Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 85 of 198
Found at i:27246016 original size:33 final size:34
Alignment explanation
Indices: 27245978--27246042 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
27245968 GTTTATTAAA
27245978 TTTAGTTCAGCTCAAATAAGTGTTAG-AATTATT
1 TTTAGTTCAGCTCAAATAAGTGTTAGTAATTATT
*
27246011 TTTAGTTCAGCTTAAATAAGTGTTAGTAATTA
1 TTTAGTTCAGCTCAAATAAGTGTTAGTAATTA
27246043 AATTGTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (34 bp):
TTTAGTTCAGCTCAAATAAGTGTTAGTAATTATT
Found at i:27252670 original size:45 final size:43
Alignment explanation
Indices: 27252619--27252715 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 43
27252609 GACACAGCCG
27252619 AATTAGTGTGTCCTGTTTAGTTTTCATTTAATTTCTTTCAATGTT
1 AATTAGTGTGTCCTGTTTAGTTTTCATTTAATTTCTTTC-AT-TT
*
27252664 AATTAGTGTGTCCTGTTTAGTTTTCATTTAATTTGTTTCATTT
1 AATTAGTGTGTCCTGTTTAGTTTTCATTTAATTTCTTTCATTT
*
27252707 AATTTGTGT
1 AATTAGTGT
27252716 CCACATTATG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
43 10 0.20
44 2 0.04
45 38 0.76
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (43 bp):
AATTAGTGTGTCCTGTTTAGTTTTCATTTAATTTCTTTCATTT
Found at i:27252702 original size:14 final size:14
Alignment explanation
Indices: 27252685--27252713 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27252675 CCTGTTTAGT
27252685 TTTCATTTAATTTG
1 TTTCATTTAATTTG
27252699 TTTCATTTAATTTG
1 TTTCATTTAATTTG
27252713 T
1 T
27252714 GTCCACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTCATTTAATTTG
Found at i:27256187 original size:12 final size:11
Alignment explanation
Indices: 27256156--27256184 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
27256146 AGTCATTGTG
27256156 AAAAAAATTGA
1 AAAAAAATTGA
27256167 AAAAAAATTGA
1 AAAAAAATTGA
27256178 AAAAAAA
1 AAAAAAA
27256185 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:27259093 original size:11 final size:11
Alignment explanation
Indices: 27259077--27259105 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
27259067 AGTCATTGTG
27259077 AAAAAAATTCA
1 AAAAAAATTCA
27259088 AAAAAAATTCA
1 AAAAAAATTCA
27259099 AAAAAAA
1 AAAAAAA
27259106 GTTTATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:27260223 original size:18 final size:18
Alignment explanation
Indices: 27260200--27260257 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
27260190 TGGAGAAATG
*
27260200 AAAGAAAAAGACATTGAA
1 AAAGAAAAAGAAATTGAA
*
27260218 AAAGAAAAAGAAATTGCA
1 AAAGAAAAAGAAATTGAA
*
27260236 AAAGAAAAGGAAATTGAA
1 AAAGAAAAAGAAATTGAA
27260254 AAAG
1 AAAG
27260258 TGAGTGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.67, C:0.03, G:0.19, T:0.10
Consensus pattern (18 bp):
AAAGAAAAAGAAATTGAA
Found at i:27260255 original size:30 final size:29
Alignment explanation
Indices: 27260221--27260301 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
27260211 CATTGAAAAA
*
27260221 GAAAAAGAAATTGCAAAAGAAAAGGAAATT
1 GAAAAAGAAATTG-AAAAGAAAAAGAAATT
** * *
27260251 GAAAAAGTGAGTGAAAAGGAAAAAGAGATT
1 GAAAAAGAAATTGAAAA-GAAAAAGAAATT
27260281 GAAAAAGAAATTGAAAGAGAA
1 GAAAAAGAAATTGAAA-AGAA
27260302 GAAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 4 0.10
30 36 0.88
31 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (29 bp):
GAAAAAGAAATTGAAAAGAAAAAGAAATT
Found at i:27260272 original size:18 final size:18
Alignment explanation
Indices: 27260251--27260290 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27260241 AAAGGAAATT
* *
27260251 GAAAAAGTGAGTGAAAAG
1 GAAAAAGAGAGTGAAAAA
*
27260269 GAAAAAGAGATTGAAAAA
1 GAAAAAGAGAGTGAAAAA
27260287 GAAA
1 GAAA
27260291 TTGAAAGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (18 bp):
GAAAAAGAGAGTGAAAAA
Found at i:27262038 original size:20 final size:20
Alignment explanation
Indices: 27262013--27262101 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
27262003 TTCCATGCGG
27262013 TTCAGCTCACTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
*
27262033 TTCAGCTCACTCGACCTCAA
1 TTCAGCTCACTCGAGCTCAA
* *
27262053 GTCAGCTCATTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
* *
27262073 GTT-AGCTCCCACGAGCTCAA
1 -TTCAGCTCACTCGAGCTCAA
27262093 TTCAGCTCA
1 TTCAGCTCA
27262102 TTGAGCTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 55 0.95
21 1 0.02
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.25
Consensus pattern (20 bp):
TTCAGCTCACTCGAGCTCAA
Found at i:27270005 original size:26 final size:26
Alignment explanation
Indices: 27269975--27270026 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
27269965 CACCACTGAA
*
27269975 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
*
27270001 TCGGGGAATCAGCCCATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
27270027 ATTTTTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.37, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:27270190 original size:104 final size:103
Alignment explanation
Indices: 27269943--27270209 Score: 385
Period size: 105 Copynumber: 2.6 Consensus size: 103
27269933 TAACCGTTAT
*
27269943 TGGTGGATCCCGCACTTAGCACCA-CCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCACGCACTTAGCACCACCCA-TGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
* **
27270007 AATCAGCCCATAGCAACCCCATTTTTCATTTCAAAGATA
65 AATCAGCACATAGCAACCCCATTTCACATTTCAAAGATA
* *
27270046 CGGTGGAT-ATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGAG
1 TGGTGGATCA-CGCACTTAGCACCACCCATG-AATCGGGGAATCAGCACTTAGCAACCCCTCG-G
*
27270110 GGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
63 GGAATCAGCACATAGCAACCCCATTTCACATTTCAAAGATA
* * **
27270151 TGGTGGATCACGCACATAGTACCACCCATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACTTAGCACCACCCATGAATCGGGGAATCAGCACTTAGCAACCCCT
27270210 TTTATATACA
Statistics
Matches: 146, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
103 23 0.16
104 60 0.41
105 62 0.42
106 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (103 bp):
TGGTGGATCACGCACTTAGCACCACCCATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCATTTCACATTTCAAAGATA
Found at i:27270572 original size:29 final size:30
Alignment explanation
Indices: 27270538--27270601 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
27270528 TAATCCACCA
*
27270538 CCCAAATTTTTG-AAAATTACAATTTTGCC
1 CCCAAACTTTTGCAAAATTACAATTTTGCC
* * * *
27270567 CCCAAACTTTTGCATAATTATACTTTTGTC
1 CCCAAACTTTTGCAAAATTACAATTTTGCC
27270597 CCCAA
1 CCCAA
27270602 GCTCGGAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (30 bp):
CCCAAACTTTTGCAAAATTACAATTTTGCC
Found at i:27272934 original size:20 final size:20
Alignment explanation
Indices: 27272889--27272937 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
27272879 ACGATCTCAA
*
27272889 TGAGCTGAATTGAGCTCGTG
1 TGAGCTGAATTGAGCTCGAG
*
27272909 -GAAGCTGACTTGAGCTCGAG
1 TG-AGCTGAATTGAGCTCGAG
27272929 TGAGCTGAA
1 TGAGCTGAA
27272938 CTGCATGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.24
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:27274377 original size:20 final size:20
Alignment explanation
Indices: 27274353--27274421 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
27274343 ACGAGCCCAA
*
27274353 TGAGCTGAATTGAGCTCGTG
1 TGAGCTGAATTGAGCTCGAG
* *
27274373 GGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
* *
27274393 TGAGCTAAATTTAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
27274413 TGAGCTGAA
1 TGAGCTGAA
27274422 CCACATGGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:27276165 original size:18 final size:18
Alignment explanation
Indices: 27276139--27276178 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27276129 TCTCTTTCAA
* *
27276139 TTTCTTTTTCAATCTCTT
1 TTTCCTTTTCAATCACTT
*
27276157 TTTCCTTTTCACTCACTT
1 TTTCCTTTTCAATCACTT
27276175 TTTC
1 TTTC
27276179 AATTTCCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCCTTTTCAATCACTT
Found at i:27276193 original size:18 final size:18
Alignment explanation
Indices: 27276172--27276229 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
27276162 TTTTCACTCA
27276172 CTTTTTCAATTTCCTTTT
1 CTTTTTCAATTTCCTTTT
*
27276190 CTTTTGCAATTTCCTTTT
1 CTTTTTCAATTTCCTTTT
* *
27276208 CTTTTTCAATGTCTTTTT
1 CTTTTTCAATTTCCTTTT
27276226 CTTT
1 CTTT
27276230 CATTTCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.66
Consensus pattern (18 bp):
CTTTTTCAATTTCCTTTT
Found at i:27280344 original size:24 final size:24
Alignment explanation
Indices: 27280308--27280365 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
27280298 TTAAAATTTG
*
27280308 TTTTTAATATGTC-TAGCTACAACA
1 TTTTAAATATGTCTTAGCT-CAACA
* *
27280332 TTTTAAATGTGTCTTTAGCTGAACA
1 TTTTAAATATGTC-TTAGCTCAACA
27280357 TTTTAAATA
1 TTTTAAATA
27280366 CAGGTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 11 0.39
25 12 0.43
26 5 0.18
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (24 bp):
TTTTAAATATGTCTTAGCTCAACA
Found at i:27281865 original size:42 final size:42
Alignment explanation
Indices: 27281809--27281891 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
27281799 AATTTGTGTG
27281809 AAACATTTCAAATTCAAACATTTGAACTCGTGTTCTTATCCA
1 AAACATTTCAAATTCAAACATTTGAACTCGTGTTCTTATCCA
* * *
27281851 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
1 AAACATTTCAAATTCAAACATTTGAACTCGTGTTCTTATCC
