Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001989.1 Hibiscus syriacus cultivar Beakdansim tig00004063_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: 499561
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 3 of 3
Found at i:414951 original size:3 final size:3
Alignment explanation
Indices: 414943--414991 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
414933 CTGCAAAATG
* *
414943 TAA TAA TAA TTAC TAC TAA TAA TAA TAA TAA TAA TAA -AA T-A TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
414987 -AA TAA
1 TAA TAA
414992 ACAAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 32 0.80
4 2 0.05
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:415668 original size:137 final size:136
Alignment explanation
Indices: 415422--415673 Score: 301
Period size: 137 Copynumber: 1.8 Consensus size: 136
415412 AATAATATGG
* * * * * *
415422 TTCCTACGTGATAAGGACAGTTGGTTATCAGGGGTGACATGGTTCCTACGTGATGAGGAGGTTTA
1 TTCCTACATGATAAGGACAGCTAGTTATCAGGGGTGACATAGCTCCTACGTGATGAGGAGGTCTA
* * * * * * *
415487 GTCGAGGGATGACACGGTTTCTACGTGATGAGGAAGGCATGCCATTTTTATTGATAAAATAGATA
66 GCCGAGGGATCACACGGTTCCTACGCGATGAGGAAGACAAGCCATCTTTATTGATAAAATAGATA
415552 ACACAA
131 ACACAA
* *
415558 TTCCTACATGATAAGGACGGCTAGTTATCAATGGGTGACATAGCTCCTACGTGATGAGGAGGTCT
1 TTCCTACATGATAAGGACAGCTAGTTATC-AGGGGTGACATAGCTCCTACGTGATGAGGAGGTCT
* * *
415623 GGCCG-GTGGATCACATGGTTCCTACGCGATGATGACA-ACAAGCCATCTTTA
65 AGCCGAG-GGATCACACGGTTCCTACGCGATGAGGA-AGACAAGCCATCTTTA
415674 GGGATTTGTT
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
136 26 0.27
137 68 0.72
138 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (136 bp):
TTCCTACATGATAAGGACAGCTAGTTATCAGGGGTGACATAGCTCCTACGTGATGAGGAGGTCTA
GCCGAGGGATCACACGGTTCCTACGCGATGAGGAAGACAAGCCATCTTTATTGATAAAATAGATA
ACACAA
Found at i:415850 original size:61 final size:64
Alignment explanation
Indices: 415774--415924 Score: 188
Period size: 61 Copynumber: 2.4 Consensus size: 64
415764 CTCAAAGATG
* *
415774 TTTGTTTCAAGAGAAACAGACTCAAAGA-TTTTTCTCAAAATAAA-TTATCTC-A-AGTCAAAA
1 TTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTCTCAAAAGAAATTTATCTCGAGAGACAAAA
* * *
415834 CTTTGTTTACAA-AGAAATAGACTCAAAGATTTTTTTTCAAAAGAAATTTGTCTCGAGAGACAAA
1 -TTTGTTT-CAAGAGAAACAGACTCAAAGATTTTTTCTCAAAAGAAATTTATCTCGAGAGACAAA
415898 A
64 A
*
415899 TTTGTTTCAAGAGAAACA-ATTCAAAG
1 TTTGTTTCAAGAGAAACAGACTCAAAG
415925 GATACTGATT
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
61 23 0.30
62 17 0.22
63 16 0.21
64 14 0.18
65 7 0.09
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (64 bp):
TTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTCTCAAAAGAAATTTATCTCGAGAGACAAAA
Found at i:418989 original size:13 final size:13
Alignment explanation
Indices: 418971--419005 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
418961 ACAATATTTA
418971 TGGATGCAAATGG
1 TGGATGCAAATGG
418984 TGGATGCAAATGG
1 TGGATGCAAATGG
*
418997 TAGATGCAA
1 TGGATGCAA
419006 TGCCCCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.23
Consensus pattern (13 bp):
TGGATGCAAATGG
Found at i:421515 original size:22 final size:21
Alignment explanation
Indices: 421479--421521 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
421469 TGCAAATGAC
*
421479 AAATAAAATATTTATAACATA
1 AAATAAAACATTTATAACATA
*
421500 AAATAACAACATTTATGACATA
1 AAATAA-AACATTTATAACATA
421522 TACATACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATAAAACATTTATAACATA
Found at i:421669 original size:30 final size:31
Alignment explanation
Indices: 421605--421792 Score: 144
Period size: 30 Copynumber: 6.3 Consensus size: 31
421595 TTGAAATTAC
* * **
421605 AAAGGACTAAAATAG-AAAAAAACATAAACAT
1 AAAGGACTAAAATAGTAAAAATA-AGAAATTT
*
421636 AAAGGACCAAAATAGTAAAAATAAG-AATTT
1 AAAGGACTAAAATAGTAAAAATAAGAAATTT
* * *
421666 AAAGGACTAAAATGGCAAAAAT-AGAAAATT
1 AAAGGACTAAAATAGTAAAAATAAGAAATTT
*
421696 AAATGG-CTAAAATAGTAAAAAT-AGAAACTT
1 AAA-GGACTAAAATAGTAAAAATAAGAAATTT
** * *
421726 -AAGGGTTTAAATA-T-AAAATACAGACATTT
1 AAAGGACTAAAATAGTAAAAATA-AGAAATTT
* *
421755 AAAGGACTAAAATAATAAAAAT-AGAAACTT
1 AAAGGACTAAAATAGTAAAAATAAGAAATTT
421785 -AAGGACTA
1 AAAGGACTA
421793 TATAGAAAAT
Statistics
Matches: 127, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.04
28 3 0.02
29 24 0.19
30 66 0.52
31 18 0.14
32 11 0.09
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.20
Consensus pattern (31 bp):
AAAGGACTAAAATAGTAAAAATAAGAAATTT
Found at i:421700 original size:21 final size:22
Alignment explanation
Indices: 421675--421715 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
421665 TAAAGGACTA
421675 AAATGGCAAAAATAG-AAAATT
1 AAATGGCAAAAATAGTAAAATT
*
421696 AAATGGCTAAAATAGTAAAA
1 AAATGGCAAAAATAGTAAAA
421716 ATAGAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.05, G:0.15, T:0.20
Consensus pattern (22 bp):
