Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001207.1 Hibiscus syriacus cultivar Beakdansim tig00002388_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: 122331
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9286 original size:3 final size:3
Alignment explanation
Indices: 9278--9303 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9268 TTTGTCATCG
9278 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
9304 ATTTCCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:10177 original size:21 final size:20
Alignment explanation
Indices: 10144--10183 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10134 TTATTAAAAC
*
10144 ATAATTTTCTTATTTATAAT
1 ATAATTTTCTTATGTATAAT
*
10164 ATAATTTTTGTTATGTATAA
1 ATAA-TTTTCTTATGTATAA
10184 ACTATGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
ATAATTTTCTTATGTATAAT
Found at i:16653 original size:20 final size:21
Alignment explanation
Indices: 16605--16665 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
16595 TTCCCCTGTG
16605 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
16628 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
*
16648 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
16666 TGCACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:20485 original size:22 final size:21
Alignment explanation
Indices: 20443--20482 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20433 GAGTTTGTTT
*
20443 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
20464 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
20483 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:23588 original size:35 final size:35
Alignment explanation
Indices: 23542--23612 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
23532 TATGCCTTCC
23542 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
1 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
23577 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
1 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
23612 A
1 A
23613 TCATCTGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (35 bp):
ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
Found at i:38251 original size:29 final size:30
Alignment explanation
Indices: 38212--38268 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
38202 TAATAATTCG
38212 AAAGTTAAATGACT-AAATTAAAAATATTT
1 AAAGTTAAATGACTAAAATTAAAAATATTT
* *
38241 AAAGTTGAATGACTAAAATTAAGAATAT
1 AAAGTTAAATGACTAAAATTAAAAATAT
38269 AGTCAAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAGTTAAATGACTAAAATTAAAAATATTT
Found at i:39740 original size:7 final size:7
Alignment explanation
Indices: 39728--39788 Score: 86
Period size: 7 Copynumber: 8.7 Consensus size: 7
39718 ACACAGAACT
*
39728 GCCTATG
1 GCCTATA
*
39735 GCCTATG
1 GCCTATA
* *
39742 GACTATG
1 GCCTATA
39749 GCCTATA
1 GCCTATA
39756 GCCTATA
1 GCCTATA
39763 GCCTATA
1 GCCTATA
39770 GCCTATA
1 GCCTATA
39777 GCCTATA
1 GCCTATA
39784 GCCTA
1 GCCTA
39789 CAGGTGGTGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (7 bp):
GCCTATA
Found at i:59407 original size:23 final size:23
Alignment explanation
Indices: 59381--59426 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
59371 CGAAAGACCG
59381 CGTAGAGA-TGCACCGAAGTGCCA
1 CGTAGA-ATTGCACCGAAGTGCCA
*
59404 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
59427 TATAATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.17
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:61650 original size:20 final size:20
Alignment explanation
Indices: 61598--61653 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
61588 AACCAATAAT
61598 AATAAACATAAAAT-AA-TTG
1 AATAAA-ATAAAATAAATTTG
*
61617 GATGAAAA-AAAATAAATTTG
1 AAT-AAAATAAAATAAATTTG
61637 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
61654 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 5 0.16
19 9 0.29
20 17 0.55
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (20 bp):
AATAAAATAAAATAAATTTG
Found at i:61772 original size:22 final size:21
Alignment explanation
Indices: 61746--61825 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 21
61736 AAACTAAAAA
61746 TATAATGAAAATA-AATAAATAG
1 TATAAT-AAAATATAA-AAATAG
61768 TATAAATAAAATAATAAAAAATA-
1 TAT-AATAAAAT-AT-AAAAATAG
