Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 124 of 230
Found at i:36124166 original size:6 final size:6
Alignment explanation
Indices: 36124148--36124243 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
36124138 AAAGATATTG
* ** * **
36124148 AAAG-A AAACAA AAAGAA AAAGAA ATTGCA AAAGAA AAAGAA ATCGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** * * *
36124195 AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
36124244 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 22, Indels: 7
0.69 0.23 0.07
Matches are distributed among these distances:
5 3 0.05
6 51 0.78
7 7 0.11
8 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:36124197 original size:18 final size:18
Alignment explanation
Indices: 36124148--36124198 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
36124138 AAAGATATTG
*
36124148 AAAGAAAAC-AAAAAGAA
1 AAAGAAATCGAAAAAGAA
* *
36124165 AAAGAAATTGCAAAAGAA
1 AAAGAAATCGAAAAAGAA
36124183 AAAGAAATCGAAAAAG
1 AAAGAAATCGAAAAAG
36124199 TGAGAGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.06
Consensus pattern (18 bp):
AAAGAAATCGAAAAAGAA
Found at i:36124225 original size:14 final size:13
Alignment explanation
Indices: 36124204--36124241 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
36124194 AAAAGTGAGA
36124204 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
36124216 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
36124231 GAAAAAGAAAA
1 GAAAAAGAAAA
36124242 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:36124255 original size:21 final size:21
Alignment explanation
Indices: 36124205--36124255 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
36124195 AAAGTGAGAG
*
36124205 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
36124226 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
36124247 AAAAAGAAA
1 AAAAAGAAA
36124256 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:36124295 original size:33 final size:33
Alignment explanation
Indices: 36124258--36124320 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
36124248 AAAAGAAATT
36124258 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
36124291 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
36124321 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:36128702 original size:20 final size:20
Alignment explanation
Indices: 36128679--36128732 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
36128669 AGTTTTTCCC
36128679 AGCTCGATTTAGCTCACATG
1 AGCTCGATTTAGCTCACATG
* ***
36128699 AGCTTGATTTAGCTCGTTTG
1 AGCTCGATTTAGCTCACATG
*
36128719 AGCTCAATTTAGCT
1 AGCTCGATTTAGCT
36128733 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
AGCTCGATTTAGCTCACATG
Found at i:36132140 original size:14 final size:14
Alignment explanation
Indices: 36132121--36132172 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
36132111 TAGCTTCTTC
36132121 TTTTTTTTCACGAA
1 TTTTTTTTCACGAA
*
36132135 TTTTTTTTCACTAA
1 TTTTTTTTCACGAA
36132149 TTTTTTTTTTCACGAA
1 --TTTTTTTTCACGAA
36132165 TTTTTTTT
1 TTTTTTTT
36132173 TCAACTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 21 0.62
16 13 0.38
ACGTcount: A:0.17, C:0.12, G:0.04, T:0.67
Consensus pattern (14 bp):
TTTTTTTTCACGAA
Found at i:36132142 original size:16 final size:16
Alignment explanation
Indices: 36132121--36132173 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
36132111 TAGCTTCTTC
36132121 TTTTTTTTCACGAA--
1 TTTTTTTTCACGAATT
*
36132135 TTTTTTTTCACTAATT
1 TTTTTTTTCACGAATT
36132151 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
36132167 TTTTTTT
1 TTTTTTT
36132174 CAACTTGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.37
16 22 0.63
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.68
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Found at i:36132230 original size:12 final size:12
Alignment explanation
Indices: 36132213--36132263 Score: 84
Period size: 12 Copynumber: 4.2 Consensus size: 12
36132203 ATGGAAACCA
36132213 AATTTTTTTTTG
1 AATTTTTTTTTG
36132225 AATTTTTTTTTG
1 AATTTTTTTTTG
36132237 AATTTTTTTTTCG
1 AATTTTTTTTT-G
*
36132250 AAATTTTTTTTG
1 AATTTTTTTTTG
36132262 AA
1 AA
36132264 GAAACTACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
12 26 0.70
13 11 0.30
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.69
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:36132256 original size:25 final size:24
Alignment explanation
