Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000692.1 Hibiscus syriacus cultivar Beakdansim tig00001349_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: 1095174
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 5 of 5
Found at i:907349 original size:23 final size:23
Alignment explanation
Indices: 907319--907367 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
907309 AGGCAAGATC
*
907319 GTGTTCGACTGATCACTATGATT
1 GTGTTCGACTGATCACTACGATT
907342 GTGTTCGACTGATCACTACGATT
1 GTGTTCGACTGATCACTACGATT
907365 GTG
1 GTG
907368 CTTACTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (23 bp):
GTGTTCGACTGATCACTACGATT
Found at i:912130 original size:2 final size:2
Alignment explanation
Indices: 912123--912176 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
912113 TTCTATTCGT
912123 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
912165 TA TA TA TA TA TA
1 TA TA TA TA TA TA
912177 CATTTCATAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:914340 original size:2 final size:2
Alignment explanation
Indices: 914333--914384 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
914323 GTACACTTGA
914333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
914375 AT AT AT AT AT
1 AT AT AT AT AT
914385 CAATTTTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:917783 original size:57 final size:57
Alignment explanation
Indices: 917695--917809 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
917685 TTAGGAATAA
917695 TCAAGGACGTAGATAACTTTAGAGAACTTTGAATCATTTCATAAAATCAAGTAACAT
1 TCAAGGACGTAGATAACTTTAGAGAACTTTGAATCATTTCATAAAATCAAGTAACAT
917752 TCAAGGACGTAGATAACTTTAGAGAACTTTGAATCATTTCATAAAATCAAGTAACAT
1 TCAAGGACGTAGATAACTTTAGAGAACTTTGAATCATTTCATAAAATCAAGTAACAT
917809 T
1 T
917810 TCCAAAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (57 bp):
TCAAGGACGTAGATAACTTTAGAGAACTTTGAATCATTTCATAAAATCAAGTAACAT
Found at i:918132 original size:39 final size:39
Alignment explanation
Indices: 918089--918172 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
918079 TTTGATCGCC
918089 CATTCTGACCCACACTAGTAGATGAACTTATCTGAGCTG
1 CATTCTGACCCACACTAGTAGATGAACTTATCTGAGCTG
*
918128 CATTCTGACCCACACTAGTAGATGAACTTATCTGATCTG
1 CATTCTGACCCACACTAGTAGATGAACTTATCTGAGCTG
918167 C-TTCTG
1 CATTCTG
918173 TTCCATTTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 5 0.11
39 39 0.89
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (39 bp):
CATTCTGACCCACACTAGTAGATGAACTTATCTGAGCTG
Found at i:918728 original size:21 final size:21
Alignment explanation
Indices: 918680--918730 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
918670 AAAAATCACC
* *
918680 TTCTCAACTTGGACGGCTGTT
1 TTCTCATCTTGGACAGCTGTT
918701 TTCTCATCTTGGACAGCTGTT
1 TTCTCATCTTGGACAGCTGTT
918722 TTCTCATCT
1 TTCTCATCT
918731 CTGATTGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (21 bp):
TTCTCATCTTGGACAGCTGTT
Found at i:923358 original size:9 final size:8
Alignment explanation
Indices: 923338--923402 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
923328 ACCCTTTTAC
923338 TTTT-TTA
1 TTTTATTA
923345 TTTTATTCA
1 TTTTATT-A
*
923354 TTTTATTT
1 TTTTATTA
*
923362 TCTTTCTTTA
1 T-TTT-ATTA
923372 TTTTAATTTA
1 TTTT-A-TTA
*
923382 TTTTATCA
1 TTTTATTA
923390 TTTTATTA
1 TTTTATTA
923398 TTTTA
1 TTTTA
923403 ATTTATTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
7 4 0.09
8 17 0.37
9 15 0.33
10 10 0.22
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTATTA
Found at i:923366 original size:26 final size:25
Alignment explanation
Indices: 923332--923418 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 25
923322 TAACTAACCC
923332 TTTTACTTTTTTATTTTATTCATTTTA
1 TTTT-CTTTTTTATTTTATT-ATTTTA
923359 TTTTCTTTCTTTATTTTA--A-TTTA
1 TTTTCTTT-TTTATTTTATTATTTTA
* * *
923382 TTTTATCATTTTATTATT-TTAATTTA
1 TTTTCT-TTTTTATT-TTATTATTTTA
923408 TTTTCTTTTTT
1 TTTTCTTTTTT
923419 TTACTAACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
23 15 0.30
24 4 0.08
25 5 0.10
26 13 0.26
27 13 0.26
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTCTTTTTTATTTTATTATTTTA
Found at i:923383 original size:10 final size:9
Alignment explanation
Indices: 923341--923421 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
923331 CTTTTACTTT
923341 TTTATTTTA
1 TTTATTTTA
*
923350 TTCATTTTA
1 TTTATTTTA
*
923359 TTT-TCTTTC
1 TTTAT-TTTA
923368 TTTATTTTAA
1 TTTATTTT-A
923378 TTTATTTTA
1 TTTATTTTA
*
923387 -TCATTTTA
1 TTTATTTTA
923395 -TTATTTTAA
1 TTTATTTT-A
*
923404 TTTATTTTC
1 TTTATTTTA
*
923413 TTTTTTTTA
1 TTTATTTTA
923422 CTAACTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
8 14 0.24
9 28 0.48
10 16 0.28
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTATTTTA
Found at i:923408 original size:36 final size:37
Alignment explanation
Indices: 923341--923411 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
923331 CTTTTACTTT
**
923341 TTTATTTTATTCATTTTATTTTCTTTCTTTATTTTAA
1 TTTATTTTATTCATTTTATTTTCTTAATTTATTTTAA
923378 TTTATTTTA-TCATTTTATTATT-TTAATTTATTTT
1 TTTATTTTATTCATTTTATT-TTCTTAATTTATTTT
923412 CTTTTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 20 0.65
37 11 0.35
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (37 bp):
TTTATTTTATTCATTTTATTTTCTTAATTTATTTTAA
Found at i:923431 original size:45 final size:46
Alignment explanation
Indices: 923336--923431 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 46
923326 TAACCCTTTT
* * *
923336 ACTTTT-TTATTTTATTCATTTTATTTTCTTTCTTTATTTTAATTT
1 ACTTTTATCATTTTATTCATTTTATTTTCTTTCTTTATTTTAACTA
*
923381 A-TTTTATCATTTTATT-ATTTTAATTTAT-TTTCTTT-TTTTTACTA
1 ACTTTTATCATTTTATTCATTTT-ATTT-TCTTTCTTTATTTTAACTA
923425 ACTTTTA
1 ACTTTTA
923432 ATTATCTCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
44 16 0.37
45 26 0.60
46 1 0.02
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (46 bp):
ACTTTTATCATTTTATTCATTTTATTTTCTTTCTTTATTTTAACTA
Found at i:928932 original size:165 final size:165
Alignment explanation
Indices: 928650--929573 Score: 1244
Period size: 165 Copynumber: 5.6 Consensus size: 165
928640 TAAAAAAAAT
* * * * * * *
928650 ATCATTTATAGCATAACTTAAGTCGAGAAGGGTTATATGCCAACC-AAAGACTTTCGAGTTCGAC
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGAC
* * * * *
928714 TACGCTCAGCTCCAAGGCATATCATTTACAACATAGCTTAAGTCGAAAAGGGCTATCTGCCGAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* *
928779 ACCCTCGAGTTTGATTATACTCAGCTTCGAGGGCAC
130 ACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* *
928815 ATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGTCACCAAAAGACCTTCAAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * * * * *
928880 ACGCTCAGCTCCAAGGCATATCATTTGCGGTATAGCTCAAGGCTAGAAGGGCTATCTTCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
928945 CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
131 CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * * *
928980 ATCATTTACAGCACAACTCAATGCTAGAAGGGTTGTCTTTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * *
929045 ACGTTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * ** * *
929110 CCTTCGAGTTCGACTACGTTCAGC-TCCAAGGCAC
131 CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * *
929144 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* *
929208 ACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * * * *
929273 CCTTCGAGTTCGATTACGCTCAGC-TCCAAGGCAT
131 CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * *
929307 ATCATTTACAGCATAACTCAGGGCTATAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGATT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * *
929372 ACGCTCAGCTCTAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
*
929437 CCCTCGAGTTCGATTACACTCAACTTCGAGGGCAC
131 CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * *
929472 ATAATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAGAAGACCTTTGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * *
929537 ACGCTCTGCTACAAGGCACATCATTTGTAGCATAGCT
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCT
929574 CAAGGCAAGA
Statistics
Matches: 667, Mismatches: 89, Indels: 6
0.88 0.12 0.01
Matches are distributed among these distances:
163 148 0.22
164 149 0.22
165 370 0.55
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:930901 original size:22 final size:21
Alignment explanation
Indices: 930827--930902 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
930817 ACCCTTTTAC
*
930827 TTTTTTACTTTATTCATTTTAT
1 TTTTTTATTTTA-TCATTTTAT
* * *
930849 TTTCTTTTTTTTTTAATTTT-T
1 TTT-TTTATTTTATCATTTTAT
* *
930870 TTTATCATTTTATCATTTTAT
1 TTTTTTATTTTATCATTTTAT
930891 TTATTTTATTTT
1 TT-TTTTATTTT
930903 TTTACTAACT
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 11 0.28
21 7 0.17
22 16 0.40
23 6 0.15
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTATTTTATCATTTTAT
Found at i:931618 original size:2 final size:2
Alignment explanation
Indices: 931611--931641 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
931601 TTTCAATTTA
931611 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 A
931642 ATCTTCAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:937653 original size:6 final size:6
Alignment explanation
Indices: 937629--937667 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
937619 TAGCTCTTCG
*
937629 TTCTCT ATTCCTCT CTCTCT TTCTCT TTCTCT TTCTCT T
1 TTCTCT -TT-CTCT TTCTCT TTCTCT TTCTCT TTCTCT T
937668 CAAATCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 22 0.76
7 3 0.10
8 4 0.14
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.62
Consensus pattern (6 bp):
TTCTCT
Found at i:938234 original size:18 final size:19
Alignment explanation
Indices: 938199--938235 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
938189 CACGGAATGT
938199 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
938219 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
938236 GGATCACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:938456 original size:32 final size:31
Alignment explanation
Indices: 938371--938456 Score: 77
Period size: 37 Copynumber: 2.6 Consensus size: 31
938361 TTGTATAATA
938371 TTAC-AAATTATAAAATATTTATATATTTTCT
1 TTACAAAATTA-AAAATATTTATATATTTTCT
*
938402 TTAAAAAATTAAATTCATAATATTTATATAATTTGT-T
1 TTACAAAATT-AA---A-AATATTTATAT-ATTT-TCT
938439 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
938457 AAAAAATGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
31 3 0.07
32 11 0.24
33 2 0.04
35 1 0.02
36 13 0.29
37 14 0.31
38 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.47
Consensus pattern (31 bp):
TTACAAAATTAAAAATATTTATATATTTTCT
Found at i:951750 original size:24 final size:20
Alignment explanation
Indices: 951694--951751 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
951684 TTTCCCTTGA
*
951694 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
951714 AGTTCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
951737 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
951752 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:955010 original size:64 final size:63
Alignment explanation
Indices: 954887--955023 Score: 143
Period size: 64 Copynumber: 2.2 Consensus size: 63
954877 TCTTTAACAT
* * * *
954887 GTGCATCGATGCACTACCCATGCATGGATACACAAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTTCATTTTAA-AGA
* * * ** *
954951 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCGATGTTTTCAT-TTTAAAGA
955014 GTGCATCGAT
1 GTGCATCGAT
955024 ACACATTGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
63 18 0.30
64 43 0.70
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:959123 original size:16 final size:16
Alignment explanation
Indices: 959102--959135 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
959092 TTTTAAAGCT
959102 TCAAACAAAATAGTGG
1 TCAAACAAAATAGTGG
959118 TCAAACAAAATAGTGG
1 TCAAACAAAATAGTGG
959134 TC
1 TC
959136 TGTTATCAAG
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:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (16 bp):
TCAAACAAAATAGTGG
Found at i:961264 original size:26 final size:26
Alignment explanation
Indices: 961228--961283 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
961218 AGCAAGGCAT
961228 TGCCGCCTATAGTGTCCTATACTTAA
1 TGCCGCCTATAGTGTCCTATACTTAA
*
961254 TGCCGCCTATAGTGTCCTATACTTGA
1 TGCCGCCTATAGTGTCCTATACTTAA
961280 TGCC
1 TGCC
961284 CCCTCCCCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.34
Consensus pattern (26 bp):
TGCCGCCTATAGTGTCCTATACTTAA
Found at i:966677 original size:11 final size:11
Alignment explanation
Indices: 966661--966687 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
966651 AGAATTCAAA
966661 GAAAACTCATC
1 GAAAACTCATC
966672 GAAAACTCATC
1 GAAAACTCATC
966683 GAAAA
1 GAAAA
966688 GAACTCCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.22, G:0.11, T:0.15
Consensus pattern (11 bp):
GAAAACTCATC
Found at i:971743 original size:27 final size:27
Alignment explanation
Indices: 971691--971745 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
971681 AAATACACAA
*
971691 ATAAATAAAATAATAAATGGTAAAAAT
1 ATAAATAAAATAATAAATGATAAAAAT
*
971718 ATAAA-AATAATAATAAATTATGAAAAAT
1 ATAAATAA-AATAATAAATGAT-AAAAAT
