Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004287.1 Hibiscus syriacus cultivar Beakdansim tig00009403_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: 112413
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:17128 original size:18 final size:18
Alignment explanation
Indices: 17091--17129 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17081 ATTAATATTT
*
17091 AATATAAAATAATTAAAA
1 AATATAAAATAATAAAAA
17109 AATATAAAATAA-AAACAA
1 AATATAAAATAATAAA-AA
17127 AAT
1 AAT
17130 GTGGTCGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AATATAAAATAATAAAAA
Found at i:19957 original size:155 final size:148
Alignment explanation
Indices: 19605--19956 Score: 352
Period size: 148 Copynumber: 2.3 Consensus size: 148
19595 GTTACATATC
* * * * * * *
19605 TATTCTATTATGGTATATGAGCATGTGATTCAAATTTGGTGAAAAAAATGACTTAAAATAAATCA
1 TATTCTACTATAGTTTAAGAGCATGTAATTCAAATTTGGT-AAAAAAA-AATTTAAAATAAATCA
* * * *
19670 TAAATTGAAAGAATAATGAGATTATGAAAAATTAAAGGACTAAATTAAAAAATATTATCAAAAAG
64 CAAATTGAAAAAATAAAGAGATTATAAAAAATTAAAGGACTAAATTAAAAAATATTATCAAAAAG
*
19735 AAGAATTGAAAATACACATT
129 AAGAATTGAAAATACACATG
* * * *
19755 TATTCTACTATAGTTTAGGAGCA--TAACTCAAATTTGGTAAAAAAAAATTTAAAATAAATGACG
1 TATTCTACTATAGTTTAAGAGCATGTAATTCAAATTTGGTAAAAAAAAATTTAAAATAAATCACA
* * *
19818 AATTGAAAAAAAATAAAGAGATTATAAAAAATTGAAGGACTACATTGAAGAAAAAAAATTGTTAT
66 AATTG--AAAAAATAAAGAGATTATAAAAAATTAAAGGACTAAATT------AAAAAA-TATTAT
* * *
19883 CAAAAAGAGGAATTGAAAGTATACATG
122 CAAAAAGAAGAATTGAAAATACACATG
* *
19910 TATTCTA-TCAT-GTTTAAGTGCATGTAATTCAAATTTGATAAAAAAAA
1 TATTCTACT-ATAGTTTAAGAGCATGTAATTCAAATTTGGTAAAAAAAA
19957 TAGACTTAAA
Statistics
Matches: 165, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
146 18 0.11
147 7 0.04
148 47 0.28
150 19 0.12
154 16 0.10
155 37 0.22
156 21 0.13
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.30
Consensus pattern (148 bp):
TATTCTACTATAGTTTAAGAGCATGTAATTCAAATTTGGTAAAAAAAAATTTAAAATAAATCACA
AATTGAAAAAATAAAGAGATTATAAAAAATTAAAGGACTAAATTAAAAAATATTATCAAAAAGAA
GAATTGAAAATACACATG
Found at i:20457 original size:4 final size:4
Alignment explanation
Indices: 20448--20482 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
20438 TTTGATACAT
20448 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
20483 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:25632 original size:26 final size:27
Alignment explanation
Indices: 25582--25635 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
25572 TTCGTGAACC
25582 AAACCCTAAACCCTGAAATCTAACTTA
1 AAACCCTAAACCCTGAAATCTAACTTA
* *
25609 AAACCCTAAA-TCTTAAATCTAACTTA
1 AAACCCTAAACCCTGAAATCTAACTTA
25635 A
1 A
25636 CATATTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (27 bp):
AAACCCTAAACCCTGAAATCTAACTTA
Found at i:32129 original size:21 final size:21
Alignment explanation
Indices: 32103--32142 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32093 CCCCCTTTGA
*
32103 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
32124 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
32143 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:36395 original size:7 final size:7
Alignment explanation
Indices: 36373--36476 Score: 87
Period size: 7 Copynumber: 15.7 Consensus size: 7
36363 TAATACCGCA
36373 CTTCTT-
1 CTTCTTC
36379 CTTC-TC
1 CTTCTTC
36385 CTTCTTC
1 CTTCTTC
36392 CTTCTTC
1 CTTCTTC
36399 CTTCTTC
1 CTTCTTC
36406 CTTCTTC
1 CTTCTTC
36413 CTTCCTT-
1 CTT-CTTC
*
36420 CTTTTTC
1 CTTCTTC
*
36427 TTTCTT-
1 CTTCTTC
36433 CTTCTT-
1 CTTCTTC
*
36439 CTTATT-
1 CTTCTTC
36445 CTTCTT-
1 CTTCTTC
**
36451 CTTCCAC
1 CTTCTTC
* *
36458 ATTCTTT
1 CTTCTTC
36465 CTTCTTC
1 CTTCTTC
36472 CTTCT
1 CTTCT
36477 CACACACTCT
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
5 1 0.01
6 29 0.37
7 46 0.58
8 3 0.04
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.61
Consensus pattern (7 bp):
CTTCTTC
Found at i:36471 original size:3 final size:3
Alignment explanation
Indices: 36373--36454 Score: 83
Period size: 3 Copynumber: 25.3 Consensus size: 3
36363 TAATACCGCA
*
36373 CTT CTT CTT CTC CTT CTT CCTT CTT CCTT CTT CCTT CTT CCTT CCTT
1 CTT CTT CTT CTT CTT CTT -CTT CTT -CTT CTT -CTT CTT -CTT -CTT
* *
36420 CTT TTT CTTT CTT CTT CTT CTT ATT CTT CTT CTT C
1 CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT C
36455 CACATTCTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
3 49 0.72
4 19 0.28
