTGGAA
* *
648338 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
648358 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
648377 GACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
648396 A
1 A
648397 CCCGACCCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 22 0.63
20 13 0.37
ACGTcount: A:0.17, C:0.24, G:0.31, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:648408 original size:14 final size:14
Alignment explanation
Indices: 648386--648432 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
648376 GGACCGGTTT
*
648386 GACCGGTCTGACCC
1 GACCCGTCTGACCC
648400 GACCCGTCTGACCC
1 GACCCGTCTGACCC
648414 GACCCGTCTGACCC
1 GACCCGTCTGACCC
648428 GACCC
1 GACCC
648433 AACCCGACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.15, C:0.49, G:0.23, T:0.13
Consensus pattern (14 bp):
GACCCGTCTGACCC
Found at i:648454 original size:17 final size:17
Alignment explanation
Indices: 648428--648465 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
648418 CGTCTGACCC
*
648428 GACCCAACCCGACTGTT
1 GACCCAACCCGACCGTT
*
648445 GACCCGACCCGACCGTT
1 GACCCAACCCGACCGTT
648462 GACC
1 GACC
648466 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.13
Consensus pattern (17 bp):
GACCCAACCCGACCGTT
Found at i:649450 original size:63 final size:63
Alignment explanation
Indices: 649348--649471 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
649338 CTAATGTGAC
* ** * *
649348 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCAACGGCCCCGAAATCATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
649411 TCTTAGGTAGGCCCAACGGCCCCGAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCAACGGCCCCGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
649472 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCAACGGCCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:653454 original size:2 final size:2
Alignment explanation
Indices: 653447--653487 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
653437 AATTTTCTAT
653447 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
653488 GGGTTAGGAT
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:660507 original size:31 final size:32
Alignment explanation
Indices: 660444--660522 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 32
660434 TCAAAAAACA
*
660444 TAAGTTTTGCTCACTTACGTTATCAATTTTAT
1 TAAGTTTTGATCACTTACGTTATCAATTTTAT
*
660476 TAAGTTTTAATCACTTACGTTATC-ATTTTAT
1 TAAGTTTTGATCACTTACGTTATCAATTTTAT
660507 TAAGTTTTGATCACTT
1 TAAGTTTTGATCACTT
660523 GGACTTTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 22 0.50
32 22 0.50
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.51
Consensus pattern (32 bp):
TAAGTTTTGATCACTTACGTTATCAATTTTAT
Found at i:669330 original size:20 final size:21
Alignment explanation
Indices: 669258--669336 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 21
669248 ATCCTTTCTA
* *
669258 TGTATTGATACACTATGAATG
1 TGTATCGATACACTCTGAATG
*
669279 TGTATCGATACATTCCTTGAATG
1 TGTATCGATACACT-C-TGAATG
669302 TGTATCGATACACTCTGAA-G
1 TGTATCGATACACTCTGAATG
*
669322 TGTACCGATACACTC
1 TGTATCGATACACTC
669337 ATCGGGATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.29
21 16 0.31
22 1 0.02
23 19 0.37
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (21 bp):
TGTATCGATACACTCTGAATG
Found at i:674447 original size:9 final size:9
Alignment explanation
Indices: 674435--674459 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
674425 TAAATAAATA
674435 ATAATATTT
1 ATAATATTT
674444 ATAATATTT
1 ATAATATTT
674453 ATAATAT
1 ATAATAT
674460 ACATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATAATATTT
Found at i:674591 original size:26 final size:26
Alignment explanation
Indices: 674562--674639 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 26
674552 TAAAAACTAC
674562 ATATTTTCAAAAAATATAATATATAT
1 ATATTTTCAAAAAATATAATATATAT
* * *
674588 ATATATT--AGAAATGT-ATACTATAT
1 ATATTTTCAAAAAATATAATA-TATAT
674612 ATATTTTCAAAAAATACTAATATATAT
1 ATATTTTCAAAAAATA-TAATATATAT
674639 A
1 A
674640 AAAACGCTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
23 3 0.07
24 17 0.41
26 11 0.27
27 7 0.17
28 3 0.07
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (26 bp):
ATATTTTCAAAAAATATAATATATAT
Found at i:676334 original size:21 final size:19
Alignment explanation
Indices: 676308--676361 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
676298 TTTTGGGCTA
676308 GAGTATCGATACTGCCAAGGG
1 GAGTATCGATACTG--AAGGG
* *
676329 GAGTATCGATATTGTAGGG
1 GAGTATCGATACTGAAGGG
676348 GTAGTATCGATACT
1 G-AGTATCGATACT
676362 CAGGGTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.17
20 11 0.38
21 13 0.45
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (19 bp):
GAGTATCGATACTGAAGGG
Found at i:677667 original size:31 final size:31
Alignment explanation
Indices: 677601--677672 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
677591 TTGTATTCAA
* * *
677601 ATAATGCATAATATGTCATGTTTGCAATCAT
1 ATAATGCACAATATGTCAGGTTTGCAATCAG
* * *
677632 ATAATGCACCATATGTCAGGTTTGCATTTAG
1 ATAATGCACAATATGTCAGGTTTGCAATCAG
677663 ATAATGCACA
1 ATAATGCACA
677673 GGAGGACCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (31 bp):
ATAATGCACAATATGTCAGGTTTGCAATCAG
Found at i:680751 original size:14 final size:14
Alignment explanation
Indices: 680732--680761 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
680722 TCTTAATTCC
*
680732 TTAAATTCTTAAAT
1 TTAAATTCCTAAAT