971746 GAAGATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.08
27 16 0.67
28 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (27 bp):
ATAAATAAAATAATAAATGATAAAAAT
Found at i:973400 original size:21 final size:21
Alignment explanation
Indices: 973374--973461 Score: 81
Period size: 23 Copynumber: 4.0 Consensus size: 21
973364 ATAAATAATA
*
973374 AAATATTTATTTATTATTCAT
1 AAATATTTATTTAATATTCAT
*
973395 AAATA-TAATTTAAATATTCAT
1 AAATATTTATTT-AATATTCAT
973416 GAATATATTTGATTT-ATAATTCAT
1 -AA-ATATTT-ATTTAAT-ATTCAT
973440 AAATATATCTATTTAATATTCA
1 AAATAT-T-TATTTAATATTCA
973462 AAACAATTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
20 5 0.09
21 13 0.24
22 6 0.11
23 17 0.31
24 10 0.18
25 4 0.07
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTATTTAATATTCAT
Found at i:977537 original size:17 final size:17
Alignment explanation
Indices: 977515--977548 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
977505 TTTTAATTAT
977515 TAAATTTTACATTTTGC
1 TAAATTTTACATTTTGC
977532 TAAATTTTACATTTTGC
1 TAAATTTTACATTTTGC
977549 CCTCTTCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
TAAATTTTACATTTTGC
Found at i:978743 original size:6 final size:6
Alignment explanation
Indices: 978732--978759 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
978722 GCGGATTACA
978732 CTCTAC CTCTAC CTCTAC CTCTAC CTCT
1 CTCTAC CTCTAC CTCTAC CTCTAC CTCT
978760 GATGAAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.50, G:0.00, T:0.36
Consensus pattern (6 bp):
CTCTAC
Found at i:979394 original size:21 final size:22
Alignment explanation
Indices: 979354--979397 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
979344 ATTGTCATAG
*
979354 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
*
979376 GGGAACCGA-TACTCTGCTACA
1 GGGAACCGATTACCCTGCTACA
979397 G
1 G
979398 TACTTCCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTACCCTGCTACA
Found at i:980177 original size:21 final size:21
Alignment explanation
Indices: 980151--980210 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
980141 CATATGAAAC
*
980151 TTGTCCCGAAGGACCATTGTA
1 TTGTCCCGAAGGACCACTGTA
980172 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
980193 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
980211 ATAACCCTCG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:980448 original size:2 final size:2
Alignment explanation
Indices: 980441--980470 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
980431 ATTCCCATAA
980441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
980471 CATTTTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:983203 original size:29 final size:31
Alignment explanation
Indices: 983156--983213 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
983146 TTGAGTCACG
983156 AAATGAAATGTTAGACACTAAACT-GAAATA
1 AAATGAAATGTTAGACACTAAACTAGAAATA
* *
983186 AAAT-AAATTTTAGGCACTAAACTAGAAA
1 AAATGAAATGTTAGACACTAAACTAGAAA
983214 AACATGCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.24
Consensus pattern (31 bp):
AAATGAAATGTTAGACACTAAACTAGAAATA
Found at i:1003828 original size:19 final size:19
Alignment explanation
Indices: 1003804--1003874 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
1003794 GAATGCCATT
*
1003804 AGTGCATCGATGCATAAGG
1 AGTGCATCCATGCATAAGG
*
1003823 AGTGCATCGATGCATAAGG
1 AGTGCATCCATGCATAAGG
1003842 AGTGCATCCATGCATAAGG
1 AGTGCATCCATGCATAAGG
1003861 AGTGCATCCATGCA
1 AGTGCATCCATGCA
1003875 CCCGCTTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (19 bp):
AGTGCATCCATGCATAAGG
Found at i:1004569 original size:38 final size:38
Alignment explanation
Indices: 1004511--1004587 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
1004501 TCGAGAGATT
* *
1004511 ATCAGTGGTCTTTCAAGACATAGTGGTTCTTCGGAACA
1 ATCAGTGGTCTTTCAAGACATAATGGTTATTCGGAACA
* *
1004549 ATCAGTGGTCCTTT-AGGACATAATGGTTATTCGGGACA
1 ATCAGTGGT-CTTTCAAGACATAATGGTTATTCGGAACA
1004587 A
1 A
1004588 ATATTCAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 30 0.88
39 4 0.12
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (38 bp):
ATCAGTGGTCTTTCAAGACATAATGGTTATTCGGAACA
Found at i:1011409 original size:18 final size:18
Alignment explanation
Indices: 1011386--1011438 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1011376 AGGGATTATC
1011386 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1011404 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1011422 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
1011439 AATATTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1014378 original size:16 final size:17
Alignment explanation
Indices: 1014354--1014386 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1014344 TTTATACCAA
1014354 TTTAAATT-AAATATTT
1 TTTAAATTAAAATATTT
*
1014370 TTTATATTAAAATATTT
1 TTTAAATTAAAATATTT
1014387 AAAATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAATTAAAATATTT
Found at i:1014746 original size:22 final size:22
Alignment explanation
Indices: 1014695--1014752 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1014685 TCACTCTCTA
* *
1014695 CGACGACATCCATCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
1014717 TGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
**
1014739 CGGTGAAATCCGTC
1 CGACGAAATCCGTC
1014753 TATCTCCATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.21
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:1015892 original size:21 final size:21
Alignment explanation
Indices: 1015868--1015919 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1015858 ACCTATTTCT
1015868 GAGGACCTAATATTATTGGTA
1 GAGGACCTAATATTATTGGTA
*
1015889 GAGGACTTAATATTATTGGTA
1 GAGGACCTAATATTATTGGTA
*
1015910 AAGGACCTAA
1 GAGGACCTAA
1015920 ATGCATAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (21 bp):
GAGGACCTAATATTATTGGTA
Found at i:1016837 original size:21 final size:21
Alignment explanation
Indices: 1016792--1016839 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1016782 AATGGTGCTT
* * *
1016792 TACGTGGTGAGGTATCTACTT
1 TACGTGGTGAGGTAGCGACTC
*
1016813 TACGTGGTGAGGTAGCGGCTC
1 TACGTGGTGAGGTAGCGACTC
1016834 TACGTG
1 TACGTG
1016840 AGATTGTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.31
Consensus pattern (21 bp):
TACGTGGTGAGGTAGCGACTC
Found at i:1017153 original size:21 final size:21
Alignment explanation
Indices: 1017122--1017240 Score: 123
Period size: 21 Copynumber: 5.7 Consensus size: 21
1017112 GATTCACCTG
* *
1017122 TCATTGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
*
1017143 -CTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCCCTC
* *
1017164 TCATCCTTCAAGAGGCCCTTC
1 TCATCGTTCAAGAGGCCCCTC
* *
1017185 TCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
*
1017206 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
1017227 CCATTGTTCGAGAG
1 TCATCGTTCAAGAG
1017241 CCCGATTCAT
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.01
21 78 0.98
22 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1017193 original size:42 final size:41
Alignment explanation
Indices: 1017128--1017227 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 41
1017118 CCTGTCATTG
*
1017128 TTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCC-CTCCTACCGTTCAAGAGGCCCCTATCATCC
* * *
1017170 TTCAAGAGGCCCTTCTCACCGTTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCTCCT-ACCGTTCAAGAGGCCCCTATCATCC
1017212 TTCAAGAGGTCCCTCC
1 TTCAAGAGG-CCCTCC
1017228 CATTGTTCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
41 4 0.08
42 42 0.82
43 5 0.10
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.25
Consensus pattern (41 bp):
TTCAAGAGGCCCTCCTACCGTTCAAGAGGCCCCTATCATCC
Found at i:1018596 original size:13 final size:14
Alignment explanation
Indices: 1018571--1018603 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1018561 AAATTGATGT
1018571 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
1018585 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
1018598 ATTTGT
1 ATTTGT
1018604 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:1018660 original size:64 final size:64
Alignment explanation
Indices: 1018582--1018732 Score: 214
Period size: 64 Copynumber: 2.4 Consensus size: 64
1018572 TTTGTAAAAG
* *
1018582 TTGATTTGT-AAAGTTGATTTGTTTAATTGATGAGGGAATCAGAATTATTTTTTGCTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA
* * *** *
1018645 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGTTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA
*
1018709 TTGATTTGTAAAAGTTTATTTGTT
1 TTGATTTGTAAAAGTTGATTTGTT
1018733 GTTTTAAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 9 0.12
64 69 0.88
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (64 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA
Found at i:1018735 original size:34 final size:37
Alignment explanation
Indices: 1018658--1018736 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
1018648 ATTTGTAAAA
*
1018658 GTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTT
1 GTTG-TTTGTTTAATTGATGTGTAAATAAGTCTTATTT
* *
1018696 TTTGTTTGTTTAATTGATTTGT-AA-AAGT-TTATTT
1 GTTGTTTGTTTAATTGATGTGTAAATAAGTCTTATTT
1018730 GTTGTTT
1 GTTGTTT
1018737 TAAATTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 12 0.32
35 3 0.08
36 2 0.05
37 17 0.46
38 3 0.08
ACGTcount: A:0.23, C:0.01, G:0.16, T:0.59
Consensus pattern (37 bp):
GTTGTTTGTTTAATTGATGTGTAAATAAGTCTTATTT
Found at i:1018841 original size:13 final size:14
Alignment explanation
Indices: 1018810--1018844 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1018800 GAAAGTCAAA
*
1018810 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
1018824 TTCGCGTTGCGA-T
1 TTCGCGTTGCGATT
1018837 TTCGCGTT
1 TTCGCGTT
1018845 TCGTTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.09, C:0.23, G:0.26, T:0.43
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:1018907 original size:19 final size:20
Alignment explanation
Indices: 1018877--1018927 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1018867 TCGCAACGTG
1018877 AATTTGACTTTCGCGTTGCA
1 AATTTGACTTTCGCGTTGCA
*
1018897 AATTT-ACTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTGCA
1018916 AATTTGACTTTC
1 AATTTGACTTTC
1018928 ACAACAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCA
Found at i:1021596 original size:12 final size:12
Alignment explanation
Indices: 1021575--1021608 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1021565 GGTTGCGGGT
*
1021575 TTTGAGATTGTG
1 TTTGATATTGTG
1021587 TTTGATATTGTG
1 TTTGATATTGTG
*
1021599 TTTGGTATTG
1 TTTGATATTG
1021609 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1022504 original size:21 final size:20
Alignment explanation
Indices: 1022447--1022507 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1022437 TGCGAAAACA
*
1022447 AAATTCGCGTTGCGAATTTAG
1 AAATTCGAGTTGCGAATTT-G
*
1022468 AAA-TCGAGTCGCGAATTTG
1 AAATTCGAGTTGCGAATTTG
*
1022487 AAATTCAGTGTTGCGAATTTG
1 AAATTC-GAGTTGCGAATTTG
1022508 GAAAAGCGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.12
20 15 0.44
21 15 0.44
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.33
Consensus pattern (20 bp):
AAATTCGAGTTGCGAATTTG
Found at i:1022543 original size:20 final size:20
Alignment explanation
Indices: 1022520--1022583 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1022510 AAAGCGCAAC
*
1022520 GCGATTTACAGATTCGCGTT
1 GCGATTTACAAATTCGCGTT
*
1022540 GCGATTTACAAATTCGTGTT
1 GCGATTTACAAATTCGCGTT
* *
1022560 GCGATTTACATATTTGCGTT
1 GCGATTTACAAATTCGCGTT
1022580 GCGA
1 GCGA
1022584 ATTTGGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (20 bp):
GCGATTTACAAATTCGCGTT
Found at i:1022547 original size:81 final size:82
Alignment explanation
Indices: 1022449--1022600 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 82
1022439 CGAAAACAAA
* *
1022449 ATTCGCGTTGCGAATTTAGAAA-TCGAGTCGCGAATTTGA-A-ATTCAGTGTTGCGAATTTGGAA
1 ATTCGCGTTGCGAATTTACAAATTCGAGTCGCG-ATTT-ACATATT-AGCGTTGCGAATTTGGAA
1022511 AAGCGCAACGCGATTTACAG
63 AAGCGCAACGCGATTTACAG
* * * *
1022531 ATTCGCGTTGCG-ATTTACAAATTCGTGTTGCGATTTACATATTTGCGTTGCGAATTTGGAAAAT
1 ATTCGCGTTGCGAATTTACAAATTCGAGTCGCGATTTACATATTAGCGTTGCGAATTTGGAAAAG
1022595 CGCAAC
66 CGCAAC
1022601 TCGAATTTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
80 1 0.02
81 37 0.61
82 23 0.38
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (82 bp):
ATTCGCGTTGCGAATTTACAAATTCGAGTCGCGATTTACATATTAGCGTTGCGAATTTGGAAAAG
CGCAACGCGATTTACAG
Found at i:1022605 original size:21 final size:21
Alignment explanation
Indices: 1022579--1022646 Score: 111
Period size: 21 Copynumber: 3.2 Consensus size: 21
1022569 ATATTTGCGT
1022579 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
1022600 CT-CGAATTTGGAAAATCGCAA
1 -TGCGAATTTGGAAAATCGCAA
*
1022621 TGGGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
1022642 TGCGA
1 TGCGA
1022647 TTTACATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24
Consensus pattern (21 bp):
TGCGAATTTGGAAAATCGCAA
Found at i:1025833 original size:2 final size:2
Alignment explanation
Indices: 1025826--1025862 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1025816 TTTAAATGAT
1025826 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 T