27281892 CTTTGAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (42 bp):
AAACATTTCAAATTCAAACATTTGAACTCGTGTTCTTATCCA
Found at i:27287953 original size:60 final size:60
Alignment explanation
Indices: 27287873--27288007 Score: 225
Period size: 60 Copynumber: 2.2 Consensus size: 60
27287863 AGATTTGAAA
*
27287873 TCTTGATTTTCTTGATTCTTGAAATCGATCCAAATAGCAAAATTGGACCAAGATTCGGTT
1 TCTTGATTTTCTTGATTCTTGAAATCGATCCAAACAGCAAAATTGGACCAAGATTCGGTT
* * * *
27287933 TCTTAATTTTCTTGATTCTTGAAATTGCTCGAAACAGCAAAATTGGACCAAGATTCGGTT
1 TCTTGATTTTCTTGATTCTTGAAATCGATCCAAACAGCAAAATTGGACCAAGATTCGGTT
27287993 TCTTGATTTTCTTGA
1 TCTTGATTTTCTTGA
27288008 AAATAAGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (60 bp):
TCTTGATTTTCTTGATTCTTGAAATCGATCCAAACAGCAAAATTGGACCAAGATTCGGTT
Found at i:27299644 original size:16 final size:17
Alignment explanation
Indices: 27299613--27299646 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
27299603 CATGTCAACA
27299613 AGTTCCACATAATGTTGG
1 AGTTCCACA-AATGTTGG
27299631 AGTTCCAC-AATGTTGG
1 AGTTCCACAAATGTTGG
27299647 CTATGTCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (17 bp):
AGTTCCACAAATGTTGG
Found at i:27315760 original size:15 final size:13
Alignment explanation
Indices: 27315742--27315791 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
27315732 TTCTTCAATT
27315742 TCTTTTTCGGTTTTC
1 TCTTTTTC--TTTTC
27315757 TCTTTTTCTTTTC
1 TCTTTTTCTTTTC
*
27315770 TCATTTTC-TTTC
1 TCTTTTTCTTTTC
*
27315782 TCATTTTCTT
1 TCTTTTTCTT
27315792 CTTTTTCGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 12 0.36
13 13 0.39
15 8 0.24
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (13 bp):
TCTTTTTCTTTTC
Found at i:27315766 original size:34 final size:34
Alignment explanation
Indices: 27315731--27315798 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
27315721 ATTTCTCTTC
* *
27315731 TTTCTTCAATTTCTTTTTCGGTTTTC-TCTTTTTCT
1 TTTC-TCAATTTCTTTCTC-ATTTTCTTCTTTTTCT
*
27315766 TTTCTCATTTTCTTTCTCATTTTCTTCTTTTTC
1 TTTCTCAATTTCTTTCTCATTTTCTTCTTTTTC
27315799 GATTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 5 0.17
34 20 0.69
35 4 0.14
ACGTcount: A:0.06, C:0.22, G:0.03, T:0.69
Consensus pattern (34 bp):
TTTCTCAATTTCTTTCTCATTTTCTTCTTTTTCT
Found at i:27315768 original size:13 final size:13
Alignment explanation
Indices: 27315752--27315791 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
27315742 TCTTTTTCGG
*
27315752 TTTTCTCTTTTTC
1 TTTTCTCATTTTC
27315765 TTTTCTCATTTTC
1 TTTTCTCATTTTC
27315778 -TTTCTCATTTTC
1 TTTTCTCATTTTC
27315790 TT
1 TT
27315792 CTTTTTCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTCTCATTTTC
Found at i:27315783 original size:12 final size:12
Alignment explanation
Indices: 27315753--27315791 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
27315743 CTTTTTCGGT
*
27315753 TTTCTCTTTTTC
1 TTTCTCATTTTC
27315765 TTTTCTCATTTTC
1 -TTTCTCATTTTC
27315778 TTTCTCATTTTC
1 TTTCTCATTTTC
27315790 TT
1 TT
27315792 CTTTTTCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTCATTTTC
Found at i:27316372 original size:53 final size:53
Alignment explanation
Indices: 27316304--27316410 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
27316294 CTCACTCCAC
*
27316304 TCATGATTTTGCTCGTTTTGGCTTTTTCTTCTCTTGAATGATCTCACGCTCTT
1 TCATGATTTTGCTCGTTTTGGCTTTTTCTTCTCTCGAATGATCTCACGCTCTT
*
27316357 TCATGCTTTTGCTCGTTTTGGCTTTTTCTTCTCTCGAATGATCTCACGCTCTT
1 TCATGATTTTGCTCGTTTTGGCTTTTTCTTCTCTCGAATGATCTCACGCTCTT
27316410 T
1 T
27316411 TACTTTTTAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.10, C:0.24, G:0.15, T:0.50
Consensus pattern (53 bp):
TCATGATTTTGCTCGTTTTGGCTTTTTCTTCTCTCGAATGATCTCACGCTCTT
Found at i:27339995 original size:12 final size:12
Alignment explanation
Indices: 27339978--27340008 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
27339968 AATCTGATTT
27339978 AATGTGTAATTC
1 AATGTGTAATTC
27339990 AATGTGTAATTC
1 AATGTGTAATTC
27340002 AATGTGT
1 AATGTGT
27340009 TTAAGGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (12 bp):
AATGTGTAATTC
Found at i:27344961 original size:18 final size:18
Alignment explanation
Indices: 27344938--27344973 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27344928 GTTTAAGCGT
27344938 GGCTGGCCAAACCATATA
1 GGCTGGCCAAACCATATA
27344956 GGCTGGCCAAACCATATA
1 GGCTGGCCAAACCATATA
27344974 TATAGGCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (18 bp):
GGCTGGCCAAACCATATA
Found at i:27358589 original size:14 final size:15
Alignment explanation
Indices: 27358537--27358589 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 15
27358527 GTTTCGTCAG
27358537 TCTTTTCTCTCTTTT
1 TCTTTTCTCTCTTTT
*
27358552 TCTTTTCACT-TTTT
1 TCTTTTCTCTCTTTT
*
27358566 T-GTTTCTCTCTTTT
1 TCTTTTCTCTCTTTT
27358580 TCTTTT-TCTC
1 TCTTTTCTCTC
27358590 GCTCAATGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 6 0.19
14 14 0.44
15 12 0.38
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.72
Consensus pattern (15 bp):
TCTTTTCTCTCTTTT
Found at i:27360323 original size:21 final size:21
Alignment explanation
Indices: 27360297--27360338 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27360287 TCTCACAACA
27360297 AAAATCTCACCAATCAATCAC
1 AAAATCTCACCAATCAATCAC
*
27360318 AAAATCTCACCAATCACTCAC
1 AAAATCTCACCAATCAATCAC
27360339 TTCGGCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAATCTCACCAATCAATCAC
Found at i:27360706 original size:11 final size:11
Alignment explanation
Indices: 27360690--27360723 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
27360680 ACAAAATAAT
27360690 TTTTTTTCAAA
1 TTTTTTTCAAA
*
27360701 TTTTTTTCGAA
1 TTTTTTTCAAA
27360712 TTTTTTTACAAA
1 TTTTTTT-CAAA
27360724 CTCATAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:27365990 original size:50 final size:50
Alignment explanation
Indices: 27365954--27366194 Score: 347
Period size: 50 Copynumber: 4.7 Consensus size: 50
27365944 AGGTGCTCAT
* ** *
27365954 GCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
27366004 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
*
27366054 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCGAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* * *
27366104 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATATCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GGTGCCAAC
*
27366160 GCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27366195 TTACCCAAAT
Statistics
Matches: 175, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
50 131 0.75
53 4 0.02
56 40 0.23
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:27366022 original size:100 final size:100
Alignment explanation
Indices: 27365897--27366194 Score: 328
Period size: 100 Copynumber: 2.9 Consensus size: 100
27365887 TTTCTTGTAT
* * * * ** *
27365897 TGCCAATGCCATATCCTAGATATGGTCTTACATCAGAGTTCTCATATAGGTGCTC-ATGCCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATCAGACCTCTCATATAGGTGC-CAACGCCATGT
* * *
27365961 CCTAGACATGGTCTTACGGGGGACCTCTCATCTTGG
65 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
** * *
27365997 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATCAGACCTCTCATATAGGTGCCAACGCCATGTC
*
27366062 CCAGACATGGTCTTACATGGGACCTCTCATCTCGG
66 CCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* ** * *
27366097 TGCCGACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATATCAATGATGCCAATGC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATCAGACCTCTC---ATAT--A-GGTGCCAACGC
* *
27366162 CATGTCCCAGACATGGTCTTACATGGGATCTCT
60 CATGTCCCAGACATGGTCTTACAGGGGACCTCT
27366195 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
99 1 0.01
100 125 0.74
103 3 0.02
106 41 0.24
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (100 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATCAGACCTCTCATATAGGTGCCAACGCCATGTC
CCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:27366091 original size:150 final size:152
Alignment explanation
Indices: 27365897--27366194 Score: 368
Period size: 150 Copynumber: 1.9 Consensus size: 152
27365887 TTTCTTGTAT
* * * ** *
27365897 TGCCAATGCCATATCCTAGATATGGTCTTACATCAGAGTTCTCATATAGGTGCTC-ATGCCATGT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATCAGACCTCTCATATAGGTGC-CGACGCCATGT
* * * *
27365961 CCTAGACATGGTCTTACGGGGGACCTCTC-ATC-TTGGTGCCAACGCCATGTCCCAGACATGGTC
65 CCCAGACATGGTCTTACAGGGGACCTCTCAATCAATGATGCCAACGCCATGTCCCAGACATGGTC
27366024 TTACATGGGACCTCTCATCTCGG
130 TTACATGGGACCTCTCATCTCGG
* ** * *
27366047 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCGACGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATCAGACCTCTCATATAGGTGCCGACGCCATGTC
* *
27366112 CCAGACATGGTCTTACATGGGACCTCTCATAATATCAATGATGCCAATGCCATGTCCCAGACATG
66 CCAGACATGGTCTTACAGGGGACCTCTC---A-ATCAATGATGCCAACGCCATGTCCCAGACATG
*
27366177 GTCTTACATGGGATCTCT
127 GTCTTACATGGGACCTCT
27366195 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
149 1 0.01
150 77 0.63
155 3 0.02
156 42 0.34
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (152 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATCAGACCTCTCATATAGGTGCCGACGCCATGTC
CCAGACATGGTCTTACAGGGGACCTCTCAATCAATGATGCCAACGCCATGTCCCAGACATGGTCT
TACATGGGACCTCTCATCTCGG
Found at i:27380292 original size:25 final size:25