680746 TTAAATTCCTAAAT
1 TTAAATTCCTAAAT
680760 TT
1 TT
680762 CTCAATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATTCCTAAAT
Found at i:681493 original size:2 final size:2
Alignment explanation
Indices: 681486--681532 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
681476 GTTTAACATT
681486 TA TA TA TA 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
681528 TA TA T
1 TA TA T
681533 TGAAAAACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:681568 original size:27 final size:29
Alignment explanation
Indices: 681538--681608 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
681528 TATATTGAAA
681538 AACAATGCAT-A-TTATTGCATCACATTT
1 AACAATGCATAATTTATTGCATCACATTT
*
681565 AACACTGCATAATCTTTATTGCATCACATTT
1 AACAATGCATAA--TTTATTGCATCACATTT
* *
681596 AACATTACATAAT
1 AACAATGCATAAT
681609 CTTTTTTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 9 0.24
28 1 0.03
29 1 0.03
31 26 0.70
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.37
Consensus pattern (29 bp):
AACAATGCATAATTTATTGCATCACATTT
Found at i:681587 original size:31 final size:31
Alignment explanation
Indices: 681549--681612 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
681539 ACAATGCATA
*
681549 TTATTGCATCACATTTAACACTGCATAATCT
1 TTATTGCATCACATTTAACACTACATAATCT
*
681580 TTATTGCATCACATTTAACATTACATAATCT
1 TTATTGCATCACATTTAACACTACATAATCT
681611 TT
1 TT
681613 TTTCTCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (31 bp):
TTATTGCATCACATTTAACACTACATAATCT
Found at i:681712 original size:22 final size:22
Alignment explanation
Indices: 681681--681739 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
681671 GGTATCAGTT
*
681681 CTTA-TTAATAACCATGAAGTG
1 CTTATTTAATAACCATAAAGTG
681702 CTTATTTAATAACCATAAAGTG
1 CTTATTTAATAACCATAAAGTG
*
681724 CTTATTTAAAAACCAT
1 CTTATTTAATAACCAT
681740 CCCATGTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (22 bp):
CTTATTTAATAACCATAAAGTG
Found at i:684144 original size:18 final size:19
Alignment explanation
Indices: 684118--684156 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
684108 AATGTAATTC
*
684118 ATTTATTTAATTTATTTTT
1 ATTTATTTAAATTATTTTT
684137 ATTT-TTTAAATTATTTTT
1 ATTTATTTAAATTATTTTT
684155 AT
1 AT
684157 AAATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTATTTAAATTATTTTT
Found at i:684152 original size:12 final size:12
Alignment explanation
Indices: 684135--684168 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
684125 TAATTTATTT
684135 TTATTTTTTAAA
1 TTATTTTTTAAA
684147 TTATTTTTATAAA
1 TTATTTTT-TAAA
684160 TTATTTTTT
1 TTATTTTTT
684169 TTAATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTTTAAA
Found at i:684154 original size:13 final size:13
Alignment explanation
Indices: 684138--684174 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
684128 TTTATTTTTA
684138 TTTTTTAAATTAT
1 TTTTTTAAATTAT
*
684151 TTTTATAAATTAT
1 TTTTTTAAATTAT
*
684164 TTTTTTTAATT
1 TTTTTTAAATT
684175 TTTCACTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTAAATTAT
Found at i:695379 original size:28 final size:27
Alignment explanation
Indices: 695335--695392 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
695325 ACAAGATTTT
* *
695335 AAACATTCAACATATT-ATCTAGTAAGA
1 AAACATTCAACACATTAAT-TAATAAGA
*
695362 AAACATTATAACACATTAATTAATAAGA
1 AAACATT-CAACACATTAATTAATAAGA
695390 AAA
1 AAA
695393 ACAACACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 7 0.27
28 17 0.65
29 2 0.08
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (27 bp):
AAACATTCAACACATTAATTAATAAGA
Found at i:696391 original size:22 final size:22
Alignment explanation
Indices: 696366--696434 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
696356 GTGGCATATG
* *
696366 GAATTTGTCCCGAAGGACTTGT
1 GAATATGTCCCGAAGGACCTGT
696388 GAATATGTCCCGAAGGACCTGT
1 GAATATGTCCCGAAGGACCTGT
* *
696410 GAATATGTCCTGAAGGACCTAT
1 GAATATGTCCCGAAGGACCTGT
696432 GAA
1 GAA
696435 ACCCTCGACT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (22 bp):
GAATATGTCCCGAAGGACCTGT
Found at i:703243 original size:22 final size:23
Alignment explanation
Indices: 703191--703243 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
703181 CACTGAGTGG
*
703191 CATATGATATTTGTCCCGAAGGAT
1 CATATGA-ATATGTCCCGAAGGAT
* *
703215 C-TGTGAATATGTTCCGAAGGA-
1 CATATGAATATGTCCCGAAGGAT
703236 CATATGAA
1 CATATGAA
703244 ACCCTCGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 4 0.17
24 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (23 bp):
CATATGAATATGTCCCGAAGGAT
Found at i:709593 original size:48 final size:49
Alignment explanation
Indices: 709536--709628 Score: 161
Period size: 48 Copynumber: 1.9 Consensus size: 49
709526 TTCCAGTATC
*
709536 ATTTATAAATTTTAAGTATGAAATATTTCTATAAT-ATTTTTCATCAAT
1 ATTTATAAATTTTAAGTATGAAATATTTATATAATAATTTTTCATCAAT
*
709584 ATTTATAAATTTTAAGTATGGAATATTTATATAATAATTTTTCAT
1 ATTTATAAATTTTAAGTATGAAATATTTATATAATAATTTTTCAT
709629 TAAGTTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
48 33 0.79
49 9 0.21
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (49 bp):
ATTTATAAATTTTAAGTATGAAATATTTATATAATAATTTTTCATCAAT
Found at i:709608 original size:24 final size:24
Alignment explanation
Indices: 709536--709614 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 24
709526 TTCCAGTATC
709536 ATTTATAAATTTTAAGTATGAAAT
1 ATTTATAAATTTTAAGTATGAAAT
*
709560 ATTTCTATAATATTTT---TCAT-CAAT
1 A-TT-TATAA-ATTTTAAGT-ATGAAAT
*