Indices: 36132213--36132263 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
36132203 ATGGAAACCA
*
36132213 AATTTTTTTTTGAATTTTTTTTTG
1 AATTTTTTTTTGAAATTTTTTTTG
36132237 AATTTTTTTTTCGAAATTTTTTTTG
1 AATTTTTTTTT-GAAATTTTTTTTG
36132262 AA
1 AA
36132264 GAAACTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.69
Consensus pattern (24 bp):
AATTTTTTTTTGAAATTTTTTTTG
Found at i:36137034 original size:15 final size:14
Alignment explanation
Indices: 36137014--36137061 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
36137004 CTCATTTTCA
36137014 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
36137029 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
36137043 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
36137058 TCTT
1 TCTT
36137062 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:36137066 original size:22 final size:21
Alignment explanation
Indices: 36137014--36137072 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
36137004 CTCATTTTCA
* *
36137014 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
36137035 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
36137056 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
36137073 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:36138142 original size:12 final size:13
Alignment explanation
Indices: 36138109--36138143 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
36138099 TTTTTTCGGA
36138109 TTTTTTTTTGAAAC
1 TTTTTTTTT-AAAC
36138123 TTTTTTTTT-AAC
1 TTTTTTTTTAAAC
36138135 TTTTTTTTT
1 TTTTTTTTT
36138144 GAAGCTACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTAAAC
Found at i:36139009 original size:13 final size:13
Alignment explanation
Indices: 36138991--36139015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36138981 TGGACATCAT
36138991 GGTGTGAACACAA
1 GGTGTGAACACAA
36139004 GGTGTGAACACA
1 GGTGTGAACACA
36139016 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:36141306 original size:10 final size:10
Alignment explanation
Indices: 36141291--36141328 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
36141281 GCTCGTTTCC
*
36141291 AGCTCACTCG
1 AGCTCAATCG
36141301 AGCTCAAGTC-
1 AGCTCAA-TCG
36141311 AGCTCAATCG
1 AGCTCAATCG
36141321 AGCTCAAT
1 AGCTCAAT
36141329 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:36141315 original size:20 final size:20
Alignment explanation
Indices: 36141290--36141327 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36141280 AGCTCGTTTC
*
36141290 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
36141310 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
36141328 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:36141334 original size:20 final size:20
Alignment explanation
Indices: 36141291--36141351 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
36141281 GCTCGTTTCC
* * *
36141291 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
36141311 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
36141331 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
36141351 A
1 A
36141352 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:36141345 original size:11 final size:10
Alignment explanation
Indices: 36141301--36141347 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
36141291 AGCTCACTCG
*
36141301 AGCTCAAGTC
1 AGCTCAATTC
36141311 AGCTCAA-TC
1 AGCTCAATTC
*
36141320 GAGCTCAATTT
1 -AGCTCAATTC
36141331 AGCTACAATTC
1 AGCT-CAATTC
36141342 AGCTCA
1 AGCTCA
36141348 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:36141852 original size:13 final size:13
Alignment explanation
Indices: 36141834--36141858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36141824 GTATTGATCA
36141834 TGTGTTCACACCT
1 TGTGTTCACACCT
36141847 TGTGTTCACACC
1 TGTGTTCACACC
36141859 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:36142847 original size:29 final size:29
Alignment explanation
Indices: 36142797--36142853 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
36142787 AAATCGTAGC
***
36142797 TTCGAAAAAAAAAAAGTTAAAAAAAAAGT
1 TTCGAAAAAAAAAAACCGAAAAAAAAAGT
*
36142826 TTCGAAAAAAAAAATCCGAAAAAAAAAG
1 TTCGAAAAAAAAAAACCGAAAAAAAAAG
36142854 AAGGAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.68, C:0.07, G:0.11, T:0.14
Consensus pattern (29 bp):
TTCGAAAAAAAAAAACCGAAAAAAAAAGT
Found at i:36142874 original size:13 final size:13
Alignment explanation
Indices: 36142802--36142879 Score: 61
Period size: 13 Copynumber: 5.8 Consensus size: 13
36142792 GTAGCTTCGA