1025863 TTCGATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1026275 original size:17 final size:16
Alignment explanation
Indices: 1026253--1026295 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1026243 AGTTTTAAAG
*
1026253 TTAAAAATAAGAAAATT
1 TTAAAAA-AACAAAATT
*
1026270 TTAAAAGAAACAAATTT
1 TTAAAA-AAACAAAATT
1026287 TTAAAAAAA
1 TTAAAAAAA
1026296 TTGTGAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (16 bp):
TTAAAAAAACAAAATT
Found at i:1030165 original size:8 final size:9
Alignment explanation
Indices: 1030145--1030192 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
1030135 ACAAAAATAT
1030145 TTTATTATA
1 TTTATTATA
1030154 TTTATT-TA
1 TTTATTATA
1030162 TTTATTAT-
1 TTTATTATA
1030170 TATTATTATA
1 T-TTATTATA
*
1030180 TTT-TTATT
1 TTTATTATA
1030188 TTTAT
1 TTTAT
1030193 AGGCCCCACA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 16 0.47
9 17 0.50
10 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTATTATA
Found at i:1030192 original size:17 final size:17
Alignment explanation
Indices: 1030145--1030192 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1030135 ACAAAAATAT
*
1030145 TTTATTATATTTATTTA
1 TTTATTATTTTTATTTA
*
1030162 TTTATTATTATTATTATA
1 TTTATTATTTTTATT-TA
1030180 TTT-TTATTTTTAT
1 TTTATTATTTTTAT
1030193 AGGCCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTATTTTTATTTA
Found at i:1030284 original size:33 final size:33
Alignment explanation
Indices: 1030241--1030323 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
1030231 GAAAATAAAT
*
1030241 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGCATTTGAGTCCTATTGAAACACTAAAAC
*
1030274 CAACGCATTTGAGTCATATTGAAACACTAAAAC
1 CAACGCATTTGAGTCCTATTGAAACACTAAAAC
1030307 CGAA-GCATTTTGAGTCC
1 C-AACGCA-TTTGAGTCC
1030324 AAGTAGGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 35 0.78
34 10 0.22
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (33 bp):
CAACGCATTTGAGTCCTATTGAAACACTAAAAC
Found at i:1030871 original size:3 final size:3
Alignment explanation
Indices: 1030858--1030921 Score: 76
Period size: 3 Copynumber: 20.0 Consensus size: 3
1030848 ATGATAATAC
1030858 ATT ATTT ATT ATT ATTT ATTT ATT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1030905 ATTT ATT ATTT ATT ATT
1 A-TT ATT A-TT ATT ATT
1030922 CATTTTTTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.04
3 38 0.68
4 16 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1030886 original size:9 final size:10
Alignment explanation
Indices: 1030858--1030926 Score: 79
Period size: 10 Copynumber: 6.7 Consensus size: 10
1030848 ATGATAATAC
1030858 ATTATTTATT
1 ATTATTTATT
1030868 ATTATTTATTT
1 ATTATTTA-TT
*
1030879 ATTTTATTATT
1 ATTAT-TTATT
1030890 ATTA-TTATT
1 ATTATTTATT
1030899 ATTA-TTATTT
1 ATTATTTA-TT
1030909 ATTATTTATT
1 ATTATTTATT
1030919 ATTCATTT
1 ATT-ATTT
1030927 TTTCTTTCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
9 12 0.23
10 19 0.37
11 18 0.35
12 3 0.06
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTATTTATT
Found at i:1035207 original size:81 final size:81
Alignment explanation
Indices: 1034958--1035836 Score: 494
Period size: 84 Copynumber: 10.7 Consensus size: 81
1034948 GCTTAAGTCG
*
1034958 AGAAGGGCTATCTGCCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
1 AGAAGGGCTATATGCCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
*
1035023 AGCATAACTCAAAGCT
66 AGCATAACTCAAGGCT
* * * * * ** * *
1035039 AGAAGGGTTATCTATCACCAAAGACCTTCGAGTTCGACTACGTTCAGC-TCCAAGGCACATCATT
1 AGAAGGGCTA--TAT-GCCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* * * * *
1035103 TGCAGCATACCTTAAGTCG
63 TACAGCATAACTCAAGGCT
* * *
1035122 AGAAGGGCTATATGTCAAATACCCTCAAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTAC
1 AGAAGGGCTATATGCCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
*
1035187 AACATAACTCAAGGCT
66 AGCATAACTCAAGGCT
* * * * * * * * *
1035203 AGAAGGGTTATCTATGACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGAATATCAT
1 AGAAGGGCTA--TATG-CC-AAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
** * * *
1035267 TTGTAGCATAACTTAAGTCG
62 TTACAGCATAACTCAAGGCT
* * * * * * * *
1035287 AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACGCTCAG-TTCCAAGGCATATCATT
1 AGAAGGGCTATATG-C--CAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* * * **
1035351 TGCAACATAGCTCAAGGAA
63 TACAGCATAACTCAAGGCT
* * * *** *
1035370 AGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGATTATGTTCAGCTTTGAGGGCACATCAT
1 AGAAGGGCTATATG-C--C-AAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
** * * *
1035435 TTGTAGCATAACTTAAGTCG
62 TTACAGCATAACTCAAGGCT
* * * * * * * * * * *
1035455 ATAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCGCATCTT
1 AGAAGGGCTATATG-C--C-AAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
** * * *
1035519 TTGTAGCATAACTTAAGTCG
62 TTACAGCATAACTCAAGGCT
* * * *
1035539 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATCACACTCAGTTTCGAGGGCACATCATTTAC
1 AGAAGGGCTATATGCCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
1035604 AGCATAACTCAAGGCT
66 AGCATAACTCAAGGCT
* * * * * * * *
1035620 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATT
1 AGAAGGGCTATATG---CCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* * * * * *
1035684 TGCAACATAGCTTAAGTCG
63 TACAGCATAACTCAAGGCT
* * * * * * * * *
1035703 AGAAGGGCTATCTACCAAAGACCTTCGAGTTCGACTCCACTCAGC-TCAAAGGCACCATCATTTG
1 AGAAGGGCTATATGCCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCA-CATCATTTA
* *
1035767 CAGCATAGCTCAAGGCA
65 CAGCATAACTCAAGGCT
** * * * * * * *
1035784 AGAAGGTATATCTGTCAAAGACCTTCGAGTTCGATTCCATTCAAC-TCGAGGGC
1 AGAAGGGCTATATGCCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
1035837 GTATCAACCG
Statistics
Matches: 643, Mismatches: 137, Indels: 36
0.79 0.17 0.04
Matches are distributed among these distances:
80 85 0.13
81 154 0.24
82 4 0.01
83 153 0.24
84 157 0.24
85 90 0.14
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (81 bp):
AGAAGGGCTATATGCCAAATACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
AGCATAACTCAAGGCT
Found at i:1035207 original size:164 final size:162
Alignment explanation
Indices: 1034936--1035819 Score: 830
Period size: 164 Copynumber: 5.4 Consensus size: 162
1034926 TAAAGAAACT
* * * * * *
1034936 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAATACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACAAAGACCTTCGAGTTCGATTACGCTCA
* * * * * * *
1035001 GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTATCACCAAAGACCT
66 GCTTCCAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGCTATCT-T-ACCAAAGACCT
*
1035066 TCGAGTTCGACTACGTTCAGCTCCAAGGCACATC
129 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * * * * * * *
1035100 ATTTGCAGCATACCTTAAGTCGAGAAGGGCTATATGTCAAATACCCTCAAGTTTGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACAAAGACCTTCGAGTTCGATTACGCTCA
* * * * *
1035165 GCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACC
66 GCTTCCAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGCTATCT-T-ACC-AAAGACC
* *
1035230 TTCGAGTTCGACTACGCTCAGCTCCAAGGAATATC
128 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
1035265 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACAAAGACCTTCGAGTTCGATTACGC
* * ** *
1035330 TCAG-TTCCAAGGCATATCATTTGCAACATAGCTCAAGGAAAGAAGGGCTAT-TTGCCAACAAAA
63 TCAGCTTCCAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGCTATCTT----ACCAAA
* * * ** *
1035393 GACCTTCGAGTTCGATTATGTTCAGCTTTGAGGGCACATC
124 GACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
* * *
1035433 ATTTGTAGCATAACTTAAGTCGATAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---AC-AAAGACCTTCGAGTTCGATTACG
* * * * * * *
1035498 CTCAGC-TCCAAGGCGCATCTTTTGTAGCATAACTTAAGTCGAGAAGGGCTATC-TGCCAAAGAC
62 CTCAGCTTCCAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGCTATCTTACCAAAGAC
* * * * *
1035561 CCTCGAGTTCGA-TCACACTCAGTTTCGAGGGCACATC
127 CTTCGAGTTCGACT-ACGCTCAG-CTCCAAGGCACATC
* * * * *
1035598 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG--A-CAAAGACCTTCGAGTTCGATTACGC
* * * *
1035663 TCAGC-TCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATC-TACCAAAGACC
63 TCAGCTTCCAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGCTATCTTACCAAAGACC
* * *
1035726 TTCGAGTTCGACTCCACTCAGCTCAAAGGCACCATC
128 TTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATC
* * * * *
1035762 ATTTGCAGCATAGCTCAAGGCAAGAA-GGTATATCTGTCAAAGACCTTCGAGTTCGATT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGT-TATCTGACAAAGACCTTCGAGTTCGATT
1035820 CCATTCAACT
Statistics
Matches: 619, Mismatches: 84, Indels: 37
0.84 0.11 0.05
Matches are distributed among these distances:
161 20 0.03
163 10 0.02
164 246 0.40
165 139 0.22
166 1 0.00
167 65 0.11
168 74 0.12
169 64 0.10
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (162 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACAAAGACCTTCGAGTTCGATTACGCTCA
GCTTCCAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGCTATCTTACCAAAGACCTTC
GAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:1036271 original size:33 final size:33
Alignment explanation
Indices: 1036234--1036298 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1036224 AAAAATAAAT
1036234 CAACGTATTTGAGTCATATTAAAACACTAAAAC
1 CAACGTATTTGAGTCATATTAAAACACTAAAAC
* *
1036267 CAACGTATTTGAGTCCTATTGAAACACTAAAA
1 CAACGTATTTGAGTCATATTAAAACACTAAAA
1036299 TCAAAGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (33 bp):
CAACGTATTTGAGTCATATTAAAACACTAAAAC
Found at i:1036861 original size:3 final size:3
Alignment explanation
Indices: 1036849--1036907 Score: 66
Period size: 3 Copynumber: 18.3 Consensus size: 3
1036839 AATGATAATA
1036849 TAT TATT TAT TAT TATT TAT TATT TAT T-T TAT TAT TAT TAT TAT TATT
1 TAT TA-T TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T
1036897 TATT TAT TAT T
1 TA-T TAT TAT T
1036908 CATTTTTTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.04
3 33 0.65
4 16 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:1038957 original size:24 final size:24
Alignment explanation
Indices: 1038920--1038965 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1038910 AGATTGAGTT
*
1038920 AAACATAAATGAACGAACATAAAC
1 AAACATAAACGAACGAACATAAAC
*
1038944 AAACATAACCGAACGAACATAA
1 AAACATAAACGAACGAACATAA
1038966 CCGAACTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.61, C:0.20, G:0.09, T:0.11
Consensus pattern (24 bp):
AAACATAAACGAACGAACATAAAC
Found at i:1038964 original size:14 final size:14
Alignment explanation
Indices: 1038945--1038971 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1038935 AACATAAACA
1038945 AACATAACCGAACG
1 AACATAACCGAACG
1038959 AACATAACCGAAC
1 AACATAACCGAAC
1038972 TTTCACGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.30, G:0.11, T:0.07
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:1039324 original size:19 final size:19
Alignment explanation
Indices: 1039302--1039340 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1039292 TAATAGTAAT
1039302 AATAATAAACAATAAATAA
1 AATAATAAACAATAAATAA
*
1039321 AATAATAAATAATAAATAA
1 AATAATAAACAATAAATAA
1039340 A
1 A
1039341 TGTTAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAATAAACAATAAATAA
Found at i:1039330 original size:7 final size:7
Alignment explanation
Indices: 1039298--1039339 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
1039288 TTAATAATAG
1039298 TAAT-AA
1 TAATAAA
1039304 TAATAAA
1 TAATAAA
*
1039311 CAATAAA
1 TAATAAA
1039318 T-A-AAA
1 TAATAAA
1039323 TAATAAA
1 TAATAAA
1039330 TAATAAA
1 TAATAAA
1039337 TAA
1 TAA
1039340 ATGTTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.13
6 6 0.19
7 21 0.68
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (7 bp):
TAATAAA
Found at i:1045697 original size:12 final size:12
Alignment explanation
Indices: 1045680--1045706 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1045670 TGGTCTGTTA
1045680 CAGTTACAGTTT
1 CAGTTACAGTTT
1045692 CAGTTACAGTTT
1 CAGTTACAGTTT
1045704 CAG
1 CAG
1045707 ACACACCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (12 bp):
CAGTTACAGTTT
Found at i:1050143 original size:193 final size:193
Alignment explanation
Indices: 1049811--1050887 Score: 1751
Period size: 193 Copynumber: 5.6 Consensus size: 193
1049801 CTTCGATTAA
* *
1049811 TCGGTTTGATATTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCACTTTCGATTATG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
** * * ** *
1049876 ACACTGTTCCTTCGTGATAAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATATGGTTCC
66 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCC
* * *
1049941 TTCGTGATGAGGAAGTCTTATTGTCTAAGGGTGACACTGCTCCTTCGTGATTAGGAGATCTGG
131 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
* * *
1050004 TCAGTTTGATGTTGAAGACGACATTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTACG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
* * **
1050069 ACGTTGTTCCTTCGTAATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATACGGTTCC
66 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCC
* *
1050134 TTCGTGATGAGGAAGTGTGATTGTCTGAGGGTGACACTACTCCTTCGTGATGAGGAGATCTGG