AAATGGCAAAAATAGTAAAATT
Found at i:421814 original size:59 final size:59
Alignment explanation
Indices: 421690--421814 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 59
421680 GCAAAAATAG
* ** * *
421690 AAAA-TTAAATGGCTAAAATAGTAAAAATAGAAACTTAAGGGTTTAAATATAAAATACA
1 AAAATTTAAATGGCTAAAATAATAAAAATAGAAACTTAAGGGACTAAATAGAAAATAAA
* * *
421748 GACATTTAAA-GGACTAAAATAATAAAAATAGAAACTTAA-GGACTATATAGAAAATAAA
1 AAAATTTAAATGG-CTAAAATAATAAAAATAGAAACTTAAGGGACTAAATAGAAAATAAA
421806 AATAATTTA
1 AA-AATTTA
421815 GAGCCCAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
58 19 0.35
59 35 0.65
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.26
Consensus pattern (59 bp):
AAAATTTAAATGGCTAAAATAATAAAAATAGAAACTTAAGGGACTAAATAGAAAATAAA
Found at i:422579 original size:20 final size:20
Alignment explanation
Indices: 422551--422598 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
422541 TTTTTTCTTT
*
422551 CTTTTTTTTCT-TTCGAATGC
1 CTTTGTTTTCTGTTCG-ATGC
* *
422571 CTTTGTTTTTTGTTCGATTC
1 CTTTGTTTTCTGTTCGATGC
422591 CTTTGTTT
1 CTTTGTTT
422599 CTCACTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.06, C:0.17, G:0.12, T:0.65
Consensus pattern (20 bp):
CTTTGTTTTCTGTTCGATGC
Found at i:428206 original size:66 final size:64
Alignment explanation
Indices: 427917--428267 Score: 182
Period size: 66 Copynumber: 5.4 Consensus size: 64
427907 TATCAGTATC
*
427917 CTTTGA-GTTGTTTCTC-TTGAAA-AAA-ATTGTCTCTC--GAGACAGTTTCTTTTGAAAAT--A
1 CTTTGAGGTTGTTTC-CATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC-TTTGAAAATAAA
427974 T
64 T
* * * * * *
427975 ATTTGA-GTCTATTT-CTTTGGAAATAAAGTTTTTTCTCTCTTGAGACACTTTCCTTTGAGAAAA
1 CTTTGAGGT-TGTTTCCATT-GAAACAAA-TTTTGTCTCTCTTGAGACAGTTT-CTTT--G-AAA
* *
428038 AAAAAC
59 ATAAAT
* ** * *
428044 CTTTGAGATCATTTCCATTAAAACAAATTTTG--TCTCTTGAGACAGTTCCTTTTGAAGAA-AAA
1 CTTTGAGGTTGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC-TTTGAA-AATAAA
428106 T
64 T
** *
428107 CTTTGAGACTGTTTCTA-TGAAA-AGAATGGTTTGTCTCTCTTGAGACAGTTTCTCTT-AAAATG
1 CTTTGAGGTTGTTTCCATTGAAACA-AAT--TTTGTCTCTCTTGAGACAGTTTCT-TTGAAAAT-
428169 AACAT
61 AA-AT
* * *
428174 CTTTGAGGTTGTTTCCATTGAAACAAATTTTGTCTAC-CTTAAGGCAGTTTCTTTGGAAATACAA
1 CTTTGAGGTTGTTTCCATTGAAACAAATTTTGTCT-CTCTTGAGACAGTTTCTTT-GAAA-A-TA
428238 AAT
62 AAT
428241 CTTTGA-GTATGTTTCTC-TTGAAACAAA
1 CTTTGAGGT-TGTTTC-CATTGAAACAAA
428268 ACATATCTTT
Statistics
Matches: 228, Mismatches: 29, Indels: 63
0.71 0.09 0.20
Matches are distributed among these distances:
57 1 0.00
58 9 0.04
59 8 0.04
60 3 0.01
61 1 0.00
62 15 0.07
63 18 0.08
64 21 0.09
65 7 0.03
66 60 0.26
67 48 0.21
68 16 0.07
69 17 0.07
70 4 0.02
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (64 bp):
CTTTGAGGTTGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTGAAAATAAAT
Found at i:428243 original size:67 final size:64
Alignment explanation
Indices: 427994--428267 Score: 191
Period size: 66 Copynumber: 4.1 Consensus size: 64
427984 TATTTCTTTG
* * * * * * **
427994 GAAATAAAGTTTTTTCTCTCTTGAGACACTTTCCTTTGAGAAAAAAAAACCTTTGAGATCATTTC
1 GAAACAAA-TTTTGTCTC-CTTGAGACAGTTT-CTTT--GAAATAAAAATCTTTGAGGTTGTTTC
428059 CATT
61 CATT
* * * ** *
428063 AAAACAAATTTTGTCT-CTTGAGACAGTTCCTTTTG-AAGAAAAATCTTTGAGACTGTTTCTA-T
1 GAAACAAATTTTGTCTCCTTGAGACAGTTTC-TTTGAAATAAAAATCTTTGAGGTTGTTTCCATT
* * *
428125 GAAA-AGAATGGTTTGTCTCTCTTGAGACAGTTTCTCTTAAAATGAACATCTTTGAGGTTGTTTC
1 GAAACA-AAT--TTTGTCTC-CTTGAGACAGTTTCT-TTGAAATAAAAATCTTTGAGGTTGTTTC
428189 CATT
61 CATT
* *
428193 GAAACAAATTTTGTCTACCTTAAGGCAGTTTCTTTGGAAATACAAAATCTTTGA-GTATGTTTCT
1 GAAACAAATTTTGTCT-CCTTGAGACAGTTTCTTT-GAAATA-AAAATCTTTGAGGT-TGTTTC-
428257 C-TT
61 CATT
428260 GAAACAAA
1 GAAACAAA
428268 ACATATCTTT
Statistics
Matches: 165, Mismatches: 25, Indels: 32
0.74 0.11 0.14
Matches are distributed among these distances:
61 1 0.01
62 7 0.04
63 20 0.12
64 8 0.05
65 4 0.02
66 55 0.33
67 47 0.28
68 16 0.10
69 7 0.04
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (64 bp):
GAAACAAATTTTGTCTCCTTGAGACAGTTTCTTTGAAATAAAAATCTTTGAGGTTGTTTCCATT
Found at i:428441 original size:39 final size:38
Alignment explanation
Indices: 428387--428627 Score: 142
Period size: 40 Copynumber: 5.8 Consensus size: 38
428377 TGGCATAATG
* *
428387 TCCTCATCATGTAGGAACCGTGTCATCCCCGAGCAGACC
1 TCCTCATCACGTAGGAACCGTGTCA-CCCCGAGCATACC
* * ** *
428426 TCCTCATCACGTAGGAGCCGTGTCACCCGTGATAACCAGCC
1 TCCTCATCACGTAGGAACCGTGTCACCC-CGAGCA-TA-CC
* * *
428467 GTCCTCATCACGTAGGAACCATGTTATCACCCTTCCTAAAGATAGCCTATCA
1 -TCCTCATCACGTAGGAACC--G-TGTCA-CC--CC----G--AGCATA-CC
**
428519 TCCTCATCACGTAGGAACCGTGTCAACCCCCGAATATACC
1 TCCTCATCACGTAGGAACCGTGTC-A-CCCCGAGCATACC
*
428559 TCCTCATCACATAGGAACCGTGTCATCCCCCGA-CTATACC
1 TCCTCATCACGTAGGAACCGTGTCA--CCCCGAGC-ATACC
*
428599 TCCTCATCACGTAGGAGCCGTGTCACCCC
1 TCCTCATCACGTAGGAACCGTGTCACCCC