709584 ATTTATAAATTTTAAGTATGGAAT
1 ATTTATAAATTTTAAGTATGAAAT
709608 ATTTATA
1 ATTTATA
709615 TAATAATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
21 5 0.11
22 5 0.11
23 4 0.09
24 17 0.38
25 4 0.09
26 5 0.11
27 5 0.11
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (24 bp):
ATTTATAAATTTTAAGTATGAAAT
Found at i:709741 original size:18 final size:18
Alignment explanation
Indices: 709720--709775 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
709710 GACATTTCAC
709720 ATTTATAAAATATTTACA
1 ATTTATAAAATATTTACA
* * *
709738 ATTT-TCATATGATTTTCA
1 ATTTATAAAAT-ATTTACA
*
709756 A-TTATAAGATATTTACA
1 ATTTATAAAATATTTACA
709773 ATT
1 ATT
709776 ATTAGATGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (18 bp):
ATTTATAAAATATTTACA
Found at i:709761 original size:35 final size:35
Alignment explanation
Indices: 709722--709824 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 35
709712 CATTTCACAT
*
709722 TTATAAAATATTTACAATTTTCATATGATTTTCAA
1 TTATAAAATATTTACAATTTTCAGATGATTTTCAA
* *
709757 TTATAAGATATTTACAATTATT-AGATGATTTTTCAG
1 TTATAAAATATTTACAATT-TTCAGATGA-TTTTCAA
* **
709793 TTATCAAATATTTACAATCATCAGATGATTTT
1 TTATAAAATATTTACAATTTTCAGATGATTTT
709825 AGTTATCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 28 0.48
36 30 0.52
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (35 bp):
TTATAAAATATTTACAATTTTCAGATGATTTTCAA
Found at i:709804 original size:36 final size:35
Alignment explanation
Indices: 709722--709852 Score: 142
Period size: 35 Copynumber: 3.7 Consensus size: 35
709712 CATTTCACAT
* * *
709722 TTATAAAATATTTACAATT-TTCATATGATTTTCAA
1 TTATCAAATATTTACAATTATT-AGATGATTTTCAG
709757 TTAT-AAGATATTTACAATTATTAGATGATTTTTCAG
1 TTATCAA-ATATTTACAATTATTAGATGA-TTTTCAG
* *
709793 TTATCAAATATTTACAATCATCAGATGATTTT-AG
1 TTATCAAATATTTACAATTATTAGATGATTTTCAG
* *
709827 TTATCAAATGTTTTACAGTTATTAGA
1 TTATCAAAT-ATTTACAATTATTAGA
709853 CATAGATTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
34 13 0.16
35 37 0.45
36 31 0.37
37 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (35 bp):
TTATCAAATATTTACAATTATTAGATGATTTTCAG
Found at i:710837 original size:22 final size:20
Alignment explanation
Indices: 710809--710850 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
710799 TTATATTATT
710809 AAGGAAAATATTTAAAGTTAAA
1 AAGGAAAATA-TTAAA-TTAAA
*
710831 AAGGAAATTATTAAATTAAA
1 AAGGAAAATATTAAATTAAA
710851 CAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (20 bp):
AAGGAAAATATTAAATTAAA
Found at i:710838 original size:21 final size:21
Alignment explanation
Indices: 710809--710850 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
710799 TTATATTATT
710809 AAGGAAAA-TATTTAAAGTTAAA
1 AAGGAAAATTA-TTAAA-TTAAA
710831 AAGG-AAATTATTAAATTAAA
1 AAGGAAAATTATTAAATTAAA
710851 CAAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
AAGGAAAATTATTAAATTAAA
Found at i:714698 original size:12 final size:12
Alignment explanation
Indices: 714681--714708 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
714671 TTGGAGTTTG
714681 AAGAATTAATTA
1 AAGAATTAATTA
714693 AAGAATTAATTA
1 AAGAATTAATTA
714705 AAGA
1 AAGA
714709 TTATTGTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (12 bp):
AAGAATTAATTA
Found at i:716734 original size:18 final size:18
Alignment explanation
Indices: 716711--716750 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
716701 ATGTTTACAA
716711 TTATCAAATAATTTTCAG
1 TTATCAAATAATTTTCAG
* *
716729 TTATCAGATGATTTTCAG
1 TTATCAAATAATTTTCAG
716747 TTAT
1 TTAT
716751 AATACGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (18 bp):
TTATCAAATAATTTTCAG
Found at i:716776 original size:19 final size:18
Alignment explanation
Indices: 716722--716777 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
716712 TATCAAATAA
* *
716722 TTTTCAGTTATCAGATGA
1 TTTTCAGTTATCAGACGT
* *
716740 TTTTCAGTTATAATACGT
1 TTTTCAGTTATCAGACGT
716758 TTTTACAGTTATCAGACGT
1 TTTT-CAGTTATCAGACGT
716777 T
1 T
716778 GATTAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
18 18 0.58
19 13 0.42
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.46
Consensus pattern (18 bp):
TTTTCAGTTATCAGACGT
Found at i:722300 original size:21 final size:21
Alignment explanation
Indices: 722271--722310 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
722261 AAATTTTATT
*
722271 TACCTAAAACATTATTATTTC
1 TACCGAAAACATTATTATTTC
**
722292 TACCGAAAATGTTATTATT
1 TACCGAAAACATTATTATT
722311 GGACGATTTA
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:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
TACCGAAAACATTATTATTTC
Found at i:722448 original size:22 final size:22
Alignment explanation
Indices: 722413--722454 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
722403 TCGAAAATAT
* * *
722413 TAAAAAATATTAATGTTTTAAG
1 TAAAAAAAAATAATATTTTAAG
722435 TAAAAAAAAATAATATTTTA
1 TAAAAAAAAATAATATTTTA
722455 GACAATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (22 bp):
TAAAAAAAAATAATATTTTAAG
Found at i:723287 original size:21 final size:21
Alignment explanation
Indices: 723262--723301 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
723252 AATCTATAAA
723262 CAAATAACAATATTAAAATGT
1 CAAATAACAATATTAAAATGT
** *
723283 CAAATTTCAATATTCAAAT
1 CAAATAACAATATTAAAAT
723302 TATAATATTA
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:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (21 bp):
CAAATAACAATATTAAAATGT
Found at i:723300 original size:74 final size:74