Alignment explanation
Indices: 27380258--27380385 Score: 100
Period size: 25 Copynumber: 5.1 Consensus size: 25
27380248 TCATGTACAA
*
27380258 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCATACGAGCTGTAAATCG
** * *
27380283 GTATGCTCATTTGACCTG-AAGATCA
1 GTATGCTCATACGAGCTGTAA-ATCG
27380308 GTATGCTC-TCACGAGC-GATAAATCG
1 GTATGCTCAT-ACGAGCTG-TAAATCG
* * * *
27380333 GTATACTCTTACGAGCTATAAATTG
1 GTATGCTCATACGAGCTGTAAATCG
* * *
27380358 GTATGTTCTTACGAGCTATAAATCG
1 GTATGCTCATACGAGCTGTAAATCG
27380383 GTA
1 GTA
27380386 ACCCTAATGA
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
24 3 0.04
25 76 0.93
26 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (25 bp):
GTATGCTCATACGAGCTGTAAATCG
Found at i:27386130 original size:17 final size:16
Alignment explanation
Indices: 27386103--27386136 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
27386093 TTATTAACCC
27386103 AAATTAAATTAGATAT
1 AAATTAAATTAGATAT
*
27386119 AAATTAAAATTAGTTAT
1 AAATT-AAATTAGATAT
27386136 A
1 A
27386137 TTATGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AAATTAAATTAGATAT
Found at i:27387412 original size:30 final size:31
Alignment explanation
Indices: 27387356--27387417 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
27387346 TAGTAATTTG
* *
27387356 TAACTATAAGGTTTTGCATGGGGGTTATCAA
1 TAACTACAAAGTTTTGCATGGGGGTTATCAA
27387387 TAACTACAAAGTTTTGCAT-GGGGTTATCAA
1 TAACTACAAAGTTTTGCATGGGGGTTATCAA
27387417 T
1 T
27387418 GATTGAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (31 bp):
TAACTACAAAGTTTTGCATGGGGGTTATCAA
Found at i:27387699 original size:29 final size:29
Alignment explanation
Indices: 27387657--27387712 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
27387647 TAAAAATGAA
27387657 TGTGATGCAATGTTGAATAAGCATTTCGC
1 TGTGATGCAATGTTGAATAAGCATTTCGC
27387686 TGTGATGCAATGTTGAATAAGCATTTC
1 TGTGATGCAATGTTGAATAAGCATTTC
27387713 TTGGTTGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (29 bp):
TGTGATGCAATGTTGAATAAGCATTTCGC
Found at i:27389017 original size:21 final size:22
Alignment explanation
Indices: 27388971--27389018 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
27388961 CTCTATCGGA
*
27388971 AAATTAGGAAAAGTTAGAAATG
1 AAATTAGGAAAAGTTAGAAATC
27388993 AAATTA-GACAAAGTTA-AAATC
1 AAATTAGGA-AAAGTTAGAAATC
27389014 AAATT
1 AAATT
27389019 CTGGTTTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.25
Consensus pattern (22 bp):
AAATTAGGAAAAGTTAGAAATC
Found at i:27402697 original size:40 final size:41
Alignment explanation
Indices: 27402653--27402749 Score: 133
Period size: 40 Copynumber: 2.4 Consensus size: 41
27402643 ATCCAGGCTA
* *
27402653 TATGCCTAGCATGCTTTAAGCCGGTGGA-AGTATCAAGCTT
1 TATGCCTAGCAGGCTTTAAGCCGGTGGACACTATCAAGCTT
* * * *
27402693 TATGCCTAGCAGGCTTTATGCCGGTGTACTCTATCAGGCTT
1 TATGCCTAGCAGGCTTTAAGCCGGTGGACACTATCAAGCTT
27402734 TATGCCTAGCAGGCTT
1 TATGCCTAGCAGGCTT
27402750 GGTGCCGGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 25 0.50
41 25 0.50
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (41 bp):
TATGCCTAGCAGGCTTTAAGCCGGTGGACACTATCAAGCTT
Found at i:27402740 original size:41 final size:40
Alignment explanation
Indices: 27402646--27402761 Score: 142
Period size: 41 Copynumber: 2.9 Consensus size: 40
27402636 CAATGATATC
* * * * *
27402646 CAGGCTATATGCCTAGCATGCTTTAAGCCGGTGGAAGTAT
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGTAACTAT
* *
27402686 CAAGCTTTATGCCTAGCAGGCTTTATGCCGGTGTACTCTAT
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGTA-ACTAT
**
27402727 CAGGCTTTATGCCTAGCAGGCTTGGTGCCGGTGTA
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGTA
27402762 TCATTTTTGG
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 30 0.46
41 35 0.54
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (40 bp):
CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGTAACTAT
Found at i:27405003 original size:20 final size:21
Alignment explanation
Indices: 27404964--27405003 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
27404954 AAAAAAGTAT
*
27404964 AAAAAGAACTAAAATGAAAAG
1 AAAAAGAACTAAAATAAAAAG
*
27404985 AAAAA-AACTAAACTAAAAA
1 AAAAAGAACTAAAATAAAAA
27405004 CCCTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.10
Consensus pattern (21 bp):
AAAAAGAACTAAAATAAAAAG
Found at i:27406775 original size:100 final size:104
Alignment explanation
Indices: 27406652--27406886 Score: 259
Period size: 100 Copynumber: 2.3 Consensus size: 104
27406642 ACTACCAATT
* * * *
27406652 CCATATCCCAGATATGGTCTTACATGGGA-GTGCCCATATCGGTGTCC-ATGCCATGCCCCAAAC
1 CCATGTCCCAGACATGGTCTTACATGGGACCT-CCCATATCGGTG-CCAACGCCATGCCCCAAAC
* *
27406715 ATGGTCTTAC-GGTGGACCTCTC-ATCTC-A-G-TGTCAACG
64 ATGGTCTTACATG-GGACCTCTCAATCTCAAGGATGCCAACG
* * * * * *
27406752 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCTCGGTGCCAACGTCATGCCCCATACAT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCCCATATCGGTGCCAACGCCATGCCCCAAACAT
*
27406817 GGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAATG
66 GGTCTTACATGGGACCTCTCA--ATCTCAAGGATGCCAACG
27406858 CCATGTCCCAGACATGGTCTTACATGGGA
1 CCATGTCCCAGACATGGTCTTACATGGGA
27406887 TCTCTTTACC
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
99 2 0.02
100 67 0.60
101 2 0.02
103 5 0.04
104 1 0.01
105 1 0.01
106 34 0.30
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (104 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCCCATATCGGTGCCAACGCCATGCCCCAAACAT
GGTCTTACATGGGACCTCTCAATCTCAAGGATGCCAACG
Found at i:27406873 original size:56 final size:52
Alignment explanation
Indices: 27406701--27406891 Score: 212
Period size: 50 Copynumber: 3.7 Consensus size: 52
27406691 CGGTGTCCAT
* * *
27406701 GCCATGCCCCAAACATGGTCTTAC-GGTGGACCTCTC-ATCTCA-GTGTCAAC
1 GCCATGCCCCAGACATGGTCTTACATG-GGACCTCTCGATCTCAGGTGCCAAC
* *
27406751 GCCATGTCCCAGACATGGTCTTACATGAGACCTCTCG-TCTC-GGTGCCAAC
1 GCCATGCCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGGTGCCAAC
* * *
27406801 GTCATGCCCCATACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGCCCCAGACATGGTCTTACATGGGACCTCTC--GATCTC-AGG-TGCCAAC
* *
27406857 GCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCATGCCCCAGACATGGTCTTACATGGGACCTCT
27406892 TTACCCAAAT
Statistics
Matches: 118, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
50 73 0.62
51 1 0.01
52 1 0.01
53 4 0.03
55 2 0.02
56 37 0.31
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (52 bp):
GCCATGCCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGGTGCCAAC
Found at i:27423697 original size:56 final size:52
Alignment explanation
Indices: 27423512--27423735 Score: 235
Period size: 50 Copynumber: 4.3 Consensus size: 52
27423502 AGTGTTATCA
** * * *
27423512 GTCTTACATGGGAGTTCTC-ATATCGG-TGCCCATGTCATGTCCCAGACATG
1 GTCTTACATGGGACCTCTCGATCTCGGATGCCAACGTCATGTCCCAGACATG
** * * *
27423562 GTCTTACGGGGGACCTCTC-ATCTTGG-TGTCAACGTCATGTCCTAGACATG
1 GTCTTACATGGGACCTCTCGATCTCGGATGCCAACGTCATGTCCCAGACATG
* * *
27423612 GTCTTACATGGGACATCTCG-TCTC-GATGCCAACGCCATGCCCCAGACATG
1 GTCTTACATGGGACCTCTCGATCTCGGATGCCAACGTCATGTCCCAGACATG
*
27423662 GTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAATGTCATGTCCCAGACATG
1 GTCTTACATGGGACCTCTC--GATCTC--GGATGCCAACGTCATGTCCCAGACATG
*
27423718 GTCTTACATGGGATCTCT
1 GTCTTACATGGGACCTCT
27423736 TTACCCAAAT
Statistics
Matches: 143, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 97 0.68
52 1 0.01
53 4 0.03
56 40 0.28
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (52 bp):
GTCTTACATGGGACCTCTCGATCTCGGATGCCAACGTCATGTCCCAGACATG
Found at i:27426081 original size:74 final size:74
Alignment explanation
Indices: 27425934--27426209 Score: 403
Period size: 75 Copynumber: 3.7 Consensus size: 74
27425924 TAGAATTCAT
* *
27425934 TTTTTGTCATTTTTTAGGTAAATTGTAAATAAGTATATTATTGATGTAAAACATACAATAGAATA
1 TTTTT-TCATTTTTTTGGTAAATTGTAAATAAGTATATTATTGATGTAAAA-ATACAATAGAATT
27425999 CATACAAACAA
64 CATACAAACAA
*
27426010 TTTTTTCATTTTTTTGGTAAATTGTAAACAAGTATATTATTGATGTAAAAATACAATAGAATTCA
1 TTTTTTCATTTTTTTGGTAAATTGTAAATAAGTATATTATTGATGTAAAAATACAATAGAATTCA
27426075 TACAAACAA
66 TACAAACAA
* * * *
27426084 TTTTTTAAATTTTTTTGATAAATTGTAAATAAGTATATTATTTATGTAAAAATACCATAGAATAT
1 TTTTTT-CATTTTTTTGGTAAATTGTAAATAAGTATATTATTGATGTAAAAATACAATAGAAT-T
* *
27426149 AATACAAATAA
64 CATACAAACAA
* *
27426160 TTTTTT-ATTTTTTT-GTAAATTGTAAATAAATATATTATGGATGTAAAAAT
1 TTTTTTCATTTTTTTGGTAAATTGTAAATAAGTATATTATTGATGTAAAAAT
27426210 TGAATACAAT
Statistics
Matches: 184, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
73 32 0.17
74 37 0.20
75 94 0.51
76 21 0.11
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (74 bp):
TTTTTTCATTTTTTTGGTAAATTGTAAATAAGTATATTATTGATGTAAAAATACAATAGAATTCA
TACAAACAA
Found at i:27426961 original size:13 final size:13
Alignment explanation
Indices: 27426945--27426997 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
27426935 TTTAAACCAA
27426945 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
27426958 ACTTCTT-AAAAGC
1 ACTT-TTCAAAAGC
***
27426971 ACTTTTCCGCAGC
1 ACTTTTCAAAAGC
27426984 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
27426997 A
1 A
27426998 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:27427039 original size:12 final size:12
Alignment explanation