61791 TATATATAAAATATAAAAATATG
1 TATA-ATAAAATATAAAAATA-G
*
61814 TATAATATAATA
1 TATAATAAAATA
61826 AAATACTAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
21 7 0.14
22 18 0.36
23 18 0.36
24 5 0.10
25 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
TATAATAAAATATAAAAATAG
Found at i:61775 original size:28 final size:28
Alignment explanation
Indices: 61742--61811 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
61732 AAAGAAACTA
*
61742 AAAATATAATGAA-AATAAATAAATAGTAT
1 AAAATATAAT-AATAAAAAATAAATA-TAT
* *
61771 -AAATAAAATAATAAAAAATATATATAT
1 AAAATATAATAATAAAAAATAAATATAT
*
61798 AAAATATAAAAATA
1 AAAATATAATAATA
61812 TGTATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (28 bp):
AAAATATAATAATAAAAAATAAATATAT
Found at i:61796 original size:25 final size:24
Alignment explanation
Indices: 61755--61922 Score: 76
Period size: 28 Copynumber: 6.5 Consensus size: 24
61745 ATATAATGAA
*
61755 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATAATATAAATAAAAT
*
61780 AATAAAAAAT-ATATATATAAAAT
1 AATAAAAAATAATATAAATAAAAT
*
61803 -ATAAAAATATGTATAATATAATAAAAT
1 AATAAAAA-AT-AAT-ATA-AATAAAAT
*
61830 ACTAAATAGTAATAATA-ATAATAATAAT
1 AATAAA-A--AATAATATA-AATAA-AAT
* *
61858 AATGAAAAATAAATATACATATAATATT
1 AATAAAAAAT-AATATA-A-ATAA-AAT
* *
61886 AACTAAAAAAGTAATCATAGA-AATAT
1 AA-TAAAAAA-TAAT-ATAAATAAAAT
61912 AA-AAAAAATAA
1 AATAAAAAATAA
61923 AGTAAGAATA
Statistics
Matches: 114, Mismatches: 13, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
22 7 0.06
23 16 0.14
24 10 0.09
25 11 0.10
26 10 0.09
27 19 0.17
28 22 0.19
29 12 0.11
30 6 0.05
31 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
AATAAAAAATAATATAAATAAAAT
Found at i:61799 original size:23 final size:23
Alignment explanation
Indices: 61755--61823 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
61745 ATATAATGAA
*
61755 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATA-TATATATAAAAT
61780 AATAAAAAATATATATATAAAAT
1 AATAAAAAATATATATATAAAAT
*
61803 -ATAAAAATATGTATAATATAA
1 AATAAAAA-ATATAT-ATATAA
61824 TAAAATACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.17
23 16 0.40
24 11 0.28
25 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAAAAAATATATATATAAAAT
Found at i:61803 original size:13 final size:12
Alignment explanation
Indices: 61740--61859 Score: 55
Period size: 10 Copynumber: 10.2 Consensus size: 12
61730 GCAAAGAAAC
61740 TAAAA-ATATAA
1 TAAAATATATAA
*
61751 TGAAA-ATA-AA
1 TAAAATATATAA
61761 T-AAATAGTATAAA
1 TAAAATA-TAT-AA
61774 TAAAATA-ATAA
1 TAAAATATATAA
61785 -AAAATATATATA
1 TAAAATATATA-A
61797 TAAAATATA-AA
1 TAAAATATATAA
* *
61808 -AATATGTATAA
1 TAAAATATATAA
*
61819 TATAATA-A-AA
1 TAAAATATATAA
61829 TACTAAATAGTAATAA
1 TA--AAATA-T-ATAA
61845 TAATAATA-ATAA
1 TAA-AATATATAA
61857 TAA
1 TAA
61860 TGAAAAATAA
Statistics
Matches: 85, Mismatches: 7, Indels: 33
0.68 0.06 0.26
Matches are distributed among these distances:
9 3 0.04
10 20 0.24
11 18 0.21
12 18 0.21
13 11 0.13
14 6 0.07
15 5 0.06
16 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (12 bp):
TAAAATATATAA
Found at i:61808 original size:21 final size:21
Alignment explanation
Indices: 61740--61817 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
61730 GCAAAGAAAC
*
61740 TAAAAATATA-AT-GAAAATA
1 TAAAAATATATATATAAAATA
*
61759 -AATAAATAGTATAAATAAAATAA
1 TAA-AAATA-TATATATAAAAT-A
61782 TAAAAAATATATATATAAAATA
1 T-AAAAATATATATATAAAATA
*
61804 TAAAAATATGTATA
1 TAAAAATATATATA
61818 ATATAATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.04
19 5 0.10
20 2 0.04
21 13 0.27
22 7 0.15
23 12 0.25
24 5 0.10
25 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAAATATATATATAAAATA
Found at i:61817 original size:19 final size:20
Alignment explanation
Indices: 61740--61881 Score: 64
Period size: 23 Copynumber: 6.8 Consensus size: 20
61730 GCAAAGAAAC
61740 TAAAA-ATATA-ATGAAAATA
1 TAAAATATATATAT-AAAATA
* *
61759 AATAAATAGTATAAATAAAATAA
1 TA-AAATA-TATATATAAAAT-A
61782 TAAAAAATATATATATAAAATA
1 T--AAAATATATATATAAAATA
* *
61804 TAAAA-ATATGTATAATATAA
1 TAAAATATATATATAAAAT-A
*
61824 TAAAATACTAAATAGTAATAATAA
1 TAAAATA-TATATA-TAA-AAT-A
61848 TAATAATA-ATA-ATGAAAA-A
1 TAA-AATATATATAT-AAAATA
*
61867 T-AAATATACATATAA
1 TAAAATATATATATAA
61882 TATTAACTAA
Statistics