Alignment explanation
Indices: 723204--723353 Score: 169
Period size: 75 Copynumber: 2.0 Consensus size: 74
723194 AATCATAAAT
*
723204 AATGTCAAATATCAAGACTCAAACAACAATATTAAATTTT-AACAGTAAAATCTATAA-ACAAAT
1 AATGTCAAATATCAAGACTCAAACAACAATATT-AATTTTAAACAATAAAATCTATAATA-AAAT
723267 AACAATATTAA
64 AACAATATTAA
* * * ** * * *
723278 AATGTCAAATTTCAATATTCAAATTATAATATTAATTTTAGAATAATAAAATCTATAATAAAATT
1 AATGTCAAATATCAAGACTCAAACAACAATATTAATTTTA-AACAATAAAATCTATAATAAAATA
*
723343 ATAATATTAA
65 ACAATATTAA
723353 A
1 A
723354 GTTGGGGTGA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
73 6 0.10
74 27 0.43
75 29 0.46
76 1 0.02
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.33
Consensus pattern (74 bp):
AATGTCAAATATCAAGACTCAAACAACAATATTAATTTTAAACAATAAAATCTATAATAAAATAA
CAATATTAA
Found at i:723347 original size:11 final size:12
Alignment explanation
Indices: 723320--723348 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
723310 TAATTTTAGA
723320 ATAATAAAATCT
1 ATAATAAAATCT
723332 ATAATAAAAT-T
1 ATAATAAAATCT
723343 ATAATA
1 ATAATA
723349 TTAAAGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAATAAAATCT
Found at i:730068 original size:18 final size:18
Alignment explanation
Indices: 730042--730088 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
730032 GCTATACAAG
*
730042 TGTGACTATTCAAAGACT
1 TGTGCCTATTCAAAGACT
730060 TGTGCCTATTCAAAGACT
1 TGTGCCTATTCAAAGACT
730078 TGTGCCTATTC
1 TGTGCCTATTC
730089 TAGATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (18 bp):
TGTGCCTATTCAAAGACT
Found at i:735108 original size:29 final size:29
Alignment explanation
Indices: 735032--735108 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 29
735022 TATATCTAGC
735032 AAAACATGAAA-TTAAATGACTAAAAATGGT
1 AAAACA-GAAATTTAAA-GACTAAAAATGGT
* * * *
735062 AAGAACATAACTTAAAAGACT-AAAATAGTT
1 AA-AACAGAAATTTAAAGACTAAAAAT-GGT
735092 AAAACAGAAATTTAAAG
1 AAAACAGAAATTTAAAG
735109 GACATAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
29 17 0.46
30 12 0.32
31 8 0.22
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.22
Consensus pattern (29 bp):
AAAACAGAAATTTAAAGACTAAAAATGGT
Found at i:735653 original size:145 final size:144
Alignment explanation
Indices: 735309--735682 Score: 437
Period size: 146 Copynumber: 2.6 Consensus size: 144
735299 CGCCGTCGTG
* * * *
735309 CCACCGTCCGATCGTCCTCAAATTTTAGTATGTTGTTTGTGTTGACATCGCGCAACTTTTGACCG
1 CCACCGTCCGATCATCCT-AAATTTTAGTATGTTGTTTGTGTAGTC-TCGCGCAACTTTTGACTG
* * * * * * * *
735374 TTCGGAATGTTGATTAGAGTTCCCAATCGCTGGCGAGAGGCCAAAAACTGTCTGGATTTGTTTTC
64 TTCAGAATGTTGATCAGAGATCCCAATCGCCGGCAAGAGACCAAAAACCGTCTGGATTAGTTTTC
* *
735439 TCCGATTCACCGTCGT
129 TCCGATCCACCGCCGT
* * *
735455 CCACCGTCTGATCATCCTAAATTTTTAGTATGTTGTTTGTGCTGGTCTCGCGCAACTTCT-AGCT
1 CCACCGTCCGATCATCCTAAA-TTTTAGTATGTTGTTTGTG-TAGTCTCGCGCAACTTTTGA-CT
* * *
735519 GTTCAGAATGTTGATCAGAGATCCCGATCGCCGGCAAGAGACCAAAAACCGTTTGGCTTAG-TTT
63 GTTCAGAATGTTGATCAGAGATCCCAATCGCCGGCAAGAGACCAAAAACCGTCTGGATTAGTTTT
* *
735583 CTTCGATCCATCGCCGT
128 CTCCGATCCACCGCCGT
* * *
735600 CCACCGTCCGATCATCCTGAATTTTCAGTATGTTGTTCGTGATAGTCTTGCGCAACTTTTGACTG
1 CCACCGTCCGATCATCCTAAATTTT-AGTATGTTGTTTGTG-TAGTCTCGCGCAACTTTTGACTG
*
735665 TTCATAATGTTGATCAGA
64 TTCAGAATGTTGATCAGA
735683 TATTCTGATC
Statistics
Matches: 194, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
144 4 0.02
145 88 0.45
146 99 0.51
147 3 0.02
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (144 bp):
CCACCGTCCGATCATCCTAAATTTTAGTATGTTGTTTGTGTAGTCTCGCGCAACTTTTGACTGTT
CAGAATGTTGATCAGAGATCCCAATCGCCGGCAAGAGACCAAAAACCGTCTGGATTAGTTTTCTC
CGATCCACCGCCGT
Found at i:736021 original size:3 final size:3
Alignment explanation
Indices: 736008--736083 Score: 73
Period size: 3 Copynumber: 24.7 Consensus size: 3
735998 TTAAGTATAG
* *
736008 TAA TAA TTAA TAA TAA TAG TAA T-A TAA CTAA TAA TAA TAA TAA TAG
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* * *
736054 CAA TAA TAG TAA TAA TAA TATT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA
736084 TTTTTTCGAC
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.03
3 49 0.83
4 8 0.14
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:736510 original size:131 final size:131
Alignment explanation
Indices: 736231--736585 Score: 412
Period size: 131 Copynumber: 2.7 Consensus size: 131
736221 GTTCGAATCG
* * * *
736231 TCTAAGGGTTGACACGACTCCTACGTGATGAGGAGGTCAGGTC-AGGTGATGAAAC-AGTTCCTA
1 TCTAA-GGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGA-GAGATGACACGA-TTCCTA
* * * * * * *
736294 CGTGATGAGGACGGAAGGTCATC-TAAGGG-TGATAACACGGTTCCTACGTGATGAGGACGGCTG
63 CGTGATGAGGACGGCAGGCCATCTTTAGGGATGATAACACAGTTCCTACATGATGAGGACGACTC
*
736357 GTTA
128 ATTA
* * * * * *
736361 TCTGAGGTTGACATGACTCCTATGTGATGAAGAGATGTGGTCGAGAGATGACACGATTCCTACAT
1 TCTAAGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGAGAGATGACACGATTCCTACGT
* *
736426 GATGAGGACGGCAGACCATCTTTAGGGATGATAACACAGTTCCTACATGATGAGGATGACTCATT
66 GATGAGGACGGCAGGCCATCTTTAGGGATGATAACACAGTTCCTACATGATGAGGACGACTCATT
736491 A
131 A
* * * * *
736492 TCTAAGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGAGGGCTGACATGGTTCTTACGT
1 TCTAAGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGAGAGATGACACGATTCCTACGT
* *
736557 GATGAGGATGACAGGCCATCTTTAGGGAT
66 GATGAGGACGGCAGGCCATCTTTAGGGAT
736586 AATGGTTTCA
Statistics
Matches: 187, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
129 64 0.34
