Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 12 of 26
Found at i:2033768 original size:43 final size:43
Alignment explanation
Indices: 2033707--2033802 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
2033697 TAAAAAAAAT
*
2033707 TATTTAAATTAATTTAAAAAT-TTATTTTATTATTTTAA-AATAA
1 TATTTAAATTAATATAAAAATATT-TTTTATTA-TTTAATAATAA
* *
2033750 TATTTATATTTATATAAAAATATTTTTTATTATTTAATAAT-A
1 TATTTAAATTAATATAAAAATATTTTTTATTATTTAATAATAA
2033792 -ATTTAAATTAA
1 TATTTAAATTAA
2033803 ATCAAATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 9 0.20
42 6 0.13
43 29 0.63
44 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (43 bp):
TATTTAAATTAATATAAAAATATTTTTTATTATTTAATAATAA
Found at i:2033769 original size:23 final size:23
Alignment explanation
Indices: 2033732--2033789 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
2033722 AAAAATTTAT
2033732 TTTATTATTT--T-AAAATAATA
1 TTTATTATTTAATAAAAATAATA
* *
2033752 TTTA-TATTTATATAAAAATATTT
1 TTTATTATTTA-ATAAAAATAATA
2033775 TTTATTATTTAATAA
1 TTTATTATTTAATAA
2033790 TAATTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 5 0.16
20 4 0.13
22 1 0.03
23 15 0.48
24 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTATTATTTAATAAAAATAATA
Found at i:2034187 original size:14 final size:14
Alignment explanation
Indices: 2034170--2034217 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
2034160 TTTATAATTT
2034170 TTAAAATATAAAAA
1 TTAAAATATAAAAA
* *
2034184 TTAAAATATTAAAT
1 TTAAAATATAAAAA
2034198 TTAATAATATAAAAA
1 TTAA-AATATAAAAA
2034213 TTAAA
1 TTAAA
2034218 TGCTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:2034433 original size:31 final size:29
Alignment explanation
Indices: 2034395--2034464 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
2034385 CTATTAAAAG
2034395 TTTTTATAGTATAGTAAA-TGAAGTTTTTTAA
1 TTTTTATA-T-TAGTAAATTGAA-TTTTTTAA
* *
2034426 TTTTTATATTATTAAATTTAATTTTTTAA
1 TTTTTATATTAGTAAATTGAATTTTTTAA
2034455 TTTTTATATT
1 TTTTTATATT
2034465 TTAAAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 24 0.67
30 4 0.11
31 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (29 bp):
TTTTTATATTAGTAAATTGAATTTTTTAA
Found at i:2036377 original size:13 final size:13
Alignment explanation
Indices: 2036359--2036386 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2036349 GACAAAGACT
2036359 CAATTCCCTCCCC
1 CAATTCCCTCCCC
2036372 CAATTCCCTCCCC
1 CAATTCCCTCCCC
2036385 CA
1 CA
2036387 GAATTTGTGA
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:0.18, C:0.61, G:0.00, T:0.21
Consensus pattern (13 bp):
CAATTCCCTCCCC
Found at i:2036448 original size:11 final size:12
Alignment explanation
Indices: 2036423--2036460 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2036413 ACTCGAGACG
2036423 AATAAAATAATA
1 AATAAAATAATA
2036435 AATAAAAT-ATA
1 AATAAAATAATA
2036446 AAT-AAATAAGTA
1 AATAAAATAA-TA
2036458 AAT
1 AAT
2036461 GACACTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.17
11 7 0.29
12 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
AATAAAATAATA
Found at i:2036893 original size:31 final size:31
Alignment explanation
Indices: 2036845--2036924 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
2036835 TTCAATTTAG
*
2036845 AATTTCTTAACCACCAGCCAAATCCAAATTA
1 AATTCCTTAACCACCAGCCAAATCCAAATTA
* ** *
2036876 AATTCCTTAGCCACCAGCCAAATTTAAATTG
1 AATTCCTTAACCACCAGCCAAATCCAAATTA
*
2036907 AATTCCCTAACCACCAGC
1 AATTCCTTAACCACCAGC
2036925 TGTCAACCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (31 bp):
AATTCCTTAACCACCAGCCAAATCCAAATTA
Found at i:2040548 original size:31 final size:31
Alignment explanation
Indices: 2040513--2040572 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2040503 TTTAATAATC
*
2040513 AATCACCAATTAAATTTAAATTAAATTTATT
1 AATCACCAATCAAATTTAAATTAAATTTATT
* *
2040544 AATCATCAATCAAATTTAAATTTAATTTA
1 AATCACCAATCAAATTTAAATTAAATTTA
2040573 ATTTATCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (31 bp):
AATCACCAATCAAATTTAAATTAAATTTATT
Found at i:2041098 original size:16 final size:16
Alignment explanation
Indices: 2041056--2041098 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
2041046 TATTAAAAAA
2041056 TAATATTTAATAA-ATT
1 TAATATTT-ATAATATT
2041072 TAA-ATTT-TAATATT
1 TAATATTTATAATATT
2041086 TAATATTTATAAT
1 TAATATTTATAAT
2041099 GTTTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.12
14 6 0.25
15 8 0.33
16 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATTTATAATATT
Found at i:2041746 original size:14 final size:14
Alignment explanation
Indices: 2041724--2041790 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 14
2041714 ATATGTTTCG
2041724 AATAAAAATATTTT
1 AATAAAAATATTTT
* *
2041738 AATATAAATTTTTT
1 AATAAAAATATTTT
2041752 AATAAAAATAAAATTTT
1 AATAAAAAT---ATTTT
2041769 AAAATAAAAATATTTT
1 --AATAAAAATATTTT
2041785 AA-AAAA
1 AATAAAA
2041791 TTTTAATCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 4 0.09
14 22 0.50
16 5 0.11
17 4 0.09
19 9 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAAAAATATTTT
Found at i:2041767 original size:19 final size:20
Alignment explanation
Indices: 2041738--2041781 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2041728 AAAATATTTT
**
2041738 AATATAAATTTTTTAATAAA
1 AATATAAATTTTAAAATAAA
2041758 AATA-AAATTTTAAAATAAA
1 AATATAAATTTTAAAATAAA
2041777 AATAT
1 AATAT
2041782 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATAAATTTTAAAATAAA
Found at i:2041944 original size:3 final size:3
Alignment explanation
Indices: 2041936--2041982 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2041926 TAAACAAAAG
2041936 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2041983 CCTGGCCTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2042332 original size:25 final size:25
Alignment explanation
Indices: 2042304--2042377 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
2042294 TAATTTTTAA
*
2042304 ATTTTTTATATAT-TTAAAAAATTAT
1 ATTTTATATATATATTAAAAAA-TAT
* *
2042329 ATTTTATATTTATATTAAAATATAT
1 ATTTTATATATATATTAAAAAATAT
** * *
2042354 ATTAAATATAAATATTTAAAAATA
1 ATTTTATATATATATTAAAAAATA
2042378 AAAAATTTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 32 0.82
26 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTTATATATATATTAAAAAATAT
Found at i:2042884 original size:17 final size:17
Alignment explanation
Indices: 2042862--2042896 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2042852 AGTTTCAATA
*
2042862 TTATTTTTTATTTAATT
1 TTATTTATTATTTAATT
*
2042879 TTATTTATTATTTGATT
1 TTATTTATTATTTAATT
2042896 T
1 T
2042897 AATTAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTATTTATTATTTAATT
Found at i:2043438 original size:28 final size:29
Alignment explanation
Indices: 2043390--2043456 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
2043380 TAAATAAATT
*
2043390 TTAATA-TA-TTTTTATCTTCATATCATA
1 TTAATATTATTTTTTATCATCATATCATA
*
2043417 TTAATATTATTTTTTAT-ATCATATTATA
1 TTAATATTATTTTTTATCATCATATCATA
* *
2043445 TTTATATCATTT
1 TTAATATTATTT
2043457 AAATCGTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.18
28 21 0.62
29 7 0.21
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (29 bp):
TTAATATTATTTTTTATCATCATATCATA
Found at i:2043743 original size:15 final size:15
Alignment explanation
Indices: 2043723--2043773 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