Matches: 97, Mismatches: 10, Indels: 33
0.69 0.07 0.24
Matches are distributed among these distances:
17 4 0.04
18 5 0.05
19 16 0.16
20 13 0.13
21 5 0.05
22 18 0.19
23 19 0.20
24 12 0.12
25 5 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (20 bp):
TAAAATATATATATAAAATA
Found at i:61845 original size:3 final size:3
Alignment explanation
Indices: 61815--61860 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
61805 AAAAATATGT
* *
61815 ATA AT- ATA ATA A-A ATA CTAA ATA GTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
61859 AT
1 AT
61861 GAAAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:61965 original size:12 final size:12
Alignment explanation
Indices: 61948--61972 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61938 ATAACGTTAG
61948 AAAATATAGTAA
1 AAAATATAGTAA
61960 AAAATATAGTAA
1 AAAATATAGTAA
61972 A
1 A
61973 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATATAGTAA
Found at i:62018 original size:29 final size:30
Alignment explanation
Indices: 61951--62018 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 30
61941 ACGTTAGAAA
*
61951 ATATAGTAAAAAATATAGTAAATAAGTAAAC
1 ATATA-TAAAAAATATAATAAATAAGTAAAC
* * *
61982 ATAGATAAAAAA-ATAATAATATAA-TATAT
1 ATATATAAAAAATATAATAA-ATAAGTAAAC
62011 ATATATAA
1 ATATATAA
62019 TAATAGGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
29 16 0.52
30 11 0.35
31 4 0.13
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.29
Consensus pattern (30 bp):
ATATATAAAAAATATAATAAATAAGTAAAC
Found at i:62035 original size:21 final size:21
Alignment explanation
Indices: 61994--62039 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
61984 AGATAAAAAA
* *
61994 ATAATAATATAATATATATAT
1 ATAATAATAGAAAATATATAT
62015 ATAATAATAGGAAAATA-ATAT
1 ATAATAATA-GAAAATATATAT
62036 ATAA
1 ATAA
62040 CGCAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATAATAGAAAATATATAT
Found at i:62086 original size:15 final size:16
Alignment explanation
Indices: 62063--62112 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
62053 AAAAAATTAT
*
62063 AACAAATAAATAAATA
1 AACATATAAATAAATA
*
62079 AA-ATATAATTAAATA
1 AACATATAAATAAATA
62094 TATACATATAAAT-AATA
1 -A-ACATATAAATAAATA
62111 AA
1 AA
62113 GGTTAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 12 0.43
16 4 0.14
17 5 0.18
18 7 0.25
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (16 bp):
AACATATAAATAAATA
Found at i:62596 original size:37 final size:37
Alignment explanation
Indices: 62503--62604 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
62493 ATGCTTGTGG
* * ** * * *
62503 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
* *
62540 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
62577 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
62605 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:63541 original size:106 final size:106
Alignment explanation
Indices: 63356--64630 Score: 2002
Period size: 106 Copynumber: 12.0 Consensus size: 106
63346 AGCATTGTTC
* * * *
63356 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
* *
63420 AACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
63462 CGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
63527 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
63568 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
63633 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
63674 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
63739 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
63780 GGAGTCCAATATCCTTTGCTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
63845 ACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
63886 -GTAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGATA-TTGTTTGTTGA
1 CG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA-AGTTGTTTGTTGA
63949 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
64 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
63992 CGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
64057 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
64098 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
64163 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
64204 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