ACGTcount: A:0.01, C:0.37, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:37570 original size:3 final size:3
Alignment explanation
Indices: 37562--37602 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
37552 GAAGTGTGTG
37562 AGA AGA AGA AGAA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A
37603 TTCTTTTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:37751 original size:3 final size:3
Alignment explanation
Indices: 37745--37832 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
37735 AAGAAGAAGA
37745 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
37793 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
37833 AGGAAGGAAG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:49971 original size:17 final size:17
Alignment explanation
Indices: 49951--49989 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
49941 ATTTCAAAGT
49951 TATAATTATATAAAAAA
1 TATAATTATATAAAAAA
* *
49968 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
49985 TATAA
1 TATAA
49990 ATAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:49994 original size:30 final size:29
Alignment explanation
Indices: 49960--50016 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
49950 TTATAATTAT
49960 ATAAAAAATATATTTATATATAAAATATAA
1 ATAAAAAATATATTTATATA-AAAATATAA
* * *
49990 ATAAAATATTTATTTATTTAAAAATAT
1 ATAAAAAATATATTTATATAAAAATAT
50017 CAGAAAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAAAAAATATATTTATATAAAAATATAA
Found at i:50133 original size:26 final size:26
Alignment explanation
Indices: 50088--50138 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
50078 CTAAAAATGT
50088 AAAAATTTAAAAGTAAAATAATTTAAG
1 AAAAATTTAAAAGTAAAAT-ATTTAAG
* *
50115 AAAAATTT-AAATTATAATATTTAA
1 AAAAATTTAAAAGTAAAATATTTAA
50139 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 8 0.36
27 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AAAAATTTAAAAGTAAAATATTTAAG
Found at i:50241 original size:24 final size:24
Alignment explanation
Indices: 50214--50269 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
50204 ACAAATAAAC
*
50214 ATTAAAATT-AATTAAATAATA-TA
1 ATTAAAATTAAAAT-AATAATACTA
*
50237 TATTAAAAATAAAATAATAATACTA
1 -ATTAAAATTAAAATAATAATACTA
50262 ATTAAAAT
1 ATTAAAAT
50270 ATTATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATTAAAATTAAAATAATAATACTA
Found at i:50252 original size:18 final size:18
Alignment explanation
Indices: 50231--50302 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
50221 TTAATTAAAT
50231 AATATATATTAAAAATAA
1 AATATATATTAAAAATAA
* * *
50249 AATA-ATAATACTAATTAA
1 AATATATATTA-AAAATAA
*
50267 AATAT-TATATAAAATTAA
1 AATATATAT-TAAAAATAA
50285 AATATAT-TTAAACAATAA
1 AATATATATTAAA-AATAA
50303 TTAAAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 9 0.21
18 31 0.72
19 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATATATTAAAAATAA
Found at i:50306 original size:11 final size:11
Alignment explanation
Indices: 50214--50319 Score: 55
Period size: 11 Copynumber: 9.6 Consensus size: 11
50204 ACAAATAAAC
50214 ATTAAAAT-TA
1 ATTAAAATATA
50224 ATTAAATAATATA
1 ATT-AA-AATATA
50237 TATTAAAA-ATAA
1 -ATTAAAATAT-A
*
50249 AATAATAATACTA
1 ATTAA-AATA-TA
50262 ATT-AAA-AT-
1 ATTAAAATATA
* *
50270 ATT-ATATAAA
1 ATTAAAATATA
50280 ATTAAAATATA
1 ATTAAAATATA
*
50291 TTTAAACA-ATA
1 ATTAAA-ATATA
*
50302 ATTAAAATAAA
1 ATTAAAATATA
50313 ATTAAAA
1 ATTAAAA
50320 CTAAATATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 25
0.69 0.08 0.23
Matches are distributed among these distances:
8 5 0.07
9 2 0.03
10 8 0.11
11 37 0.50
12 10 0.14
13 8 0.11
14 4 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTAAAATATA
Found at i:51602 original size:3 final size:3
Alignment explanation
Indices: 51594--51687 Score: 122
Period size: 3 Copynumber: 32.0 Consensus size: 3
51584 ATATTTATTA
* *
51594 AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT AAT AAT ATT TAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
**
51637 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
51685 AAT
1 AAT
51688 TTAAGTAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
2 6 0.08
3 70 0.89
4 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:51636 original size:15 final size:15
Alignment explanation
Indices: 51582--51687 Score: 96
Period size: 15 Copynumber: 7.3 Consensus size: 15
51572 TTTGGGTTTG
*
51582 TAATATTTATTA-AA