428628 TAGATAACCA
Statistics
Matches: 159, Mismatches: 24, Indels: 39
0.72 0.11 0.18
Matches are distributed among these distances:
38 7 0.04
39 27 0.17
40 60 0.38
41 5 0.03
42 18 0.11
43 1 0.01
44 1 0.01
45 4 0.03
46 2 0.01
47 2 0.01
48 4 0.03
49 5 0.03
51 20 0.13
52 2 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (38 bp):
TCCTCATCACGTAGGAACCGTGTCACCCCGAGCATACC
Found at i:428574 original size:40 final size:40
Alignment explanation
Indices: 428519--428627 Score: 175
Period size: 40 Copynumber: 2.8 Consensus size: 40
428509 TAGCCTATCA
428519 TCCTCATCACGTAGGAACCGTGTCAACCCCCGAATATACC
1 TCCTCATCACGTAGGAACCGTGTCAACCCCCGAATATACC
* * *
428559 TCCTCATCACATAGGAACCGTGTCATCCCCCGACTATACC
1 TCCTCATCACGTAGGAACCGTGTCAACCCCCGAATATACC
*
428599 TCCTCATCACGTAGGAGCCGTGTC-ACCCC
1 TCCTCATCACGTAGGAACCGTGTCAACCCC
428628 TAGATAACCA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 4 0.06
40 59 0.94
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.21
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCAACCCCCGAATATACC
Found at i:428737 original size:173 final size:172
Alignment explanation
Indices: 428387--428756 Score: 467
Period size: 173 Copynumber: 2.1 Consensus size: 172
428377 TGGCATAATG
*
428387 TCCTCATCATGTAGGAACCGTGTCATCCCCGAGCAGACCTCCTCATCACGTAGGAGCCGTGTCAC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCGAGCAGACCTCCTCATCACGTAGGAGCCGTGTCAC
* *
428452 CCGTGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCCTTCCTAAAGATAGCCTAT
66 CCCTGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCCTTCCTAAAGATAGCCTAA
* * *
428517 CATCCTCATCACGTAGGAACCGTGTCAACCCCCGAATATACC
131 CATCCTCATCACGTAGGAACCGTGTCAACCACCGAACAGACC
* *
428559 TCCTCATCACATAGGAACCGTGTCATCCCCCGA-CTATACCTCCTCATCACGTAGGAGCCGTGTC
1 TCCTCATCACGTAGGAACCGTGTCAT-CCCCGAGC-AGACCTCCTCATCACGTAGGAGCCGTGTC
* ** * * * *
428623 ACCCCTAGATAACCAGTCGTCCTCATCGTGTAGGAACCGTGTTGTCTCCCTTCCTAAAGATGGCC
64 ACCCCT-GATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCCTTCCTAAAGATAGCC
** * * * * *
428688 ATAAC-TTTTCATCA-GTATGAGCCGTGTCATCCACCGACCAGATC
128 -TAACATCCTCATCACGTAGGAACCGTGTCAACCACCGAACAGACC
**
428732 TCCTCATCACGTAGGATTCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
428757 CCCTTAGAAG
Statistics
Matches: 169, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
172 25 0.15
173 83 0.49
174 58 0.34
175 3 0.02
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (172 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCGAGCAGACCTCCTCATCACGTAGGAGCCGTGTCAC
CCCTGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCCTTCCTAAAGATAGCCTAA
CATCCTCATCACGTAGGAACCGTGTCAACCACCGAACAGACC
Found at i:428967 original size:13 final size:13
Alignment explanation
Indices: 428949--428979 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
428939 GGTCAAAAAA
*
428949 TATTATTATTTAT
1 TATTATTATTAAT
428962 TATTATTATTAAT
1 TATTATTATTAAT
428975 TATTA
1 TATTA
428980 CAATCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATTATTAAT
Found at i:440201 original size:3 final size:3
Alignment explanation
Indices: 440193--440240 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
440183 TCGTCTGACC
* *
440193 TTA TTA TTA TTA TTA TT- TTA TT- TT- TTA TT- TTA TTG TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
440237 TTA T
1 TTA T
440241 CAATATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 8 0.21
3 30 0.79
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:442050 original size:134 final size:132
Alignment explanation
Indices: 441810--442916 Score: 1216
Period size: 134 Copynumber: 8.3 Consensus size: 132
441800 AATCGACCTT
* *
441810 GATTCAATCTTCCCTG-AGTAAAAGTGGAATGAATCAACGTCCCA-AGTTCTGATTTTCCCTCAA
1 GATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACATCCCATA--TCTGATTTTCCCTCAA
* ** * *
441873 GAAGAAATG-GAACAAATCATTCTC-TTCTAATATTTGATATTCCCTAAGTAACAGTGGAACATG
63 GAAG-AA-GCGAACATATCCCTCTCTTTC-AAGATTTGATATTCCCTAAGTAACAGTGGAACAAG
* *
441936 TTTGCGTC
125 TCTGCCTC
* *
441944 GATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATCCTCATATTTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCC-CATATCTGATTTTCCCTCAAGA
* * **
442009 AGAAGCAGAACATATCCCTCTCTTTCAAGATTTTATATTCCCTGAGTAACAGTGGAACAAACCTG
65 AGAAGC-GAACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTG
442074 CCTC
129 CCTC
* * * * * * *
442078 GATTTAATCTTTCCTG-AGTAACAATGGAATGAATCAACGTCCCTAGATCTAATTTTCTCTCAAG
1 GATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACATCCC-ATATCTGATTTTCCCTCAAG
* * * *
442142 AAGAAGTGGAACAAATCCATCAT-TTCCAAGATTTGATATTCCCTAAGTAACAGTGG-ACAAGTC
64 AAGAAG-CGAACATATCCCTC-TCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTC
442205 TGCCTC
127 TGCCTC
* * * *
442211 GATTCAATCTTCCCT-AGAGAACAGTGGAATAAATCAACGTCCCCAGATCTGATTTTCCCTAAAA
1 GATTCAATCTTCCCTGA-AGAACAGTGGAATGAATCAACAT-CCCATATCTGATTTTCCCT-CAA
