Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008049.1 Hibiscus syriacus cultivar Beakdansim tig00110542_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: 95889
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6477 original size:9 final size:9
Alignment explanation
Indices: 6463--6492 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
6453 TGATCAAAGA
6463 ATTTAATTT
1 ATTTAATTT
6472 ATTTAATTT
1 ATTTAATTT
6481 ATTTAATTT
1 ATTTAATTT
6490 ATT
1 ATT
6493 GTTCGATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTAATTT
Found at i:14607 original size:15 final size:14
Alignment explanation
Indices: 14587--14624 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
14577 GCCTGACCCA
14587 ATAATTTAAATATAT
1 ATAATTTAAATAT-T
14602 ATAATTTAAA-ATT
1 ATAATTTAAATATT
14615 A-AATTTAAAT
1 ATAATTTAAAT
14625 CTGTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.36
13 2 0.09
14 2 0.09
15 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAATTTAAATATT
Found at i:17176 original size:95 final size:93
Alignment explanation
Indices: 16982--17176 Score: 245
Period size: 95 Copynumber: 2.1 Consensus size: 93
16972 TTTTGTCAAT
*
16982 TTGATATTGGCTACATTAGCTTATGGTTTGTACGGGTATGCTATCAACATATCCTTACTGGTTGT
1 TTGATATTGGCTACATTAGCTTATGGTTTATACGGGTATGCTATCAACATATCCTTACTGGTTGT
* *
17047 AGCATGAAAGCAAAAATTATCCTACTCGAT
66 AGCACGAAAGCAAAAATTA--CTACTCGAC
* *
17077 TTGATATTGGCTACGTTAGCTTATGGTTTATACGGGTATGTTATCGAACATGGTTATCCTTACTG
1 TTGATATTGGCTACATTAGCTTATGGTTTATACGGGTATGCTATC-AACA----TATCCTTACTG
17142 GTTGTAGCACGAAAG-AAAAAGTTA-T-C-CGAC
61 GTTGTAGCACGAAAGCAAAAA-TTACTACTCGAC
17172 TTGAT
1 TTGAT
17177 TTTTCTCCAG
Statistics
Matches: 89, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
95 50 0.56
96 5 0.06
97 1 0.01
99 5 0.06
100 28 0.31
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (93 bp):
TTGATATTGGCTACATTAGCTTATGGTTTATACGGGTATGCTATCAACATATCCTTACTGGTTGT
AGCACGAAAGCAAAAATTACTACTCGAC
Found at i:26253 original size:39 final size:39
Alignment explanation
Indices: 26210--26331 Score: 217
Period size: 39 Copynumber: 3.1 Consensus size: 39
26200 CATGCTTCCG
*
26210 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCC
1 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
26249 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
1 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
* *
26288 CAGCAAATGCCAGCAGGCCAGATGGGTTCAATGTACCCT
1 CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
26327 CAGCA
1 CAGCA
26332 GCAGATTTAC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.27, C:0.30, G:0.29, T:0.15
Consensus pattern (39 bp):
CAGCAAATGCCAGCGGGCCAGATGGGTGCAATGTACCCT
Found at i:28876 original size:163 final size:165
Alignment explanation
Indices: 28644--28955 Score: 448
Period size: 167 Copynumber: 1.9 Consensus size: 165
28634 TTCGGATATG
** * *
28644 AAACAGTTTTCTTTTAGAATTGAATATACTTGTGTCTAGAGACATACTTGTATTCAATATTCTCC
1 AAACAGTTTTCTTTTAGAATTGAATATACTCATGTCTAGAGACATACTTATATTCAATATTCACC
* * *
28709 TTTGAATCCTGGG-TACATTGTTGTTTTGATTTTTTCTTAATTATGTAGCCTTCTTTAGTATAGG
66 TTTGAATCCTGGGATACATTGTTGTTTTGATATTGTCTGAATTATGTAGCCTTCTTTAGTATAGG
*
28773 GACCGTCGGAGACACCGATCGAAGGCGCAGAAATA
131 GACCATCGGAGACACCGATCGAAGGCGCAGAAATA
** * * *
28808 AAACAGTTTT-TTTTTTAATTGAATATACTCATGTCTAGATACTTACTTATATTCGATATTCACC
1 AAACAGTTTTCTTTTAGAATTGAATATACTCATGTCTAGAGACATACTTATATTCAATATTCACC
*
28872 TTTGAATCCTGGGTACATACATTGTTGTTTTGATATTGTCTGAATTATGTAGCCTTCTTTTGTAT
66 TTTGAATCCTGGG---ATACATTGTTGTTTTGATATTGTCTGAATTATGTAGCCTTCTTTAGTAT
*
28937 AGGGACCATCTGAGACACC
128 AGGGACCATCGGAGACACC
28956 TTACGAAGGC
Statistics
Matches: 129, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
163 58 0.45
164 10 0.08
167 61 0.47
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (165 bp):
AAACAGTTTTCTTTTAGAATTGAATATACTCATGTCTAGAGACATACTTATATTCAATATTCACC
TTTGAATCCTGGGATACATTGTTGTTTTGATATTGTCTGAATTATGTAGCCTTCTTTAGTATAGG
GACCATCGGAGACACCGATCGAAGGCGCAGAAATA