2043713 CACTACCTAT
*
2043723 ATATAATATAATATA
1 ATATAATATAATATG
2043738 ATATAATATAATATG
1 ATATAATATAATATG
*
2043753 ATATGATATAATATG
1 ATATAATATAATATG
2043768 ATATAA
1 ATATAA
2043774 ATTTTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
ATATAATATAATATG
Found at i:2043788 original size:5 final size:5
Alignment explanation
Indices: 2043723--2043773 Score: 75
Period size: 5 Copynumber: 10.2 Consensus size: 5
2043713 CACTACCTAT
* * *
2043723 ATATA ATATA ATATA ATATA ATATA ATATG ATATG ATATA ATATG ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2043773 A
1 A
2043774 ATTTTTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:2044764 original size:2 final size:2
Alignment explanation
Indices: 2044757--2044785 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2044747 GCATCCAAAT
2044757 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2044786 GAGTTCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2046197 original size:18 final size:18
Alignment explanation
Indices: 2046176--2046216 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2046166 TTTAATTTTT
*
2046176 AAAATCTTTTAAATATAA
1 AAAATCTTTTAAAAATAA
* *
2046194 AAAAACTTTTAAAAATTA
1 AAAATCTTTTAAAAATAA
2046212 AAAAT
1 AAAAT
2046217 ACTTGTTGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATCTTTTAAAAATAA
Found at i:2048574 original size:2 final size:2
Alignment explanation
Indices: 2048567--2048601 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2048557 GCCATATCTA
*
2048567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2048602 GAGCGAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2048611 original size:2 final size:2
Alignment explanation
Indices: 2048601--2048633 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2048591 ATATATTTAT
*
2048601 AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2048634 AGCAATGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2050040 original size:18 final size:18
Alignment explanation
Indices: 2050019--2050085 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
2050009 CACATAATAT
2050019 AAATATATAAATATATTA
1 AAATATATAAATATATTA
* *
2050037 AAATTTATAAAAATA-T-
1 AAATATATAAATATATTA
*
2050053 AAAT-TATTAATATATTA
1 AAATATATAAATATATTA
2050070 AAATTTATATAAATAT
1 AAA--TATATAAATAT
2050086 TATGTTATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
15 8 0.21
16 5 0.13
17 4 0.10
18 13 0.33
19 1 0.03
20 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAAATATATTA
Found at i:2050070 original size:8 final size:8
Alignment explanation
Indices: 2050015--2050067 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
2050005 ATATCACATA
2050015 ATATAAAT
1 ATATAAAT
2050023 ATATAAAT
1 ATATAAAT
2050031 ATATTAAAAT
1 ATA-T-AAAT
* *
2050041 TTATAAAA
1 ATATAAAT
2050049 ATATAAAT
1 ATATAAAT
*
2050057 -TATTAAT
1 ATATAAAT
2050064 ATAT
1 ATAT
2050068 TAAAATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 6 0.16
8 23 0.62
9 2 0.05
10 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:2050070 original size:33 final size:34
Alignment explanation
Indices: 2050014--2050085 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
2050004 AATATCACAT
2050014 AATATAAATATATAAATATATTAAAATTTATAAA
1 AATATAAATATATAAATATATTAAAATTTATAAA
* *
2050048 AATATAAAT-TATTAATATATTAAAATTTATATA
1 AATATAAATATATAAATATATTAAAATTTATAAA
2050081 AATAT
1 AATAT
2050086 TATGTTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 27 0.75
34 9 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
AATATAAATATATAAATATATTAAAATTTATAAA
Found at i:2050112 original size:11 final size:11
Alignment explanation
Indices: 2050096--2050121 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2050086 TATGTTATGT
2050096 TAAAAATAATA
1 TAAAAATAATA
2050107 TAAAAATAATA
1 TAAAAATAATA
2050118 TAAA
1 TAAA
2050122 TATACGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:2051154 original size:18 final size:17
Alignment explanation
Indices: 2051126--2051165 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2051116 TATTTAAAAT
2051126 ATTTT-ATATTTATATAA
1 ATTTTAATATTTATAT-A
*
2051143 ATTTTAATATTTTTATA
1 ATTTTAATATTTATATA
2051160 ATTTTA
1 ATTTTA
2051166 TTATATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTAATATTTATATA
Found at i:2051199 original size:14 final size:14
Alignment explanation
Indices: 2051182--2051218 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
2051172 AAATTGTAAA
2051182 ATATTCATATTTTT
1 ATATTCATATTTTT
2051196 ATATT-ATA-TTTT
1 ATATTCATATTTTT
2051208 ATA-TCATATTT
1 ATATTCATATTT
2051219 AATTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.05
12 10 0.48
13 5 0.24
14 5 0.24
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTCATATTTTT
Found at i:2051201 original size:33 final size:32
Alignment explanation
Indices: 2051124--2051204 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
2051114 TATATTTAAA
* * * *
2051124 ATATTTTATATTTATATAAATTTTAATATTTTT
1 ATATTTTATA-TTATATAAATTGTAAAATATTC
*
2051157 ATAATTT-TATTATATAAATTGTAAAATATTC
1 ATATTTTATATTATATAAATTGTAAAATATTC
2051188 ATATTTTTATATTATAT
1 ATA-TTTTATATTATAT
2051205 TTTATATCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 21 0.52
32 5 0.12
33 14 0.35
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (32 bp):
ATATTTTATATTATATAAATTGTAAAATATTC
Found at i:2051228 original size:21 final size:23
Alignment explanation
Indices: 2051193--2051243 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
2051183 TATTCATATT
2051193 TTTATATTATATTTTATATCATA
1 TTTATATTATATTTTATATCATA
*
2051216 TTTA-ATT-TATTTTATATTATA
1 TTTATATTATATTTTATATCATA
2051237 TTTATAT
1 TTTATAT
2051244 ATTATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 17 0.65
22 5 0.19
23 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATATTATATTTTATATCATA
Found at i:2052040 original size:4 final size:4
Alignment explanation
Indices: 2052033--2052059 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2052023 TATATATATA
2052033 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2052060 ATGTATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2058404 original size:21 final size:20
Alignment explanation
Indices: 2058375--2058415 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2058365 ATAATAAAAT
2058375 ATTAATTTTAAATA-TATTTA
1 ATTAATTTTAAA-ACTATTTA
2058395 ATTAATTTTTAAAACTATTTA
1 ATTAA-TTTTAAAACTATTTA
2058416 TACATTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTAATTTTAAAACTATTTA
Found at i:2058674 original size:15 final size:14
Alignment explanation
Indices: 2058646--2058682 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2058636 ATTTTTTGAA
2058646 TTAAA-TTT-AAAT
1 TTAAATTTTAAAAT
2058658 TTAAAATTTTAAAAT
1 TT-AAATTTTAAAAT
2058673 TTAAATTTTA
1 TTAAATTTTA
2058683 TTAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 3 0.14
14 11 0.50
15 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAATTTTAAAAT
Found at i:2059828 original size:11 final size:10
Alignment explanation
Indices: 2059809--2059851 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
2059799 TAAATTAATA
*
2059809 TTTTAATATAT
1 TTTTCATAT-T
2059820 TTTTCATATT
1 TTTTCATATT
2059830 TTTT-ATATT
1 TTTTCATATT
2059839 TTTATCATATT
1 TTT-TCATATT
2059850 TT
1 TT