131 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
** *
1050197 TCGGTTTGATGTTGAAGATAACACTGCTCATCCGCGATGAAGAGATCAGGTCGCTTTCGATTATG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
*
1050262 ACGTTGTTCCTTCGTGATGAGAAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCC
66 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCC
1050327 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
131 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
*
1050390 TCGGTTTAATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
* * *
1050455 ACG-TATTCATTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGATTCC
66 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCC
*
1050519 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGATATCTGG
131 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
* * * *
1050582 TCAGTTTGATGTTGAAGACGACACTGCTCATCTGCGATGAAGAGATCGGGTCGTTTTCGAGTATG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
* * *
1050647 ACGTTGTTCCTTCATGATGAGGAAATTAGGTTAATCTGGAGATAATTTGGGGACAATACGGTTCC
66 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCC
1050712 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
131 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
** *
1050775 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCATTTTCGAGTATG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
** * *
1050840 ACACTATTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATGATTT
66 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTT
1050888 CATTCAGAAA
Statistics
Matches: 824, Mismatches: 59, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
192 182 0.22
193 642 0.78
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (193 bp):
TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCC
TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
Found at i:1050659 original size:385 final size:385
Alignment explanation
Indices: 1049814--1050887 Score: 1752
Period size: 385 Copynumber: 2.8 Consensus size: 385
1049804 CGATTAATCG
* * *
1049814 GTTTGATATTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCACTTTCGATTATGACA
1 GTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGACG
* * * ** *
1049879 CTGTTCCTTCGTGATAAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATATGGTTCCTTC
66 TTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCCTTC
* * * *
1049944 GTGATGAGGAAGTCTTATTGTCTAAGGGTGACACTGCTCCTTCGTGATTAGGAGATCTGGTCAGT
131 GTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGT
* *
1050009 TTGATGTTGAAGACGACATTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTACGACGTT
196 TTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGACG-T
* * * ** *
1050074 GTTCCTTCGTAATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATACGGTTCCTTCGT
260 ATTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGATTCCTTCGT
* *
1050139 GATGAGGAAGTGTGATTGTCTGAGGGTGACACTACTCCTTCGTGATGAGGAGATCTGGTCG
325 GATGAGGAAGTCTGATTGTCTGAGGGTGACACTACTCCTTCGTGATGAGGAGATCTGGTCA
** *
1050200 GTTTGATGTTGAAGATAACACTGCTCATCCGCGATGAAGAGATCAGGTCGCTTTCGATTATGACG
1 GTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGACG
*
1050265 TTGTTCCTTCGTGATGAGAAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCCTTC
66 TTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCCTTC
1050330 GTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGT
131 GTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGT
*
1050395 TTAATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGACGTA
196 TTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGACGTA
*
1050460 TTCATTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGATTCCTTCGTG
261 TTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGATTCCTTCGTG
* *
1050525 ATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGATATCTGGTCA
326 ATGAGGAAGTCTGATTGTCTGAGGGTGACACTACTCCTTCGTGATGAGGAGATCTGGTCA
* * *
1050585 GTTTGATGTTGAAGACGACACTGCTCATCTGCGATGAAGAGATCGGGTCGTTTTCGAGTATGACG
1 GTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGACG
* * *
1050650 TTGTTCCTTCATGATGAGGAAATTAGGTTAATCTGGAGATAATTTGGGGACAATACGGTTCCTTC
66 TTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCCTTC
1050715 GTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGT
131 GTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGT
** * *
1050780 TTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCATTTTCGAGTATGACACT
196 TTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGAC-GT
*
1050845 ATTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATGATTT
260 ATTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTT
1050888 CATTCAGAAA
Statistics
Matches: 639, Mismatches: 48, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
385 359 0.56
386 280 0.44
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (385 bp):
GTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGACG
TTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCCTTC
GTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGT
TTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATGACGTA
TTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGATTCCTTCGTG
ATGAGGAAGTCTGATTGTCTGAGGGTGACACTACTCCTTCGTGATGAGGAGATCTGGTCA
Found at i:1063934 original size:19 final size:18
Alignment explanation
Indices: 1063910--1063954 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1063900 ACATGTGCTG
*
1063910 GTGCTGGTAAGTAGAGCAT
1 GTGCTGGT-ACTAGAGCAT
*
1063929 GTGCTGGTACTGGAGCAT
1 GTGCTGGTACTAGAGCAT
1063947 GTGCTGGT
1 GTGCTGGT
1063955 GCTGGTGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.18, C:0.13, G:0.40, T:0.29
Consensus pattern (18 bp):
GTGCTGGTACTAGAGCAT
Found at i:1063946 original size:18 final size:18
Alignment explanation
Indices: 1063923--1063959 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1063913 CTGGTAAGTA
1063923 GAGCATGTGCTGGTACTG
1 GAGCATGTGCTGGTACTG
*
1063941 GAGCATGTGCTGGTGCTG
1 GAGCATGTGCTGGTACTG
1063959 G
1 G
1063960 TGTGGAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (18 bp):
GAGCATGTGCTGGTACTG
Found at i:1063980 original size:24 final size:24
Alignment explanation
Indices: 1063901--1063996 Score: 74
Period size: 24 Copynumber: 4.0 Consensus size: 24
1063891 TGTGCAGCCA
*
1063901 CATGTGCTGGTGCTGGTA-AGTAGAG
1 CATGTGCTGGTG-TGG-AGAGTGGAG
* *
1063926 CATGTGCTGGTACTGGAGCA-T-GTG
1 CATGTGCTGGT-GTGGAG-AGTGGAG
1063950 C-TGGTGCTGGTGTGGAGAGTGGAG
1 CAT-GTGCTGGTGTGGAGAGTGGAG
* *
1063974 CATGTGCTGGAGTGGATAGTGGA
1 CATGTGCTGGTGTGGAGAGTGGA
1063997 AATTGTACAG
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