Found at i:33609 original size:30 final size:30
Alignment explanation
Indices: 33575--33635 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
33565 ATTCTACAAG
33575 TAAAGACTTCAACTTTTTATTTATTTATTT
1 TAAAGACTTCAACTTTTTATTTATTTATTT
33605 TAAAGACTTCAACTTTTTATTTATTTATTT
1 TAAAGACTTCAACTTTTTATTTATTTATTT
33635 T
1 T
33636 CACACCCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (30 bp):
TAAAGACTTCAACTTTTTATTTATTTATTT
Found at i:42067 original size:2 final size:2
Alignment explanation
Indices: 42060--42088 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42050 TCAGCTGTAA
42060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42089 GTATTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43966 original size:2 final size:2
Alignment explanation
Indices: 43959--43993 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43949 ATGAATCCTA
43959 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 A
43994 ATTGTCGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44122 original size:2 final size:2
Alignment explanation
Indices: 44115--44143 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44105 TGTGTCCTAT
44115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44144 TCTTTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44629 original size:59 final size:59
Alignment explanation
Indices: 44496--44632 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 59
44486 CTTCATTTTA
* * * *
44496 AATTGATCCTTAAACTTTTAAAATTTTAATTTCATCCCTAAAATATTATCCTCGTTCTG
1 AATTGATCCTTAAACTTTTAAAATTCTAATTTCATCCCTAAAATATGATCCTCATTCAG
* * * * *
44555 CATTAATTCTTAAACTTTTAAACATTCTAATTTCATCCC-AAACTATGA-CTTTCATTCAG
1 AATTGATCCTTAAACTTTTAAA-ATTCTAATTTCATCCCTAAAATATGATC-CTCATTCAG
*
44614 AATTGATCCTCAAACTTTT
1 AATTGATCCTTAAACTTTT
44633 GAATCTTCCG
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
58 1 0.02
59 47 0.75
60 15 0.24
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.42
Consensus pattern (59 bp):
AATTGATCCTTAAACTTTTAAAATTCTAATTTCATCCCTAAAATATGATCCTCATTCAG
Found at i:47661 original size:13 final size:14
Alignment explanation
Indices: 47643--47677 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
47633 TCTATATCTT
*
47643 ACCCTAACTTA-AA
1 ACCCTAAATTATAA
47656 ACCCTAAATTATAA
1 ACCCTAAATTATAA
47670 ACCCTAAA
1 ACCCTAAA
47678 GTAGGGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (14 bp):
ACCCTAAATTATAA
Found at i:56769 original size:140 final size:139
Alignment explanation
Indices: 56548--56824 Score: 412
Period size: 140 Copynumber: 2.0 Consensus size: 139
56538 TTTCTATAGT
* * *
56548 AAACCCAATTTATTATTTCCTTCCTTATTATATTGTCGTATTAATTTAGTCTTGGAAGTTATTCA
1 AAACCCAATTTATTATTTCCATCCCTATTATATTGTCGCATTAATTTAGTCTTGGAAGTTATTCA
* * *
56613 ATTGCATCACTTTAGATCCTACCCCTAACTTAAAAC-CTAAAATTATATATCATAAACCCTAAAC
66 ATTGCATCACTCTAGATCATACCCCTAACTTAAAACTC-AAAATTATAAATCATAAACCCTAAAC
*
56677 CCTAAACTTA
130 CATAAACTTA
* * *
56687 AAACCCTAATTTATTATTTTCATCCCTATTATATTTTCGCATTAATTTAGTCTTTGAAGTTATTC
1 AAACCC-AATTTATTATTTCCATCCCTATTATATTGTCGCATTAATTTAGTCTTGGAAGTTATTC
* * *
56752 AATTGCATCACTCTAGATCATATCCCTAACTTAAAACTCAAAATTATAAATCATAAACCTTAAAT
65 AATTGCATCACTCTAGATCATACCCCTAACTTAAAACTCAAAATTATAAATCATAAACCCTAAAC
56817 CATAAACT
130 CATAAACT
56825 CATAAACCTT
Statistics
Matches: 123, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
139 6 0.05
140 116 0.94
141 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.39
Consensus pattern (139 bp):
AAACCCAATTTATTATTTCCATCCCTATTATATTGTCGCATTAATTTAGTCTTGGAAGTTATTCA
ATTGCATCACTCTAGATCATACCCCTAACTTAAAACTCAAAATTATAAATCATAAACCCTAAACC
ATAAACTTA
Found at i:59560 original size:179 final size:179
Alignment explanation
Indices: 59260--59610 Score: 639
Period size: 179 Copynumber: 2.0 Consensus size: 179
59250 ATACCTGAAA
* *
59260 TTTAGTTTTTGTTTCATTTTAGTACAACCAAAGCATATCTTATTGTTTTGAACGATTATTTTAAT
1 TTTAGTTTTTGTTTCATTTTAGTACAACAAAAGCATATCTTATTGTTTTGAACGATTAATTTAAT
*