2059852 ATATGATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 8 0.28
10 6 0.21
11 15 0.52
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTCATATT
Found at i:2059836 original size:18 final size:18
Alignment explanation
Indices: 2059815--2059855 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2059805 AATATTTTAA
*
2059815 TATATTTTTCAT-ATTTTT
1 TATATTTTT-ATCATATTT
2059833 TATATTTTTATCATATTT
1 TATATTTTTATCATATTT
2059851 TATAT
1 TATAT
2059856 GATAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TATATTTTTATCATATTT
Found at i:2059837 original size:20 final size:20
Alignment explanation
Indices: 2059809--2059851 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2059799 TAAATTAATA
2059809 TTTTAATATATTTT-TCATAT
1 TTTTAATAT-TTTTATCATAT
*
2059829 TTTTTATATTTTTATCATAT
1 TTTTAATATTTTTATCATAT
2059849 TTT
1 TTT
2059852 ATATGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAATATTTTTATCATAT
Found at i:2059902 original size:22 final size:22
Alignment explanation
Indices: 2059871--2059912 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2059861 AATTAAAATA
*
2059871 AATTTTTATTTAATAATTTAAT
1 AATTTATATTTAATAATTTAAT
* *
2059893 AATTTATATTTTATATTTTA
1 AATTTATATTTAATAATTTA
2059913 TCTATTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTTATATTTAATAATTTAAT
Found at i:2059956 original size:13 final size:12
Alignment explanation
Indices: 2059894--2059972 Score: 63
Period size: 13 Copynumber: 6.2 Consensus size: 12
2059884 TAATTTAATA
*
2059894 ATTTATATTTTAT
1 ATTTATA-TATAT
*
2059907 ATTTTATCTATTAT
1 A-TTTATATA-TAT
2059921 ATTTATATATAAT
1 ATTTATATAT-AT
2059934 CATTTA-ATATAT
1 -ATTTATATATAT
2059946 AGTTTATATATAT
1 A-TTTATATATAT
*
2059959 ATGTAT-TATAT
1 ATTTATATATAT
2059970 ATT
1 ATT
2059973 ATAATTTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
11 8 0.15
12 11 0.20
13 22 0.40
14 14 0.25
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:2060996 original size:19 final size:20
Alignment explanation
Indices: 2060952--2061001 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2060942 TTTATTAAAA
**
2060952 TATAATATATTAAATATAAT
1 TATAATATAAAAAATATAAT
2060972 TATAAT-TAAAAAATATAA-
1 TATAATATAAAAAATATAAT
2060990 TATTAATATAAA
1 TA-TAATATAAA
2061002 TATATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATAATATAAAAAATATAAT
Found at i:2061160 original size:20 final size:19
Alignment explanation
Indices: 2061135--2061173 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
2061125 AATTTATATT
2061135 TAAA-TTTAATTATAGAAATA
1 TAAATTTTAA-TATA-AAATA
2061155 TAAATTTTAATATAAAATA
1 TAAATTTTAATATAAAATA
2061174 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAATTTTAATATAAAATA
Found at i:2061161 original size:26 final size:26
Alignment explanation
Indices: 2061112--2061161 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2061102 TTAAAATATT
* *
2061112 ATTTAATTATTAAAATTTATATTTAA
1 ATTTAATTATTAAAATATAAATTTAA
2061138 ATTTAATTA-TAGAAATATAAATTT
1 ATTTAATTATTA-AAATATAAATTT
2061162 TAATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTAATTATTAAAATATAAATTTAA
Found at i:2062187 original size:10 final size:10
Alignment explanation
Indices: 2062172--2062247 Score: 52
Period size: 10 Copynumber: 7.6 Consensus size: 10
2062162 ATTTATATTA
2062172 TAATTTAAAT
1 TAATTTAAAT
2062182 TAATTTATAAT
1 TAATTTA-AAT
2062193 T-A-TTAAA-
1 TAATTTAAAT
2062200 TAATTTATAA-
1 TAATTTA-AAT
* *
2062210 AAATATAAATAT
1 TAAT-TTAA-AT
*
2062222 TAATTTAATT
1 TAATTTAAAT
*
2062232 TAATTTAATT
1 TAATTTAAAT
2062242 TAATTT
1 TAATTT
2062248 TTAATTTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
7 1 0.02
8 3 0.06
9 6 0.11
10 31 0.57
11 10 0.19
12 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:2062218 original size:19 final size:18
Alignment explanation
Indices: 2062176--2062220 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2062166 ATATTATAAT
**
2062176 TTAAATTAATTTATAATTA
1 TTAAA-TAATTTATAAAAA
2062195 TTAAATAATTTATAAAAA
1 TTAAATAATTTATAAAAA
2062213 TATAAATA
1 T-TAAATA
2062221 TTAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATAATTTATAAAAA
Found at i:2062231 original size:5 final size:5
Alignment explanation
Indices: 2062221--2062247 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2062211 AATATAAATA
2062221 TTAAT TTAAT TTAAT TTAAT TTAAT TT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TT
2062248 TTAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTAAT
Found at i:2063290 original size:29 final size:30
Alignment explanation
Indices: 2063254--2063314 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
2063244 AATATTAAAA
**
2063254 TTAAAAAT-TATTTAATATATTTTAAAATT
1 TTAAAAATATATAAAATATATTTTAAAATT
2063283 TTAAAAATAATATAAAATATATTTTAAAATT
1 TTAAAAAT-ATATAAAATATATTTTAAAATT
2063314 T
1 T
2063315 AAACATCCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.29
31 20 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAAAAATATATAAAATATATTTTAAAATT
Found at i:2063667 original size:25 final size:25
Alignment explanation
Indices: 2063633--2063709 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 25
2063623 ATTTAAATAT
*
2063633 AAATTTAAATTTTATTTATAAATTAA
1 AAATATAAA-TTTATTTATAAATTAA
2063659 AAATA-AAA-TTATTTGAGTATAA-TAA
1 AAATATAAATTTATTT-A-TA-AATTAA
2063684 AAATATAAAATTT-TTTATAAATTAA
1 AAATAT-AAATTTATTTATAAATTAA
2063709 A
1 A
2063710 TAAATTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
23 6 0.14
24 3 0.07
25 19 0.44
26 7 0.16
27 6 0.14
28 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.43
Consensus pattern (25 bp):
AAATATAAATTTATTTATAAATTAA
Found at i:2067593 original size:28 final size:30
Alignment explanation
Indices: 2067547--2067602 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
2067537 ATTTTTTATT
*
2067547 TATTATAATTATAAAAATATAAAATTTAAA
1 TATTATAATTATAAAAATAAAAAATTTAAA
*
2067577 TATTA-AATT-TAATAATAAAAAATTTA
1 TATTATAATTATAAAAATAAAAAATTTA
2067603 CATAATTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
29 4 0.17
30 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TATTATAATTATAAAAATAAAAAATTTAAA
Found at i:2068441 original size:15 final size:15
Alignment explanation
Indices: 2068423--2068451 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2068413 TTTTTATTGC
2068423 TTTTGTTTTTTTTTT
1 TTTTGTTTTTTTTTT
2068438 TTTTGTTTTTTTTT
1 TTTTGTTTTTTTTT
2068452 CTCTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (15 bp):
TTTTGTTTTTTTTTT
Found at i:2072475 original size:41 final size:41
Alignment explanation
Indices: 2072411--2072498 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 41
2072401 ATGTTGGAAT
2072411 TTGATTTGAAATATAAATCGAATTGATTGAACTTA-TTTTA
1 TTGATTTGAAATATAAATCGAATTGATTGAACTTACTTTTA
* * *
2072451 TTCGATTTGAGATATAAATTGAATTGATTGAGCTTACTTTTA
1 TT-GATTTGAAATATAAATCGAATTGATTGAACTTACTTTTA
2072493 TTGATT
1 TTGATT
2072499 CGATTTGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 2 0.05
41 34 0.79
42 7 0.16
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.47
Consensus pattern (41 bp):
TTGATTTGAAATATAAATCGAATTGATTGAACTTACTTTTA
Found at i:2072520 original size:23 final size:23
Alignment explanation
Indices: 2072488--2072536 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
2072478 TTGAGCTTAC
* *
2072488 TTTTATTGATTCGATTTGGTTTG
1 TTTTAATGATTCGACTTGGTTTG