36142802 AAAAAAAAAAGTT-
1 AAAAAAAAAA-TTG
*
36142815 AAAAAAAAAGTTTCG
1 AAAAAAAAA-ATT-G
*
36142830 AAAAAAAAAATCCG
1 AAAAAAAAAAT-TG
*
36142844 AAAAAAAAAGA-AG
1 AAAAAAAAA-ATTG
*
36142857 GAAAAAAAAATTG
1 AAAAAAAAAATTG
36142870 AAAAAAAAAA
1 AAAAAAAAAA
36142880 ATTGCATACG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
12 1 0.02
13 30 0.58
14 11 0.21
15 10 0.19
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:36142875 original size:14 final size:14
Alignment explanation
Indices: 36142800--36142883 Score: 61
Period size: 14 Copynumber: 6.1 Consensus size: 14
36142790 TCGTAGCTTC
36142800 GAAAAAAAAAAAGTT
1 GAAAAAAAAAAA-TT
**
36142815 -AAAAAAAAAGTTT
1 GAAAAAAAAAAATT
*
36142828 CG-AAAAAAAAAATCC
1 -GAAAAAAAAAAAT-T
36142843 GAAAAAAAAAGAA--
1 GAAAAAAAAA-AATT
*
36142856 G-GAAAAAAAAATT
1 GAAAAAAAAAAATT
36142869 GAAAAAAAAAAATT
1 GAAAAAAAAAAATT
36142883 G
1 G
36142884 CATACGGTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
11 2 0.04
12 7 0.13
13 4 0.07
14 31 0.57
15 8 0.15
16 2 0.04
ACGTcount: A:0.73, C:0.04, G:0.12, T:0.12
Consensus pattern (14 bp):
GAAAAAAAAAAATT
Found at i:36143857 original size:18 final size:18
Alignment explanation
Indices: 36143819--36143860 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36143809 AAATCGAAAG
* **
36143819 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
36143837 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
36143855 AAAAGA
1 AAAAGA
36143861 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:36145569 original size:10 final size:10
Alignment explanation
Indices: 36145554--36145591 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
36145544 GCTCGTTTCC
*
36145554 AGCTCACTCG
1 AGCTCAATCG
36145564 AGCTCAAGTC-
1 AGCTCAA-TCG
36145574 AGCTCAATCG
1 AGCTCAATCG
36145584 AGCTCAAT
1 AGCTCAAT
36145592 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:36145578 original size:20 final size:20
Alignment explanation
Indices: 36145553--36145590 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36145543 AGCTCGTTTC
*
36145553 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
36145573 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
36145591 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:36145597 original size:20 final size:20
Alignment explanation
Indices: 36145554--36145614 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
36145544 GCTCGTTTCC
* * *
36145554 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
36145574 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
36145594 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
36145614 A
1 A
36145615 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:36145608 original size:11 final size:10
Alignment explanation
Indices: 36145564--36145610 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
36145554 AGCTCACTCG
*
36145564 AGCTCAAGTC
1 AGCTCAATTC
36145574 AGCTCAA-TC
1 AGCTCAATTC
*
36145583 GAGCTCAATTT
1 -AGCTCAATTC
36145594 AGCTACAATTC
1 AGCT-CAATTC
36145605 AGCTCA
1 AGCTCA
36145611 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:36146115 original size:13 final size:13
Alignment explanation
Indices: 36146097--36146121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36146087 GTATTGATCA
36146097 TGTGTTCACACCT
1 TGTGTTCACACCT
36146110 TGTGTTCACACC
1 TGTGTTCACACC
36146122 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:36147694 original size:52 final size:52
Alignment explanation
Indices: 36147611--36147711 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
36147601 TAAGGAAACG
* * *
36147611 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
36147663 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAA
36147712 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
Found at i:36152728 original size:20 final size:19
Alignment explanation
Indices: 36152705--36152769 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
36152695 AAGCTCAAAC
36152705 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
36152725 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
36152745 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
36152765 GAGCT
1 GAGCT
36152770 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:36154056 original size:17 final size:18
Alignment explanation
Indices: 36154034--36154067 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36154024 ACAACACTCC
*
36154034 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