59325 ATTACATTAATAAATCATAGAAAATAATTAAATCCGGGGCTTAAATTTTAAAAAGTAAAAAGTAT
66 ATTACATTAATAAATCATAGAAAATAATTAAATCCGGGGCTTAAATTTTAAAAAGTAAAAAGTAG
*
59390 GATTGAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGCATGGAG
131 GATTAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGCATGGAG
*
59439 TTTAGTTTTTGTTTCATTTTAGTACAACAAAAGTATATCTTATTGTTTTGAACGATTAATTTAAT
1 TTTAGTTTTTGTTTCATTTTAGTACAACAAAAGCATATCTTATTGTTTTGAACGATTAATTTAAT
* *
59504 ATTATATTAATAAATCATAGAAAATAATTAAATTCGGGGCTTAAATTTTAAAAAGTAAAAAGTAG
66 ATTACATTAATAAATCATAGAAAATAATTAAATCCGGGGCTTAAATTTTAAAAAGTAAAAAGTAG
59569 GATTAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTG
131 GATTAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTG
59611 AGATTAAAAA
Statistics
Matches: 165, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
179 165 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (179 bp):
TTTAGTTTTTGTTTCATTTTAGTACAACAAAAGCATATCTTATTGTTTTGAACGATTAATTTAAT
ATTACATTAATAAATCATAGAAAATAATTAAATCCGGGGCTTAAATTTTAAAAAGTAAAAAGTAG
GATTAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGCATGGAG
Found at i:59621 original size:44 final size:43
Alignment explanation
Indices: 59558--60028 Score: 317
Period size: 43 Copynumber: 11.0 Consensus size: 43
59548 ATTTTAAAAA
*
59558 GTAAAAAGT-AGGATTAAAAAAATTAGGGGCCTCAATTATAAAG
1 GTAAAAAGTGA-GATTAAAAAAATTAAGGGCCTCAATTATAAAG
* *
59601 GTAAAAAGTGAGATT-AAAAAATT-AGAGGACTCAATTTTAAAG
1 GTAAAAAGTGAGATTAAAAAAATTAAG-GGCCTCAATTATAAAG
* * * *
59643 G-AAAATGTG-GTATT-GAAAAATT-AGGGAGCT-ACATTGTATAA-
1 GTAAAAAGTGAG-ATTAAAAAAATTAAGGG-CCTCA-ATTATA-AAG
* * * **
59684 GTAAAAGGTG-GTATTGAAAAAATTAGGGGCCTCAATTATAATT
1 GTAAAAAGTGAG-ATTAAAAAAATTAAGGGCCTCAATTATAAAG
* * * *
59727 ATTACAAGTGAGATTAAAAAAATTAAGGGCCTCAATTGTAAAG
1 GTAAAAAGTGAGATTAAAAAAATTAAGGGCCTCAATTATAAAG
* *
59770 GTAAAAAGTGAGATTGCAAAAAA-TAAGAG-CTCAATTATAAAG
1 GTAAAAAGTGAGATT-AAAAAAATTAAGGGCCTCAATTATAAAG
* * * * *
59812 ATAAAAAGTGGGATTGAAAAAAATTAA-GGCAATCAATTATATAT
1 GTAAAAAGTGAGATT-AAAAAAATTAAGGGC-CTCAATTATAAAG
*
59856 GTAAAAAAGTGAGATTAAAAAAATTAAGAGCCTCAATTATAAA-
1 GT-AAAAAGTGAGATTAAAAAAATTAAGGGCCTCAATTATAAAG
* * * **
59899 G-ACAAAAGATCAAATAAAAAAAATTTAAGGTACTCAATTATAAAG
1 GTA-AAAAG-TGAGATTAAAAAAA-TTAAGGGCCTCAATTATAAAG
* * * * *
59944 ATAAAAAGTAAAATTAAAAAAATT-AGAGCCTTCTATTATAAAG
1 GTAAAAAGTGAGATTAAAAAAATTAAGGGCC-TCAATTATAAAG
** * * ** * *
59987 AAAAAAAGTTAAATGGAAAAAATTAAAGGACTCAATTATAAA
1 GTAAAAAGTGAGATTAAAAAAATTAAGGGCCTCAATTATAAA
60029 AATAAAAAAT
Statistics
Matches: 342, Mismatches: 61, Indels: 50
0.75 0.13 0.11
Matches are distributed among these distances:
40 4 0.01
41 29 0.08
42 79 0.23
43 134 0.39
44 76 0.22
45 19 0.06
46 1 0.00
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (43 bp):
GTAAAAAGTGAGATTAAAAAAATTAAGGGCCTCAATTATAAAG
Found at i:60007 original size:87 final size:85
Alignment explanation
Indices: 59573--60036 Score: 288
Period size: 87 Copynumber: 5.4 Consensus size: 85
59563 AAGTAGGATT
* * * *
59573 AAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGAGGACTCAATT
1 AAAAAAATTA-AGGACTCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTAGA-GCCTCAATT
* * * *** *
59637 TTAAAG-GAAAATGTGGTATTG
64 ATAAAGAAAAAAAGTCAAATAG
* * * * *
59658 --AAAAATTAGGGAGCT-ACATTGTATAAG-TAAAAGGTG-GTATTGAAAAAATTAGGGGCCTCA
1 AAAAAAATTAAGGA-CTCA-ATTATA-AAGATAAAAAGTGAG-ATTAAAAAAATTA-GAGCCTCA
** ** * * * *
59718 ATTATAATTATTACAAGTGAGAT-T
61 ATTATAAAGAAAAAAAGTCAAATAG
* * * * *
59742 AAAAAAATTAAGGGCCTCAATTGTAAAGGTAAAAAGTGAGATTGCAAAAAATAAGAG-CTCAATT
1 AAAAAAATTAA-GGACTCAATTATAAAGATAAAAAGTGAGATT-AAAAAAATTAGAGCCTCAATT
* *** *
59806 ATAAAGATAAAAAGTGGGATTG
64 ATAAAGAAAAAAAGTCAAATAG
* *
59828 AAAAAAATTAAGGCAATCAATTATATATG-TAAAAAAGTGAGATTAAAAAAATTAAGAGCCTCAA
1 AAAAAAATTAAGG-ACTCAATTATA-AAGAT-AAAAAGTGAGATTAAAAAAATT-AGAGCCTCAA
*
59892 TTATAAAG-ACAAAAGATCAAATA-
62 TTATAAAGAAAAAAAG-TCAAATAG
* * *
59915 AAAAAAATTTAAGGTACTCAATTATAAAGATAAAAAGTAAAATTAAAAAAATTAGAGCCTTCTAT
1 AAAAAAA-TTAAGG-ACTCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTAGAGCC-TCAAT