1 TAATATTTATAATAA
*
51596 TAATA-ATATAAT-A
1 TAATATTTATAATAA
*
51609 T-ATATAATATAATAA
1 TAATAT-TTATAATAA
51624 TAATATTTATAATAA
1 TAATATTTATAATAA
* *
51639 TAATAATAATAATAA
1 TAATATTTATAATAA
* *
51654 TAATAATAATAATAA
1 TAATATTTATAATAA
51669 TAAT-TTTAATAATAA
1 TAATATTT-ATAATAA
51684 TAAT
1 TAAT
51688 TTAAGTAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
12 3 0.04
13 6 0.08
14 13 0.16
15 53 0.67
16 4 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATATTTATAATAA
Found at i:52280 original size:76 final size:76
Alignment explanation
Indices: 51844--52253 Score: 766
Period size: 76 Copynumber: 5.4 Consensus size: 76
51834 GTCTTAAAAA
* * *
51844 AAACATCATGCACTGCAGGACTTACAGATGACCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51909 AGGCTTTTTGG
66 AGGCTTTTTGG
51920 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51985 AGGCTTTTTGG
66 AGGCTTTTTGG
*
51996 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
52061 AGGCTTTTTGG
66 AGGCTTTTTGG
*
52072 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
52137 AGGATTTTTGG
66 AGGCTTTTTGG
52148 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
52213 AGGCTTTTTGG
66 AGGCTTTTTGG
52224 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
52254 TGGGAAATAG
Statistics
Matches: 325, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 325 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:52959 original size:22 final size:22
Alignment explanation
Indices: 52934--52986 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
52924 TAAAGCTTTT
52934 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
*
52956 ATCTTTAAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
52978 ATCTTTGAA
1 ATCTTTGAA
52987 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:55895 original size:114 final size:114
Alignment explanation
Indices: 55562--55872 Score: 534
Period size: 114 Copynumber: 2.7 Consensus size: 114
55552 TGATCGGTTC
* * * *
55562 TGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGGTCTC
1 TGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGAGTCTC
*
55627 CTTATTTCTACTATGAGCAAATTCATCTTTTAAATCCAATGATTGATTT
66 CTTATTTCTACTATGAGCAAATTCATCTTTTAAATCTAATGATTGATTT
*
55676 TGAGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGAGTCTC
1 TGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGAGTCTC
*
55741 CTTATTTCTACTATGAACAAATTCATCTTTTAAATCTAATGATTGATTT
66 CTTATTTCTACTATGAGCAAATTCATCTTTTAAATCTAATGATTGATTT
* *
55790 TGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTT
1 TGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGAGTCTC
55855 CTTATTTCTAC-ATGAGCA
66 CTTATTTCTACTATGAGCA
55873 CATGGCACTT
Statistics
Matches: 186, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
113 6 0.03
114 180 0.97
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (114 bp):
TGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGAGTCTC
CTTATTTCTACTATGAGCAAATTCATCTTTTAAATCTAATGATTGATTT
Found at i:57943 original size:16 final size:15
Alignment explanation
Indices: 57922--57953 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
57912 TCAATTTTCC
57922 TTTTTCTTCTTCTCTT
1 TTTTTCTTCTT-TCTT
57938 TTTTTCTTCTTTCTT
1 TTTTTCTTCTTTCTT
57953 T
1 T
57954 GTTGGACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTCTTTCTT
Found at i:60434 original size:8 final size:7
Alignment explanation
Indices: 60406--60444 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
60396 TAAAAGTATG
60406 AATGCAA
1 AATGCAA
*
60413 AATGAAA
1 AATGCAA
60420 AATGCAA
1 AATGCAA
60427 AGATGCAA
1 A-ATGCAA
60435 AATG-AA
1 AATGCAA
60441 AATG
1 AATG
60445 TATATATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:63029 original size:17 final size:17
Alignment explanation
Indices: 63009--63047 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
62999 ATTTCAAAGT
63009 TATAATTATATAAAAAA
1 TATAATTATATAAAAAA
* *
63026 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
63043 TATAA
1 TATAA
63048 ATAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:63191 original size:26 final size:26
Alignment explanation
Indices: 63146--63196 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
63136 CTAAAAATGT
63146 AAAAATTTAAAAGTAAAATAATTTAAG
1 AAAAATTTAAAAGTAAAAT-ATTTAAG
* *
63173 AAAAATTT-AAATTATAATATTTAA
1 AAAAATTTAAAAGTAAAATATTTAA
63197 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 8 0.36