36154051 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
36154068 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:36154175 original size:15 final size:16
Alignment explanation
Indices: 36154150--36154181 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
36154140 TATCTCACAC
36154150 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
36154166 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
36154181 T
1 T
36154182 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:36155130 original size:31 final size:28
Alignment explanation
Indices: 36155088--36155158 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 28
36155078 GCAAGACTTC
*
36155088 TCAC-TTTTTTTTAACTTGATTTTTTTT
1 TCACTTTTTTTTTAACTCGATTTTTTTT
**
36155115 GGTCACCTTTTTTTTTTGCTCGATTTTTTTT
1 --TCA-CTTTTTTTTTAACTCGATTTTTTTT
36155146 TCACTTTTTTTTT
1 TCACTTTTTTTTT
36155159 GAATTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.27
29 6 0.16
30 1 0.03
31 20 0.54
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (28 bp):
TCACTTTTTTTTTAACTCGATTTTTTTT
Found at i:36155153 original size:12 final size:12
Alignment explanation
Indices: 36155137--36155175 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
36155127 TTTTTGCTCG
36155137 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
36155149 CTTTTTTTTTGA
1 ATTTTTTTTTCA
36155161 ATTTTTTTTTTCA
1 A-TTTTTTTTTCA
36155174 AT
1 AT
36155176 CAATTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:36155195 original size:15 final size:15
Alignment explanation
Indices: 36155150--36155197 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 15
36155140 TTTTTTTCAC
36155150 TTTTTTTTT-G-AAT
1 TTTTTTTTTCGAAAT
*
36155163 TTTTTTTTTCAATCAAT
1 TTTTTTTTTCGA--AAT
36155180 TTTTTTTTTCGAAAT
1 TTTTTTTTTCGAAAT
36155195 TTT
1 TTT
36155198 CTTGATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 9 0.31
15 6 0.21
17 14 0.48
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (15 bp):
TTTTTTTTTCGAAAT
Found at i:36156850 original size:20 final size:19
Alignment explanation
Indices: 36156827--36156891 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
36156817 AAGCTCAAAC
36156827 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
36156847 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
36156867 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
36156887 GAGCT
1 GAGCT
36156892 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:36158221 original size:20 final size:20
Alignment explanation
Indices: 36158175--36158212 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36158165 AGCTCGTTTC
*
36158175 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
*
36158195 CAACTCACTCAAGCTCAA
1 CAGCTCACTCAAGCTCAA
36158213 TTTAGCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:36160412 original size:23 final size:22
Alignment explanation
Indices: 36160361--36160412 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
36160351 CCTCGTCTTT
*
36160361 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
36160383 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
36160406 TTCTTTT
1 TTCTTTT
36160413 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:36164039 original size:20 final size:20
Alignment explanation
Indices: 36164014--36164068 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
36164004 ACGAGTTAAA
* **
36164014 TTGAGCTTGAATGAGCTGGC
1 TTGAGCTCGAATGAGCTAAC
*
36164034 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
36164054 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
36164069 TTGAACCACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:36165391 original size:15 final size:16
Alignment explanation
Indices: 36165352--36165392 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
36165342 AACAACACTC
36165352 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
36165368 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
36165382 CTTTCTTTTTC
1 CTTTCTTTTTC
36165393 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:36165587 original size:17 final size:15
Alignment explanation
Indices: 36165550--36165588 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
36165540 TATCTCCCAC
36165550 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
36165566 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
36165583 TCATTT
1 TCATTT
36165589 TCTCACTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:36166478 original size:27 final size:27