130 11 0.06
131 112 0.60
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (131 bp):
TCTAAGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGAGAGATGACACGATTCCTACGT
GATGAGGACGGCAGGCCATCTTTAGGGATGATAACACAGTTCCTACATGATGAGGACGACTCATT
A
Found at i:736719 original size:35 final size:36
Alignment explanation
Indices: 736621--736835 Score: 220
Period size: 36 Copynumber: 6.0 Consensus size: 36
736611 TAAATGATGC
* * * *
736621 TTCAAGAGAAGCTGTCTCAAAAGAGATAAAATATGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* ** *
736657 TTCAAGGGAAACTGTCTCATTAAAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
736693 TTCAA-AAAAAATGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * *
736728 TTCAAGAGAAACCGTCTCAAGAAAGACAAAACTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
736764 TTCAA-AAAAAATGTCTCAAGAGAGACGAAATTTTAT
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGT
*
736800 TTCAATG-GAAACTGTCTCAAGGGAGACAAAAATTTG
1 TTCAA-GAGAAACTGTCTCAAGAGAGAC-AAAATTTG
736836 AAATCGTGTA
Statistics
Matches: 144, Mismatches: 31, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
35 46 0.32
36 75 0.52
37 23 0.16
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:736723 original size:71 final size:71
Alignment explanation
Indices: 736633--736830 Score: 270
Period size: 71 Copynumber: 2.8 Consensus size: 71
736623 CAAGAGAAGC
* * * ** *
736633 TGTCTCAAAAGAGATAAAATATGTTTCAAGGGAAACTGTCTCATTAAAGACAAAATTTGTTTCAA
1 TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAACTTGTTTCAA
736698 AAAAAA
66 AAAAAA
* *
736704 TGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACCGTCTCAAGAAAGACAAAACTTGTTTCAA
1 TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAACTTGTTTCAA
736769 AAAAAA
66 AAAAAA
* * * **
736775 TGTCTCAAGAGAGACGAAATTTTATTTCAATGGAAACTGTCTCAAGGGAGACAAAA
1 TGTCTCAAGAGAGAC-AAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAA
736831 ATTTGAAATC
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 78 0.70
72 33 0.30
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (71 bp):
TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAACTTGTTTCAA
AAAAAA
Found at i:739581 original size:6 final size:6
Alignment explanation
Indices: 739570--739598 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
739560 TGATGGATTT
739570 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
739599 TTTAATCAAG
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:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:742120 original size:30 final size:29
Alignment explanation
Indices: 742045--742121 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
742035 TAGATCTAGC
*
742045 AAAACATGAAATTAAATGACTAAAAATGGT
1 AAAACAT-AAATTAAAAGACTAAAAATGGT
* *
742075 AAGAACATAACTTAAAAGACTAAAACA-GTT
1 AA-AACATAAATTAAAAGACTAAAA-ATGGT
*
742105 AAAACATAAATTTAAAG
1 AAAACATAAATTAAAAG
742122 GACATAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 13 0.32
30 21 0.52
31 6 0.15
ACGTcount: A:0.58, C:0.09, G:0.10, T:0.22
Consensus pattern (29 bp):
AAAACATAAATTAAAAGACTAAAAATGGT
Found at i:752932 original size:14 final size:14
Alignment explanation
Indices: 752851--752933 Score: 57
Period size: 14 Copynumber: 6.2 Consensus size: 14
752841 TGGGTCTGGA
*
752851 GAACATAAATGAAC
1 GAACATAAACGAAC
* * *
752865 AAACACAAATGAAC
1 GAACATAAACGAAC
752879 GAACATAAAC--A-
1 GAACATAAACGAAC
* *
752890 -AACTTAAACGAAT
1 GAACATAAACGAAC
* * *
752903 AAACATAAATGGAC
1 GAACATAAACGAAC
752917 GAACATAAACGAAC
1 GAACATAAACGAAC
752931 GAA
1 GAA
752934 TTACCGAACG
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
10 8 0.15
12 2 0.04
14 42 0.81
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.12
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:756632 original size:12 final size:12
Alignment explanation
Indices: 756615--756665 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
756605 TTACCTTTGT
756615 TATTATTATTTA
1 TATTATTATTTA
756627 TATTA-TATTT-
1 TATTATTATTTA
756637 TATTATATATTTCA
1 TATTAT-TATTT-A
* *
756651 TGTCATTATTTA
1 TATTATTATTTA
756663 TAT
1 TAT
756666 ATAGGTATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.16
11 5 0.16
12 13 0.41
13 5 0.16
14 4 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:757167 original size:4 final size:4
Alignment explanation
Indices: 757158--757183 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
757148 ATTTTCTTGG
757158 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
757184 GCTTCTTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:768700 original size:98 final size:98
Alignment explanation
Indices: 768437--769183 Score: 1056
Period size: 98 Copynumber: 7.4 Consensus size: 98
768427 CCCAGAGTTG
768437 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC-AGCGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGG
* *
768501 GACCGCTGGCTGTCAACAGACATTTCTCAATTTCAGAGCCA
65 GACCGCTGGTTGTCAATA-A-A-----CAATTTCAGAGCCA
768542 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
768607 ACCGCTGGTTGTCAATAAACAATTTCAGGGCCA
66 ACCGCTGGTTGTCAATAAACAATTTCAGAGCCA
*
768640 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
768705 ACCGCTGGTTGTCAATAAACAATTTCAGGGCCA
66 ACCGCTGGTTGTCAATAAACAATTTCAGAGCCA
* *
768738 ATTTCAGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
768803 ACCGCTGGTTGTCAATAAACAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAATTTCAGAGCCA
768836 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