*
59980 TATAAAGAAAAAAAGTTAAAT-G
63 TATAAAGAAAAAAAGTCAAATAG
* *
60002 GAAAAAATTAAAGGACTCAATTATAAAAATAAAAA
1 AAAAAAATT-AAGGACTCAATTATAAAGATAAAAA
60037 ATTAGGAGTA
Statistics
Matches: 303, Mismatches: 49, Indels: 53
0.75 0.12 0.13
Matches are distributed among these distances:
82 5 0.02
83 26 0.09
84 23 0.08
85 35 0.12
86 84 0.28
87 91 0.30
88 39 0.13
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (85 bp):
AAAAAAATTAAGGACTCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTAGAGCCTCAATTAT
AAAGAAAAAAAGTCAAATAG
Found at i:60037 original size:44 final size:43
Alignment explanation
Indices: 59739--60037 Score: 211
Period size: 44 Copynumber: 6.9 Consensus size: 43
59729 TACAAGTGAG
* * * * *
59739 ATTAAAAAAATTAAGGGCCTCAATTGTAAAGGT-AAAAAGTGAG
1 ATTAAAAAAATTAA-GGACTCAATTATAAAGATAAAAAAGTAAA
* ***
59782 ATTGCAAAAAA-TAA-GAGCTCAATTATAAAGAT-AAAAAGTGGG
1 ATT-AAAAAAATTAAGGA-CTCAATTATAAAGATAAAAAAGTAAA
* * * *
59824 ATTGAAAAAAATTAAGGCAATCAATTATATATG-TAAAAAAGTGAG
1 ATT-AAAAAAATTAAGG-ACTCAATTATA-AAGATAAAAAAGTAAA
* * * *
59869 ATTAAAAAAATTAAGAGCCTCAATTATAAAGACAAAAGA-TCAA
1 ATTAAAAAAATTAAG-GACTCAATTATAAAGATAAAAAAGTAAA
*
59912 ATAAAAAAAATTTAAGGTACTCAATTATAAAGAT-AAAAAGTAAA
1 ATTAAAAAAA-TTAAGG-ACTCAATTATAAAGATAAAAAAGTAAA
* * *
59956 ATTAAAAAAATT-AGAGCCTTCTATTATAAAGA-AAAAAAGTTAA
1 ATTAAAAAAATTAAG-GAC-TCAATTATAAAGATAAAAAAGTAAA
** *
59999 ATGGAAAAAATTAAAGGACTCAATTATAAAAATAAAAAA
1 ATTAAAAAAATT-AAGGACTCAATTATAAAGATAAAAAA
60038 TTAGGAGTAC
Statistics
Matches: 208, Mismatches: 30, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
41 1 0.00
42 35 0.17
43 72 0.35
44 82 0.39
45 18 0.09
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (43 bp):
ATTAAAAAAATTAAGGACTCAATTATAAAGATAAAAAAGTAAA
Found at i:62650 original size:61 final size:61
Alignment explanation
Indices: 62585--62723 Score: 158
Period size: 61 Copynumber: 2.3 Consensus size: 61
62575 GTCCCCGAAT
* * * *
62585 TATGACTTTCATT-TCAAATTAGTCCTTAAACTTTTAAATATTCTG-ATTTCATCCCCCATAC
1 TATGACTCTCATTCT-AAAGTAGTCCTTAAACTCTTAAACATT-TGAATTTCATCCCCCATAC
* *
62646 TATGACTCTCATTCTAAAGTAGTCCTTAAACTCTTGAACATTTGAATTTCAT-CCCCAAAC
1 TATGACTCTCATTCTAAAGTAGTCCTTAAACTCTTAAACATTTGAATTTCATCCCCCATAC
* * *
62706 TACGAATATCATTCTAAA
1 TATGACTCTCATTCTAAA
62724 TTGGTCCATG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
60 24 0.36
61 42 0.63
62 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.38
Consensus pattern (61 bp):
TATGACTCTCATTCTAAAGTAGTCCTTAAACTCTTAAACATTTGAATTTCATCCCCCATAC
Found at i:67591 original size:4 final size:4
Alignment explanation
Indices: 67575--67611 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
67565 AAGCTCCAAG
*
67575 ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
67612 TTACATGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:71257 original size:20 final size:20
Alignment explanation
Indices: 71163--71531 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
71153 GATTTTCCAT
* ** *
71163 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
71183 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
71203 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
71223 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
71243 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
71263 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
71283 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
71303 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
71323 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
71343 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
71363 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
71383 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
71403 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
71423 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
71443 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
71463 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