27 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AAAAATTTAAAAGTAAAATATTTAAG
Found at i:63299 original size:24 final size:24
Alignment explanation
Indices: 63272--63327 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
63262 ACAAATAAAC
*
63272 ATTAAAATTAATCA-AATAATA-TA
1 ATTAAAATTAA-AATAATAATACTA
*
63295 TATTAAAAATAAAATAATAATACTA
1 -ATTAAAATTAAAATAATAATACTA
63320 ATTAAAAT
1 ATTAAAAT
63328 ATTATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 24 0.89
25 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (24 bp):
ATTAAAATTAAAATAATAATACTA
Found at i:63310 original size:18 final size:18
Alignment explanation
Indices: 63289--63360 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
63279 TTAATCAAAT
63289 AATATATATTAAAAATAA
1 AATATATATTAAAAATAA
* * *
63307 AATA-ATAATACTAATTAA
1 AATATATATTA-AAAATAA
*
63325 AATAT-TATATAAAATTAA
1 AATATATAT-TAAAAATAA
63343 AATATAT-TTAAACAATAA
1 AATATATATTAAA-AATAA
63361 TTAAAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 9 0.21
18 31 0.72
19 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATATATTAAAAATAA
Found at i:64659 original size:3 final size:3
Alignment explanation
Indices: 64651--64725 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
64641 ATATTTATTA
* *
64651 AAT AAT AAT -AT AAT ATAT ATAT AAT -AT AAT AAT AAT ATT TAT AAT
1 AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
**
64696 AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
64726 TTAAGTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 4 0.07
3 50 0.82
4 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:64709 original size:24 final size:24
Alignment explanation
Indices: 64639--64725 Score: 112
Period size: 22 Copynumber: 3.8 Consensus size: 24
64629 TTTGGGTTTG
*
64639 TAATATTTATTA-AATAATAAT-A
1 TAATATTTATAATAATAATAATAA
*
64661 TAATATATAT-ATAAT-ATAATAA
1 TAATATTTATAATAATAATAATAA
64683 TAATATTTATAATAATAATAATAA
1 TAATATTTATAATAATAATAATAA
64707 TAAT-TTTAATAATAATAAT
1 TAATATTT-ATAATAATAAT
64726 TTAAGTAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
21 6 0.10
22 22 0.38
23 8 0.14
24 22 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATATTTATAATAATAATAATAA
Found at i:68813 original size:153 final size:153
Alignment explanation
Indices: 68481--68892 Score: 581
Period size: 153 Copynumber: 2.7 Consensus size: 153
68471 CCACGACCTG
*
68481 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACTTTCTTCTCCTCAATTCGATCAACAA
1 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
* * * * *
68546 CCTTATCAGCTTGAGCTTCACTGATTTTCTTCTTCTTCTTGGTTTTCGCTTTGACAACTTTCGAT
66 CCTTGTCATCTTGAGCTTCACT-A-----ATCTTCTTCTTGGATTTCGCTTCGACAACTTTCGAT
* *
68611 GTTTGGGAAGCACTTGGTGGTTCAACATA
125 ATTTGGGAAGCACTTGGCGGTTCAACATA
* ** *
68640 TTTATCCTCAGCCCTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTTGATTCGATCAACAG
1 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
*
68705 CCTTGTCATCTTGAGCTTCACTAATCTTCTTCTTGGATTTCTCTTCGACAACTTTCGATATTTGG
66 CCTTGTCATCTTGAGCTTCACTAATCTTCTTCTTGGATTTCGCTTCGACAACTTTCGATATTTGG
68770 GAAGCACTTGGCGGTTCAACATA
131 GAAGCACTTGGCGGTTCAACATA
* * * *
68793 TTTTTCTTCAGCCTTCTTTTCCTCTACATTTTCGTCAACCTTCTTCTCCTCAATTCGATCCACAA
1 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
* * * *
68858 CCTTGTTATCTTGAGCTTCATTGATCCTCTTCTTG
66 CCTTGTCATCTTGAGCTTCACTAATCTTCTTCTTG
68893 TTCTTGGTTT
Statistics
Matches: 228, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
153 147 0.64
158 1 0.00
159 80 0.35
ACGTcount: A:0.18, C:0.28, G:0.11, T:0.42
Consensus pattern (153 bp):
TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCAACAA
CCTTGTCATCTTGAGCTTCACTAATCTTCTTCTTGGATTTCGCTTCGACAACTTTCGATATTTGG
GAAGCACTTGGCGGTTCAACATA
Found at i:78903 original size:36 final size:36
Alignment explanation
Indices: 78859--79016 Score: 177
Period size: 36 Copynumber: 4.5 Consensus size: 36
78849 GAGCATGAGG
* *
78859 ATGCAACATGCATTTATGTAGATGCATAAACCATGC
1 ATGCAACATACATTTATGCAGATGCATAAACCATGC
*
78895 AT-CAAACATACATTTATGCAGATACA-AATACCATGC
1 ATGC-AACATACATTTATGCAGATGCATAA-ACCATGC
*
78931 ATGCAACATACATGTATGCAGATGC-T--ACCATGC
1 ATGCAACATACATTTATGCAGATGCATAAACCATGC
* *
78964 ATGCAACATACATTTATGCAGATACA-AATGCCATGC
1 ATGCAACATACATTTATGCAGATGCATAA-ACCATGC
79000 A-GCTAACATACATTTAT
1 ATGC-AACATACATTTAT
79017 ACATATACAA
Statistics
Matches: 105, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
33 30 0.29