2072511 TTTTAATGATTCGACTTGGTTTG
1 TTTTAATGATTCGACTTGGTTTG
2072534 TTT
1 TTT
2072537 ATTAAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.14, C:0.06, G:0.20, T:0.59
Consensus pattern (23 bp):
TTTTAATGATTCGACTTGGTTTG
Found at i:2074092 original size:17 final size:17
Alignment explanation
Indices: 2074071--2074104 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2074061 ATAATTAATT
*
2074071 ATTTTAATT-ATTTAAA
1 ATTTTTATTGATTTAAA
2074087 ATTTTTATTGATTTAAA
1 ATTTTTATTGATTTAAA
2074104 A
1 A
2074105 ATTATGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTTATTGATTTAAA
Found at i:2075585 original size:25 final size:24
Alignment explanation
Indices: 2075548--2075594 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2075538 TGTGATTCAT
*
2075548 ATTTAAATAAAAATTATTTATTTTA
1 ATTTAAATAAAAAATA-TTATTTTA
* *
2075573 ATTTAATTTAAAAATATTATTT
1 ATTTAAATAAAAAATATTATTT
2075595 ATCAAAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTAAATAAAAAATATTATTTTA
Found at i:2076467 original size:16 final size:15
Alignment explanation
Indices: 2076448--2076508 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 15
2076438 TGATTTAATT
2076448 AATTAAAATTTTAAAA
1 AATT-AAATTTTAAAA
**
2076464 AATTATTTTTTATTAAA
1 AATTAAATTTTA--AAA
2076481 ATATT-AATTTTAAAA
1 A-ATTAAATTTTAAAA
2076496 AATTAATATTTTA
1 AATTAA-ATTTTA
2076509 TATTTTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 3 0.08
15 11 0.31
16 10 0.28
17 9 0.25
18 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTAAATTTTAAAA
Found at i:2076495 original size:14 final size:14
Alignment explanation
Indices: 2076454--2076502 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
2076444 AATTAATTAA
2076454 AATTTTAAAAAATT
1 AATTTTAAAAAATT
*
2076468 ATTTTTTATTAAAATATT
1 A-ATTTTA--AAAA-ATT
2076486 AATTTTAAAAAATT
1 AATTTTAAAAAATT
2076500 AAT
1 AAT
2076503 ATTTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 7 0.24
15 9 0.31
17 9 0.31
18 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTTAAAAAATT
Found at i:2076981 original size:13 final size:13
Alignment explanation
Indices: 2076942--2076988 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
2076932 TTATTTATAT
2076942 TTAA-TAATATAAA
1 TTAATTAATA-AAA
2076955 TATAATT-A-AAAA
1 T-TAATTAATAAAA
2076967 TTAATTAATAAAA
1 TTAATTAATAAAA
2076980 TTAATTAAT
1 TTAATTAAT
2076989 TCAATCCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 15 0.50
14 4 0.13
15 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAATTAATAAAA
Found at i:2078609 original size:13 final size:13
Alignment explanation
Indices: 2078591--2078615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2078581 GTAATTAGTT
2078591 TTAAAAAATATTC
1 TTAAAAAATATTC
2078604 TTAAAAAATATT
1 TTAAAAAATATT
2078616 AGATAACAAA
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAAAAAATATTC
Found at i:2081461 original size:23 final size:23
Alignment explanation
Indices: 2081433--2081483 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
2081423 TTATTGGTAT
2081433 GATTTCACTCACGGTAGTTAATA
1 GATTTCACTCACGGTAGTTAATA
2081456 GATTTCACTCACGGTAGTTAATA
1 GATTTCACTCACGGTAGTTAATA
2081479 GATTT
1 GATTT
2081484 TGGGTTCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (23 bp):
GATTTCACTCACGGTAGTTAATA
Found at i:2082569 original size:18 final size:19
Alignment explanation
Indices: 2082543--2082607 Score: 91
Period size: 18 Copynumber: 3.6 Consensus size: 19
2082533 CGATGATGAT
2082543 GATGATTCTGAGGATGAAA
1 GATGATTCTGAGGATGAAA
*
2082562 G-TGGTTCTGAGGA-GAAA
1 GATGATTCTGAGGATGAAA
2082579 GATGATTCTGAGGATG-AA
1 GATGATTCTGAGGATGAAA
*
2082597 GATGAGTCTGA
1 GATGATTCTGA
2082608 TGAGGTTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 5 0.12
18 34 0.83
19 2 0.05
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.26
Consensus pattern (19 bp):
GATGATTCTGAGGATGAAA
Found at i:2082942 original size:3 final size:3
Alignment explanation
Indices: 2082934--2082969 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2082924 GTCTATTTGA
2082934 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2082970 TGATAAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2086170 original size:13 final size:12
Alignment explanation
Indices: 2086142--2086184 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
2086132 GCTGCAAACC
2086142 TTATTTATAAAA
1 TTATTTATAAAA
2086154 TTATTTATAATAA
1 TTATTTATAA-AA
*
2086167 TTATGTTTTAAATA
1 TTAT-TTATAAA-A
2086181 TTAT
1 TTAT
2086185 ATATTATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 10 0.37
13 7 0.26
14 10 0.37
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTTATAAAA
Found at i:2086685 original size:2 final size:2
Alignment explanation
Indices: 2086678--2086708 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2086668 CCACTTGGAT
2086678 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 T
2086709 GAAAATACCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2089108 original size:2 final size:2
Alignment explanation
Indices: 2089101--2089143 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2089091 AATAGTAGCA
2089101 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2089143 A
1 A
2089144 TTACGAGATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2092010 original size:28 final size:25
Alignment explanation
Indices: 2091958--2092012 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
2091948 AAATAAAAAA
* *
2091958 AAACAAAAAACAAAAGAATCAATAT
1 AAACAAAAAAAAAAAGAAACAATAT
2091983 AAACAGAAAAAAAAAATGAAACACATAT
1 AAACA-AAAAAAAAAA-GAAACA-ATAT
2092011 AA
1 AA
2092013 TGCTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 9 0.36
27 5 0.20
28 6 0.24
ACGTcount: A:0.73, C:0.11, G:0.05, T:0.11
Consensus pattern (25 bp):
AAACAAAAAAAAAAAGAAACAATAT
Found at i:2094064 original size:39 final size:38
Alignment explanation
Indices: 2094008--2094125 Score: 146
Period size: 39 Copynumber: 3.0 Consensus size: 38
2093998 AACCAAGGAC
*
2094008 AACAAAGCCTGCAACTCCAAAGCAAGCAAGGGAAAAGAA
1 AACAAAGCTTGCAACTCCAAAGCAAGCAA-GGAAAAGAA
** * *
2094047 GCCAAAGCTTGCAACTCCAAAGCAAACCAAGAAAAAGAA
1 AACAAAGCTTGCAACTCCAAAGC-AAGCAAGGAAAAGAA
* *
2094086 AACAAAGCTTGCAGCTCCAAAGAAAGCTAAGGAAAAGAA
1 AACAAAGCTTGCAACTCCAAAGCAAGC-AAGGAAAAGAA
2094125 A
1 A
2094126 TCTGATAATG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 3 0.05
39 58 0.88
40 5 0.08
ACGTcount: A:0.52, C:0.22, G:0.19, T:0.08
Consensus pattern (38 bp):
AACAAAGCTTGCAACTCCAAAGCAAGCAAGGAAAAGAA
Found at i:2099399 original size:2 final size:2
Alignment explanation
Indices: 2099392--2099418 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2099382 ATTTCGTGTA
2099392 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 A
2099419 AAAACTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2100178 original size:22 final size:22
Alignment explanation
Indices: 2100147--2100188 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2100137 CAGATGTAGG
*
2100147 TTTTT-TTTTTTTTTCATTTTCA
1 TTTTTATTTTTATTT-ATTTTCA
2100169 TTTTTATTTTTATTTATTTT
1 TTTTTATTTTTATTTATTTT
2100189 AATATTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTATTTTTATTTATTTTCA
Found at i:2100425 original size:7 final size:7
Alignment explanation
Indices: 2100400--2100439 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
2100390 ATAATTATAT