71483 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
71503 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
71523 AATCACAAC
1 AATCGCAAC
71532 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:72241 original size:24 final size:24
Alignment explanation
Indices: 72202--72248 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
72192 AAATTTGGTC
72202 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
72226 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
72249 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:74764 original size:19 final size:19
Alignment explanation
Indices: 74742--75065 Score: 371
Period size: 19 Copynumber: 18.4 Consensus size: 19
74732 CGGAAAATAC
*
74742 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
74761 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
74775 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
74795 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
74809 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
74828 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
74847 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
74866 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
74880 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
74899 AATCGCAATGCG-AA-GAA
1 AATCGCAATGCGAAATGAA
*
74916 AATCG-AA-CCG-AAT---
1 AATCGCAATGCGAAATGAA
*
74929 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
74948 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
74967 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
74986 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
75005 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
75019 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
75039 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
75058 AATCGCAA
1 AATCGCAA
75066 CGAGATAATC
Statistics
Matches: 265, Mismatches: 11, Indels: 58
0.79 0.03 0.17
Matches are distributed among these distances:
13 5 0.02
14 42 0.16
15 8 0.03
16 12 0.05
17 21 0.08
18 6 0.02
19 147 0.55
20 24 0.09
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:74962 original size:120 final size:124
Alignment explanation
Indices: 74770--75046 Score: 394
Period size: 120 Copynumber: 2.3 Consensus size: 124
74760 AAATCCCAAC
74770 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
*
74835 ATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
66 ATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
74894 ATGAAAATCGCAATGC-G-AA-GAAAATCG-AACCGA-ATAATCGCAATGCGAAATTAAAATCGC
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAAATGAAAATCGC
*
74954 AATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
65 AATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
75017 A-G--AATCGCAATGCGGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA
75047 TGCGAAATGA
Statistics
Matches: 139, Mismatches: 4, Indels: 20
0.85 0.02 0.12
Matches are distributed among these distances:
120 77 0.55
121 12 0.09
122 7 0.05
123 14 0.10
124 19 0.14
125 10 0.07
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (124 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
ATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:74991 original size:139 final size:144
Alignment explanation
Indices: 74809--75097 Score: 502
Period size: 139 Copynumber: 2.0 Consensus size: 144
74799 GCAACGAGAG
*
74809 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
*
74874 CGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG-AA-GAAAATCG-AACCGA-ATAATCG
66 CGAAAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCG
74934 CAATGCGAAATTA-A
130 CAATGCGAAATTATA
74948 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
75013 CGAAAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
66 CGAAAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
75078 AATGCGAAATTATA
131 AATGCGAAATTATA
75092 AA-CGCA
1 AATCGCA
75098 TTGCGATTTT
Statistics