35 5 0.05
36 69 0.66
37 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.27
Consensus pattern (36 bp):
ATGCAACATACATTTATGCAGATGCATAAACCATGC
Found at i:78949 original size:15 final size:15
Alignment explanation
Indices: 78926--78976 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
78916 ATACAAATAC
78926 CATGCATGCAACATA
1 CATGCATGCAACATA
*
78941 CATGTATGCAGATGC-TA
1 CATGCATGCA-A--CATA
78958 CCATGCATGCAACATA
1 -CATGCATGCAACATA
78974 CAT
1 CAT
78977 TTATGCAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 13 0.45
16 3 0.10
17 3 0.10
18 10 0.34
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (15 bp):
CATGCATGCAACATA
Found at i:78973 original size:69 final size:71
Alignment explanation
Indices: 78859--79012 Score: 217
Period size: 69 Copynumber: 2.2 Consensus size: 71
78849 GAGCATGAGG
* * *
78859 ATGCAACATGCATTTATGTAGATGCATAAACCATGCATCAAACATACATTTATGCAGATACAAAT
1 ATGCAACATACATGTATGCAGATGCAT-AACCATGCATCAAACATACATTTATGCAGATACAAAT
78924 ACCATGC
65 ACCATGC
78931 ATGCAACATACATGTATGCAGATGC-T-ACCATGCATGC-AACATACATTTATGCAGATACAAAT
1 ATGCAACATACATGTATGCAGATGCATAACCATGCAT-CAAACATACATTTATGCAGATACAAAT
*
78993 GCCATGC
65 ACCATGC
79000 A-GCTAACATACAT
1 ATGC-AACATACAT
79013 TTATACATAT
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
68 2 0.03
69 50 0.66
70 1 0.01
71 1 0.01
72 22 0.29
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (71 bp):
ATGCAACATACATGTATGCAGATGCATAACCATGCATCAAACATACATTTATGCAGATACAAATA
CCATGC
Found at i:79025 original size:36 final size:35
Alignment explanation
Indices: 78861--79043 Score: 176
Period size: 36 Copynumber: 5.2 Consensus size: 35
78851 GCATGAGGAT
* ** *
78861 GCAACATGCATTTATGTAGATGCATAA-ACCATGCA
1 GCAACATACATTTATACAGATACA-AATACCATGCA
* *
78896 TCAAACATACATTTATGCAGATACAAATACCATGCA
1 GC-AACATACATTTATACAGATACAAATACCATGCA
* * *
78932 TGCAACATACATGTATGCAGATGC---TACCATGCA
1 -GCAACATACATTTATACAGATACAAATACCATGCA
* *
78965 TGCAACATACATTTATGCAGATACAAATGCCATGCA
1 -GCAACATACATTTATACAGATACAAATACCATGCA
*
79001 GCTAACATACATTTATACATATACAAATACCATGCA
1 GC-AACATACATTTATACAGATACAAATACCATGCA
79037 GCCAACA
1 G-CAACA
79044 CATTCATGAA
Statistics
Matches: 127, Mismatches: 13, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
33 31 0.24
35 5 0.04
36 89 0.70
37 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (35 bp):
GCAACATACATTTATACAGATACAAATACCATGCA
Found at i:88253 original size:6 final size:6
Alignment explanation
Indices: 88242--88278 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
88232 TCGGCTCGGC
88242 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
88279 TTTTAGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:88541 original size:22 final size:22
Alignment explanation
Indices: 88516--88570 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
88506 TCAGGAGTTA
* *
88516 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
88538 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
88560 CGGGAGTTATA
1 CAGGAGTTATA
88571 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:93868 original size:21 final size:21
Alignment explanation
Indices: 93842--93885 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
93832 ATTCTGGGCT
* *
93842 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
93863 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
93884 AG
1 AG
93886 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:94987 original size:31 final size:31
Alignment explanation
Indices: 94893--95000 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
94883 AGTCGAGGGT
* *
94893 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
94924 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
94955 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
94986 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
95001 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:94998 original size:30 final size:30
Alignment explanation
Indices: 94946--95041 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
94936 CTAAGGAACA
* *
94946 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* *
94977 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * *
95007 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
*
95036 TCTGGA
1 TATGGA
95042 TATGTCCTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 29 0.52
31 9 0.16