768901 ACCGCTGGTTGTCAATAAACAATTTC----CCA
66 ACCGCTGGTTGTCAATAAACAATTTCAGAGCCA
*
768930 ATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
768995 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAAT--A-AA-----CAATTTCAGAGCCA
* * * * *
769036 ATTTCAACTTCACAACGAAGGAGATTGGGC-CCAGACAACACAAGTTCAACTTCACAATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
769100 ACCGCTGGTTGTCAACAAGTAATTTCCCGGTTTTAGAGCCA
66 ACCGCTGGTTGTCAATAAACAATTT--C------AGAGCCA
* * * *
769141 ATTTCAACTTCACAGCGAAGGATATTGGCCTCAAAACAACGCA
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
769184 TCTTGCATTG
Statistics
Matches: 594, Mismatches: 26, Indels: 43
0.90 0.04 0.06
Matches are distributed among these distances:
94 83 0.14
96 1 0.00
97 7 0.01
98 293 0.49
99 1 0.00
102 8 0.01
103 2 0.00
104 1 0.00
105 158 0.27
106 40 0.07
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (98 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAATAAACAATTTCAGAGCCA
Found at i:768899 original size:43 final size:43
Alignment explanation
Indices: 768838--768993 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
768828 CAGAGCCAAT
768838 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
768881 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
*
768932 TTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
768975 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
768994 GACCGCTGGT
Statistics
Matches: 83, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
43 38 0.46
44 3 0.04
45 3 0.04
46 7 0.08
48 7 0.08
49 2 0.02
50 3 0.04
51 20 0.24
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:769688 original size:17 final size:18
Alignment explanation
Indices: 769668--769705 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
769658 TTCATTCATA
769668 TATTACATTTA-TTTATT
1 TATTACATTTATTTTATT
**
769685 TATTATTTTTATTTTATT
1 TATTACATTTATTTTATT
769703 TAT
1 TAT
769706 GCTTCTTCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTACATTTATTTTATT
Found at i:771289 original size:2 final size:2
Alignment explanation
Indices: 771282--771308 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
771272 AGTATTGCAT
771282 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
771309 TTGTGTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:775133 original size:2 final size:2
Alignment explanation
Indices: 775128--775155 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
775118 AATATTGTTA
775128 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
775156 TTAATGGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:776566 original size:18 final size:20
Alignment explanation
Indices: 776526--776566 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
776516 AGATACGTGG
776526 TAATATTAATAATTTTTGCAA
1 TAATATTAATAATTTTT-CAA
776547 TAATATTAA-AATTTTT-AA
1 TAATATTAATAATTTTTCAA
776565 TA
1 TA
776567 TTAATTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATATTAATAATTTTTCAA
Found at i:777918 original size:82 final size:82
Alignment explanation
Indices: 777778--778387 Score: 760
Period size: 82 Copynumber: 7.3 Consensus size: 82
777768 TAACTTTGAA
* ** *
777778 AAGCAAAGGATGTGAATATTGTAGATTCTATGATT-TCAATGGAAATTATTTCAGTTTATCTGAG
1 AAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTC--T--AAAATATTTCAGTTTATCTGAG
777842 TTGATGTGAAATATCAATGAC
62 TTGATGTGAAATATCAATGAC
* * *
777863 AAGCAAAGGATGTGAATAGTGTAAATTCCCTTATTCTCTAAAATATTTTAGTTTATCTGAGTTGA
1 AAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAGTTTATCTGAGTTGA
777928 TGTGAAATATCAATGAC
66 TGTGAAATATCAATGAC
* * * * * * * * *
777945 AAGTAAAAGACGTGAATAATATAGATTCTCTTATT-TCAATGGAAATTATTTCAGTTTATCTTAG
1 AAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTC--T--AAAATATTTCAGTTTATCTGAG
778009 TTGATGTGAAATATCAATGAC
62 TTGATGTGAAATATCAATGAC
* *
778030 AAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAATTTATCTGAGTTGA
1 AAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAGTTTATCTGAGTTGA
* * *
778095 TGTGAAATGTTAATGAT
66 TGTGAAATATCAATGAC
* *
778112 AAGCAAAGGATGTGAATAGTGTAGATTCTCTGATT-TCAAAGGAAATTATTTCAGTTTATCTGAG
1 AAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTC-TA--AAA-TATTTCAGTTTATCTGAG
778176 TTGATGTGAAATATCAATGAC
62 TTGATGTGAAATATCAATGAC
* * * * * *
778197 AAACAAATGATATGAATAGTGTAGATTCCATGATTCTCTAAAATATTTCAATTTATCTTAGTTGA
1 AAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAGTTTATCTGAGTTGA
*
778262 TGTGAAATGTCAATGAC
66 TGTGAAATATCAATGAC
* * *
778279 AAACAAATGG-TGTGAATAGTGTAGATTCCCTGATTCTCTACAATATTTCAGTTAATCTGAGTTG
1 AAGCAAA-GGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAGTTTATCTGAGTTG
*
778343 ATGTGAAATGTCAATGAC
65 ATGTGAAATATCAATGAC
*
778361 AAGCAAATGATGTGAATAGTGTAGATT
1 AAGCAAAGGATGTGAATAGTGTAGATT
778388 GTCTACAAGG
Statistics
Matches: 457, Mismatches: 55, Indels: 29
0.84 0.10 0.05
Matches are distributed among these distances:
81 5 0.01
82 272 0.60
83 5 0.01
84 5 0.01
85 164 0.36
86 6 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (82 bp):
AAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAGTTTATCTGAGTTGA
TGTGAAATATCAATGAC
Found at i:778068 original size:167 final size:167
Alignment explanation
Indices: 777778--778387 Score: 906
Period size: 167 Copynumber: 3.7 Consensus size: 167
777768 TAACTTTGAA
* * *
777778 AAGCAAAGGATGTGAATATTGTAGATTCTATGATTTCAATGGAAATTATTTCAGTTTATCTGAGT
1 AAGCAAAAGATGTGAATAGTGTAGATTCTCTGATTTCAATGGAAATTATTTCAGTTTATCTGAGT