Matches: 142, Mismatches: 2, Indels: 8
0.93 0.01 0.05
Matches are distributed among these distances:
139 80 0.56
140 20 0.14
141 2 0.01
142 11 0.08
143 26 0.18
144 3 0.02
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (144 bp):
AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAAAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
AATGCGAAATTATA
Found at i:75184 original size:19 final size:19
Alignment explanation
Indices: 75094--75176 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
75084 AAATTATAAA
75094 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
75113 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
75133 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
75149 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
75166 CGCATTGCGAT
1 CGCATTGCGAT
75177 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:75302 original size:14 final size:14
Alignment explanation
Indices: 75283--75319 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
75273 CATCAATTAC
75283 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
75297 ACAAATCATCTTTT
1 ACAAATCAACTTTT
75311 ACAAATCAA
1 ACAAATCAA
75320 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:75331 original size:12 final size:12
Alignment explanation
Indices: 75314--75385 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
75304 ATCTTTTACA
75314 AATCAATTAAAC
1 AATCAATTAAAC
*
75326 AATCAA--AAATTG
1 AATCAATTAAA--C
**
75338 AATCAACTTTTAC
1 AATCAA-TTAAAC
75351 AAATCAATTAAAC
1 A-ATCAATTAAAC
75364 AATCAA--AAAC
1 AATCAATTAAAC
75374 AATCAATTAAAC
1 AATCAATTAAAC
75386 TATTGAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
10 13 0.28
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.57, C:0.17, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:75348 original size:38 final size:38
Alignment explanation
Indices: 75300--75372 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
75290 AACTTTTACA
*
75300 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
75338 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
75373 CAATCAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:77255 original size:14 final size:14
Alignment explanation
Indices: 77236--77292 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
77226 GCGAAATGAA
*
77236 AATCGCAACGACAG
1 AATCGCAACGAAAG
77250 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
77267 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
77283 AATCGCAACG
1 AATCGCAACG
77293 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:77263 original size:33 final size:33
Alignment explanation
Indices: 77217--77309 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
77207 GCGAAACCAA
*
77217 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
77250 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
77283 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
77310 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:77274 original size:19 final size:19
Alignment explanation
Indices: 77180--77314 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
77170 TAGTTTACTT
* *
77180 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
77200 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
77219 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
77238 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
77252 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
77271 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
77285 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
77304 TCGCAATGCGA
1 TCGCAACGCGA
77315 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:77332 original size:19 final size:19
Alignment explanation
Indices: 77310--77438 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
77300 AAAATCGCAA
77310 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
**
77329 TGCGAACTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
77343 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