2100400 AATTAAA
1 AATTAAA
*
2100407 AAGTTGAA
1 AA-TTAAA
2100415 AATTAAA
1 AATTAAA
2100422 AATTAAA
1 AATTAAA
2100429 AATTAAA
1 AATTAAA
2100436 AATT
1 AATT
2100440 TAATTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (7 bp):
AATTAAA
Found at i:2100458 original size:19 final size:19
Alignment explanation
Indices: 2100399--2100448 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
2100389 TATAATTATA
*
2100399 TAATTAAAAAGTTGAAAATT
1 TAATTAAAAA-TTAAAAATT
*
2100419 AAAAATTAAAAATTAAAAATT
1 --TAATTAAAAATTAAAAATT
2100440 TAATTAAAA
1 TAATTAAAA
2100449 TTTTATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
21 8 0.32
22 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
TAATTAAAAATTAAAAATT
Found at i:2100474 original size:27 final size:26
Alignment explanation
Indices: 2100392--2100482 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
2100382 ATTTTTTTAT
*
2100392 AATTATATAATTAAAAAGTTGAAAATTAA
1 AATTTTATAATTAAAAAG-T-AAAA-TAA
* * * * * *
2100421 AAATTAAAAATTAAAAATTTAATTAA
1 AATTTTATAATTAAAAAGTAAAATAA
2100447 AATTTTATAATTAAAAAAGTAAAATAA
1 AATTTTATAATT-AAAAAGTAAAATAA
2100474 AATTTTATA
1 AATTTTATA
2100483 TTTTTAAGCA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
26 12 0.25
27 22 0.46
28 1 0.02
29 13 0.27
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (26 bp):
AATTTTATAATTAAAAAGTAAAATAA
Found at i:2105255 original size:27 final size:27
Alignment explanation
Indices: 2105209--2105260 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
2105199 AAACATTTTA
2105209 TTTTATTAAATAATATTAA-TAAATAT
1 TTTTATTAAATAATATTAATTAAATAT
*
2105235 TTTTATTTTAATAAT-TATAATTAAAT
1 TTTTA-TTAAATAATAT-TAATTAAAT
2105261 TTAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 6 0.27
27 11 0.50
28 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTATTAAATAATATTAATTAAATAT
Found at i:2105272 original size:25 final size:25
Alignment explanation
Indices: 2105248--2105301 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
2105238 TATTTTAATA
**
2105248 ATTATAAT-TAAATTTAAATAAAAT
1 ATTATAATATAAATAAAAATAAAAT
*
2105272 ATTATTATATAAATAAAAATAAAAT
1 ATTATAATATAAATAAAAATAAAAT
*
2105297 TTTAT
1 ATTAT
2105302 TTATTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTATAATATAAATAAAAATAAAAT
Found at i:2113946 original size:3 final size:3
Alignment explanation
Indices: 2113938--2113968 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2113928 TGTATACCTA
*
2113938 AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2113969 TGGTTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2114909 original size:17 final size:18
Alignment explanation
Indices: 2114889--2114929 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
2114879 ATGTTATCTC
2114889 ATTTTAAAAAAATA-ATT
1 ATTTTAAAAAAATATATT
*
2114906 A-TTTAAAATAATATATT
1 ATTTTAAAAAAATATATT
*
2114923 TTTTTAA
1 ATTTTAA
2114930 TATTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTAAAAAAATATATT
Found at i:2115087 original size:18 final size:19
Alignment explanation
Indices: 2115064--2115173 Score: 64
Period size: 18 Copynumber: 6.3 Consensus size: 19
2115054 CTATAAGTCA
2115064 AATTAAATTAT-ATATATT
1 AATTAAATTATAATATATT
*
2115082 AATTAAATT-TAATTTATT
1 AATTAAATTATAATATATT
* *
2115100 -ATTAAATTAATAAAAAATT
1 AATTAAATT-ATAATATATT
*
2115119 ATTTAAATT-TAAT-TA-T
1 AATTAAATTATAATATATT
2115135 -A--AAATATATAA-ATATT
1 AATTAAAT-TATAATATATT
*
2115151 AATATAAA--ATAATATTTT
1 AAT-TAAATTATAATATATT
2115169 AATTA
1 AATTA
2115174 TGAAATAAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 27
0.66 0.08 0.25
Matches are distributed among these distances:
13 4 0.06
14 1 0.01
15 5 0.07
16 2 0.03
17 17 0.24
18 25 0.36
19 6 0.09
20 10 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTAAATTATAATATATT
Found at i:2115146 original size:21 final size:21
Alignment explanation
Indices: 2115113--2115180 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
2115103 AAATTAATAA
*
2115113 AAAATTATTTAAATTTAATTAT
1 AAAA-TATATAAATTTAATTAT
2115135 AAAATATATAAATATTAA-TAT
1 AAAATATATAAAT-TTAATTAT
*
2115156 AAAATA-AT-ATTTTAATTAT
1 AAAATATATAAATTTAATTAT
*
2115175 GAAATA
1 AAAATA
2115181 AGTTTCTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.10
19 10 0.24
20 2 0.05
21 17 0.41
22 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
AAAATATATAAATTTAATTAT
Found at i:2115165 original size:22 final size:21
Alignment explanation
Indices: 2115105--2115161 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2115095 TTATTATTAA
* *
2115105 ATTAATAAAAAATTATTTAAAT
1 ATTAATATAAAA-TATATAAAT
2115127 -TTAATTATAAAATATATAAAT
1 ATTAA-TATAAAATATATAAAT
2115148 ATTAATATAAAATA
1 ATTAATATAAAATA
2115162 ATATTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAATATAAAATATATAAAT
Found at i:2118376 original size:2 final size:2
Alignment explanation
Indices: 2118369--2118405 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2118359 ACACTTGATT
2118369 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
2118406 TGCCATTGTT
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:2118530 original size:21 final size:22
Alignment explanation
Indices: 2118492--2118532 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2118482 TTTTTTTACA
*
2118492 AAAAAAATTATAATTTTAAAAT
1 AAAAAAATTATAAATTTAAAAT
*
2118514 AAAAAATTTA-AAATTTAAA
1 AAAAAAATTATAAATTTAAA
2118533 CTTACTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAAAATTATAAATTTAAAAT
Found at i:2120648 original size:2 final size:2
Alignment explanation
Indices: 2120641--2120677 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2120631 TCATTCTGTA
2120641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2120678 CATTGAAATA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2122061 original size:250 final size:250
Alignment explanation
Indices: 2121620--2122112 Score: 986
Period size: 250 Copynumber: 2.0 Consensus size: 250
2121610 GCTTTCAAAG
2121620 ACTATGTTATTTAAATCACTAACTTGAGATCAGGTGTTCGTCGATTTTGACAAATTGGTTGCAGT
1 ACTATGTTATTTAAATCACTAACTTGAGATCAGGTGTTCGTCGATTTTGACAAATTGGTTGCAGT
2121685 AACATTGTAATTGTAAAGAAATAAGGCTTGCTTTCATCATGAATCATTTCATAATAGATGCTTCC
66 AACATTGTAATTGTAAAGAAATAAGGCTTGCTTTCATCATGAATCATTTCATAATAGATGCTTCC
2121750 GTAGATTGAAGGCCCAAAGTAACTGCTAATATCATCCGGAGATTCATCAGAACAATGATAGAAAA
131 GTAGATTGAAGGCCCAAAGTAACTGCTAATATCATCCGGAGATTCATCAGAACAATGATAGAAAA
2121815 CAAGGGAAATAGGAAACTAATGACCTTATCTTCTGCAAAAAAAAAAAAGGGAAAT
196 CAAGGGAAATAGGAAACTAATGACCTTATCTTCTGCAAAAAAAAAAAAGGGAAAT
2121870 ACTATGTTATTTAAATCACTAACTTGAGATCAGGTGTTCGTCGATTTTGACAAATTGGTTGCAGT
1 ACTATGTTATTTAAATCACTAACTTGAGATCAGGTGTTCGTCGATTTTGACAAATTGGTTGCAGT
2121935 AACATTGTAATTGTAAAGAAATAAGGCTTGCTTTCATCATGAATCATTTCATAATAGATGCTTCC
66 AACATTGTAATTGTAAAGAAATAAGGCTTGCTTTCATCATGAATCATTTCATAATAGATGCTTCC
2122000 GTAGATTGAAGGCCCAAAGTAACTGCTAATATCATCCGGAGATTCATCAGAACAATGATAGAAAA
131 GTAGATTGAAGGCCCAAAGTAACTGCTAATATCATCCGGAGATTCATCAGAACAATGATAGAAAA
2122065 CAAGGGAAATAGGAAACTAATGACCTTATCTTCTGCAAAAAAAAAAAA
196 CAAGGGAAATAGGAAACTAATGACCTTATCTTCTGCAAAAAAAAAAAA
2122113 AAGAAAAAAA
Statistics
Matches: 243, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 243 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (250 bp):
ACTATGTTATTTAAATCACTAACTTGAGATCAGGTGTTCGTCGATTTTGACAAATTGGTTGCAGT