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:98271 original size:5 final size:5
Alignment explanation
Indices: 98255--98286 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
98245 TTTTAAAAAA
98255 TCGGG TTCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG -TCGGG TCGGG TCGGG TCGGG TCGGG T
98287 TTTTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:99326 original size:21 final size:21
Alignment explanation
Indices: 99291--99334 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
99281 ATTCTGGGCT
* *
99291 AGGGGAATCGGTACC-CATTCA
1 AGGGGAACCGATACCTC-TTCA
99312 AGGGGAACCGATACCTCTTCA
1 AGGGGAACCGATACCTCTTCA
99333 AG
1 AG
99335 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
AGGGGAACCGATACCTCTTCA
Found at i:100453 original size:31 final size:31
Alignment explanation
Indices: 100359--100466 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
100349 AGTCGAGGGT
* *
100359 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
100390 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
100421 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
100452 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
100467 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:100464 original size:30 final size:30
Alignment explanation
Indices: 100412--100507 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
100402 CTAAGGAACA
* *
100412 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* *
100443 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * * *
100473 TCTGGATAGTTTCCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
*
100502 TCTGGA
1 TATGGA
100508 TATGTCCTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 29 0.52
31 9 0.16
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:102249 original size:5 final size:5
Alignment explanation
Indices: 102230--102271 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
102220 GTCCGTCCGT
* * *
102230 CTCGG CTCGT CTCGG CTCGG CACGG CACGG CTCGG CT-GG CTC
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTC
102272 TCGTGGTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.05, C:0.40, G:0.36, T:0.19
Consensus pattern (5 bp):
CTCGG
Found at i:102283 original size:6 final size:6
Alignment explanation
Indices: 102272--102322 Score: 68
Period size: 6 Copynumber: 8.2 Consensus size: 6
102262 CGGCTGGCTC
102272 TCGTGG TCGTGG TCG-GG TCGAGGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TC---GTGG TCGTGG TCGTGG TCGTGG TCGTGG
102322 T
1 T
102323 AATAGTGTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 4 0.10
6 32 0.78
8 1 0.02
9 4 0.10
ACGTcount: A:0.02, C:0.16, G:0.51, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:102299 original size:20 final size:21
Alignment explanation
Indices: 102274--102312 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
102264 GCTGGCTCTC
102274 GTGGTCGTGGTCG-GGTCGAG
1 GTGGTCGTGGTCGTGGTCGAG
102294 GTGGTCGTGGTCGTGGTCG
1 GTGGTCGTGGTCGTGGTCG
102313 TGGTCGTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.03, C:0.15, G:0.54, T:0.28
Consensus pattern (21 bp):
GTGGTCGTGGTCGTGGTCGAG
Found at i:103642 original size:2 final size:2
Alignment explanation
Indices: 103631--103678 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
103621 ATCGCGAGCA
*
103631 AT AT -T AT AT AT AT AT AT AG AT AT AT AT AT AT A- 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
103671 AT AT AT AT
1 AT AT AT AT
103679 TAAAAATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104240 original size:2 final size:2
Alignment explanation
Indices: 104233--104286 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
104223 AAGTAGAAAC
104233 AT AT AT AT AT AT AT AT AT A- 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
*
104274 AT CT A- AT AT AT AT
1 AT AT AT AT AT AT AT
104287 CATTGTATTC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104271 original size:27 final size:27
Alignment explanation
Indices: 104233--104286 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
104223 AAGTAGAAAC
104233 ATATATATATATATATATAATATATAT
1 ATATATATATATATATATAATATATAT
*
104260 ATATATATATATATATCTAATATATAT
1 ATATATATATATATATATAATATATAT
104287 CATTGTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATATATATATATATAATATATAT
Found at i:104387 original size:13 final size:13
Alignment explanation
Indices: 104369--104393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104359 ATTATGAATG