64269 ACCAGTGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
64310 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTG--A
64375 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
64 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
64418 AGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGGTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
64483 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
64524 AGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
64589 ACCAGTC-GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
64630 C
1 C
64631 TAGTGGCACG
Statistics
Matches: 1094, Mismatches: 66, Indels: 18
0.93 0.06 0.02
Matches are distributed among these distances:
105 3 0.00
106 990 0.90
107 3 0.00
108 98 0.09
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:65619 original size:22 final size:22
Alignment explanation
Indices: 65594--65649 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
65584 TTGTGTTTGG
*
65594 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
65616 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
65638 TCAAATGTTTGA
1 TCAAAGGTTTGA
65650 TGGGGTAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:66282 original size:16 final size:16
Alignment explanation
Indices: 66263--66314 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
66253 TTCTTTTTGA
66263 TTTTTGTTCTTTCTTT
1 TTTTTGTTCTTTCTTT
66279 TTTTTG-T-TTTCTTCT
1 TTTTTGTTCTTTCTT-T
66294 TTTTTGCTTCTTTTCTTT
1 TTTTTG-TTC-TTTCTTT
66312 TTT
1 TTT
66315 GTTTTTGCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.19
15 8 0.26
16 6 0.19
17 1 0.03
18 4 0.13
19 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTTGTTCTTTCTTT
Found at i:66315 original size:16 final size:15
Alignment explanation
Indices: 66263--66317 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 15
66253 TTCTTTTTGA
*
66263 TTTTTGTTCTTTCTTT
1 TTTTTGTTCTTT-TCT
66279 TTTTTGTT-TTCTTCT
1 TTTTTGTTCTT-TTCT
66294 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
66310 TTTTTGTT
1 TTTTTGTT
66318 TTTGCCCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
15 12 0.34
16 21 0.60
17 2 0.06
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:66328 original size:32 final size:31
Alignment explanation
Indices: 66263--66334 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 31
66253 TTCTTTTTGA
* *
66263 TTTTTGTTCTTTCTTTTTTTTGTTTTCTTCT
1 TTTTTGTTCTTTCTTTTTTTTGTTTGCTCCT
66294 TTTTTGCTTCTTTTCTTTTTTGTT-TTTGC-CC-
1 TTTTTG-TTC-TTTCTTTTTT-TTGTTTGCTCCT
66325 TTTTTGTTCT
1 TTTTTGTTCT
66335 GATTAAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
29 1 0.03
30 3 0.08
31 12 0.33
32 4 0.11
33 14 0.39
34 2 0.06
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.76
Consensus pattern (31 bp):
TTTTTGTTCTTTCTTTTTTTTGTTTGCTCCT
Found at i:66329 original size:31 final size:31
Alignment explanation
Indices: 66263--66334 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
66253 TTCTTTTTGA
* * *
66263 TTTTTGTTCTTTCTTTTTTTTGTTTTCTTCT
1 TTTTTGTTCTTTCTCTTTTTTGTTTTCTCCC
66294 TTTTTGCTTCTTT-TCTTTTTTGTTTT-TGCCC
1 TTTTTG-TTCTTTCTCTTTTTTGTTTTCT-CCC
66325 TTTTTGTTCT
1 TTTTTGTTCT
66335 GATTAAATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 5 0.14
31 25 0.69
32 6 0.17
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.76
Consensus pattern (31 bp):
TTTTTGTTCTTTCTCTTTTTTGTTTTCTCCC
Found at i:69631 original size:4 final size:4
Alignment explanation
Indices: 69622--69657 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
69612 AATGTTAGTA
69622 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
69658 GACAAAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:69813 original size:20 final size:20
Alignment explanation
Indices: 69784--69829 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
69774 TCGAGATCTC
*
69784 CTTGCTGGTGCCCCCTTGGG
1 CTTGCCGGTGCCCCCTTGGG
*
69804 CTTGCCGGTGCCCTCTTGGG
1 CTTGCCGGTGCCCCCTTGGG
69824 CTTGCC
1 CTTGCC
69830 AGACCCTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.00, C:0.37, G:0.33, T:0.30
Consensus pattern (20 bp):
CTTGCCGGTGCCCCCTTGGG
Found at i:70694 original size:20 final size:19
Alignment explanation
Indices: 70644--70699 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
70634 AACCAATAAT