AACATTGTAATTGTAAAGAAATAAGGCTTGCTTTCATCATGAATCATTTCATAATAGATGCTTCC
GTAGATTGAAGGCCCAAAGTAACTGCTAATATCATCCGGAGATTCATCAGAACAATGATAGAAAA
CAAGGGAAATAGGAAACTAATGACCTTATCTTCTGCAAAAAAAAAAAAGGGAAAT
Found at i:2122751 original size:2 final size:2
Alignment explanation
Indices: 2122739--2122802 Score: 64
Period size: 2 Copynumber: 33.0 Consensus size: 2
2122729 ATAAATAATT
*
2122739 TA TA T- TA TA TA TA T- TC TGA TA TA T- TCA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA TA TA TA TA
*
2122780 TA TA TA TA TA TA TT TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
2122803 AAATTATAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
1 4 0.08
2 47 0.89
3 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2125562 original size:29 final size:30
Alignment explanation
Indices: 2125524--2125580 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
2125514 TATATTAAAA
*
2125524 ATTATATTATTAAA-TATAATTCATATTTTG
1 ATTATATTA-TAAACTATAATTAATATTTTG
*
2125554 ATTA-ATTATAAACTATATTTAATATTT
1 ATTATATTATAAACTATAATTAATATTT
2125581 ATTTAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 16 0.67
30 4 0.17
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTATATTATAAACTATAATTAATATTTTG
Found at i:2126884 original size:21 final size:22
Alignment explanation
Indices: 2126840--2126886 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2126830 TATCTAATTA
* *
2126840 TAAATATAAAAATATAATTTTT
1 TAAATATAAAAATAAAAATTTT
*
2126862 TAAATAT-AAATTAAAAATTTT
1 TAAATATAAAAATAAAAATTTT
2126883 TAAA
1 TAAA
2126887 AATTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATAAAAATAAAAATTTT
Found at i:2126893 original size:22 final size:22
Alignment explanation
Indices: 2126840--2126899 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
2126830 TATCTAATTA
* * * *
2126840 TAAATATAAAAATATAATTTTT
1 TAAAAATAAATATAAAAATTTT
*
2126862 TAAATATAAAT-TAAAAATTTT
1 TAAAAATAAATATAAAAATTTT
2126883 TAAAAATTAAATATAAA
1 TAAAAA-TAAATATAAA
2126900 CATATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 13 0.41
22 15 0.47
23 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATAAATATAAAAATTTT
Found at i:2128096 original size:20 final size:21
Alignment explanation
Indices: 2128062--2128100 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2128052 TCTTTTTAAT
2128062 ATTTTTAAATAATAAAAATCA
1 ATTTTTAAATAATAAAAATCA
2128083 ATTTTTAAAT-ATAAAAAT
1 ATTTTTAAATAATAAAAAT
2128101 TAAAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTTTAAATAATAAAAATCA
Found at i:2132269 original size:25 final size:23
Alignment explanation
Indices: 2132236--2132282 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2132226 AAATTTATAA
2132236 ATATGTTAAATTAAATTTAAAAAAC
1 ATATGTTAAA--AAATTTAAAAAAC
*
2132261 ATATTTTAAAAAATTTAAAAAA
1 ATATGTTAAAAAATTTAAAAAA
2132283 ATAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATGTTAAAAAATTTAAAAAAC
Found at i:2133846 original size:19 final size:21
Alignment explanation
Indices: 2133799--2133847 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
2133789 TGAAAACTTA
2133799 AAAATAATATATAAATATTTTT
1 AAAATAAT-TATAAATATTTTT
*
2133821 -AATTAATT-TAAAT-TTTTT
1 AAAATAATTATAAATATTTTT
2133839 AAAATAATT
1 AAAATAATT
2133848 CATCATCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
20 1 0.04
21 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATAATTATAAATATTTTT
Found at i:2137627 original size:10 final size:10
Alignment explanation
Indices: 2137612--2137643 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2137602 TTAATTTTTG
2137612 TAATTTAAAT
1 TAATTTAAAT
2137622 TAATTTAAAT
1 TAATTTAAAT
*
2137632 AAATTTAAAT
1 TAATTTAAAT
2137642 TA
1 TA
2137644 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:2137710 original size:22 final size:21
Alignment explanation
Indices: 2137671--2137715 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2137661 TAATATTTTT
*
2137671 ATTTAAAATTTAATTATATAA
1 ATTTAAAATTTAATTATAAAA
2137692 ATTTATAAATATTAA-TATAAAA
1 ATTTA-AAAT-TTAATTATAAAA
2137714 AT
1 AT
2137716 ATTTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 12 0.57
23 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTAAAATTTAATTATAAAA
Found at i:2138340 original size:141 final size:142
Alignment explanation
Indices: 2138195--2138478 Score: 525
Period size: 142 Copynumber: 2.0 Consensus size: 142
2138185 ATTGACGTCA
*
2138195 AAATTATTGTTCACGAAAATAATACATGTGTATAATTT-TGTATAATTAATGGTTTTTCTTTCTT
1 AAATTATTGTTCACGAAAATAATACATGTGTATAATTTATGTATAATTAATGGCTTTTCTTTCTT
*
2138259 TTTTTTAAGTGATTTAATTAAGATGAGATACTAATAATTGGTTTTTATTTATTTATTTATTTGCT
66 TTTTTAAAGTGATTTAATTAAGATGAGATACTAATAATTGGTTTTTATTTATTTATTTATTTGCT
2138324 TATTTCATATAT
131 TATTTCATATAT
* *
2138336 AAATTATTGTTCACGAAAATAATATATGTGTATAATTTATGTATAATTAATGGCTTTTCTTTGTT
1 AAATTATTGTTCACGAAAATAATACATGTGTATAATTTATGTATAATTAATGGCTTTTCTTTCTT
2138401 TTTTTAAAGTGATTTAATTAAGATGAGATACTAATAATTGGTTTTTATTTATTTATTTATTTGCT
66 TTTTTAAAGTGATTTAATTAAGATGAGATACTAATAATTGGTTTTTATTTATTTATTTATTTGCT
2138466 TATTTCATATAT
131 TATTTCATATAT
2138478 A
1 A
2138479 TTTTACAGTT
Statistics
Matches: 138, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
141 37 0.27
142 101 0.73
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (142 bp):
AAATTATTGTTCACGAAAATAATACATGTGTATAATTTATGTATAATTAATGGCTTTTCTTTCTT
TTTTTAAAGTGATTTAATTAAGATGAGATACTAATAATTGGTTTTTATTTATTTATTTATTTGCT
TATTTCATATAT
Found at i:2139831 original size:6 final size:6
Alignment explanation
Indices: 2139820--2139845 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2139810 TAATTTACAA
2139820 TATATT TATATT TATATT TATATT TA
1 TATATT TATATT TATATT TATATT TA
2139846 CAATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TATATT
Found at i:2140953 original size:16 final size:16
Alignment explanation
Indices: 2140910--2140954 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
2140900 AATTTAATAA
2140910 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
2140926 TTTGATAA--TAAATTAT
1 TTT-A-AATTTAAATTAT
2140942 TTTAAATTTAAAT
1 TTTAAATTTAAAT
2140955 GAATTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.08
15 1 0.04
16 19 0.76
17 1 0.04
18 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:2141267 original size:2 final size:2
Alignment explanation
Indices: 2141260--2141284 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2141250 CTTTTGTTTC
2141260 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 T
2141285 GGATTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2141890 original size:42 final size:42
Alignment explanation
Indices: 2141829--2141914 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
2141819 GAACAGTAAT
* *
2141829 ATTTTTCATCAACTACCTTAACATTTTCACTTCAAATATGTC
1 ATTTTTCATCAACTACCTTAACACTTTCACTTCAAATATATC
* *
2141871 ATTTTTCATCAACTGCCTTAACGCTTTCACTTCAAATATATC
1 ATTTTTCATCAACTACCTTAACACTTTCACTTCAAATATATC
2141913 AT
1 AT
2141915 AAACCCAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.42
Consensus pattern (42 bp):
ATTTTTCATCAACTACCTTAACACTTTCACTTCAAATATATC
Found at i:2144743 original size:19 final size:19
Alignment explanation
Indices: 2144719--2144759 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2144709 TTATGTTAAT
*
2144719 ATTAAATTA-TTTTTATTTA
1 ATTAAA-TACTTTTAATTTA
2144738 ATTAAATACTTTTAATTTA
1 ATTAAATACTTTTAATTTA