* * *
777843 TGATGTGAAATATCAATGACAAGCAAAGGATGTGAATAGTGTAAATTCCCTTATTCTCTAAAATA
66 TGATGTGAAATATCAATGACAAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATA
* * *
777908 TTTTAGTTTATCTGAGTTGATGTGAAATATCAATGAC
131 TTTCAATTTATCTGAGTTGATGTGAAATGTCAATGAC
* * * * * *
777945 AAGTAAAAGACGTGAATAATATAGATTCTCTTATTTCAATGGAAATTATTTCAGTTTATCTTAGT
1 AAGCAAAAGATGTGAATAGTGTAGATTCTCTGATTTCAATGGAAATTATTTCAGTTTATCTGAGT
778010 TGATGTGAAATATCAATGACAAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATA
66 TGATGTGAAATATCAATGACAAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATA
* *
778075 TTTCAATTTATCTGAGTTGATGTGAAATGTTAATGAT
131 TTTCAATTTATCTGAGTTGATGTGAAATGTCAATGAC
* *
778112 AAGCAAAGGATGTGAATAGTGTAGATTCTCTGATTTCAAAGGAAATTATTTCAGTTTATCTGAGT
1 AAGCAAAAGATGTGAATAGTGTAGATTCTCTGATTTCAATGGAAATTATTTCAGTTTATCTGAGT
* * *
778177 TGATGTGAAATATCAATGACAAACAAATGATATGAATAGTGTAGATTCCATGATTCTCTAAAATA
66 TGATGTGAAATATCAATGACAAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATA
*
778242 TTTCAATTTATCTTAGTTGATGTGAAATGTCAATGAC
131 TTTCAATTTATCTGAGTTGATGTGAAATGTCAATGAC
* * * * *
778279 AAACAAATGGTGTGAATAGTGTAGATTCCCTGATTCTC--T--ACAA-TATTTCAGTTAATCTGA
1 AAGCAAAAGATGTGAATAGTGTAGATTCTCTGATT-TCAATGGA-AATTATTTCAGTTTATCTGA
*
778339 GTTGATGTGAAATGTCAATGACAAGCAAATGATGTGAATAGTGTAGATT
64 GTTGATGTGAAATATCAATGACAAGCAAATGATGTGAATAGTGTAGATT
778388 GTCTACAAGG
Statistics
Matches: 402, Mismatches: 39, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
164 63 0.16
165 2 0.00
167 335 0.83
168 2 0.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (167 bp):
AAGCAAAAGATGTGAATAGTGTAGATTCTCTGATTTCAATGGAAATTATTTCAGTTTATCTGAGT
TGATGTGAAATATCAATGACAAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATA
TTTCAATTTATCTGAGTTGATGTGAAATGTCAATGAC
Found at i:778256 original size:249 final size:247
Alignment explanation
Indices: 777778--778387 Score: 807
Period size: 249 Copynumber: 2.4 Consensus size: 247
777768 TAACTTTGAA
* * ** *
777778 AAGCAAAGGATGTGAATATTGTAGATTCTATGATT-TCAATGGAAATTATTTCAGTTTATCTGAG
1 AAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTC--T--AAAATATTTCAGTTTATCTGAG
* * * *
777842 TTGATGTGAAATATCAATGACAAGCAAAGGATGTGAATAGTGTAAATTCCCTTATTCTCTAAAAT
62 TTGATGTGAAATGTCAATGACAAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTCAAAAAT
* ** *
777907 ATTTTAGTTTATCTGAGTTGATGTGAAATATCAATGACAAGTAAAAGACGTGAATAATATAGATT
127 ATTTCAGTTTATCTGAGTTGATGTGAAATATCAATGACAAACAAAAGACATGAATAATATAGATT
* * *
777972 CTCTTATTTCAATGGAAATTATTTCAGTTTATCTTAGTTGATGTGAAATATCAATGAC
192 CTCTGATTTC-AT-GAAAATATTTCAATTTATCTTAGTTGATGTGAAATATCAATGAC
*
778030 AAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAATTTATCTGAGTTGA
1 AAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAGTTTATCTGAGTTGA
* * *
778095 TGTGAAATGTTAATGATAAGCAAAGGATGTGAATAGTGTAGATTCTCTGATT-TCAAAGGAAATT
66 TGTGAAATGTCAATGACAAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTC-AA--AAA-T
* * * *
778159 ATTTCAGTTTATCTGAGTTGATGTGAAATATCAATGACAAACAAATGATATGAATAGTGTAGATT
127 ATTTCAGTTTATCTGAGTTGATGTGAAATATCAATGACAAACAAAAGACATGAATAATATAGATT
*
778224 C-CATGATTCTC-T-AAAATATTTCAATTTATCTTAGTTGATGTGAAATGTCAATGAC
192 CTC-TGATT-TCATGAAAATATTTCAATTTATCTTAGTTGATGTGAAATATCAATGAC
* * * *
778279 AAACAAATGGTGTGAATAGTGTAGATTCCCTGATTCTCTACAATATTTCAGTTAATCTGAGTTGA
1 AAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAGTTTATCTGAGTTGA
*
778344 TGTGAAATGTCAATGACAAGCAAATGATGTGAATAGTGTAGATT
66 TGTGAAATGTCAATGACAAGCAAAGGATGTGAATAGTGTAGATT
778388 GTCTACAAGG
Statistics
Matches: 318, Mismatches: 33, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
248 2 0.01
249 212 0.67
251 6 0.02
252 94 0.30
253 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (247 bp):
AAGCAAATGATGTGAATAGTGTAGATTCCCTGATTCTCTAAAATATTTCAGTTTATCTGAGTTGA
TGTGAAATGTCAATGACAAGCAAAGGATGTGAATAGTGTAGATTCCCTGATTCTCAAAAATATTT
CAGTTTATCTGAGTTGATGTGAAATATCAATGACAAACAAAAGACATGAATAATATAGATTCTCT
GATTTCATGAAAATATTTCAATTTATCTTAGTTGATGTGAAATATCAATGAC
Found at i:781552 original size:24 final size:24
Alignment explanation
Indices: 781525--781584 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
781515 TTCTCTTTTG
*
781525 TCTTATTCTTCTCTTCCATTTTCA
1 TCTTCTTCTTCTCTTCCATTTTCA
781549 TCTTCTTCTTCTCTTCCATTTTCA
1 TCTTCTTCTTCTCTTCCATTTTCA
781573 TCTTCTTCTTCT
1 TCTTCTTCTTCT
781585 TATGCTCCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (24 bp):
TCTTCTTCTTCTCTTCCATTTTCA
Found at i:785148 original size:190 final size:190
Alignment explanation
Indices: 784825--785205 Score: 762
Period size: 190 Copynumber: 2.0 Consensus size: 190
784815 CAACGGCGCC
784825 CGCAACTATCCGGCTTCGGGTAGCTCCTGTCTCCTCCCAATCATACTTAACCCCAACGAAAACCG
1 CGCAACTATCCGGCTTCGGGTAGCTCCTGTCTCCTCCCAATCATACTTAACCCCAACGAAAACCG
784890 CCGAGTGATTCCGGCGGAGGTTTTGGTATGCGGAGGAACGGCGCACGACGCGTACCCAAAGGCCG
66 CCGAGTGATTCCGGCGGAGGTTTTGGTATGCGGAGGAACGGCGCACGACGCGTACCCAAAGGCCG
784955 AAAAACTGCGGCCCAAGGTGTTCGTCCCGGGGAACACCGATTGTGCCCGCATGGATATCA
131 AAAAACTGCGGCCCAAGGTGTTCGTCCCGGGGAACACCGATTGTGCCCGCATGGATATCA
785015 CGCAACTATCCGGCTTCGGGTAGCTCCTGTCTCCTCCCAATCATACTTAACCCCAACGAAAACCG
1 CGCAACTATCCGGCTTCGGGTAGCTCCTGTCTCCTCCCAATCATACTTAACCCCAACGAAAACCG
785080 CCGAGTGATTCCGGCGGAGGTTTTGGTATGCGGAGGAACGGCGCACGACGCGTACCCAAAGGCCG
66 CCGAGTGATTCCGGCGGAGGTTTTGGTATGCGGAGGAACGGCGCACGACGCGTACCCAAAGGCCG
785145 AAAAACTGCGGCCCAAGGTGTTCGTCCCGGGGAACACCGATTGTGCCCGCATGGATATCA