* * * * *
442275 AAAGAAGTGGAATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
63 GAAGAAG-CGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTC
442340 TG-CTC
127 TGCCTC
* * *
442345 GATTCAATCTTCTCTG-AGTAACAGTGGAATGAATCAACATTCCTAAATCTGATTTTCCCTCAAG
1 GATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACA-TCCCATATCTGATTTTCCCTCAAG
* * * *
442409 AAGAAGCAGAACATATCCCTCT-TTTCCAAGATTTGATATTCCCTGAGTAATAGTGGAATAAGTT
64 AAGAAGC-GAACATATCCCTCTCTTT-CAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTC
*
442473 TTCCTC
127 TGCCTC
* * * *
442479 GATTCAATCTTCACTGGAA-AACAATGGAATAAATCAACATCCCCATATATGATTTTCCCTCAAG
1 GATTCAATCTTCCCT-GAAGAACAGTGGAATGAATCAACAT-CCCATATCTGATTTTCCCTCAAG
* * * * * * *
442543 AAGAAGCGAAACAAACCCCTCTCTTTCAAG-TTTTATATTCCTTGAGCAATAGTGGAACAAGTCT
64 AAGAAGCG-AACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCT
*
442607 TCCTC
128 GCCTC
* * * * *
442612 GATTCAATCTTCCCTG-AGTAATAGTGGAACGAATCAACGTCCCTTGATCTAATTTTCCCTCAAG
1 GATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACATCCCAT-ATCTGATTTTCCCTCAAG
*
442676 AAGAAGCGAAACATATCCCTCTCTTTTAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCT
64 AAGAAGCG-AACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCT
442741 GCCTC
128 GCCTC
* * * * * *
442746 GATTCATTTTTCCATGAAGAGCAGTGGAATGAATCAACATCCCCATATTTGATGTTCCCTCAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACAT-CCCATATCTGATTTTCCCTCAAGA
* *
442811 AGAAGCGAAACATATCCCTCTCTTCCAAGATTTGATTTTCCCTAAGTAACAGTGGAACAAGTCTG
65 AGAAGCG-AACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTG
442876 CCTC
129 CCTC
* * *
442880 AATTCAATCTTCCCTAAAGAACAGTGAAATGAATCAA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAA
442917 TGTTTCTCGG
Statistics
Matches: 831, Mismatches: 109, Indels: 66
0.83 0.11 0.07
Matches are distributed among these distances:
131 1 0.00
132 9 0.01
133 230 0.28
134 561 0.68
135 28 0.03
136 2 0.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (132 bp):
GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCATATCTGATTTTCCCTCAAGAA
GAAGCGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTGCC
TC
Found at i:442437 original size:267 final size:268
Alignment explanation
Indices: 441810--442916 Score: 1404
Period size: 267 Copynumber: 4.1 Consensus size: 268
441800 AATCGACCTT
* * *
441810 GATTCAATCTTCCCTGAGTAAAAGTGGAATGAATCAACGTCCC-AAGTTCTGATTTTCCCTCAAG
1 GATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCTAA-ATCTAATTTTCCCTCAAG
** ** * * * * *
441874 AAGAAATGGAACAAATCATTCTCTTCTAATATTTGATATTCCCTAAGTAACAGTGGAACATGTTT
65 AAGAAGCGGAACAAATCCCTCTTTTCCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCT
* * *
441939 GCGTCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATCCTCATATTTGATTTTCCCT
130 GCCTCGATTCAATCTTCCCTGAAGAACAATGGAATAAATCAACATCCCCATATTTGATTTTCCCT
*
442004 CAAGAAGAAGC-AGAACATATCCCTCTCTTTCAAGATTTTATATTCCCTGAGTAACAGTGGAACA
195 CAAGAAGAAGCGA-AACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
**
442068 AACCTGCCTC
259 AGTCTGCCTC
* * * * *
442078 GATTTAATCTTTCCTGAGTAACAATGGAATGAATCAACGTCCCTAGATCTAATTTTCTCTCAAGA
1 GATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCTAAATCTAATTTTCCCTCAAGA
* * *
442143 AGAAGTGGAACAAATCCATCATTTCCAAGATTTGATATTCCCTAAGTAACAGTGG-ACAAGTCTG
66 AGAAGCGGAACAAATCCCTCTTTTCCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTG
* * * *
442207 CCTCGATTCAATCTTCCCT-AGAGAACAGTGGAATAAATCAACGTCCCCAGATCTGATTTTCCCT
131 CCTCGATTCAATCTTCCCTGA-AGAACAATGGAATAAATCAACATCCCCATATTTGATTTTCCCT
* * * * * *
442271 AAAAAAAGAAGTGGAATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
195 -CAAGAAGAAGCGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
442336 AGTCTG-CTC
259 AGTCTGCCTC
* * * *
442345 GATTCAATCTTCTCTGAGTAACAGTGGAATGAATCAACATTCCTAAATCTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCTAAATCTAATTTTCCCTCAAGA
* * * * * * *
442410 AGAAGCAGAACATATCCCTCTTTTCCAAGATTTGATATTCCCTGAGTAATAGTGGAATAAGTTTT
66 AGAAGCGGAACAAATCCCTCTTTTCCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTG
* *
442475 CCTCGATTCAATCTTCACTGGAA-AACAATGGAATAAATCAACATCCCCATATATGATTTTCCCT
131 CCTCGATTCAATCTTCCCT-GAAGAACAATGGAATAAATCAACATCCCCATATTTGATTTTCCCT
* * * * * *
442539 CAAGAAGAAGCGAAACAAACCCCTCTCTTTCAAG-TTTTATATTCCTTGAGCAATAGTGGAACAA
195 CAAGAAGAAGCGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
*
442603 GTCTTCCTC
260 GTCTGCCTC
* * **
442612 GATTCAATCTTCCCTGAGTAATAGTGGAACGAATCAACGTCCCTTGATCTAATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCTAAATCTAATTTTCCCTCAAGA
* * *
442677 AGAAGCGAAACATATCCCTCTCTTT-TAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCT
66 AGAAGCGGAACAAATCCCTCT-TTTCCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCT
* * * * * * *
442741 GCCTCGATTCATTTTTCCATGAAGAGCAGTGGAATGAATCAACATCCCCATATTTGATGTTCCCT