Indices: 27427016--27427055 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
27427006 CTAGCCCTTT
*
27427016 ATCTTCACCTCC
1 ATCTCCACCTCC
*
27427028 ATCTCCATCTCC
1 ATCTCCACCTCC
*
27427040 ACCTCCACCTCC
1 ATCTCCACCTCC
27427052 ATCT
1 ATCT
27427056 TGATCTTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.53, G:0.00, T:0.30
Consensus pattern (12 bp):
ATCTCCACCTCC
Found at i:27427042 original size:18 final size:18
Alignment explanation
Indices: 27427016--27427055 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
27427006 CTAGCCCTTT
* *
27427016 ATCTTCACCTCCATCTCC
1 ATCTCCACCTCCACCTCC
27427034 ATCTCCACCTCCACCTCC
1 ATCTCCACCTCCACCTCC
27427052 ATCT
1 ATCT
27427056 TGATCTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.53, G:0.00, T:0.30
Consensus pattern (18 bp):
ATCTCCACCTCCACCTCC
Found at i:27429230 original size:33 final size:33
Alignment explanation
Indices: 27429187--27429251 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
27429177 TGAAAAATAT
*
27429187 TGAGAATAAAATAATTGAGAGAATAGGATTGAC
1 TGAGAATAAAAGAATTGAGAGAATAGGATTGAC
*
27429220 TGAGATTAAAAGAATTGAGAGAATAGGATTGA
1 TGAGAATAAAAGAATTGAGAGAATAGGATTGA
27429252 ATGGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.25
Consensus pattern (33 bp):
TGAGAATAAAAGAATTGAGAGAATAGGATTGAC
Found at i:27429334 original size:23 final size:22
Alignment explanation
Indices: 27429291--27429342 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
27429281 ATATATAGGG
*
27429291 AAAAAAAGTAATCACTAGAGAGA
1 AAAAAAAGTAACCACTAGAGA-A
* *
27429314 AAAAAAAGTAACCATTGGAGAA
1 AAAAAAAGTAACCACTAGAGAA
*
27429336 AAGAAAA
1 AAAAAAA
27429343 TGTTAACGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.63, C:0.08, G:0.17, T:0.12
Consensus pattern (22 bp):
AAAAAAAGTAACCACTAGAGAA
Found at i:27429778 original size:22 final size:23
Alignment explanation
Indices: 27429753--27429795 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
27429743 ATGATTTTAA
*
27429753 TGGAATGTAATT-TTTAGAAATG
1 TGGAATGTAATTATTGAGAAATG
27429775 TGGAATGTAATTATTGAGAAA
1 TGGAATGTAATTATTGAGAAA
27429796 ATTATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (23 bp):
TGGAATGTAATTATTGAGAAATG
Found at i:27430036 original size:22 final size:21
Alignment explanation
Indices: 27430008--27430050 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
27429998 TAATAATAAA
*
27430008 TTTTAATTGATATTGTTTAATT
1 TTTTAATTGATAATG-TTAATT
*
27430030 TTTTAATTTATAATGTTAATT
1 TTTTAATTGATAATGTTAATT
27430051 GAAATCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTAATTGATAATGTTAATT
Found at i:27431065 original size:34 final size:33
Alignment explanation
Indices: 27431002--27431065 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 33
27430992 TTAAAAGTAT
* *
27431002 ATTTTTATATTATTTTTAATTTAATTTTTAAGA
1 ATTTTTATATTATTTTTAATTAAAATTTTAAGA
*
27431035 ATTTTATATATT-TTTATTTATTAAAATTTTA
1 ATTTT-TATATTATTT-TTAATTAAAATTTTA
27431066 TATATAGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
33 8 0.31
34 18 0.69
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (33 bp):
ATTTTTATATTATTTTTAATTAAAATTTTAAGA
Found at i:27431929 original size:17 final size:17
Alignment explanation
Indices: 27431909--27431944 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27431899 ATTTTCCCAT
* *
27431909 ATTTTTGGTATTTTATA
1 ATTTTTGATAGTTTATA
27431926 ATTTTTGATAGTTTATA
1 ATTTTTGATAGTTTATA
27431943 AT
1 AT
27431945 AATATTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (17 bp):
ATTTTTGATAGTTTATA
Found at i:27433161 original size:11 final size:11
Alignment explanation
Indices: 27433145--27433187 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
27433135 TTAATTAGAT
27433145 AAATTTTAATA
1 AAATTTTAATA
27433156 AAATTTTAATA
1 AAATTTTAATA
*
27433167 AGATATTTTATTA
1 A-A-ATTTTAATA
*
27433180 ATATTTTA
1 AAATTTTA
27433188 TTATAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 18 0.64
12 1 0.04
13 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
AAATTTTAATA
Found at i:27435596 original size:56 final size:57
Alignment explanation
Indices: 27435536--27435720 Score: 144
Period size: 64 Copynumber: 3.1 Consensus size: 57
27435526 TTCAAAATAT
27435536 TTTTATTACTTTCCTATTTCAATT-ATTTTTTATTACTGCTTTATTTATCTATAAAA
1 TTTTATTACTTTCCTATTTCAATTGATTTTTTATTACTGCTTTATTTATCTATAAAA
* * * * *
27435592 TTTTA-GA-TGTTCACTATTTATCATATATTGATTTATTGTATTAATAG-TTAATATTATTTTTC
1 TTTTATTACT-TTC-CTA-TT-TC--A-ATTGATTT-TT-TATTACT-GCTTTAT-TTATCTAT-
27435654 AAAATA
54 -AAA-A
* *
27435660 TCTTTATTACTTCCCTATTTCAATTGTTTTTTTATTACTGCTTTATTTATCTATAAAA
1 T-TTTATTACTTTCCTATTTCAATTGATTTTTTATTACTGCTTTATTTATCTATAAAA
27435718 TTT
1 TTT
27435721 AAGATCTTTA
Statistics
Matches: 98, Mismatches: 12, Indels: 37
0.67 0.08 0.25
Matches are distributed among these distances:
54 1 0.01
55 4 0.04
56 8 0.08
57 4 0.04
58 4 0.04
59 3 0.03
60 1 0.01
61 10 0.10
62 14 0.14
63 4 0.04
64 17 0.17
65 8 0.08
67 5 0.05
68 4 0.04
69 7 0.07
70 3 0.03
71 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (57 bp):
TTTTATTACTTTCCTATTTCAATTGATTTTTTATTACTGCTTTATTTATCTATAAAA
Found at i:27435681 original size:125 final size:124
Alignment explanation
Indices: 27435427--27435745 Score: 457
Period size: 125 Copynumber: 2.6 Consensus size: 124
27435417 GCTATATTTT
** * * * *
27435427 CCTATTTCAATTAACTTTTATTATTGCTTTGTTTATTTAT-AAATTTTAATATCTTCACTATTTA
1 CCTATTTCAATTATTTTTTATTACTGCTTTATTTATCTATAAAATTTT-AGATCTTCACTATTTA
* *
27435491 TC--ATA-TATTTATTCTATTAATAGTTAATATTATTTTTCAAAATATTTTTATTACTTT
65 TCATATATTATTTATTCTATTAATAGTTAATATTATTTTTCAAAATATCTTTATTACTTC
*
27435548 CCTATTTCAATTATTTTTTATTACTGCTTTATTTATCTATAAAATTTTAGATGTTCACTATTTAT
1 CCTATTTCAATTATTTTTTATTACTGCTTTATTTATCTATAAAATTTTAGATCTTCACTATTTAT
*
27435613 CATATATTGATTTATTGTATTAATAGTTAATATTATTTTTCAAAATATCTTTATTACTTC
66 CATATATT-ATTTATTCTATTAATAGTTAATATTATTTTTCAAAATATCTTTATTACTTC
* * * *
27435673 CCTATTTCAATTGTTTTTTTATTACTGCTTTATTTATCTATAAAATTTAAGATCTTTACTATTGA
1 CCTATTTCAATT-ATTTTTTATTACTGCTTTATTTATCTATAAAATTTTAGATCTTCACTATTTA
27435738 TCATATAT
65 TCATATAT
27435746 ATAATGATTT
Statistics
Matches: 177, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
121 51 0.29
122 7 0.04
123 3 0.02
124 1 0.01
125 60 0.34
126 55 0.31
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (124 bp):
CCTATTTCAATTATTTTTTATTACTGCTTTATTTATCTATAAAATTTTAGATCTTCACTATTTAT
CATATATTATTTATTCTATTAATAGTTAATATTATTTTTCAAAATATCTTTATTACTTC
Found at i:27445317 original size:43 final size:42
Alignment explanation
Indices: 27445162--27445326 Score: 154
Period size: 43 Copynumber: 3.9 Consensus size: 42
27445152 ATATGGTTAC
* *
27445162 CGAGATTACGTGTAAGACCCTATCTAGGATATGGCATCGATA
1 CGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
* * *
27445204 TGAGACTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGATA
1 CGAGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* * * * * *
27445247 TGTGATTTCGTGTAAGATCATGGT-TGGGCTATTGGCATCGATA
1 CGAGATTACGTGTAAGACCAT-ATCTGGGATA-TGGCATCGATA
* * *
27445290 CGAGATTACATATAAGACCATATTTGGGATATGGCAT
1 CGAGATTACGTGTAAGACCATATCTGGGATATGGCAT
27445327 TGTTACGGTA
Statistics
Matches: 101, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 32 0.32
43 67 0.66
44 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (42 bp):
CGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:27449960 original size:16 final size:16
Alignment explanation
Indices: 27449939--27449969 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27449929 TTTCTAGTAT
27449939 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTG
27449955 TTTATTTACTAGCGT
1 TTTATTTACTAGCGT
27449970 ATTTGCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (16 bp):
TTTATTTACTAGCGTG
Found at i:27452246 original size:17 final size:18
Alignment explanation
Indices: 27452207--27452278 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 18
27452197 AAAAATTTTA
* *
27452207 CAAAAATTATTAAAAATA
1 CAAAAATTACTAAAAATT
*
27452225 GAAAAATTA-TAAAAATT
1 CAAAAATTACTAAAAATT
27452242 CAAAAACTATA-TAAAAAGTT
1 CAAAAA-T-TACTAAAAA-TT
*
27452262 -AAAATTTACTAAAAATT
1 CAAAAATTACTAAAAATT
27452279 TTAAAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
17 16 0.35
18 16 0.35
19 12 0.26
20 2 0.04
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
CAAAAATTACTAAAAATT
Found at i:27453697 original size:48 final size:48
Alignment explanation
Indices: 27453637--27453734 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
27453627 TGAAAGGTTT
*
27453637 TAGCATGGGTTCATATCTTATGATTCTCGATAGGAATGATAACCAAAC
1 TAGCATGGGTTCATATCTCATGATTCTCGATAGGAATGATAACCAAAC
* *
27453685 TAGCGTGGGTTCATATCTCATGATTCTCGATAGGAATGATAACCAGAC
1 TAGCATGGGTTCATATCTCATGATTCTCGATAGGAATGATAACCAAAC
27453733 TA
1 TA
27453735 AGGCTAAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (48 bp):
TAGCATGGGTTCATATCTCATGATTCTCGATAGGAATGATAACCAAAC
Found at i:27460730 original size:4 final size:4
Alignment explanation
Indices: 27460721--27460783 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
27460711 GTAAGGGCAG
27460721 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
27460769 CATA CATA CATA CAT
1 CATA CATA CATA CAT
27460784 TCACATATAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:27465413 original size:41 final size:41