2144757 ATT
1 ATT
2144760 TTAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTAAATACTTTTAATTTA
Found at i:2145428 original size:30 final size:28
Alignment explanation
Indices: 2145393--2145468 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
2145383 ATTTTACTTG
*
2145393 AATAAATTTTTAGATTTTAATTATATTTTA
1 AATAAATTTTTAGA-TTTAATTATA-ATTA
* * *
2145423 AATAAATTATTATATTTATTTATAATTA
1 AATAAATTTTTAGATTTAATTATAATTA
2145451 AATAAGA-TTTTA-ATTTAA
1 AATAA-ATTTTTAGATTTAA
2145469 ATAAAATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.13
28 12 0.31
29 10 0.26
30 12 0.31
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AATAAATTTTTAGATTTAATTATAATTA
Found at i:2145443 original size:23 final size:21
Alignment explanation
Indices: 2145416--2145483 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
2145406 ATTTTAATTA
2145416 TATTTTAAATAAATTATTATATT
1 TATTTTAAATAAA-TATTAT-TT
* **
2145439 TATTTATAATTAAATAAGATTT
1 TATTT-TAAATAAATATTATTT
*
2145461 TAATTTAAATAAAATATTGATTT
1 TATTTTAAAT-AAATATT-ATTT
2145484 AGATTAAAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.11
22 11 0.31
23 13 0.37
24 7 0.20
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TATTTTAAATAAATATTATTT
Found at i:2145464 original size:16 final size:18
Alignment explanation
Indices: 2145440--2145472 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2145430 TATTATATTT
2145440 ATTTATAA-TTAAATAAG
1 ATTTATAATTTAAATAAG
2145457 ATTT-TAATTTAAATAA
1 ATTTATAATTTAAATAA
2145473 AATATTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
ATTTATAATTTAAATAAG
Found at i:2145518 original size:28 final size:28
Alignment explanation
Indices: 2145487--2145567 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
2145477 TTGATTTAGA
2145487 TTAAAGTTTATTATATATAAATTAAAAT
1 TTAAAGTTTATTATATATAAATTAAAAT
** *
2145515 TTAAAAATTATTTAAATATAAATT-AAAT
1 TTAAAGTTTA-TTATATATAAATTAAAAT
* *
2145543 TAAAAGTTTATT-TAAATAAATTAAA
1 TTAAAGTTTATTATATATAAATTAAA
2145568 GTTGAAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
26 8 0.19
27 4 0.09
28 19 0.44
29 12 0.28
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
TTAAAGTTTATTATATATAAATTAAAAT
Found at i:2145575 original size:28 final size:25
Alignment explanation
Indices: 2145486--2145590 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 25
2145476 ATTGATTTAG
* *
2145486 ATTAAAGTTTATTATATATAAATTAAA
1 ATTAAAATTTATT-TAAATAAATT-AA
*
2145513 ATTTAAAAATTATTTAAATATAAATTAA
1 A-TTAAAATTTATTT-AA-ATAAATTAA
2145541 ATTAAAAGTTTATTTAAATAAATTAA
1 ATTAAAA-TTTATTTAAATAAATTAA
* *
2145567 AGTTGAAAATTTATATAAGTAAAT
1 A-TT-AAAATTTATTTAAATAAAT
2145591 AAAAAATATT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
26 10 0.15
27 25 0.38
28 24 0.36
29 7 0.11
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (25 bp):
ATTAAAATTTATTTAAATAAATTAA
Found at i:2145951 original size:5 final size:5
Alignment explanation
Indices: 2145943--2146009 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
2145933 ATTATAATAA
* ** *
2145943 TTATT TTATT TTATT TTATT TTAATT TT-TA TTAAA TAATT ATTATT TTA--
1 TTATT TTATT TTATT TTATT TT-ATT TTATT TTATT TTATT -TTATT TTATT
*
2145992 TAATT TTATT TTATT TTA
1 TTATT TTATT TTATT TTA
2146010 ATAAATTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
3 2 0.04
4 3 0.06
5 35 0.71
6 9 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (5 bp):
TTATT
Found at i:2145984 original size:38 final size:39
Alignment explanation
Indices: 2145932--2146008 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
2145922 TAAATCAATA
*
2145932 TATTATAATAATTATT-TTATT-TTATTTTATTTTAATTTT
1 TATTATAATAATTATTATT-TTATAATTTTATTTT-ATTTT
2145971 TATTA-AATAATTATTATTTTATAATTTTATTTTATTTT
1 TATTATAATAATTATTATTTTATAATTTTATTTTATTTT
2146009 AATAAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
38 17 0.49
39 18 0.51
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (39 bp):
TATTATAATAATTATTATTTTATAATTTTATTTTATTTT
Found at i:2152126 original size:89 final size:85
Alignment explanation
Indices: 2151966--2152292 Score: 287
Period size: 89 Copynumber: 3.8 Consensus size: 85
2151956 CAGCTCAACA
* * * * ** *
2151966 TCAAGACATAGCGACTTCCAAGCTCACATATCGAGGCATTTCAAATCATTTATAGTTGTATCCCT
1 TCAAGACATA-CAAATTCCAAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTATCCCT
*
2152031 GTGTCTTTCATAACCAGTCCAAAG
65 GTGTCTTTCA-AA-CA-TACAAAG
* *
2152055 TCAAGACATACTAAATTCCAAGCTCACGTGTCAAGGCATTTCAAATTGTTTATAGTCGTATCTCT
1 TCAAGACATAC-AAATTCCAAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTATCCCT
* *
2152120 GAGTCTTTC--ACATGC--AG
65 GTGTCTTTCAAACATACAAAG
* * *
2152137 CTCAATG---T-CAAATCCCGAGCTCACATGTCAAGGCATTTC-AATCT-TTTATAGTCGTGTCC
1 -TCAA-GACATACAAATTCCAAGCTCACATGTCAAGGCATTTCAAAT-TGTTTATAGTCGTATCC
*
2152196 CTGTGTCTTTCACAATCAATACAATG
63 CTGTGTCTTTCA-AA-C-ATACAAAG
* *** *
2152222 TCAACACATACCCGCTTCCTAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTATCCCT
1 TCAAGACATA-CAAATTCCAAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTATCCCT
2152287 GTGTCT
65 GTGTCT
2152293 ATGATTCCTT
Statistics
Matches: 194, Mismatches: 26, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
78 26 0.13
79 28 0.14
80 1 0.01
81 2 0.01
82 3 0.02
83 7 0.04
84 7 0.04
85 3 0.02
86 2 0.01
88 28 0.14
89 87 0.45
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (85 bp):
TCAAGACATACAAATTCCAAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTATCCCTG
TGTCTTTCAAACATACAAAG
Found at i:2152263 original size:167 final size:168
Alignment explanation
Indices: 2151986--2152292 Score: 436
Period size: 167 Copynumber: 1.8 Consensus size: 168
2151976 GCGACTTCCA
* * * * *
2151986 AGCTCACATATCGAGGCATTTCAAATCATTTATAGTTGTATCCCTGTGTCTTTCATAACCAGTCC
1 AGCTCACATATCAAGGCATTTCAAATCATTTATAGTCGTATCCCTGTGTCTTTCACAACCAATAC
* * *
2152051 AAAGTCAAGACATACTAAATTCCAAGCTCACGTGTCAAGGCATTTCAAATTGTTTATAGTCGTAT
66 AAAGTCAACACATACCAAATTCCAAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTAT
*
2152116 CTCTGAGTCTTTCACATGCAGCTCAATGTCAAATCCCG
131 CCCTGAGTCTTTCACATGCAGCTCAATGTCAAATCCCG
* * * *
2152154 AGCTCACATGTCAAGGCATTTC-AATCTTTTATAGTCGTGTCCCTGTGTCTTTCACAATCAATAC
1 AGCTCACATATCAAGGCATTTCAAATCATTTATAGTCGTATCCCTGTGTCTTTCACAACCAATAC
* *** *
2152218 AATGTCAACACATACCCGCTTCCTAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTAT
66 AAAGTCAACACATACCAAATTCCAAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTAT
*
2152283 CCCTGTGTCT
131 CCCTGAGTCT
2152293 ATGATTCCTT
Statistics
Matches: 120, Mismatches: 19, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
167 100 0.83
168 20 0.17
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (168 bp):
AGCTCACATATCAAGGCATTTCAAATCATTTATAGTCGTATCCCTGTGTCTTTCACAACCAATAC
AAAGTCAACACATACCAAATTCCAAGCTCACATGTCAAGGCATTTCAAATTGTTTATAGTCGTAT
CCCTGAGTCTTTCACATGCAGCTCAATGTCAAATCCCG
Found at i:2154512 original size:20 final size:20
Alignment explanation
Indices: 2154487--2154542 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
2154477 TTTATTAAAG
2154487 TATTTTTTTAATTTTATAAT
1 TATTTTTTTAATTTTATAAT
* * *
2154507 TATTTTTAT-ATATTCTAAT
1 TATTTTTTTAATTTTATAAT
2154526 TAATTTTTTTTAATTTT
1 T-A-TTTTTTTAATTTT
2154543 TATGATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 9 0.32
20 9 0.32
21 6 0.21
22 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTTTTTAATTTTATAAT
Found at i:2154529 original size:31 final size:31
Alignment explanation
Indices: 2154493--2154562 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2154483 AAAGTATTTT
2154493 TTTAATTTTATAATT-ATTTTTAT-ATATTCTAA
1 TTTAATTTT-T-ATTAATTTTTATGATATT-TAA
*
2154525 -TTAATTTTTTTTAATTTTTATGATATTTAA
1 TTTAATTTTTATTAATTTTTATGATATTTAA
2154555 TTTAATTT
1 TTTAATTT
2154563 AATCTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 2 0.06
30 12 0.35
31 20 0.59
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (31 bp):
TTTAATTTTTATTAATTTTTATGATATTTAA
Found at i:2154579 original size:35 final size:30
Alignment explanation
Indices: 2154510--2154583 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 30
2154500 TTATAATTAT
*
2154510 TTTTATATATTCTAATTAATTTTTTTTAAT
1 TTTTATATATTCTAATTAATTTTTTTTAAA
2154540 TTTTATGATATT-TAATTTAATTTAATCTTTTAAAA
1 TTTTAT-ATATTCTAA-TTAATTT--T-TTTT-AAA
2154575 TTTTATATA
1 TTTTATATA
2154584 ATATAAACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
30 9 0.24
31 12 0.32
33 1 0.03
34 7 0.19
35 8 0.22
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTATATATTCTAATTAATTTTTTTTAAA
Found at i:2155138 original size:17 final size:17
Alignment explanation
Indices: 2155098--2155139 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2155088 TTTACACTAT
2155098 ATATATAT-ATACACAC
1 ATATATATGATACACAC
* * *
2155114 ACATATATGATGCATAC
1 ATATATATGATACACAC
2155131 ATATATATG
1 ATATATATG
2155140 TATGTACGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (17 bp):
ATATATATGATACACAC
Found at i:2155143 original size:4 final size:4
Alignment explanation
Indices: 2155136--2155170 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2155126 CATACATATA
*
2155136 TATG TATG TACG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
2155171 CAGTTACAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:2160277 original size:25 final size:28
Alignment explanation
Indices: 2160247--2160313 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
2160237 GATTCAATTG
2160247 ATAATAAATTTTAAAAAATT-AATAT-T
1 ATAATAAATTTTAAAAAATTAAATATAT
*
2160273 A-AATATAATTAATAAAAAATTAAATATAT
1 ATAATA-AATT-TTAAAAAATTAAATATAT
*
2160302 ATAATTAATTTT
1 ATAATAAATTTT
2160314 TATCAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
25 4 0.12
26 5 0.15
27 9 0.27
28 6 0.18
29 6 0.18
30 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAATAAATTTTAAAAAATTAAATATAT
Found at i:2160288 original size:27 final size:25
Alignment explanation
Indices: 2160258--2160310 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 25
2160248 TAATAAATTT
2160258 TAAAAAATTAATATTAAATATAATTAA
1 TAAAAAATTAA-A-TAAATATAATTAA
*
2160285 TAAAAAATTAAATATATATAATTAA
1 TAAAAAATTAAATAAATATAATTAA
2160310 T
1 T
2160311 TTTTATCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 13 0.52
26 1 0.04
27 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAAAATTAAATAAATATAATTAA
Found at i:2161165 original size:15 final size:15
Alignment explanation
Indices: 2161147--2161206 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
2161137 GATACAACAT
2161147 AAAAAATAAATATTA
1 AAAAAATAAATATTA
*
2161162 AAAAATTATAAT-TTA
1 AAAAAATA-AATATTA
*
2161177 AAAATAAAAAATATTA
1 AAAA-AATAAATATTA
* * *
2161193 TAAATATAAGTATT
1 AAAAAATAAATATT
2161207 TTAATTTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 24 0.69
16 11 0.31
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAAAATAAATATTA
Found at i:2163923 original size:2 final size:2
Alignment explanation
Indices: 2163883--2163907 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2163873 TGACAGCAAC
2163883 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 A
2163908 CGCACACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2164390 original size:6 final size:6
Alignment explanation
Indices: 2164379--2164409 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2164369 TTTAAAATGA
2164379 TTATAT TTATAT TTATAT TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT TTATAT T
2164410 AAATATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:2166587 original size:99 final size:99
Alignment explanation
Indices: 2166403--2166597 Score: 282
Period size: 99 Copynumber: 2.0 Consensus size: 99
2166393 CGGCGACATA
* * * *
2166403 GGCTCCGTCTACTTGGCCGAACTCAAGTCTCAACCTGACATCAATGCAGCGAACACAAACAAGAA
1 GGCTCCGTCTACTTAGCCGAACTCAAGTCTCAACCCGACACCAATGCAGCCAACACAAACAAGAA
*
2166468 CAACAGCAACAAAAATAGCAAAAACGAAGTCCTC
66 CAACAGCAACAAAAACAGCAAAAACGAAGTCCTC
* * *
2166502 GGCTCCGTCTACTTATCCGACCTCAAGTCTCAACCCGACACCAATGGAGCCAACACAAACAAGAA
1 GGCTCCGTCTACTTAGCCGAACTCAAGTCTCAACCCGACACCAATGCAGCCAACACAAACAAGAA
* * * *
2166567 CAAGAGCAACAAAAGCAGCAAGAATGAAGTC
66 CAACAGCAACAAAAACAGCAAAAACGAAGTC
2166598 GTTTTTGCAG
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 84 1.00
ACGTcount: A:0.40, C:0.30, G:0.17, T:0.13
Consensus pattern (99 bp):
GGCTCCGTCTACTTAGCCGAACTCAAGTCTCAACCCGACACCAATGCAGCCAACACAAACAAGAA
CAACAGCAACAAAAACAGCAAAAACGAAGTCCTC
Found at i:2167029 original size:17 final size:18
Alignment explanation
Indices: 2166993--2167029 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2166983 GTAATAAAAG
2166993 ATTTATTAATAAATTAAA
1 ATTTATTAATAAATTAAA
2167011 ATTTATATAA-AAA-TAAA
1 ATTTAT-TAATAAATTAAA
2167028 AT
1 AT
2167030 AATTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTATTAATAAATTAAA
Found at i:2167395 original size:2 final size:2
Alignment explanation
Indices: 2167388--2167420 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2167378 TTAAGCACTT
2167388 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2167421 CCAGCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2176378 original size:2 final size:2
Alignment explanation
Indices: 2176371--2176409 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2176361 GAGCAATGAA
*
2176371 AT AT AT AT AT AT AT AT TT AT -T 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
2176410 TTATTAGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2176401 original size:23 final size:23
Alignment explanation
Indices: 2176371--2176415 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2176361 GAGCAATGAA
2176371 ATATATATATATATATTTATTAT
1 ATATATATATATATATTTATTAT
2176394 ATATATATATATATATTTATTA
1 ATATATATATATATATTTATTA
2176416 GTCATTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATATATATATATATTTATTAT
Found at i:2185739 original size:16 final size:16
Alignment explanation
Indices: 2185718--2185749 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2185708 AGGCCCTTAA
2185718 GGTATGTCAGTGATTT
1 GGTATGTCAGTGATTT
2185734 GGTATGTCAGTGATTT
1 GGTATGTCAGTGATTT
2185750 TCCATCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (16 bp):
GGTATGTCAGTGATTT
Found at i:2193242 original size:42 final size:42
Alignment explanation
Indices: 2193195--2193286 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
2193185 AACTAATCAG
2193195 AATTATATAAAAAGTTATT-AAAAATATTACAAATGATATTGA
1 AATTATATAAAAAGTT-TTCAAAAATATTACAAATGATATTGA
* * * *
2193237 AATTATATAAAAAGTTTTCAAAATTATTAGAAATGCTATTGT
1 AATTATATAAAAAGTTTTCAAAAATATTACAAATGATATTGA
2193279 AATTATAT
1 AATTATAT
2193287 CAAGGGTTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (42 bp):
AATTATATAAAAAGTTTTCAAAAATATTACAAATGATATTGA
Done.