77362 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
77376 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
77395 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
77414 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
77434 TGCGA
1 TGCGA
77439 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:77400 original size:33 final size:34
Alignment explanation
Indices: 77310--77401 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 34
77300 AAAATCGCAA
*
77310 TGCGATTTTGGTTTCGCGTTGCGA-ACTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
77343 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
77376 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
77402 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.45
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:77771 original size:92 final size:93
Alignment explanation
Indices: 77482--77860 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
77472 TTGAATGGAT
77482 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
77546 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
77574 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
77639 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
77667 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
77731 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
77759 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
77824 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
77852 AAATTTACT
1 AAATTTACT
77861 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 108 0.38
93 177 0.62
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:77794 original size:185 final size:185
Alignment explanation
Indices: 77482--77860 Score: 742
Period size: 185 Copynumber: 2.0 Consensus size: 185
77472 TTGAATGGAT
77482 AAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
77547 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
77612 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
77667 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
77731 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
77796 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
77852 AAATTTACT
1 AAATTTACT
77861 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 171 0.89
186 22 0.11
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:79583 original size:14 final size:14
Alignment explanation
Indices: 79564--79653 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
79554 TTGAAATGAA
79564 AATCGCAACGAGAG
1 AATCGCAACGAGAG
79578 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
79595 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
79611 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
79630 AATCGCAACGAGAG
1 AATCGCAACGAGAG
79644 AATCGCAACG
1 AATCGCAACG
79654 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:79601 original size:33 final size:33
Alignment explanation
Indices: 79556--79670 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
79546 TCTTTTGGTT
79556 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
79589 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
79622 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
79655 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
79671 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:79602 original size:19 final size:18
Alignment explanation
Indices: 79563--79675 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
79553 GTTGAAATGA
79563 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
79578 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
79595 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
79611 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
79628 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
79644 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
79661 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