22 1 0.02
23 7 0.12
24 33 0.57
25 16 0.28
26 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.44, T:0.27
Consensus pattern (24 bp):
CATGTGCTGGTGTGGAGAGTGGAG
Found at i:1064592 original size:34 final size:36
Alignment explanation
Indices: 1064466--1064629 Score: 167
Period size: 34 Copynumber: 4.6 Consensus size: 36
1064456 TTTTAAGAAT
*
1064466 ATATAATATATATAGTTTTTAAAACGGTTTTGAAAAC
1 ATATAATATATATA-TTTTTAAAACGATTTTGAAAAC
* * * *
1064503 ATATAATATATGATCTTTTAAAAATGGTTTTGAAAAC
1 ATATAATATAT-ATATTTTTAAAACGATTTTGAAAAC
*
1064540 GTATAATATATATA--TTTAAAACGATTTTGAAAAC
1 ATATAATATATATATTTTTAAAACGATTTTGAAAAC
* *
1064574 ATATAATATA-AT-TTTTTAAAACATATTTTTAAAA-
1 ATATAATATATATATTTTTAAAAC-GATTTTGAAAAC
*
1064608 ATATAGTATTATATAGTTTTTA
1 ATATAATA-TATATA-TTTTTA
1064630 TTATTATATT
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
33 2 0.02
34 41 0.38
35 11 0.10
36 4 0.04
37 41 0.38
38 8 0.07
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
ATATAATATATATATTTTTAAAACGATTTTGAAAAC
Found at i:1064621 original size:71 final size:71
Alignment explanation
Indices: 1064455--1064629 Score: 192
Period size: 71 Copynumber: 2.4 Consensus size: 71
1064445 TCAAATATAG
* * *
1064455 TTTTTAAGAATATATAATATATATAGTTTTTAAAACGGTTTTGAAAACATATAATATATGATCTT
1 TTTTTAAAAATATAT-AT-TATATAGTATTTAAAACGATTTTGAAAACATATAATATA-GATCTT
*
1064520 TTAAAAATG
63 TTAAAAATA
* * ** * *
1064529 GTTTTGAAAACGTATAATATATA-TATTTAAAACGATTTTGAAAACATATAATATA-ATTTTTTA
1 TTTTTAAAAATATATATTATATAGTATTTAAAACGATTTTGAAAACATATAATATAGATCTTTTA
1064592 AAACATA
66 AAA-ATA
*
1064599 TTTTTAAAAATATAGTATTATATAGTTTTTA
1 TTTTTAAAAATATA-TATTATATAGTATTTA
1064630 TTATTATATT
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
69 10 0.12
70 12 0.15
71 38 0.46
72 11 0.13
73 1 0.01
74 10 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (71 bp):
TTTTTAAAAATATATATTATATAGTATTTAAAACGATTTTGAAAACATATAATATAGATCTTTTA
AAAATA
Found at i:1064633 original size:14 final size:13
Alignment explanation
Indices: 1064614--1064683 Score: 54
Period size: 14 Copynumber: 5.3 Consensus size: 13
1064604 AAAAATATAG
1064614 TATTATATAGTTTT
1 TATTATATA-TTTT
*
1064628 TATTAT-TATATT
1 TATTATATATTTT
* *
1064640 TAGTATATATTAT
1 TATTATATATTTT
*
1064653 TATTTATATATTAT
1 TA-TTATATATTTT
*
1064667 TATT-TATTTTATT
1 TATTATATATT-TT
1064680 TATT
1 TATT
1064684 TATCTCATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
12 13 0.28
13 15 0.33
14 18 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TATTATATATTTT
Found at i:1064678 original size:23 final size:26
Alignment explanation
Indices: 1064643--1064706 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 26
1064633 TTATATTTAG
1064643 TATA-TATTATTATTTATATAT-T-AT
1 TATATTATT-TTATTTATATATCTCAT
*
1064667 TAT-TTATTTTATTTATTTATCTCAT
1 TATATTATTTTATTTATATATCTCAT
*
1064692 TTTATTATTTTATTT
1 TATATTATTTTATTT
1064707 CAGATCCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 11 0.32
24 8 0.24
25 4 0.12
26 11 0.32
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (26 bp):
TATATTATTTTATTTATATATCTCAT
Found at i:1065965 original size:37 final size:37
Alignment explanation
Indices: 1065880--1065996 Score: 152
Period size: 37 Copynumber: 3.3 Consensus size: 37
1065870 TAAATTATTA
* * *
1065880 TTTTTTATTTATTCTAAAATTTAATA-TTTCTT--TC
1 TTTTTTATTTCTTTTAAAATTTAATATTTTCTTCATT
* *
1065914 CTTTTTATTTCTTTTAAAAATTAATATTTTCTTCATT
1 TTTTTTATTTCTTTTAAAATTTAATATTTTCTTCATT
*
1065951 TTTTTTATTTCTTTTAAAATTTAACATTTTCTTCA-T
1 TTTTTTATTTCTTTTAAAATTTAATATTTTCTTCATT
1065987 TTTTTTATTT
1 TTTTTTATTT
1065997 ATTTCTCTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
34 22 0.31
35 6 0.08
36 11 0.15
37 33 0.46
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (37 bp):
TTTTTTATTTCTTTTAAAATTTAATATTTTCTTCATT
Found at i:1073277 original size:6 final size:6
Alignment explanation
Indices: 1073266--1073290 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1073256 CCACCGAAGC
1073266 TGGTTT TGGTTT TGGTTT TGGTTT T
1 TGGTTT TGGTTT TGGTTT TGGTTT T
1073291 TGTCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (6 bp):
TGGTTT
Found at i:1074192 original size:51 final size:47
Alignment explanation
Indices: 1074098--1074215 Score: 118
Period size: 49 Copynumber: 2.5 Consensus size: 47
1074088 GAAATAATCA
* * *
1074098 AAATAAAAAAAATAAT--TAAATATATATATGTTAATAATAGGTATAC
1 AAATAAATAAAATAATAGTATATATATATATATTAATAATAGGTAT-C
*
1074144 AAATAAAATAAAA-AATACGTATATATATATATATATACATAA-ATGGTATG
1 AAAT-AAATAAAATAATA-GTATATATATATATAT-TA-ATAATA-GGTATC
1074194 AAATAAATAAAATAATAGTATA
1 AAATAAATAAAATAATAGTATA
1074216 AGTATTAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
46 7 0.12
47 7 0.12
49 26 0.43
50 11 0.18
51 9 0.15
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (47 bp):
AAATAAATAAAATAATAGTATATATATATATATTAATAATAGGTATC
Found at i:1077272 original size:8 final size:7
Alignment explanation
Indices: 1077244--1077278 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1077234 ACCCACCTTA
1077244 TTTTTCT
1 TTTTTCT
*
1077251 TTTCTCT
1 TTTTTCT
1077258 TTTTTCT
1 TTTTTCT
1077265 TTTGTTCT
1 TTT-TTCT
1077273 TTTTTC
1 TTTTTC
1077279 AATTTAGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:1089908 original size:26 final size:28
Alignment explanation
Indices: 1089872--1089937 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
1089862 GATTTAACAA
* *
1089872 AAAGGGGGAGAAGTG-TA-AAATGTTTT
1 AAAGGGGGAGAAATGTTAGAAATGTTAT
1089898 AAAGGGGGAGAAATGTTAGAAATGTTAT
1 AAAGGGGGAGAAATGTTAGAAATGTTAT
1089926 AGTAAGGGGGAG
1 A--AAGGGGGAG
1089938 TAATTTCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 14 0.41
27 2 0.06
28 9 0.26
30 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.38, T:0.23
Consensus pattern (28 bp):
AAAGGGGGAGAAATGTTAGAAATGTTAT
Found at i:1090297 original size:20 final size:20
Alignment explanation
Indices: 1090272--1090311 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1090262 TTTTTAAGGG
1090272 CATGCACCGATGCACCAATT
1 CATGCACCGATGCACCAATT
* *
1090292 CATGCATCGATGCATCAATT
1 CATGCACCGATGCACCAATT
1090312 AATATCTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (20 bp):
CATGCACCGATGCACCAATT
Found at i:1090369 original size:18 final size:18
Alignment explanation
Indices: 1090346--1090386 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1090336 TTATGCATCA
1090346 ATGCACTCAGTGCATTTG
1 ATGCACTCAGTGCATTTG
1090364 ATGCACTCAGTGCATTTG
1 ATGCACTCAGTGCATTTG
1090382 ATGCA
1 ATGCA
1090387 TCGATGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (18 bp):
ATGCACTCAGTGCATTTG
Done.