Alignment explanation
Indices: 27465365--27465645 Score: 393
Period size: 41 Copynumber: 6.9 Consensus size: 41
27465355 TAACAAATTT
*
27465365 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCTCTAATGCTC
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
27465406 GGTGCTTTAGCGGCGTTTCTAAAAAAACGCCGCTAATGCTC
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
27465447 GGTGCTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTC
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * ** *
27465488 GGTGCTTTAGCGGCGTTTTTGAAAAAGTGACATTAATGCTG
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
27465529 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCT-
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* ** *
27465569 GGGGCATTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTT
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
27465610 GGGGCTCTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
27465646 AAACATTTTA
Statistics
Matches: 213, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 37 0.17
41 176 0.83
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (41 bp):
GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:27466014 original size:15 final size:15
Alignment explanation
Indices: 27465994--27466040 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
27465984 TATTTTAAGG
*
27465994 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
27466009 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
27466023 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
27466037 TTTA
1 TTTA
27466041 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:27466061 original size:21 final size:21
Alignment explanation
Indices: 27466024--27466100 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
27466014 GGATTATGAA
*
27466024 TTAGGGATTATGGTTTAAGGG
1 TTAGGGATTAAGGTTTAAGGG
*
27466045 TT-GGGATTTAAGGTTTAGGGG
1 TTAGGGA-TTAAGGTTTAAGGG
*
27466066 TTAGGGGTTAAGGGTTTAAGGG
1 TTAGGGATTAA-GGTTTAAGGG
*
27466088 TTTAGGGGTTAAG
1 -TTAGGGATTAAG
27466101 AGTTAGAGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.08
21 20 0.42
22 13 0.27
23 11 0.23
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (21 bp):
TTAGGGATTAAGGTTTAAGGG
Found at i:27466079 original size:15 final size:15
Alignment explanation
Indices: 27466052--27466100 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
27466042 GGGTTGGGAT
27466052 TTAA-GGTTTAGGGG
1 TTAAGGGTTTAGGGG
* * *
27466066 TTAGGGGTTAAGGGT
1 TTAAGGGTTTAGGGG
27466081 TTAAGGGTTTAGGGG
1 TTAAGGGTTTAGGGG
27466096 TTAAG
1 TTAAG
27466101 AGTTAGAGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 3 0.11
15 25 0.89
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (15 bp):
TTAAGGGTTTAGGGG
Found at i:27466196 original size:25 final size:25
Alignment explanation
Indices: 27466164--27466211 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
27466154 AGATTAATTA
* *
27466164 TTTTTTAATTTATATTTTAAATATG
1 TTTTTTAATTTACATATTAAATATG
27466189 TTTTTTAATTTACATATTAAATA
1 TTTTTTAATTTACATATTAAATA
27466212 ATTTCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTTTAATTTACATATTAAATATG
Found at i:27466396 original size:7 final size:7
Alignment explanation
Indices: 27466386--27466447 Score: 79
Period size: 7 Copynumber: 8.9 Consensus size: 7
27466376 GATTTAAGGT
27466386 TTAGGGG
1 TTAGGGG
*
27466393 TTAGGAG
1 TTAGGGG
*
27466400 TTAGGAG
1 TTAGGGG
27466407 TTAGGGG
1 TTAGGGG
*
27466414 TTAGGAG
1 TTAGGGG
27466421 TTAGGGG
1 TTAGGGG
27466428 TTAGGGG
1 TTAGGGG
* *
27466435 TTAAGAG
1 TTAGGGG
27466442 TTAGGG
1 TTAGGG
27466448 ATTTAAGGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.23, C:0.00, G:0.48, T:0.29
Consensus pattern (7 bp):
TTAGGGG
Found at i:27466447 original size:21 final size:21
Alignment explanation
Indices: 27466386--27466447 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
27466376 GATTTAAGGT
*
27466386 TTAGGGGTTAGGAGTTAGGAG
1 TTAGGGGTTAGGAGTTAGGGG
27466407 TTAGGGGTTAGGAGTTAGGGG
1 TTAGGGGTTAGGAGTTAGGGG
*
27466428 TTAGGGGTTAAGAGTTAGGG
1 TTAGGGGTTAGGAGTTAGGG
27466448 ATTTAAGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.00, G:0.48, T:0.29
Consensus pattern (21 bp):
TTAGGGGTTAGGAGTTAGGGG
Found at i:27466818 original size:19 final size:20
Alignment explanation
Indices: 27466796--27466838 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
27466786 ATTATAAGAA
*
27466796 AAAAATAAAATACAAAAA-T
1 AAAAATAAAATAAAAAAACT
*
27466815 AAAAATGAAATAAAAAAACT
1 AAAAATAAAATAAAAAAACT
27466835 AAAA
1 AAAA
27466839 TTTATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAATAAAATAAAAAAACT
Found at i:27471436 original size:43 final size:43
Alignment explanation
Indices: 27471384--27471657 Score: 347
Period size: 43 Copynumber: 6.4 Consensus size: 43
27471374 TTTTTGTGAG
* * *
27471384 AAGCACCGCTAAAGGTATCGAGTTATAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
* *
27471427 AAGCGCCGCTAAAGGTATCGAGCTATAGCGACGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
* * *
27471470 AAGCGCCGCTAAAGGTCGT-GACCTATAGCGGCATTTGTGGGAA
1 AAGCGCCGCTAAAGGTC-TCGAGCTATAGCGGCGTTTGTGGAAA
* *
27471513 AAGCGCCGCTAAAGCTCTTGAGCTATAGCGGCGTTTGT-GAGAA
1 AAGCGCCGCTAAAGGTCTCGAGCTATAGCGGCGTTTGTGGA-AA
* * * *
27471556 AAGCGCCGCTAAATGTCTTGAGCTATAGTGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
* * * *
27471599 AAGCGCCGCTAAAGGTCTCGAGATATAGCAGCGTTTTTGG-GA
1 AAGCGCCGCTAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
27471641 AAGCGCCGCTAAAGGTC
1 AAGCGCCGCTAAAGGTC
27471658 AATGTCTTTA
Statistics
Matches: 204, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
42 20 0.10
43 182 0.89
44 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTCGAGCTATAGCGGCGTTTGTGGAAA
Found at i:27472257 original size:14 final size:14
Alignment explanation
Indices: 27472238--27472275 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
27472228 CCAGAAAAGT
*
27472238 AAATCATTTTCTAG
1 AAATCATTTTCCAG
27472252 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
27472266 AAAACATTTT
1 AAATCATTTT
27472276 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:27473018 original size:33 final size:33
Alignment explanation
Indices: 27472976--27473042 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
27472966 TAGCATATAA
27472976 ATGGTAGACCAAAACTCTATTCACTATCCAAAC
1 ATGGTAGACCAAAACTCTATTCACTATCCAAAC
27473009 ATGGTAGACCAAAACTCTATTCACTATCCAAAC
1 ATGGTAGACCAAAACTCTATTCACTATCCAAAC
27473042 A
1 A
27473043 AATCTTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24
Consensus pattern (33 bp):
ATGGTAGACCAAAACTCTATTCACTATCCAAAC
Found at i:27478634 original size:14 final size:14
Alignment explanation
Indices: 27478617--27478650 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
27478607 TAGTATTCAT
*
27478617 AATATTTTATTAAA
1 AATATTTTAATAAA
27478631 AATATTTTAATAAA
1 AATATTTTAATAAA
*
27478645 TATATT
1 AATATT
27478651 ATTTTTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTTTAATAAA
Found at i:27478714 original size:17 final size:17
Alignment explanation
Indices: 27478658--27478716 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
27478648 ATTATTTTTG
27478658 TAAATATT-TAATAATA
1 TAAATATTATAATAATA
*
27478674 -AAA-GTTATAATACAAATA
1 TAAATATTATAAT---AATA
*
27478692 TGAATATTATAATAATA
1 TAAATATTATAATAATA
27478709 TAAATATT
1 TAAATATT
27478717 TTTTATCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
17 11 0.33
18 4 0.12
19 2 0.06
20 7 0.21
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATATTATAATAATA
Found at i:27482891 original size:21 final size:21
Alignment explanation
Indices: 27482830--27482899 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
27482820 AGAGTCTAGG
* *
27482830 CCATGTG-AAGAGTCTACATGA
1 CCATGTGAAAGAGGC-ACACGA
* **
27482851 CCGTGTGAAAGAGGGGCACG-
1 CCATGTGAAAGAGGCACACGA
27482871 CCTATGTGAAAGAGGCACACGA
1 CC-ATGTGAAAGAGGCACACGA
27482893 CCATGTG
1 CCATGTG
27482900 GCGGAGACAC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.05
21 29 0.76
22 7 0.18
ACGTcount: A:0.30, C:0.21, G:0.31, T:0.17
Consensus pattern (21 bp):
CCATGTGAAAGAGGCACACGA
Found at i:27486079 original size:38 final size:38
Alignment explanation
Indices: 27486037--27486112 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
27486027 TACCAAAAGT
*
27486037 TAGTTTGCTTTATATACCGAGAAGTTTGAGGGATAATG
1 TAGTTTGCTTTATATACCGAGAAGTCTGAGGGATAATG
27486075 TAGTTTGCTTTATATACCGAGAAGTCTGAGGGATAATG
1 TAGTTTGCTTTATATACCGAGAAGTCTGAGGGATAATG
27486113 AGATGTATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36
Consensus pattern (38 bp):
TAGTTTGCTTTATATACCGAGAAGTCTGAGGGATAATG
Found at i:27486935 original size:24 final size:25
Alignment explanation
Indices: 27486879--27486935 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
27486869 TAAAAAGTTT
*
27486879 TAACAGGAAGCTCACAAGAACCATA
1 TAACGGGAAGCTCACAAGAACCATA
* *
27486904 TAACGGGAAGCTCACAAGATCTA-A
1 TAACGGGAAGCTCACAAGAACCATA
27486928 TAACGGGA
1 TAACGGGA
27486936 CTCTCTTTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCACAAGAACCATA
Found at i:27490023 original size:180 final size:180
Alignment explanation
Indices: 27489721--27490084 Score: 728