131 AAAAACTGCGGCCCAAGGTGTTCGTCCCGGGGAACACCGATTGTGCCCGCATGGATATCA
785205 C
1 C
785206 CAAGAGAAAT
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 191 1.00
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.18
Consensus pattern (190 bp):
CGCAACTATCCGGCTTCGGGTAGCTCCTGTCTCCTCCCAATCATACTTAACCCCAACGAAAACCG
CCGAGTGATTCCGGCGGAGGTTTTGGTATGCGGAGGAACGGCGCACGACGCGTACCCAAAGGCCG
AAAAACTGCGGCCCAAGGTGTTCGTCCCGGGGAACACCGATTGTGCCCGCATGGATATCA
Found at i:786919 original size:25 final size:25
Alignment explanation
Indices: 786891--786946 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
786881 ATATTATTTC
786891 TTCTTCTTCTTCTCCAGGTTACTTT
1 TTCTTCTTCTTCTCCAGGTTACTTT
786916 TTCTTCTTCTTCTCCAGGTTACTTT
1 TTCTTCTTCTTCTCCAGGTTACTTT
786941 TTCTTC
1 TTCTTC
786947 CTCCTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.07, C:0.29, G:0.07, T:0.57
Consensus pattern (25 bp):
TTCTTCTTCTTCTCCAGGTTACTTT
Found at i:788073 original size:19 final size:19
Alignment explanation
Indices: 788049--788098 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
788039 AAAAAAAGGA
788049 GGAGAAGAAGAAATAACCT
1 GGAGAAGAAGAAATAACCT
788068 GGAGAAGAAGAAATAACCT
1 GGAGAAGAAGAAATAACCT
*
788087 GAAGAAGAAGAA
1 GGAGAAGAAGAA
788099 GGGGTGGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (19 bp):
GGAGAAGAAGAAATAACCT
Found at i:788589 original size:19 final size:18
Alignment explanation
Indices: 788560--788600 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
788550 GCTCTCATCT
788560 TTATTATAAATCAATTTA
1 TTATTATAAATCAATTTA
*
788578 TTATTCATAAATCATTTTA
1 TTATT-ATAAATCAATTTA
788597 TTAT
1 TTAT
788601 AAAGCCCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTATAAATCAATTTA
Found at i:788965 original size:18 final size:17
Alignment explanation
Indices: 788944--788977 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
788934 TAGTGAGTTG
788944 TTATAAAATATATTTTTA
1 TTAT-AAATATATTTTTA
*
788962 TTATAATTATATTTTT
1 TTATAAATATATTTTT
788978 TATTTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATAAATATATTTTTA
Found at i:788978 original size:18 final size:18
Alignment explanation
Indices: 788951--788998 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
788941 TTGTTATAAA
788951 ATATATTTTTATTATAA-TT
1 ATAT-TTTTTATT-TAATTT
788970 ATATTTTTTATTTAATTT
1 ATATTTTTTATTTAATTT
*
788988 GTATTTTTTAT
1 ATATTTTTTAT
788999 ATTTGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.11
18 20 0.74
19 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
ATATTTTTTATTTAATTT
Found at i:789004 original size:15 final size:15
Alignment explanation
Indices: 788952--789009 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
788942 TGTTATAAAA
*
788952 TATATTTTTATTATAAT
1 TATATTTGTATTAT--T
788969 TATATTT-T-TTATT
1 TATATTTGTATTATT
*
788982 TA-ATTTGTATTTTT
1 TATATTTGTATTATT
788996 TATATTTGTATTAT
1 TATATTTGTATTAT
789010 AGTTTAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 4 0.11
13 4 0.11
14 6 0.17
15 14 0.39
16 1 0.03
17 7 0.19
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TATATTTGTATTATT
Found at i:789156 original size:59 final size:59
Alignment explanation
Indices: 789085--789217 Score: 151
Period size: 59 Copynumber: 2.3 Consensus size: 59
789075 ATGTTATTTT
* * * *
789085 AAATTTTAAATGAGTGATTGTGGTTAAATTAGAATAATTAAAATATTATCATAAAATTC
1 AAATATTAAATGAGTGATTGTAGTTAAATCAAAATAATTAAAATATTATCATAAAATTC
* * * * * * *
789144 -AATCGTTAAATGAATGATTTTAGTTCAATCAAAATAATTAAAATATTTTCTTAATATTC
1 AAAT-ATTAAATGAGTGATTGTAGTTAAATCAAAATAATTAAAATATTATCATAAAATTC
789203 AAATATTAAATGAGT
1 AAATATTAAATGAGT
789218 TATCTTAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
58 3 0.05
59 54 0.90
60 3 0.05
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (59 bp):
AAATATTAAATGAGTGATTGTAGTTAAATCAAAATAATTAAAATATTATCATAAAATTC
Found at i:790031 original size:15 final size:15
Alignment explanation
Indices: 790011--790077 Score: 89
Period size: 15 Copynumber: 4.5 Consensus size: 15
790001 TGAGACATTA
*
790011 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
*
790026 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
* *
790041 CCCGCCCCACATTCT
1 CCCGCCCCACATCCG
790056 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
*
790071 CCTGCCC
1 CCCGCCC
790078 AGCTAAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.09, C:0.66, G:0.15, T:0.10
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:791461 original size:41 final size:41
Alignment explanation
Indices: 791380--791462 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
791370 ATAACCCATA
* *
791380 ATTGGTTATTTTTTCATCCTTAGTAAAAAGAGAACGACATT
1 ATTGATTATTTTTTCATCCTTAGTAAAAAGACAACGACATT
* *
791421 ATTGATTATTTTTTCATCCTTAGTAAAAATACAACTACATT
1 ATTGATTATTTTTTCATCCTTAGTAAAAAGACAACGACATT
791462 A
1 A
791463 GCTTTGATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (41 bp):
ATTGATTATTTTTTCATCCTTAGTAAAAAGACAACGACATT
Found at i:791551 original size:27 final size:25
Alignment explanation
Indices: 791490--791554 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
791480 CGTCACTATT
* *
791490 ATCTTAATTTTTTCTTTATTTTTTT
1 ATCTTATTTTTTTCTTTATTTTTTA
*
791515 ATCATGTATTTTTTTCTTTGTTTTTAATA
1 ATC-T-TATTTTTTTCTTTATTTTT--TA
791544 ATCTTATTTTT
1 ATCTTATTTTT
791555 ATGGTATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.09
26 1 0.03
27 24 0.73
28 1 0.03
29 4 0.12
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (25 bp):
ATCTTATTTTTTTCTTTATTTTTTA
Done.