130 GCCTCGATTCAATCTTCCCTGAAGAACAATGGAATAAATCAACATCCCCATATTTGATTTTCCCT
* * *
442806 CAAGAAGAAGCGAAACATATCCCTCTCTTCCAAGATTTGATTTTCCCTAAGTAACAGTGGAACAA
195 CAAGAAGAAGCGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
442871 GTCTGCCTC
260 GTCTGCCTC
* * *
442880 AATTCAATCTTCCCTAAAG-AACAGTGAAATGAATCAA
1 GATTCAATCTTCCCT-GAGTAACAGTGGAATGAATCAA
442917 TGTTTCTCGG
Statistics
Matches: 718, Mismatches: 109, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
266 34 0.05
267 391 0.54
268 288 0.40
269 4 0.01
270 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (268 bp):
GATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCTAAATCTAATTTTCCCTCAAGA
AGAAGCGGAACAAATCCCTCTTTTCCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTG
CCTCGATTCAATCTTCCCTGAAGAACAATGGAATAAATCAACATCCCCATATTTGATTTTCCCTC
AAGAAGAAGCGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
TCTGCCTC
Found at i:442516 original size:401 final size:398
Alignment explanation
Indices: 441810--442892 Score: 1374
Period size: 401 Copynumber: 2.7 Consensus size: 398
441800 AATCGACCTT
*
441810 GATTCAATCTTCCCTGAGTAAAAGTGGAATGAATCAACGTCCCAAGTTCTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAGTAAAAGTGGAATGAATCAACGTCCCAAGATCTGATTTTCCCTCAAGA
* ** * * *
441875 AGAAATGGAACAAATCATTCTC-TTCTAATATTTGATATTCCCTAAGTAACAGTGGAACATGTTT
66 AGAAGTGGAACAAATCCCTCTCTTTC-AAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCT
*
441939 GCGTCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACA-TCCTCATATTTGATTTTCCC
130 GC-TCGATTCAATCTT-CCTGAAGAACAGTGGAATGAATCAACATTCCT-ATATTTGATTTTCCC
*
442003 TCAAGAAGAAGCAGAACATATCCCTCTCTTT-CAAGATTTTATATTCCCTGAGTAACAGTGGAAC
192 TCAAGAAGAAGCAGAACATATCCCTCT-TTTCCAAGATTTGATATTCCCTGAGTAACAGTGGAAC
** * * * * * *
442067 AAACCTGCCTCGATTTAATCTTTCCTGAGTAACAATGGAATGAATCAACGTCCCTAGATCTAATT
256 AAGTCTGCCTCGATTCAATC-TTCCTGAGAAACAATGGAATAAATCAACATCCCCAGATATAATT
* * * * *
442132 TTCTCTCAAGAAGAAGTGGAACAAATCCATCAT-TTCCAAGATTTGATATTCCCTAAGTAACAGT
320 TTCCCTCAAGAAGAAGCGAAACAAACCCATC-TCTTCCAAG-TTTGATATTCCCTAAGCAACAGT
442196 GG-ACAAGTCTGCCTC
383 GGAACAAGTCTGCCTC
* * * *
442211 GATTCAATCTTCCCTAGAG-AACAGTGGAATAAATCAACGTCCCCAGATCTGATTTTCCCTAAAA
1 GATTCAATCTTCCCT-GAGTAAAAGTGGAATGAATCAACGTCCCAAGATCTGATTTTCCCT-CAA
* * * *
442275 AAAGAAGTGGAATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
64 GAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTC
* *
442340 TGCTCGATTCAATCTTCTCTG-AGTAACAGTGGAATGAATCAACATTCCTAAATCTGATTTTCCC
129 TGCTCGATTCAATCTTC-CTGAAG-AACAGTGGAATGAATCAACATTCCTATATTTGATTTTCCC
* *
442404 TCAAGAAGAAGCAGAACATATCCCTCTTTTCCAAGATTTGATATTCCCTGAGTAATAGTGGAATA
192 TCAAGAAGAAGCAGAACATATCCCTCTTTTCCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
* * * *
442469 AGTTTTCCTCGATTCAATCTTCACTG-GAAAACAATGGAATAAATCAACATCCCCATATATGATT
257 AGTCTGCCTCGATTCAATCTTC-CTGAG-AAACAATGGAATAAATCAACATCCCCAGATATAATT
* * * * * *
442533 TTCCCTCAAGAAGAAGCGAAACAAACCCCTCTCTTTCAAGTTTTATATTCCTTGAGCAATAGTGG
320 TTCCCTCAAGAAGAAGCGAAACAAACCCATCTCTTCCAAGTTTGATATTCCCTAAGCAACAGTGG
*
442598 AACAAGTCTTCCTC
385 AACAAGTCTGCCTC
* * ** *
442612 GATTCAATCTTCCCTGAGTAATAGTGGAACGAATCAACGTCCCTTGATCTAATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAGTAAAAGTGGAATGAATCAACGTCCCAAGATCTGATTTTCCCTCAAGA
* * * *
442677 AGAAGCGAAACATATCCCTCTCTTTTAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTG
66 AGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTG
* * * * * *
442742 CCTCGATTCATTTTTCCATGAAGAGCAGTGGAATGAATCAACATCCCCATATTTGATGTTCCCTC
131 -CTCGATTCAATCTTCC-TGAAGAACAGTGGAATGAATCAACATTCCTATATTTGATTTTCCCTC
* * *
442807 AAGAAGAAGC-GAAACATATCCCTCTCTTCCAAGATTTGATTTTCCCTAAGTAACAGTGGAACAA
194 AAGAAGAAGCAG-AACATATCCCTCTTTTCCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
*
442871 GTCTGCCTCAATTCAATCTTCC
258 GTCTGCCTCGATTCAATCTTCC
442893 CTAAAGAACA
Statistics
Matches: 591, Mismatches: 75, Indels: 33
0.85 0.11 0.05
Matches are distributed among these distances:
400 99 0.17
401 424 0.72
402 65 0.11
403 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (398 bp):
GATTCAATCTTCCCTGAGTAAAAGTGGAATGAATCAACGTCCCAAGATCTGATTTTCCCTCAAGA
AGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCTG
CTCGATTCAATCTTCCTGAAGAACAGTGGAATGAATCAACATTCCTATATTTGATTTTCCCTCAA
GAAGAAGCAGAACATATCCCTCTTTTCCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
TGCCTCGATTCAATCTTCCTGAGAAACAATGGAATAAATCAACATCCCCAGATATAATTTTCCCT
CAAGAAGAAGCGAAACAAACCCATCTCTTCCAAGTTTGATATTCCCTAAGCAACAGTGGAACAAG
TCTGCCTC
Found at i:443984 original size:14 final size:13
Alignment explanation
Indices: 443955--443980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
443945 TCTCTCTCTA
443955 AAATGAAAAAAAT
1 AAATGAAAAAAAT
443968 AAATGAAAAAAAT
1 AAATGAAAAAAAT
443981 TAAAAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAATGAAAAAAAT
Found at i:445461 original size:131 final size:130
Alignment explanation
Indices: 445105--445454 Score: 416
Period size: 131 Copynumber: 2.7 Consensus size: 130
445095 GAGAATAGTA
* * *
445105 ATATATTTTCATTTTAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGACAT-ATTCTATTCT
1 ATATATTTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGTATGAGACGTCATT-TATTCT
* * * * * * *
445169 CGATTGAAAATAATTTGATATTACCGTTTTCTCTCGAATTAATATTGATTTTTAAGATGAAATAG
65 CGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGATG-AATAA
445234 TG
129 TG
* * ** * *
445236 ATATATTCTCATTTCGATTGGAGCGATAAATGACTGCTTTAAGGTATGAGATGTCATTTATTATC
1 ATATATTTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGTATGAGACGTCATTTATTCTC
* * *
445301 GATTAGAAATTATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAGACATG-ATAA
66 GATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAG--ATGAATAA
445365 TG
129 TG
* * * * * * *
445367 ATATCTTTTCATTTCCAGTGGAGTAATAAATGACTGTTTTAAGATATGAGAGGTCGTTTATTCTC
1 ATATATTTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGTATGAGACGTCATTTATTCTC
445432 GATTGGAAATAATTAGATATTAT
66 GATTGGAAATAATTAGATATTAT
445455 TATTTTCTAT
Statistics
Matches: 184, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
131 178 0.97
132 3 0.02
133 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (130 bp):
ATATATTTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGTATGAGACGTCATTTATTCTC
GATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGATGAATAATG
Found at i:450938 original size:32 final size:30
Alignment explanation
Indices: 450814--450930 Score: 85
Period size: 32 Copynumber: 3.8 Consensus size: 30
450804 AAAAGATTTT
* * *
450814 TAATCATTAAAAATT-TAAAAC-ATATAAAA
1 TAATCATT-AAACTTATCAAACTATACAAAA
* * * *
450843 TTATCAGTAAATTTATCGAACTGATACAAAA
1 TAATCATTAAACTTATCAAACT-ATACAAAA
* **
450874 TAATCATTAAACGTTATTAAGTTAATACAAAA
1 TAATCATTAAAC-TTATCAAACT-ATACAAAA
450906 TAATCATTAAAACTTATCAAACTAT
1 TAATCATT-AAACTTATCAAACTAT
450931 TATAAAATGA
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
28 5 0.08
29 10 0.15
31 18 0.27
32 29 0.44
33 4 0.06
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (30 bp):
TAATCATTAAACTTATCAAACTATACAAAA
Found at i:452970 original size:3 final size:3
Alignment explanation
Indices: 452964--453003 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
452954 AATAATAATA
*
452964 ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
453004 CTTACAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:462539 original size:54 final size:54
Alignment explanation
Indices: 462380--462590 Score: 261
Period size: 54 Copynumber: 4.0 Consensus size: 54
462370 TGATTGAGAA
* * *
462380 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
* *
462434 ATCTGGGTAGAAGCCACA-G-GA-AAT-AATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
462484 ATCTGGGCAGAAGCCACATGAAAGAATTAATGTCTTGTCAAATATTTTATGAAC
1 ATCTGGGCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
462538 ATCTGAGAAGAAACCACATGAGATG-ATGAATGTGTTGTCAAATGTTTTACGAA
1 ATCTGGGCAGAAGCCACATGA-AAGAATGAATGTGTTGTCAAATGTTTTACGAA
462591 TCAGTTCTTC
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
50 42 0.31
51 3 0.02
52 2 0.01
53 4 0.03
54 82 0.61
55 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:462975 original size:22 final size:23
Alignment explanation
Indices: 462950--463030 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 23
462940 CTACATCTAC
* *
462950 ATTCTTCAAATATAATAGATT-T
1 ATTCTTCAAAGATGATAGATTCT
*
462972 ATTCTTCACAGATGATAGATTCT
1 ATTCTTCAAAGATGATAGATTCT
*
462995 -CTCTTCAAAGATGATAGATTCT
1 ATTCTTCAAAGATGATAGATTCT
*
463017 CTT-TTCAAAGATGA
1 ATTCTTCAAAGATGA
463031 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
22 49 0.96
23 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (23 bp):
ATTCTTCAAAGATGATAGATTCT
Found at i:463729 original size:45 final size:45
Alignment explanation
Indices: 463658--464053 Score: 476
Period size: 45 Copynumber: 8.8 Consensus size: 45
463648 CTATTTCCCA
* * * * *
463658 CATCTATAAGACCTACAGTGCAGGATGTTTTCAAAGCATTCAGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
463703 CATCCACAAGACCTTTAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
** * * **
463748 CATCTGTAAGACCTTCAGTGCATGTTGTTTTCAAAGTCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
** *
463793 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
463838 CATCTC-TAAGACCTTCAGTGCATGAT-ATTTCAAAACCTTCGGGT
1 CATC-CATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
463882 CATCCATAAGACCTACAGTGTAGGATGTTTTCAAAACCTTCGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * * *
463927 CATCCATAAGACCTACAGAGCAGGATGTTTTCAAAGCCTTTGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