70644 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
70663 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
70683 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
70700 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:71608 original size:37 final size:37
Alignment explanation
Indices: 71567--71655 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
71557 GGATCCTATC
** *
71567 TTTAGGAGTTTAAATAATAGTTGAATTCTATCATATT
1 TTTAGGAGTTTAAATAATAGTAAAATTATATCATATT
** *
71604 TTTAGGAGTTTAAATTCTAGTAAAATTATATCCTATT
1 TTTAGGAGTTTAAATAATAGTAAAATTATATCATATT
* *
71641 TTTAAGAATTTAAAT
1 TTTAGGAGTTTAAAT
71656 TTTAGTAGGA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGTAAAATTATATCATATT
Found at i:71842 original size:3 final size:3
Alignment explanation
Indices: 71834--71868 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
71824 ATTTCTCCAA
71834 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
71869 CAATTATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:71939 original size:13 final size:14
Alignment explanation
Indices: 71908--71940 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
71898 AGGATATATC
71908 AAAATATTGTTTTT
1 AAAATATTGTTTTT
71922 AAAATATT-TTTTT
1 AAAATATTGTTTTT
*
71935 GAAATA
1 AAAATA
71941 ATTTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
AAAATATTGTTTTT
Found at i:76904 original size:19 final size:20
Alignment explanation
Indices: 76877--76914 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
76867 AATTTTTTTT
*
76877 AATTTTCATATCA-ACATTA
1 AATTATCATATCACACATTA
76896 AATTATCATATCACACATT
1 AATTATCATATCACACATT
76915 TTCAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATCATATCACACATTA
Found at i:84040 original size:12 final size:12
Alignment explanation
Indices: 84023--84054 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
84013 TTATGTTCCT
84023 AGGAAAGGATAG
1 AGGAAAGGATAG
*
84035 AGGAAAAGATAG
1 AGGAAAGGATAG
84047 AGGAAAGG
1 AGGAAAGG
84055 TTGGCAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.41, T:0.06
Consensus pattern (12 bp):
AGGAAAGGATAG
Found at i:95134 original size:20 final size:20
Alignment explanation
Indices: 95100--95141 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
95090 TAAACTTTAA
*
95100 TAATGCATATTTATTTTAATT
1 TAATGCATATATATTTT-ATT
95121 TAATG-ATATATATTTTATT
1 TAATGCATATATATTTTATT
95140 TA
1 TA
95142 TTGACCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
TAATGCATATATATTTTATT
Found at i:95550 original size:15 final size:14
Alignment explanation
Indices: 95525--95558 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
95515 CCCTATTCAT
95525 AATTTAAATTTTAA
1 AATTTAAATTTTAA
95539 AATTTAAAATTTTAA
1 AATTT-AAATTTTAA
*
95554 TATTT
1 AATTT
95559 CACCTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTAAATTTTAA
Found at i:98755 original size:31 final size:32
Alignment explanation
Indices: 98711--98795 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 32
98701 CAAGTCAGAT
* * *
98711 ATCGAGTCGAATAAAAAAAATTTAA-ACTCAA
1 ATCGAATCAAATAAAAAAAATATAATACTCAA
98742 ATCGAATCAAATAAAAAAAATATAATACTCAA
1 ATCGAATCAAATAAAAAAAATATAATACTCAA
* *
98774 ATCAAATTCAGATAAACAAAAA
1 ATCGAA-TCAAATAAA-AAAAA
98796 ATGTAACCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 22 0.48
32 11 0.24
33 8 0.17
34 5 0.11
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (32 bp):
ATCGAATCAAATAAAAAAAATATAATACTCAA
Found at i:111595 original size:137 final size:137
Alignment explanation
Indices: 111323--111588 Score: 356
Period size: 137 Copynumber: 1.9 Consensus size: 137
111313 TAAATCGAGT
*
111323 AACTAGAAGAAGTCTACCTACCAAGAAGACGAGTCAGACACCTGCCTACTGAGGTAACGAGTTGG
1 AACTAGAAGAAGTCTACCTACCAAGAAGACGAGTCAGACACCTGCCTACTGAGGTAACAAGTTGG
* * **
111388 ACTCGAGACGATTCGATGCTGAAGCCAGTAGTTGAAGATCATGAACCAACTCAAAGGATTTCTGG
66 ACTCGAGACGATTCAATGCAGAAGCCAACAGTTGAAGATCATGAACCAACTCAAAGGATTTCTGG
111453 AAGTAGG
131 AAGTAGG
* * * * * ** **
111460 AACTAGAGGGAGTCTATCTACCAAGGAGACGA-TCCAGGCATTTGCCTGTTGAGGTAACAAGTTG
1 AACTAGAAGAAGTCTACCTACCAAGAAGACGAGT-CAGACACCTGCCTACTGAGGTAACAAGTTG
* *
111524 GACTCGAGACGATTCAATGCAGAAGCCAACAGTTGAAGATCGTGAACCAGCTCGAAA-GATTTCT
65 GACTCGAGACGATTCAATGCAGAAGCCAACAGTTGAAGATCATGAACCAACTC-AAAGGATTTCT
111588 G
129 G
111589 AGAGTAGAAG