Alignment explanation
Indices: 36166436--36166502 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
36166426 TTTCAATCAC
* *
36166436 TCTTTTTTTTTCAATTTCGATTTTTTT
1 TCTTTTTTTTTTAATTTCGAATTTTTT
36166463 TCTTTTTTTTTTAATTTCGAATTTTTT
1 TCTTTTTTTTTTAATTTCGAATTTTTT
36166490 TCTTCTTTTTTTT
1 TCTT-TTTTTTTT
36166503 TCTTCAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 29 0.78
28 8 0.22
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (27 bp):
TCTTTTTTTTTTAATTTCGAATTTTTT
Found at i:36166564 original size:11 final size:10
Alignment explanation
Indices: 36166548--36166600 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
36166538 GAATACAAAC
36166548 TTTTTTTTGAA
1 TTTTTTTT-AA
*
36166559 TTTTTTTCAAA
1 TTTTTTT-TAA
36166570 TTTTTTTTCAA
1 TTTTTTTT-AA
*
36166581 GTTTTTTTTTA
1 -TTTTTTTTAA
36166592 TTTTTTTTA
1 TTTTTTTTA
36166601 CAAACCGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 8 0.23
11 19 0.54
12 8 0.23
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:36166565 original size:12 final size:12
Alignment explanation
Indices: 36166559--36166599 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
36166549 TTTTTTTGAA
*
36166559 TTTTTTTCAAAT
1 TTTTTTTCAATT
36166571 TTTTTTTCAAGTT
1 TTTTTTTCAA-TT
36166584 TTTTTTT--ATT
1 TTTTTTTCAATT
36166594 TTTTTT
1 TTTTTT
36166600 ACAAACCGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 8 0.30
11 1 0.04
12 10 0.37
13 8 0.30
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:36168321 original size:20 final size:19
Alignment explanation
Indices: 36168298--36168362 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
36168288 AAGCTCAAAC
36168298 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
36168318 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
36168338 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
36168358 GAGCT
1 GAGCT
36168363 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:36170383 original size:18 final size:18
Alignment explanation
Indices: 36170362--36170396 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36170352 TTTTTCTTTT
36170362 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
36170380 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
36170397 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:36171345 original size:13 final size:13
Alignment explanation
Indices: 36171329--36171376 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
36171319 TTTTTTTTCA
36171329 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*
36171342 TTTTTTTTCAATCAAT
1 TTTTTTTTGAAT---T
*
36171358 TTTTTTTCGAATT
1 TTTTTTTTGAATT
36171371 TTTTTT
1 TTTTTT
36171377 GATTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 18 0.62
16 11 0.38
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:36171370 original size:12 final size:11
Alignment explanation
Indices: 36171355--36171387 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
36171345 TTTTTCAATC
36171355 AATTTTTTTTCG
1 AATTTTTTTT-G
36171367 AATTTTTTTTG
1 AATTTTTTTTG
36171378 -ATTTTTTTTG
1 AATTTTTTTTG
36171388 TTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 1 0.05
12 10 0.48
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:36172904 original size:20 final size:19
Alignment explanation
Indices: 36172881--36172945 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
36172871 AAGCTCAAAC
36172881 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
36172901 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
36172921 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
36172941 GAGCT
1 GAGCT
36172946 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:36174086 original size:56 final size:56
Alignment explanation
Indices: 36173981--36174087 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
36173971 ATTAATGCCG
* * * * *
36173981 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCTGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCTGT
36174037 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
36174088 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCTGT
Found at i:36174736 original size:20 final size:20
Alignment explanation
Indices: 36174711--36174765 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
36174701 ACGAGTTAAA
* *
36174711 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
36174731 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