***
463972 CATATGTAAGACCTAT-AGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
1 CATCCATAAGACCT-TCAGTGCAGGATGTTTTC-AAAA-CCTTCGGGT
*
464019 CATCCATAAGACCTTCAGTGCTGGATGTTTT-AAAA
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAA
464054 TAGTAATTTA
Statistics
Matches: 305, Mismatches: 39, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.00
44 38 0.12
45 229 0.75
46 4 0.01
47 33 0.11
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (45 bp):
CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
Found at i:464001 original size:179 final size:182
Alignment explanation
Indices: 463658--464053 Score: 525
Period size: 179 Copynumber: 2.2 Consensus size: 182
463648 CTATTTCCCA
* * * * **
463658 CATCTATAAGACCTACAGTGCAGGATGTTTTCAAAGCATTCAGGTCATCCACAAGACCTTTAGTG
1 CATCTCTAAGACCTTCAGTGCAGGATGATTTCAAAACATTCAGGTCATCCACAAGACCTACAGTG
** * * * * *
463723 CAGGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGTTGTTTTCAAAGTCTT
66 CAGGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGAGCAGGATGTTTTCAAAGCCTT
* *
463788 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGT
131 CGGGTCATATGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
* * * *
463838 CATCTCTAAGACCTTCAGTGCATGAT-ATTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
1 CATCTCTAAGACCTTCAGTGCAGGATGATTTCAAAACATTCAGGTCATCCACAAGACCTACAGTG
*
463902 TAGGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGAGCAGGATGTTTTCAAAGCCTT
66 CAGGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGAGCAGGATGTTTTCAAAGCCTT
*
463967 TGGGTCATATGTAAGACCTAT-AGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
131 CGGGTCATATGTAAGACCT-TCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
* *
464019 CATC-CATAAGACCTTCAGTGCTGGATG-TTTTAAAA
1 CATCTC-TAAGACCTTCAGTGCAGGATGATTTCAAAA
464054 TAGTAATTTA
Statistics
Matches: 187, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
179 120 0.64
180 29 0.16
181 38 0.20
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (182 bp):
CATCTCTAAGACCTTCAGTGCAGGATGATTTCAAAACATTCAGGTCATCCACAAGACCTACAGTG
CAGGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGAGCAGGATGTTTTCAAAGCCTT
CGGGTCATATGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
Found at i:464159 original size:39 final size:39
Alignment explanation
Indices: 464105--464626 Score: 715
Period size: 39 Copynumber: 13.4 Consensus size: 39
464095 CCAGATGGAT
* *
464105 TTCATAATCTAAAGAACTCGTCTGAAGAGGAACAAGGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
* * *
464144 TTCATAATTTGAAGAACTCGT-TAGAAGAGAAAAAAAGAG
1 TTCATAATCTGAAGAACTCGTCT-GAAGAGGAAAAAGGAG
464183 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
*
464222 TTCATAATCTGAAGAACTCGTCTGAA-AAGAAAAAGGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
* ** * *
464260 TTCATAAACTGAAGAACTCAACTGAAGAGGAAGAAGGAC
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
* *
464299 TTCATAATCTGAAGAACTCCTCTGAAGAGGAAAAAAGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
464338 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
* *
464377 TTCATAATCTGAAGAACTCGTCTGAAAAGGAAGAAGGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
**
464416 TTCATAATCTGAAGAACTTATCTGAAGAGGAAAAAGGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
* ** *
464455 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAATCAA
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
*
464494 TTCATAATATGAAGAACTCGTCTGAAGAGGAAAAAGGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
* * *
464533 TTCATAATCTAAAGAACTCGTTTGAAGAGGAAGAAGGAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
** * * * * * *
464572 TTCATTGTCTTAAGAACTCATCTAAAAAGGAAGAAGAAG
1 TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
*
464611 TTCATAGTCTGAAGAA
1 TTCATAATCTGAAGAA
464627 ATTATTCAAC
Statistics
Matches: 426, Mismatches: 54, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
38 35 0.08
39 390 0.92
40 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.22
Consensus pattern (39 bp):
TTCATAATCTGAAGAACTCGTCTGAAGAGGAAAAAGGAG
Found at i:464817 original size:15 final size:15
Alignment explanation
Indices: 464797--464826 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
464787 TAATTTTTCC
464797 ATTATTATTATTACT
1 ATTATTATTATTACT
464812 ATTATTATTATTACT
1 ATTATTATTATTACT
464827 TACTTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTATTATTACT
Found at i:467774 original size:37 final size:37
Alignment explanation
Indices: 467721--467825 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
467711 CATTTTCGTC
467721 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
467758 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
467795 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
467826 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:468187 original size:18 final size:18