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
136 1 0.01
137 107 0.96
138 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (137 bp):
AACTAGAAGAAGTCTACCTACCAAGAAGACGAGTCAGACACCTGCCTACTGAGGTAACAAGTTGG
ACTCGAGACGATTCAATGCAGAAGCCAACAGTTGAAGATCATGAACCAACTCAAAGGATTTCTGG
AAGTAGG
Found at i:114042 original size:74 final size:75
Alignment explanation
Indices: 113952--114163 Score: 214
Period size: 75 Copynumber: 2.8 Consensus size: 75
113942 CAATATAAAT
* ** * * **
113952 TTTGTCTCGCTTGAGACAGTTTCA-TTTAATACAAAAGATTT-ATCTCATTGGAGATTGTTTTTC
1 TTTGTCTCACTTGAGACAGTTTCACTCGAA-ACAAAACATTTCATCTCACTCAAGATTGTTTTTC
114015 TTAAAAC-AGA
65 TTAAAACAAGA
* * * * * *
114025 CTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGACATTTCATTTGACTCAAGATTGTTTTTC
1 -TTTGTCTCACTTGAGACAGTTTCACTCGAAACAAAACATTTCATCTCACTCAAGATTGTTTTTC
114090 TTAAAACAAGA
65 TTAAAACAAGA
* * * * *
114101 TTTGTCTCTCTTGAGACAGTTTTTACTCGAAAGAATACATTTCATTTCACTCAAGATTGTTTT
1 TTTGTCTCACTTGAGACAG-TTTCACTCGAAACAAAACATTTCATCTCACTCAAGATTGTTTT
114164 AAAGAATATT
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
74 29 0.25
75 44 0.38
76 44 0.38
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (75 bp):
TTTGTCTCACTTGAGACAGTTTCACTCGAAACAAAACATTTCATCTCACTCAAGATTGTTTTTCT
TAAAACAAGA
Found at i:114047 original size:36 final size:36
Alignment explanation
Indices: 113994--114124 Score: 88
Period size: 36 Copynumber: 3.6 Consensus size: 36
113984 AAAAGATTTA
*
113994 TCTCA-TTGGAGATTGTTTTTCTTAAAACAGACTTTG
1 TCTCACTT-GAGACTGTTTTTCTTAAAACAGACTTTG
* * *
114030 TCTCACTTGAGACTGTTTTACTCGAAAGA-AGACATTTCA
1 TCTCACTTGAGACTGTTTTTCT-TAAA-ACAGAC-TTT-G
* * ** *
114069 TTTGACTCAAGATTGTTTTTCTTAAAACAAGA-TTTG
1 TCTCACTTGAGACTGTTTTTCTTAAAAC-AGACTTTG
* *
114105 TCTCTCTTGAGACAGTTTTT
1 TCTCACTTGAGACTGTTTTT
114125 ACTCGAAAGA
Statistics
Matches: 69, Mismatches: 19, Indels: 14
0.68 0.19 0.14
Matches are distributed among these distances:
36 30 0.43
37 13 0.19
38 7 0.10
39 19 0.28
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (36 bp):
TCTCACTTGAGACTGTTTTTCTTAAAACAGACTTTG
Found at i:114093 original size:75 final size:76
Alignment explanation
Indices: 114003--114163 Score: 263
Period size: 76 Copynumber: 2.1 Consensus size: 76
113993 ATCTCATTGG
*
114003 AGATTGTTTTTCTTAAAAC-AGACTTTGTCTCACTTGAGACTG-TTTTACTCGAAAGAAGACATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACAGTTTTTACTCGAAAGAAGACATT
*
114066 TCATTTGACTCA
65 TCATTTCACTCA
* *
114078 AGATTGTTTTTCTTAAAACAAGATTTGTCTCTCTTGAGACAGTTTTTACTCGAAAGAATACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTTTACTCGAAAGAAGACATTT
114143 CATTTCACTCA
66 CATTTCACTCA
114154 AGATTGTTTT
1 AGATTGTTTT
114164 AAAGAATATT
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
75 36 0.45
76 44 0.55
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTTTACTCGAAAGAAGACATTT
CATTTCACTCA
Found at i:114222 original size:39 final size:40
Alignment explanation
Indices: 114168--114284 Score: 155
Period size: 39 Copynumber: 3.0 Consensus size: 40
114158 TGTTTTAAAG
*
114168 AATATTGTATCTCGCTTGAGATAGTTTCCCTTGAAACA-A
1 AATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACATA
* *
114207 AATATTTTATCTCGCTTGAGATAGTTTCCCTGGAAACATG
1 AATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACATA
* * * **
114247 AAGATTTTGTCTCTCTTGAGGCAGTTTCCCTTGAAACA
1 AATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
114285 CCAATCTTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 36 0.53
40 32 0.47
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (40 bp):
AATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACATA
Found at i:114338 original size:66 final size:68
Alignment explanation
Indices: 114222--114349 Score: 188
Period size: 66 Copynumber: 1.9 Consensus size: 68
114212 TTTATCTCGC
* *
114222 TTGAGATAGTTTCCCTGGAAACATGAAGATTTTGTCTCTCTTGAGGCAGTTTCCCTTGAAACACC
1 TTGAGATAGTTTCCCTGGAAACA--AAGATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACACC
114287 AATCT
64 AATCT
* *
114292 TTGAGATTGTTTCCCTTGAAAC-AA-ATTTTGTCTCACTTGAGACAGTTTCCCTTGAAAC
1 TTGAGATAGTTTCCCTGGAAACAAAGATTTTGTCTCACTTGAGACAGTTTCCCTTGAAAC
114350 GAGTTTTGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
66 32 0.59
67 2 0.04
70 20 0.37