79676 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:79706 original size:14 final size:14
Alignment explanation
Indices: 79687--79741 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
79677 TTTGGTTTCG
79687 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
79701 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
79720 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
79734 CGTTGCGA
1 CGTTGCGA
79742 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:79903 original size:33 final size:33
Alignment explanation
Indices: 79861--79931 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
79851 AATACTAACT
*
79861 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
79894 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
79927 TGAAA
1 TGAAA
79932 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:80162 original size:22 final size:22
Alignment explanation
Indices: 80110--80164 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
80100 TGGTTGTGAG
**
80110 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
80132 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
80154 GGATTTCTTCG
1 GGATTTCTTCG
80165 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:80335 original size:20 final size:20
Alignment explanation
Indices: 80310--80503 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
80300 CTTTAAATAT
80310 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
80330 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
80352 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
80371 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
80391 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
80411 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
80431 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
80451 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
80471 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
80491 CGCGTTGCGATTT
1 CGCGTTGCGATTT
80504 GGAAAATCGC
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:80497 original size:60 final size:60
Alignment explanation
Indices: 80310--80503 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
80300 CTTTAAATAT
**
80310 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
80371 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
80431 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
80491 CGCGTTGCGATTT
1 CGCGTTGCGATTT
80504 GGAAAATCGC
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:80513 original size:20 final size:20
Alignment explanation
Indices: 80470--80565 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 20
80460 ATTTATGTGT
* * *
80470 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTGCAAAA
*
80490 TCGCGTTGCGATTTGGAAAA
1 TCGCGTTGCGATTTGCAAAA
** * **
80510 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCG-ATTTGCAAAA
* * *
80531 TCGCATCGCGATTTTCAAGAA
1 TCGCGTTGCGATTTGCAA-AA
80552 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
80566 TGGAAACTGA
Statistics
Matches: 57, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 29 0.51
21 28 0.49
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGATTTGCAAAA
Found at i:80582 original size:20 final size:20
Alignment explanation
Indices: 80557--80608 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
80547 AAGAATCGCG
*
80557 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
80577 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
80597 TTGCGATTCTGG
1 TTGCGATTCTGG
80609 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:84738 original size:29 final size:29
Alignment explanation
Indices: 84696--84755 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
84686 TTCCGTGTGA
* *
84696 CTCGATCCCACGACTTCAAGGTTAAAAAC
1 CTCGATCCCACGACCTCAAAGTTAAAAAC
*
84725 CTCGATCCCACGACCTCAAAGTTAAGAAC
1 CTCGATCCCACGACCTCAAAGTTAAAAAC
84754 CT
1 CT
84756 TATGATCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (29 bp):
CTCGATCCCACGACCTCAAAGTTAAAAAC
Done.