Alignment explanation
Indices: 468164--468213 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
468154 TATTAGTCCC
468164 TTTATTTATTA-TATTTCA
1 TTTATTTATTATTA-TTCA
468182 TTTATTT-TTATTATTCA
1 TTTATTTATTATTATTCA
468199 TGTTA-TTATTATTAT
1 T-TTATTTATTATTAT
468214 ATGTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATTTATTATTATTCA
Found at i:469680 original size:138 final size:139
Alignment explanation
Indices: 469429--469696 Score: 323
Period size: 138 Copynumber: 1.9 Consensus size: 139
469419 CTAAGTTCCG
* * *
469429 AAATGGAAATTCACAAACTCCTTATGAATTCCATGATGCACACACAGTGCCAAAAGTACATATAT
1 AAATGGAAATTCAAAAACTCATTATGAATACCATGATGCACACACAGTGCCAAAAGTACATATAT
* * *
469494 ATAGTAATGATATGAAAATACAATATATGCATTAGAAAAAATCCATCGATAACCATTCATACACA
66 ATACT-ATGATACGAAAATACAACATATGCATTAGAAAAAATCCATCGATAACCA-TCATACACA
469559 AATACATGTCA
129 AATACATGTCA
* * *
469570 AAATGGTAATTCAAAAACTCATTATGAATACCATGGTTG-A-ACATCTAGTGCCGAAAGTACATA
1 AAATGGAAATTCAAAAACTCATTATGAATACCAT-GATGCACACA-C-AGTGCCAAAAGTACATA
* ** *
469633 TA-ATACT-T-ATACGAAAATGCAACATATGCATTA-AACAAAATTGATCGATAACCATCATATA
63 TATATACTATGATACGAAAATACAACATATGCATTAGAA-AAAATCCATCGATAACCATCATACA
469694 CAA
127 CAA
469697 TGTATATCTC
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
137 11 0.10
138 38 0.35
139 1 0.01
140 3 0.03
141 36 0.33
142 21 0.19
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (139 bp):
AAATGGAAATTCAAAAACTCATTATGAATACCATGATGCACACACAGTGCCAAAAGTACATATAT
ATACTATGATACGAAAATACAACATATGCATTAGAAAAAATCCATCGATAACCATCATACACAAA
TACATGTCA
Found at i:476419 original size:138 final size:138
Alignment explanation
Indices: 476171--476491 Score: 461
Period size: 138 Copynumber: 2.3 Consensus size: 138
476161 GCATAATAAT
476171 ACAAAATCGATCT-ATAACCATTCATACACAAATGTATGA-CAAAATGGTAATTCAAAAACTCAT
1 ACAAAATCGAT-TGATAACCATTCATACACAAATGTAT-ATCAAAATGGTAATTCAAAAACTCAT
* *
476234 TATGAATACCATGGTTGCACATCTAGTGCCGAAAGTACATATAGTACTGATACAAAAATGCAATA
64 TATGAATACCATGGTTGCACATCTAGTGCCGAAAATACATATAGTACTGATACAAAAATGCAACA
*
476299 TATGCATTAG
129 TATGCATTAA
* * *
476309 ACAAAATCGATTGATAACCATTCATACACAAATGTATATCGAAATGGTAATTCACAAACTCATTT
1 ACAAAATCGATTGATAACCATTCATACACAAATGTATATCAAAATGGTAATTCAAAAACTCATTA
* * * *
476374 TGAATACCATGGTTGCACATCTAGTGCCTAAAATACATATAGTACTGATTCGAAATTGCAACATA
66 TGAATACCATGGTTGCACATCTAGTGCCGAAAATACATATAGTACTGATACAAAAATGCAACATA
476439 TGCATTAA
131 TGCATTAA
* * * *
476447 ATAAAATCGATCGATAACC-TTCATATAC-AATATATATCCAAAATG
1 ACAAAATCGATTGATAACCATTCATACACAAATGTATAT-CAAAATG
476492 TACCTATGAT
Statistics
Matches: 165, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
136 8 0.05
137 16 0.10
138 141 0.85
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (138 bp):
ACAAAATCGATTGATAACCATTCATACACAAATGTATATCAAAATGGTAATTCAAAAACTCATTA
TGAATACCATGGTTGCACATCTAGTGCCGAAAATACATATAGTACTGATACAAAAATGCAACATA
TGCATTAA
Found at i:477747 original size:9 final size:9
Alignment explanation
Indices: 477735--477767 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
477725 TGTTTTTCAG
*
477735 CTTTTTTCC
1 CTTTTTCCC
477744 C-TTTTCCC
1 CTTTTTCCC
477752 CTTTTTCCC
1 CTTTTTCCC
477761 CTTTTTC
1 CTTTTTC
477768 AACCCTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (9 bp):
CTTTTTCCC
Found at i:478542 original size:13 final size:13
Alignment explanation
Indices: 478524--478549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
478514 AAGTGCACCC
478524 GGTATCGATACCA
1 GGTATCGATACCA
478537 GGTATCGATACCA
1 GGTATCGATACCA
478550 CCCTGCAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
GGTATCGATACCA
Found at i:492012 original size:24 final size:24
Alignment explanation
Indices: 491983--492028 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
491973 GGGAGTTCAA
491983 AGAAAA-AAAAAAGAAGAAAAATTC
1 AGAAAAGAAAAAA-AAGAAAAATTC
*
492007 AGAAAAGAATAAAAAGAAAAAT
1 AGAAAAGAAAAAAAAGAAAAAT
492029 AGAATTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.09
Consensus pattern (24 bp):
AGAAAAGAAAAAAAAGAAAAATTC
Found at i:492034 original size:29 final size:27
Alignment explanation
Indices: 491990--492044 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
491980 CAAAGAAAAA
*
491990 AAAAAGAAGAAAAA-TTCAGAAAAGAAT
1 AAAAAGAAAAAAAATTTCA-AAAAGAAT
492017 AAAAAGAAAAATAGAATTTCAAAAAGAA
1 AAAAAGAAAAA-A-AATTTCAAAAAGAA
492045 AGCAATGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.42
28 1 0.04
29 9 0.38
30 4 0.17
ACGTcount: A:0.71, C:0.04, G:0.13, T:0.13
Consensus pattern (27 bp):
AAAAAGAAAAAAAATTTCAAAAAGAAT
Found at i:494974 original size:2 final size:2
Alignment explanation
Indices: 494967--495008 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
494957 ATTTATTTTC
*
494967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
495008 A
1 A
495009 GTTATTATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.