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (68 bp):
TTGAGATAGTTTCCCTGGAAACAAAGATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACACCAA
TCT
Found at i:114400 original size:21 final size:20
Alignment explanation
Indices: 114306--114475 Score: 74
Period size: 21 Copynumber: 9.2 Consensus size: 20
114296 GATTGTTTCC
* *
114306 CTTGAAACAAATTTTGTCTCA
1 CTTGAAAC-AGTTTTGTCTCT
*
114327 CTTGAGACAG--TT-TC-C-
1 CTTGAAACAGTTTTGTCTCT
114342 CTTGAAACGAGTTTTGTCTCT
1 CTTGAAAC-AGTTTTGTCTCT
* *
114363 CTTGAGACAG----CT-TCT
1 CTTGAAACAGTTTTGTCTCT
114378 CTTGAAACGAGTTTTGTCTCT
1 CTTGAAAC-AGTTTTGTCTCT
* *
114399 CTTGAGACAG----CT-TCT
1 CTTGAAACAGTTTTGTCTCT
114414 CTTGAAACAAGTTTTGTCTCT
1 CTTGAAAC-AGTTTTGTCTCT
*
114435 CTTGAGACAG--TT-TC-C-
1 CTTGAAACAGTTTTGTCTCT
*
114450 CTTGAAACAAGTTTTGTCTAT
1 CTTGAAAC-AGTTTTGTCTCT
114471 CTTGA
1 CTTGA
114476 GATAATTTCC
Statistics
Matches: 111, Mismatches: 14, Indels: 48
0.64 0.08 0.28
Matches are distributed among these distances:
15 34 0.31
16 12 0.11
17 4 0.04
18 8 0.07
19 4 0.04
20 10 0.09
21 39 0.35
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (20 bp):
CTTGAAACAGTTTTGTCTCT
Found at i:114591 original size:67 final size:67
Alignment explanation
Indices: 114495--114666 Score: 210
Period size: 66 Copynumber: 2.6 Consensus size: 67
114485 CCTTGAATTT
*
114495 TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGA-AT-ATGTTTCTCTTGAA-
1 TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAGATCGT-TTTC-CTTGAAC
114557 AAGAA
64 AA-AA
* * ** *
114562 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAC-CGATCTTTGAGATCGTTTTCCTTGAACTA
1 TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAGATCGTTTTCCTTGAACAA
114626 AA
66 AA
*
114628 TTTTGTCTCGA-TGGAGACAGTTTCTCTTGAAACACAAAA
1 TTTTGTCTC-ACTTGAGACAGTTTCTCTTGAAACACAAAA
114667 ACTTGGATTG
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
66 47 0.53
67 41 0.46
68 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (67 bp):
TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAGATCGTTTTCCTTGAACAA
AA
Found at i:114593 original size:36 final size:36
Alignment explanation
Indices: 114177--114528 Score: 301
Period size: 36 Copynumber: 9.8 Consensus size: 36
114167 GAATATTGTA
* * *
114177 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTTTA
1 TCTCTCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTTG
* * *
114216 TCTCGCTTGAGATAGTTTCCCTGGAAACATGAAGATTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAAC---AA-ATTTTG
*
114256 TCTCTCTTGAGGCAGTTTCCCTTGAAACACCAA-----
1 TCTCTCTTGAGACAGTTTCCCTTGAAACA--AATTTTG
**
114289 --TCT-TTGAGATTGTTTCCCTTGAAACAAATTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* * *
114322 TCTCACTTGAGACAGTTTCCCTTGAAACGAGTTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* * * *
114358 TCTCTCTTGAGACAGCTTCTCTTGAAACGAGTTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* * *
114394 TCTCTCTTGAGACAGCTTCTCTTGAAACAAGTTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
*
114430 TCTCTCTTGAGACAGTTTCCCTTGAAACAAGTTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* * * ***
114466 TCTATCTTGAGATAATTTCCCTTG-AA-TTTTTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* *
114500 TCTCACTTGAGACAGTTTCTCTTGAAACA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACA
114529 CAAAATCTTT
Statistics
Matches: 265, Mismatches: 35, Indels: 29
0.81 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
30 20 0.08
31 3 0.01
34 24 0.09
35 6 0.02
36 149 0.56
37 1 0.00
38 1 0.00
39 28 0.11
40 31 0.12
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (36 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
Found at i:115231 original size:91 final size:91
Alignment explanation
Indices: 115069--115442 Score: 529
Period size: 91 Copynumber: 4.1 Consensus size: 91
115059 CCAATCAACA
* * *
115069 TTCCAGCGGAGAGTTCATAATGAGAAGAACTCGTCCAAGGAGGGAGAAGAAGTTCATAATGAGAA
1 TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
*
115134 TAACTTGTTCAACCTTATCTCAGCAT
66 GAACTTGTTCAACCTTATCTCAGCAT
*
115160 TTCCTGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
1 TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
* *
115225 CAACTTGTTCAACCTT-TACTCAGTAT
66 GAACTTGTTCAACCTTAT-CTCAGCAT
* * * *