104369 TTAAAATCTCTTA
1 TTAAAATCTCTTA
104382 TTAAAATCTCTT
1 TTAAAATCTCTT
104394 CTAACAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAAATCTCTTA
Found at i:105833 original size:32 final size:32
Alignment explanation
Indices: 105790--105854 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
105780 GAAGACAAAG
*
105790 ATTATCTTTAAAAGACGATTGATATATTTAAA
1 ATTATCCTTAAAAGACGATTGATATATTTAAA
105822 ATTATCCTTAAAAGACGATTGATATATTTAAA
1 ATTATCCTTAAAAGACGATTGATATATTTAAA
105854 A
1 A
105855 AATTTATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (32 bp):
ATTATCCTTAAAAGACGATTGATATATTTAAA
Found at i:105961 original size:13 final size:13
Alignment explanation
Indices: 105945--105972 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
105935 AAGACACTTT
105945 AAATGAAACATTA
1 AAATGAAACATTA
105958 AAATGAAACATTA
1 AAATGAAACATTA
105971 AA
1 AA
105973 GAGACACGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAATGAAACATTA
Found at i:106796 original size:17 final size:18
Alignment explanation
Indices: 106770--106810 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
106760 CATTCTCAAA
*
106770 AATC-TTATT-CATTGGT
1 AATCTTTATTCCACTGGT
106786 AATCTTTATTCCCACTGGT
1 AATCTTTATT-CCACTGGT
106805 AATCTT
1 AATCTT
106811 ACATTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 5 0.24
19 12 0.57
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (18 bp):
AATCTTTATTCCACTGGT
Found at i:107601 original size:20 final size:20
Alignment explanation
Indices: 107576--107668 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
107566 TTTTCCCAAT
107576 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
107596 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
107616 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
107637 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
107658 TCGCAATGCGA
1 TCGCAATGCGA
107669 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:107618 original size:41 final size:41
Alignment explanation
Indices: 107573--107668 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
107563 CGATTTTCCC
*
107573 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
107614 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
107655 AAATCGCAATGCGA
1 AATTCGCAATGCGA
107669 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:107681 original size:41 final size:41
Alignment explanation
Indices: 107595--107726 Score: 117
Period size: 41 Copynumber: 3.2 Consensus size: 41
107585 GAATAAGTAA
* * * *
107595 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
107636 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
107677 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
107718 TTCGCAACG
1 ATCGCAACG
107727 AGATACTGAC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 70 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:107682 original size:20 final size:20
Alignment explanation
Indices: 107657--107751 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
107647 AATTGAGAAA
*
107657 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
107677 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
107698 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
107718 TTCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
107738 TTCGCAACGCGATA
1 ATCGCAACGCGATA
107752 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:107965 original size:22 final size:22
Alignment explanation
Indices: 107937--107980 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
107927 CACTCTCTCA
107937 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
107959 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
107981 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:108265 original size:20 final size:20
Alignment explanation
Indices: 108240--108277 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
108230 CGATTCTCTC
108240 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
108260 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
108278 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:110144 original size:19 final size:20
Alignment explanation
Indices: 110090--110156 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
110080 TAGTTTACTT
* *
110090 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
110110 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