Period size: 180 Copynumber: 2.0 Consensus size: 180
27489711 TGCCTTCAGC
27489721 ATATACTATATGTCCAAGGAATCCAACTTCCTGAAGCCAAAATTCACATTTACTGAATTTGGCAT
1 ATATACTATATGTCCAAGGAATCCAACTTCCTGAAGCCAAAATTCACATTTACTGAATTTGGCAT
27489786 ACAGTTGTTTCTCACGTAGAGTTTACATCACAATTCTCAAATGATCAACATGTTCATTTTCATCT
66 ACAGTTGTTTCTCACGTAGAGTTTACATCACAATTCTCAAATGATCAACATGTTCATTTTCATCT
27489851 TGGGAGTATACCAGAATATTATCAGTAAACACCACAACAAATCTATCCAG
131 TGGGAGTATACCAGAATATTATCAGTAAACACCACAACAAATCTATCCAG
27489901 ATATACTATATGTCCAAGGAATCCAACTTCCTGAAGCCAAAATTCACATTTACTGAATTTGGCAT
1 ATATACTATATGTCCAAGGAATCCAACTTCCTGAAGCCAAAATTCACATTTACTGAATTTGGCAT
27489966 ACAGTTGTTTCTCACGTAGAGTTTACATCACAATTCTCAAATGATCAACATGTTCATTTTCATCT
66 ACAGTTGTTTCTCACGTAGAGTTTACATCACAATTCTCAAATGATCAACATGTTCATTTTCATCT
27490031 TGGGAGTATACCAGAATATTATCAGTAAACACCACAACAAATCTATCCAG
131 TGGGAGTATACCAGAATATTATCAGTAAACACCACAACAAATCTATCCAG
27490081 ATAT
1 ATAT
27490085 GGTCTAAAAA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 184 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.31
Consensus pattern (180 bp):
ATATACTATATGTCCAAGGAATCCAACTTCCTGAAGCCAAAATTCACATTTACTGAATTTGGCAT
ACAGTTGTTTCTCACGTAGAGTTTACATCACAATTCTCAAATGATCAACATGTTCATTTTCATCT
TGGGAGTATACCAGAATATTATCAGTAAACACCACAACAAATCTATCCAG
Found at i:27494288 original size:33 final size:34
Alignment explanation
Indices: 27494246--27494327 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 34
27494236 TAACAATAAT
27494246 GGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GGTAACAGTATTCGACACACAAAGTGCCGAATCG
*
27494280 GTAACAGTAACAGTATTCGACACACAAAGTGTCGAATC-
1 G-----GTAACAGTATTCGACACACAAAGTGCCGAATCG
27494318 GGTAACAGTA
1 GGTAACAGTA
27494328 ACAGTAACAG
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
33 9 0.21
34 1 0.02
38 1 0.02
39 31 0.74
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.20
Consensus pattern (34 bp):
GGTAACAGTATTCGACACACAAAGTGCCGAATCG
Found at i:27494303 original size:84 final size:84
Alignment explanation
Indices: 27494194--27494378 Score: 282
Period size: 84 Copynumber: 2.2 Consensus size: 84
27494184 GTAACGGTAG
* **
27494194 CAGTAACAGTAACAGTATTCAACACACAAAGTGAT-GAATCTGTAACAATAATGGTAACAGTATT
1 CAGTAACAGTAACAGTATTCAACACACAAAGTG-TCGAATCGGTAACAATAACAGTAACAGTATT
27494258 CGACACACAAAGTGCCGAAT
65 CGACACACAAAGTGCCGAAT
* * *
27494278 CGGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCGGTAACAGTAACAGTAACAGTATTC
1 CAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCGGTAACAATAACAGTAACAGTATTC
*
27494343 GACACACAGAGTGCCGAAT
66 GACACACAAAGTGCCGAAT
*
27494362 CAGTAATAGTAACAGTA
1 CAGTAACAGTAACAGTA
27494379 ACAGTAGTCG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
83 1 0.01
84 90 0.99
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (84 bp):
CAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCGGTAACAATAACAGTAACAGTATTC
GACACACAAAGTGCCGAAT
Found at i:27494361 original size:45 final size:45
Alignment explanation
Indices: 27494188--27494384 Score: 244
Period size: 45 Copynumber: 4.5 Consensus size: 45
27494178 TAATCAGTAA
* * **
27494188 CGGTAGCAGTAACAGTAACAGTATTCAACACACAAAGTGATGAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* * **
27494233 CTGTAACAATAATGGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
*
27494278 C-G-----GTAACAGTAACAGTATTCGACACACAAAGTGTCGAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
*
27494317 CGGTAACAGTAACAGTAACAGTATTCGACACACAGAGTGCCGAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
27494362 CAGTAATAGTAACAGTAACAGTA
1 CGGTAACAGTAACAGTAACAGTA
27494385 GTCGGCATAT
Statistics
Matches: 130, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 34 0.26
40 1 0.01
44 1 0.01
45 94 0.72
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (45 bp):
CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:27511358 original size:20 final size:19
Alignment explanation
Indices: 27511333--27511376 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
27511323 TTAATCCATA
27511333 TAATTATAAC-AAGACATAAT
1 TAATTA-AACTAAGAC-TAAT
*
27511353 TAATTAAACTAAGTCTAAT
1 TAATTAAACTAAGACTAAT
27511372 TAATT
1 TAATT
27511377 CGGTTTGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (19 bp):
TAATTAAACTAAGACTAAT
Found at i:27513220 original size:21 final size:22
Alignment explanation
Indices: 27513154--27513250 Score: 67
Period size: 21 Copynumber: 4.5 Consensus size: 22
27513144 CCCTACTGAA
* *
27513154 AGGTACATCACACTT-CTCAAG
1 AGGTACAACACCCTTACTCAAG
* * * *
27513175 TGGTACAACACCTTTCCGTC--T
1 AGGTACAACACCCTTAC-TCAAG
27513196 AGGTACAACACCCTT-CTCAAG
1 AGGTACAACACCCTTACTCAAG
** *
27513217 AGGTACAACACTTTTACTCAAA
1 AGGTACAACACCCTTACTCAAG
*
27513239 AAGTACAACACC
1 AGGTACAACACC
27513251 TTTCCAACTG
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.03
20 1 0.02
21 37 0.64
22 16 0.28
23 2 0.03
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.24
Consensus pattern (22 bp):
AGGTACAACACCCTTACTCAAG
Found at i:27513745 original size:30 final size:28
Alignment explanation
Indices: 27513706--27513762 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
27513696 AAGTAATTTG
* *
27513706 TAAAGGGTTTTAGTTAAGCCTCATAAAAAC
1 TAAAAGGTTTAAGTTAAG-C-CATAAAAAC
27513736 TAAAAGGTTTAAGTTAAGCCATAAAAA
1 TAAAAGGTTTAAGTTAAGCCATAAAAA
27513763 TTAGGGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.32
29 1 0.04
30 16 0.64
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.28
Consensus pattern (28 bp):
TAAAAGGTTTAAGTTAAGCCATAAAAAC
Found at i:27528486 original size:28 final size:28
Alignment explanation
Indices: 27528451--27528516 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
27528441 ATAAAAAATA
27528451 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
*
27528479 ACCAAAATATTATAATTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
27528507 ACCAAAATAT
1 ACCAAAATAT
27528517 ACCACAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:27528626 original size:27 final size:26
Alignment explanation
Indices: 27528581--27528634 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
27528571 CCAATCACAT
27528581 TGGCGGCACCAAAAGTGCCAAAGAGAC
1 TGGCGGCACCAAAAGTGCCAAA-AGAC
*
27528608 TGGCGGCACC-AATGATGCCAAAAGAC
1 TGGCGGCACCAAAAG-TGCCAAAAGAC
27528634 T
1 T
27528635 AAAATGTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.35, C:0.26, G:0.28, T:0.11
Consensus pattern (26 bp):
TGGCGGCACCAAAAGTGCCAAAAGAC
Found at i:27529230 original size:18 final size:19
Alignment explanation
Indices: 27529201--27529293 Score: 100
Period size: 18 Copynumber: 5.0 Consensus size: 19
27529191 TCTAATTAAG
*
27529201 TAATAACTCTATTTTAATT
1 TAATAACACTATTTTAATT
* *
27529220 TAATAA-ACTATTCTCATT
1 TAATAACACTATTTTAATT
**
27529238 TAATAATTCTATTTTAATT
1 TAATAACACTATTTTAATT
* *
27529257 TAATAA-ACTATTCTCATT
1 TAATAACACTATTTTAATT
*
27529275 TAATAACTCTATTTTAATT
1 TAATAACACTATTTTAATT
27529294 GAAAAAAAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
18 30 0.50
19 30 0.50
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAACACTATTTTAATT
Found at i:27529242 original size:37 final size:37
Alignment explanation
Indices: 27529201--27529293 Score: 177
Period size: 37 Copynumber: 2.5 Consensus size: 37
27529191 TCTAATTAAG
27529201 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
*
27529238 TAATAATTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
27529275 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
27529294 GAAAAAAAGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.51
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
Found at i:27576746 original size:37 final size:37
Alignment explanation
Indices: 27576696--27576770 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
27576686 CAAATTTATT
27576696 AAAAGAGTATAGGAGAGAAGGAAAAAGGAAACATACA
1 AAAAGAGTATAGGAGAGAAGGAAAAAGGAAACATACA
27576733 AAAAGAGTATAGGAGAGAAGGAAAAAGGAAACATACA
1 AAAAGAGTATAGGAGAGAAGGAAAAAGGAAACATACA
27576770 A
1 A
27576771 GGATTAGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.60, C:0.05, G:0.27, T:0.08
Consensus pattern (37 bp):
AAAAGAGTATAGGAGAGAAGGAAAAAGGAAACATACA
Found at i:27579936 original size:21 final size:21
Alignment explanation
Indices: 27579906--27579952 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
27579896 ACGGGGGTTG
*
27579906 TGGTTGCTCCGGT-GGAGATTC
1 TGGTTCCTCCGGTAGGAGA-TC
*
27579927 TGGTTCCTCCGGTAGGGGATC
1 TGGTTCCTCCGGTAGGAGATC
27579948 TGGTT
1 TGGTT
27579953 GTCGATGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.09, C:0.19, G:0.38, T:0.34
Consensus pattern (21 bp):
TGGTTCCTCCGGTAGGAGATC
Found at i:27582815 original size:18 final size:17
Alignment explanation
Indices: 27582782--27582820 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
27582772 TTTTATAAAT
27582782 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
27582800 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
27582817 TGTG
1 TGTG
27582821 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:27583081 original size:23 final size:23
Alignment explanation
Indices: 27583046--27583167 Score: 183
Period size: 23 Copynumber: 5.3 Consensus size: 23
27583036 AGTGTTATTG
* *
27583046 ATCAATGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