115251 TTCCACTTGAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAATAAGTTCATAATGAGAA
1 TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
*
115316 GAACTTGTTCAACCTTGGT-TCAAG-AT
66 GAACTTGTTCAACCTT-ATCTC-AGCAT
* *
115342 TTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAAGAAGTTCATATTGAGAA
1 TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
* * ** *
115407 GAATTTCTTCAACCTTAGATCATCAT
66 GAACTTGTTCAACCTTATCTCAGCAT
115433 TTCCAGTGGA
1 TTCCAGTGGA
115443 AAGACCAGGA
Statistics
Matches: 255, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
90 2 0.01
91 250 0.98
92 2 0.01
93 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (91 bp):
TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTATCTCAGCAT
Found at i:118393 original size:29 final size:30
Alignment explanation
Indices: 118350--118419 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
118340 GCCATGTTAG
** ** *
118350 ATAAAATGGTAAGAAATTAATTAATTAAAT
1 ATAAAATGAAAAGAAACAAATTAAGTAAAT
118380 -TAAAATGAAAAGAAACAAATTAAGTAAAT
1 ATAAAATGAAAAGAAACAAATTAAGTAAAT
118409 GATAAAATGAA
1 -ATAAAATGAA
118420 GAAAGCAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 24 0.73
31 9 0.27
ACGTcount: A:0.61, C:0.01, G:0.11, T:0.26
Consensus pattern (30 bp):
ATAAAATGAAAAGAAACAAATTAAGTAAAT
Found at i:118421 original size:29 final size:30
Alignment explanation
Indices: 118349--118428 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
118339 AGCCATGTTA
* ** *
118349 GATAAAATGGTAAGAAATTAATTAATTAAAT
1 GATAAAAT-GAAAGAAACAAATTAAGTAAAT
118380 --TAAAATGAAAAGAAACAAATTAAGTAAAT
1 GATAAAATG-AAAGAAACAAATTAAGTAAAT
118409 GATAAAATG-AAGAAAGCAAA
1 GATAAAATGAAAGAAA-CAAA
118429 GATAAAATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
28 1 0.02
29 29 0.71
30 4 0.10
31 7 0.17
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.23
Consensus pattern (30 bp):
GATAAAATGAAAGAAACAAATTAAGTAAAT
Found at i:118493 original size:23 final size:25
Alignment explanation
Indices: 118433--118495 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
118423 AGCAAAGATA
* *
118433 AAATAGTAAGTAAAAAAACAAATAAT
1 AAATA-TAAATAAAAAAACAAATAAG
* *
118459 AAATATATATAAAAAAAGAAA-AAG
1 AAATATAAATAAAAAAACAAATAAG
118483 AAA-ATAAATAAAA
1 AAATATAAATAAAA
118496 CAAATAAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 9 0.28
24 5 0.16
25 13 0.41
26 5 0.16
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (25 bp):
AAATATAAATAAAAAAACAAATAAG
Found at i:118809 original size:2 final size:2
Alignment explanation
Indices: 118802--118847 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
118792 CTTGTGTAGA
118802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
118845 AT A
1 AT A
118848 GTAAAAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:118914 original size:21 final size:21
Alignment explanation
Indices: 118883--118937 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
118873 AATAAAAAAG
*
118883 AAAATAAATATATAATGA-TAAT
1 AAAA-AAATATATAA-AATTAAT
*
118905 AAAAAAATATAGAAAATTAAT
1 AAAAAAATATATAAAATTAAT
*
118926 AGAAAAATATAT
1 AAAAAAATATAT
118938 GTATAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAAAATATATAAAATTAAT
Found at i:119031 original size:2 final size:2
Alignment explanation
Indices: 119024--119062 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
119014 GAGCATACGC
* * *
119024 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
119063 AAAATAATAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:119143 original size:20 final size:22
Alignment explanation
Indices: 119106--119152 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
119096 GAATGAGAAG
119106 TAAAAAATATAATAATAATAAA
1 TAAAAAATATAATAATAATAAA
119128 TAAAAAATATATATAAT-ATAAA
1 TAAAAAATATA-ATAATAATAAA
119150 TAA
1 TAA
119153 GTAGAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAAATATAATAATAATAAA
Found at i:119800 original size:37 final size:37
Alignment explanation
Indices: 119759--119863 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
119749 GTGCTTGTGG
* * *
119759 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
119796 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
119833 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
119864 GACGAAAAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Done.