110130 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
110149 TCGCAACG
1 TCGCAACG
110157 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:110164 original size:14 final size:14
Alignment explanation
Indices: 110145--110202 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
110135 ATGCGAAATG
110145 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
110159 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
110175 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
110191 AAAATCACAACG
1 AAAATCGCAACG
110203 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:110187 original size:32 final size:33
Alignment explanation
Indices: 110129--110219 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
110119 GGAAATGGCT
*
110129 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
110162 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
110194 ATCACAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
110220 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:110224 original size:19 final size:18
Alignment explanation
Indices: 110129--110224 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
110119 GGAAATGGCT
110129 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
110148 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
110162 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
*
110180 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
*
110194 ATCACAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
110213 ATCGCAATGCGA
1 ATCGCAA-GCGA
110225 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.19
19 20 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:110270 original size:18 final size:16
Alignment explanation
Indices: 110243--110309 Score: 66
Period size: 18 Copynumber: 4.0 Consensus size: 16
110233 TCGTGTTGCG
110243 ATTTGTCGTTGCGATTT
1 ATTTG-CGTTGCGATTT
110260 CATTTAGCGTTGCGATTT
1 -ATTT-GCGTTGCGATTT
*
110278 -TGT-CGTTGCGATTTT
1 ATTTGCGTTGCGA-TTT
110293 ATTTCGCGTTGCGATTT
1 ATTT-GCGTTGCGATTT
110310 TGTCGTTACG
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 8 0.19
15 3 0.07
16 4 0.10
17 3 0.07
18 23 0.55
19 1 0.02
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.49
Consensus pattern (16 bp):
ATTTGCGTTGCGATTT
Found at i:110280 original size:32 final size:32
Alignment explanation
Indices: 110231--110340 Score: 159
Period size: 32 Copynumber: 3.4 Consensus size: 32
110221 GCGATTTGTG
*
110231 TTTCGTGTTGCGA-TTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
* *
110262 TTTAGCGTTGCGATTTTGTCGTTGCGATTTTA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
*
110294 TTTCGCGTTGCGATTTTGTCGTTACGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
110327 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
110341 AGCCATTTCC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
31 11 0.16
32 42 0.60
33 17 0.24
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:110286 original size:14 final size:14
Alignment explanation
Indices: 110237--110324 Score: 70
Period size: 14 Copynumber: 5.8 Consensus size: 14
110227 TGTGTTTCGT
110237 GTTGCGA-TTTGTC
1 GTTGCGATTTTGTC
*
110250 GTTGCGATTTCATTTAGC
1 GTTGCGATTT--TGT--C
110268 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
*
110282 GTTGCGATTTTATTTCGC
1 GTTGCGA-TTT-TGT--C
110300 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
*
110314 GTTACGATTTT
1 GTTGCGATTTT
110325 CATTTCGCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
13 7 0.11
14 21 0.34
15 3 0.05
16 8 0.13
17 3 0.05
18 19 0.31
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:110359 original size:20 final size:19
Alignment explanation
Indices: 110325--110380 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
110315 TTACGATTTT
*
110325 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
110344 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
110364 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
110381 TTTAAGTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:112412 original size:19 final size:19
Alignment explanation
Indices: 112358--112405 Score: 89
Period size: 18 Copynumber: 2.6 Consensus size: 19
112348 ATCGCAACGA
112358 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
112377 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
112395 GAAAATCGCAA
1 GAAAATCGCAA
112406 CGAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Done.