27583069 TTCAGTGGTAGCTAT-GGCTACAT
1 ATCAGTGGTAGCT-TCGGCTACAT
27583092 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
27583115 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
27583138 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
27583161 ATCAGTG
1 ATCAGTG
27583168 TGGCACTTAT
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
22 1 0.01
23 88 0.98
24 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:27583103 original size:46 final size:46
Alignment explanation
Indices: 27583046--27583167 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
27583036 AGTGTTATTG
* * *
27583046 ATCAATGGTAGCTTTGGCTACATTTCAGTGGTAGCTATGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
27583092 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
27583138 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
27583168 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:27585667 original size:11 final size:11
Alignment explanation
Indices: 27585651--27585696 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
27585641 TAAAGCTTTC
*
27585651 TTGAGAGGAAT
1 TTGAGAGAAAT
27585662 TTGAGAGAAAT
1 TTGAGAGAAAT
27585673 TTGAGAGAATAT
1 TTGAGAGAA-AT
*
27585685 TGGAGAGAAAT
1 TTGAGAGAAAT
27585696 T
1 T
27585697 AAATTTTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.28
Consensus pattern (11 bp):
TTGAGAGAAAT
Found at i:27585676 original size:22 final size:23
Alignment explanation
Indices: 27585651--27585696 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
27585641 TAAAGCTTTC
27585651 TTGAGAGGAAT-TT-GAGAGAAAT
1 TTGAGA-GAATATTGGAGAGAAAT
27585673 TTGAGAGAATATTGGAGAGAAAT
1 TTGAGAGAATATTGGAGAGAAAT
27585696 T
1 T
27585697 AAATTTTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.28
Consensus pattern (23 bp):
TTGAGAGAATATTGGAGAGAAAT
Found at i:27586504 original size:28 final size:29
Alignment explanation
Indices: 27586458--27586529 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
27586448 AAAGTCAAAA
* * *
27586458 TAAATTTTATAAAAA-TTAATAA-AGTATT
1 TAAATTTTA-AAAAATTTAAAAAGAGAACT
27586486 TAAATTTTAAAAAATTTAAAAAGAGAACT
1 TAAATTTTAAAAAATTTAAAAAGAGAACT
*
27586515 TAAATTTTCAAAAAT
1 TAAATTTTAAAAAAT
27586530 ACATTCTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 5 0.13
28 15 0.39
29 18 0.47
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (29 bp):
TAAATTTTAAAAAATTTAAAAAGAGAACT
Found at i:27586719 original size:20 final size:20
Alignment explanation
Indices: 27586694--27586737 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
27586684 TTAAATAATA
*
27586694 TTTTTTATATTTTTTTCAAT
1 TTTTTTATATTATTTTCAAT
*
27586714 TTTTTTATATTATTTTGAAT
1 TTTTTTATATTATTTTCAAT
27586734 TTTT
1 TTTT
27586738 GAAATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTTATATTATTTTCAAT
Found at i:27586765 original size:31 final size:31
Alignment explanation
Indices: 27586717--27586775 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
27586707 TTTCAATTTT
27586717 TTTATATTATTTTGAATTTT-TGAAATTTATA
1 TTTATATTATTTTGAATTTTAT-AAATTTATA
27586748 TTTATA-TATTTTAGAATTTTATAAATTT
1 TTTATATTATTTT-GAATTTTATAAATTT
27586776 TAAATCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 6 0.23
31 19 0.73
32 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (31 bp):
TTTATATTATTTTGAATTTTATAAATTTATA
Found at i:27586788 original size:10 final size:9
Alignment explanation
Indices: 27586693--27586805 Score: 50
Period size: 10 Copynumber: 11.9 Consensus size: 9
27586683 CTTAAATAAT
27586693 ATTTTTTATA
1 ATTTTTTA-A
*
27586703 TTTTTTTCAA
1 ATTTTTT-AA
* *
27586713 TTTTTTTAT
1 ATTTTTTAA
*
27586722 ATTATTTTGA
1 ATT-TTTTAA
*
27586732 ATTTTTGAA
1 ATTTTTTAA
*
27586741 ATTTATATTTAT
1 A-TT-T-TTTAA
*
27586753 ATATTTTAGA
1 ATTTTTTA-A
*
27586763 ATTTTATAA
1 ATTTTTTAA
27586772 A--TTTTAA
1 ATTTTTTAA
27586779 ATCTTTTTAA
1 AT-TTTTTAA
*
27586789 ATTTTTTGA
1 ATTTTTTAA
*
27586798 ATTATTTA
1 ATTTTTTA
27586806 TGTATTACAT
Statistics
Matches: 77, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
7 6 0.08
9 26 0.34
10 38 0.49
11 3 0.04
12 4 0.05
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:27586789 original size:17 final size:17
Alignment explanation
Indices: 27586748--27586793 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
27586738 GAAATTTATA
*
27586748 TTTATATATTTTAGAAT
1 TTTATAAATTTTAGAAT
27586765 TTTATAAATTTTA-AAT
1 TTTATAAATTTTAGAAT
*
27586781 CTTTTTAAATTTT
1 -TTTATAAATTTT
27586794 TTGAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTATAAATTTTAGAAT
Found at i:27588216 original size:12 final size:12
Alignment explanation
Indices: 27588199--27588223 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27588189 TCATGGTGAG
27588199 AAGATTAATTCA
1 AAGATTAATTCA
27588211 AAGATTAATTCA
1 AAGATTAATTCA
27588223 A
1 A
27588224 TTTTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AAGATTAATTCA
Found at i:27595281 original size:21 final size:22
Alignment explanation
Indices: 27595227--27595281 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
27595217 TGTTTTTGGA
* *
27595227 TAAATTTGAGTAAATATGTGAT
1 TAAATTAGATTAAATATGTGAT
* *
27595249 TAAATAAG-TTAAATTTGT-AT
1 TAAATTAGATTAAATATGTGAT
27595269 TAAATTAGATTAA
1 TAAATTAGATTAA
27595282 GAAAAGAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 9 0.33
21 12 0.44
22 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
TAAATTAGATTAAATATGTGAT
Found at i:27595642 original size:44 final size:42
Alignment explanation
Indices: 27595570--27595704 Score: 141
Period size: 44 Copynumber: 3.1 Consensus size: 42
27595560 ACATAGGACT
* *
27595570 TCGATATGTGATTTCGTGTAAGATCATGTCTGGTACATTGGCA
1 TCGATATGAGATTTCGTGTAAGACCATGTCTGG-ACATTGGCA
* *
27595613 TCGATTTGAGATTTACGTGTAAGACCATGTCTAAGACATTGGCA
1 TCGATATGAGATTT-CGTGTAAGACCATGTCT-GGACATTGGCA
* *
27595657 TCG-TAT-ATGATTTCGTGTAAGATCC-TGTCTGGGATAGTGGCA
1 TCGATATGA-GATTTCGTGTAAGA-CCATGTCT-GGACATTGGCA
27595699 TCGATA
1 TCGATA
27595705 GTTGATTACA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
42 26 0.33
43 23 0.29
44 28 0.36
45 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (42 bp):
TCGATATGAGATTTCGTGTAAGACCATGTCTGGACATTGGCA
Found at i:27602858 original size:43 final size:43
Alignment explanation
Indices: 27602796--27602886 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 43
27602786 TAAAAAATAG
* *
27602796 AGGAAGCTACGT-AAAAAAAATCACTACCAGGAAACAACAAAAA
1 AGGAAACTACGTAAAAAAAAATCACTACCAAGAAACAAC-AAAA
** * *
27602839 AGGAAACTACGTAGGAAAAAATCACTATCAAGAAACGACAAAA
1 AGGAAACTACGTAAAAAAAAATCACTACCAAGAAACAACAAAA
27602882 AGGAA
1 AGGAA
27602887 GTTATGTGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 20 0.49
44 21 0.51
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.10
Consensus pattern (43 bp):
AGGAAACTACGTAAAAAAAAATCACTACCAAGAAACAACAAAA
Found at i:27602874 original size:44 final size:42
Alignment explanation
Indices: 27602796--27602886 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 42
27602786 TAAAAAATAG
* *
27602796 AGGAAGCTACGTAAAAAAAATCACTACCAGGAAACAACAAAAA
1 AGGAAACTACGTAAAAAAAATCACTACCAAGAAACAAC-AAAA
* * *
27602839 AGGAAACTACGTAGGAAAAAATCACTATCAAGAAACGACAAAA
1 AGGAAACTACGTA-AAAAAAATCACTACCAAGAAACAACAAAA
27602882 AGGAA
1 AGGAA
27602887 GTTATGTGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 21 0.50
44 21 0.50
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.10
Consensus pattern (42 bp):
AGGAAACTACGTAAAAAAAATCACTACCAAGAAACAACAAAA
Found at i:27605334 original size:33 final size:33
Alignment explanation
Indices: 27605297--27605404 Score: 153
Period size: 33 Copynumber: 3.3 Consensus size: 33
27605287 TCGAGTCAAT
**
27605297 TCACACCAATGCTCATAAGAGCTAATCTGACCA
1 TCACACCAATGCTCATAAGAGCTAATCCAACCA
*
27605330 TCACACCAATGCTCATAAGAGCTAAACCAACCA
1 TCACACCAATGCTCATAAGAGCTAATCCAACCA
* * *
27605363 TCACACTAATGCTCATAAAAGCTAATCCAACTA
1 TCACACCAATGCTCATAAGAGCTAATCCAACCA
*
27605396 GCACACCAA
1 TCACACCAA
27605405 AAAGAGAGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.41, C:0.31, G:0.09, T:0.19
Consensus pattern (33 bp):
TCACACCAATGCTCATAAGAGCTAATCCAACCA
Found at i:27625970 original size:51 final size:52
Alignment explanation
Indices: 27625756--27626097 Score: 314
Period size: 51 Copynumber: 6.8 Consensus size: 52
27625746 TTTTATCATT
* *
27625756 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGA--TTAGTTTTAC
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTAC
* * *
27625806 AG-TTCACATAGTAGCCTTCACATAGTACTACACACGTGATCA-AGTTTTAC
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTAC
* * * * *
27625856 GGCT-CACATAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTT-C
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTAC
* * * * *
27625906 CGGTATC-CATAGTAGCCTTCACTTAGTACCACACATGTAACCATAG-TTTAC
1 CGATA-CACATAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTAC
* * * ***
27625957 CGATACACGTAGTAGCTTTCACACAGTACTACACACGTG-CTCA-AAACTT-C
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTGAC-CATAGTTTTAC
* * * *
27626007 TCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCAT--TATTTAT
1 -CGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCATAGT-TTTAC
* *
27626059 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTG
27626098 TTCATCGATA
Statistics
Matches: 237, Mismatches: 40, Indels: 29
0.77 0.13 0.09
Matches are distributed among these distances:
49 35 0.15
50 56 0.24
51 144 0.61
52 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (52 bp):
CGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTAC
Found at i:27625995 original size:102 final size:103
Alignment explanation
Indices: 27625756--27626097 Score: 407
Period size: 102 Copynumber: 3.4 Consensus size: 103
27625746 TTTTATCATT
* ** * * *
27625756 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGA--TTAGTTTTACAGT-TCACATAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTCCGGTATCACATAGT
* * *
27625818 AGCCTTCACATAGTACTACACACGTGATCA-AGTTTTAC
66 AGCCTTCACTTAGTACTACACATGTGACCATAG-TTTAC
* * * * *
27625856 GGCT-CACATAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTCCGGTATC-CATAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTCCGGTATCACATAGT
* *
27625919 AGCCTTCACTTAGTACCACACATGTAACCATAGTTTAC
66 AGCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
* *
27625957 CGATACACGTAGTAGCTTTCACACAGTACTACACACGTG-CTCAAAAC-TTCTCGGTA-CACATA
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGAC-CAAAGCTTTC-CGGTATCACATA
*
27626019 GTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTAT
64 GTAGCCTTCACTTAGTACTACACATGTGACCA-TAGTTTAC
27626059 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
27626098 TTCATCGATA
Statistics
Matches: 208, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
99 33 0.16
100 2 0.01
101 51 0.25
102 120 0.58
103 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (103 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTCCGGTATCACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
Found at i:27626072 original size:153 final size:149
Alignment explanation
Indices: 27625754--27626096 Score: 363
Period size: 153 Copynumber: 2.3 Consensus size: 149
27625744 ATTTTTATCA
* * * *
27625754 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATTAGTTTTACAGTTCACATAGTA
1 TTCGATACACGTAGTAGCCTTCACATAGTACCACACACGTAAATAGTTTTACAGTACACATAGTA
* * *
27625819 GCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCTCACATAGTAGCCTTCACATAGTAC
66 GCCTTCACACAGTACTACACACGTGATCAACTTCTACGGCTCACATAGTAGCCTTCACATAGTAC
*
27625884 TACATACGTGACCAAAGCTT
131 TACACACGTGACCAAA-CTT
* * * * * * *
27625904 TCCGGTATC-CATAGTAGCCTTCACTTAGTACCACACATGTAACCATAG-TTTACCGATACACGT
1 TTCGATA-CACGTAGTAGCCTTCACATAGTACCACACACGTAA--ATAGTTTTACAG-TACACAT
* *
27625967 AGTAGCTTTCACACAGTACTACACACGTGCTCAAAACTTCT-CGG-TACACATAGTAGCCTTCAC
62 AGTAGCCTTCACACAGTACTACACACGTGATC--AACTTCTACGGCT-CACATAGTAGCCTTCAC
* * *
27626030 TTAGTACTACACATGTGACCATTA-TT
124 ATAGTACTACACACGTGACCA-AACTT
* *
27626056 TATCGATACACGTAGTAGCCTTCACACAGTACTACACACGT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACCACACACGT
27626097 GTTCATCGAT
Statistics
Matches: 156, Mismatches: 27, Indels: 17
0.78 0.14 0.09
Matches are distributed among these distances:
150 33 0.21
151 7 0.04
152 42 0.27
153 68 0.44
154 6 0.04
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (149 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACCACACACGTAAATAGTTTTACAGTACACATAGTA
GCCTTCACACAGTACTACACACGTGATCAACTTCTACGGCTCACATAGTAGCCTTCACATAGTAC
TACACACGTGACCAAACTT
Found at i:27627901 original size:138 final size:137
Alignment explanation
Indices: 27627731--27627995 Score: 440
Period size: 138 Copynumber: 1.9 Consensus size: 137
27627721 CATAGAAAAA
**
27627731 AATTAATATATGAATTTGGTTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * *
27627796 TAAATAATTATATTAATTAATTTCTGTCAAAATATAAAAGGCATGGAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAA-TTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
27627861 AAGAATAT
130 AAGAATAT
* *
27627869 AATTAATATATGAATTTAATTCATACACAATATTAATTGTATATATTTTACTGAATTTATTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* *
27627934 TAAACAGTTATATTAATTAATTCAGTCAAAATATAAAAGACATGGCAATTAATATTCTTTTG
66 TAAACAATTATATTAATTAATTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTG
27627996 AAAATATAAC
Statistics
Matches: 118, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
137 39 0.33
138 79 0.67
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (137 bp):
AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
TAAACAATTATATTAATTAATTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAA
AGAATAT
Found at i:27629061 original size:44 final size:44
Alignment explanation
Indices: 27628993--27629083 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
27628983 AACTATAGTT
** *
27628993 TTAGTTTCCCACTTAAACTCTGATTAATGTAAGTTATTTTAATA
1 TTAGTTTCAAACTTAAACTCTGATTAATGTAAGTTATTTGAATA
* * *
27629037 TTAGTTTCAAACTTAAACTTTGATTAGTGTAGGTTATTTGAATA
1 TTAGTTTCAAACTTAAACTCTGATTAATGTAAGTTATTTGAATA
27629081 TTA
1 TTA
27629084 TTTGACCTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (44 bp):
TTAGTTTCAAACTTAAACTCTGATTAATGTAAGTTATTTGAATA
Found at i:27630562 original size:158 final size:160
Alignment explanation
Indices: 27630259--27630580 Score: 431
Period size: 158 Copynumber: 2.0 Consensus size: 160
27630249 GGATTCGGGG
* * *
27630259 TGTTCTTTCCACATGTGTGTCCCAACAGGGTCTGGTTATTCACATACAATTCAATTGAAGGTGGA
1 TGTTCGTTCCACATGTGTGTCCCAACAGGGACTAGTTATTCACATACAATTCAATTGAAGGTGGA
* *
27630324 GTTGTATGCCTAGGGAATGACTTACCTAGTAAAGTAACTAGTGTTGGTACTATTCAAATCAGGAT
66 GTTGTATGCCTAGAGAATGACTTACCTAGTAAAGTAACGAGTGTTGGTACTATTCAAATCAGGAT
* * *
27630389 GCACGATAGGACAATCAGGACACTGTCAGA
131 GCACGAGAGGACAATCAAGACACTATCAGA
*
27630419 TGTTCGTTCCACATGTGT-T-CCAACAGGGACTAGTT-CTCTACATACAATT-AAGTTGAAGGTG
1 TGTTCGTTCCACATGTGTGTCCCAACAGGGACTAGTTATTC-ACATACAATTCAA-TTGAAGGTG
* * * * *
27630480 GATTTGTGTGCCTAGAGAATGACTTACCTAGTAAAGTAACCGA-TGTTGTTACTGTTCAGATCAG
64 GAGTTGTATGCCTAGAGAATGACTTACCTAGTAAAGTAA-CGAGTGTTGGTACTATTCAAATCAG
*
27630544 GATGCATGACGA-GACAATCAAGACACTATCAGA
128 GATGCACGA-GAGGACAATCAAGACACTATCAGA
27630577 TGTT
1 TGTT
27630581 AGAAATATGT
Statistics
Matches: 143, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
157 4 0.03
158 118 0.83
159 4 0.03
160 17 0.12
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (160 bp):
TGTTCGTTCCACATGTGTGTCCCAACAGGGACTAGTTATTCACATACAATTCAATTGAAGGTGGA
GTTGTATGCCTAGAGAATGACTTACCTAGTAAAGTAACGAGTGTTGGTACTATTCAAATCAGGAT
GCACGAGAGGACAATCAAGACACTATCAGA
Found at i:27631191 original size:44 final size:44
Alignment explanation
Indices: 27631133--27631219 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
27631123 TCTATTTTTA
27631133 GTTTCCCACTTAAACTCTAAATAGTGTAGGTTATTTTAATATTT
1 GTTTCCCACTTAAACTCTAAATAGTGTAGGTTATTTTAATATTT
* * *
27631177 GTTTCCCACTTAAACTTTGATTAGTGTAGGTTATTTTAATATT
1 GTTTCCCACTTAAACTCTAAATAGTGTAGGTTATTTTAATATT
27631220 ATTTGACCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (44 bp):
GTTTCCCACTTAAACTCTAAATAGTGTAGGTTATTTTAATATTT
Found at i:27635932 original size:25 final size:27
Alignment explanation
Indices: 27635904--27635971 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
27635894 AAAATTGGTA
27635904 AGACATTTTCCATTCT-TCTCT-A-AGC
1 AGACATTTTCCATTCTCT-TCTAAGAGC
27635929 AGACATTTTCCATTCTCTTCTAAGTAGC
1 AGACATTTTCCATTCTCTTCTAAG-AGC
27635957 AGACATTTTCCATTC
1 AGACATTTTCCATTC
27635972 CTCAAAGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
25 19 0.49
26 2 0.05
28 18 0.46
ACGTcount: A:0.25, C:0.26, G:0.09, T:0.40
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAAGAGC
Found at i:27640054 original size:35 final size:36
Alignment explanation
Indices: 27640006--27640074 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
27639996 ATTTGTTAGA
27640006 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
27640042 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
27640075 ATGGTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:27641380 original size:14 final size:14
Alignment explanation
Indices: 27641361--27641388 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27641351 ACAATTTATT
27641361 AATATATATTAATA
1 AATATATATTAATA
27641375 AATATATATTAATA
1 AATATATATTAATA
27641389 TATGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:27641523 original size:20 final size:20
Alignment explanation
Indices: 27641498--27641537 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27641488 AATATTTTCC
*
27641498 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
27641518 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
27641538 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:27641543 original size:34 final size:35
Alignment explanation
Indices: 27641486--27641552 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
27641476 CAAACACCAA
*
27641486 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
27641521 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
27641553 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:27641544 original size:14 final size:14
Alignment explanation
Indices: 27641521--27641560 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27641511 ACAGAAAAGT
*
27641521 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
27641535 AAATCATTTTACGG
1 AAAACATTTTACAG
27641549 AAAACATTTTAC
1 AAAACATTTTAC
27641561 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Done.