36174751 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
36174766 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:36182825 original size:31 final size:31
Alignment explanation
Indices: 36182787--36182848 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
36182777 CAAGTACATT
36182787 GCTTATTCTAGAATTTGACCATTGGAGCTCC
1 GCTTATTCTAGAATTTGACCATTGGAGCTCC
36182818 GCTTATTCTAGAATTTGACCATTGGAGCTCC
1 GCTTATTCTAGAATTTGACCATTGGAGCTCC
36182849 CTATTCAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (31 bp):
GCTTATTCTAGAATTTGACCATTGGAGCTCC
Found at i:36183314 original size:23 final size:23
Alignment explanation
Indices: 36183288--36183372 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
36183278 AAACATTATA
* *
36183288 CCATTTCCTACCTACACGAAAAC
1 CCATTTCGTACCTAAACGAAAAC
* ** *
36183311 CCATTTCGTACCAAAACCTATA-
1 CCATTTCGTACCTAAACGAAAAC
36183333 CCATTTCGTACCTAAACGAAAAC
1 CCATTTCGTACCTAAACGAAAAC
* *
36183356 CCATTTCATACCAAAAC
1 CCATTTCGTACCTAAAC
36183373 CTATACCATT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 18 0.37
23 31 0.63
ACGTcount: A:0.38, C:0.34, G:0.05, T:0.24
Consensus pattern (23 bp):
CCATTTCGTACCTAAACGAAAAC
Found at i:36183333 original size:45 final size:45
Alignment explanation
Indices: 36183265--36183382 Score: 175
Period size: 45 Copynumber: 2.6 Consensus size: 45
36183255 ACCTTTTGAT
* *
36183265 CCATTTACGTACC-AAACATTATACCATTTCCTACCTACACGAAAAC
1 CCATTT-CGTACCAAAAC-CTATACCATTTCCTACCTAAACGAAAAC
*
36183311 CCATTTCGTACCAAAACCTATACCATTTCGTACCTAAACGAAAAC
1 CCATTTCGTACCAAAACCTATACCATTTCCTACCTAAACGAAAAC
*
36183356 CCATTTCATACCAAAACCTATACCATT
1 CCATTTCGTACCAAAACCTATACCATT
36183383 CCATAACTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
45 57 0.85
46 10 0.15
ACGTcount: A:0.37, C:0.32, G:0.04, T:0.26
Consensus pattern (45 bp):
CCATTTCGTACCAAAACCTATACCATTTCCTACCTAAACGAAAAC
Found at i:36183339 original size:22 final size:22
Alignment explanation
Indices: 36183311--36183423 Score: 95
Period size: 22 Copynumber: 5.1 Consensus size: 22
36183301 ACACGAAAAC
*
36183311 CCATTTCGTACCAAAACCTATA
1 CCATTTCGTACCAAAACCTAAA
* **
36183333 CCATTTCGTACCTAAACGAAAA
1 CCATTTCGTACCAAAACCTAAA
* *
36183355 CCCATTTCATACCAAAACCTATA
1 -CCATTTCGTACCAAAACCTAAA
* * * *
36183378 CCATTCCATAACTAAACCTAAA
1 CCATTTCGTACCAAAACCTAAA
*
36183400 CCATATTCG-ACC-AAACTTAAA
1 CCAT-TTCGTACCAAAACCTAAA
36183421 CCA
1 CCA
36183424 ATTCTTTCTA
Statistics
Matches: 72, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
21 11 0.15
22 42 0.58
23 19 0.26
ACGTcount: A:0.41, C:0.32, G:0.04, T:0.24
Consensus pattern (22 bp):
CCATTTCGTACCAAAACCTAAA
Found at i:36183393 original size:45 final size:44
Alignment explanation
Indices: 36183284--36183394 Score: 159
Period size: 45 Copynumber: 2.5 Consensus size: 44
36183274 TACCAAACAT
* *
36183284 TATACCATTTCCTACCTACACGAAAACCCATTTCGTACCAAAACC
1 TATACCA-TTCCTACCTAAACGAAAACCCATTTCATACCAAAACC
*
36183329 TATACCATTTCGTACCTAAACGAAAACCCATTTCATACCAAAACC
1 TATACCA-TTCCTACCTAAACGAAAACCCATTTCATACCAAAACC
*
36183374 TATACCATTCCATAACTAAAC
1 TATACCATTCC-TACCTAAAC
36183395 CTAAACCATA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 3 0.05
45 57 0.95
ACGTcount: A:0.39, C:0.32, G:0.04, T:0.25
Consensus pattern (44 bp):
TATACCATTCCTACCTAAACGAAAACCCATTTCATACCAAAACC
Found at i:36186005 original size:13 final size:13
Alignment explanation
Indices: 36185987--36186077 Score: 51
Period size: 12 Copynumber: 6.7 Consensus size: 13
36185977 TTGGAGTAAC
36185987 AAAAAAAAATC-A
1 AAAAAAAAATCAA
*
36185999 AAAAAAAATTCGAA
1 AAAAAAAAATC-AA
*
36186013 AAAAAAAATTGATTGAA
1 AAAAAAAA---A-TCAA
*
36186030 AAAAAAAATTC-A
1 AAAAAAAAATCAA
* *
36186042 AAAAAAAAGTGAA
1 AAAAAAAAATCAA
* *
36186055 AAAAAAAATTGAA
1 AAAAAAAAATCAA
36186068 TAAAAAAAAA
1 -AAAAAAAAA
36186078 GGTGAGCAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
12 20 0.32
13 14 0.23
14 17 0.27
17 10 0.16
18 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATCAA
Found at i:36186044 original size:25 final size:25
Alignment explanation
Indices: 36185986--36186075 Score: 85
Period size: 25 Copynumber: 3.4 Consensus size: 25
36185976 ATTGGAGTAA
*
36185986 CAAAAAAAAA-T-CAAAAAAAAATT
1 CAAAAAAAAAGTGAAAAAAAAAATT
36186009 CGAAAAAAAAAATTGATTGAAAAAAAAAATT
1 C--AAAAAAAAA--G--TGAAAAAAAAAATT
36186040 CAAAAAAAAAGTGAAAAAAAAAATT
1 CAAAAAAAAAGTGAAAAAAAAAATT
*
36186065 GAATAAAAAAA
1 CAA-AAAAAAA
36186076 AAGGTGAGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
23 1 0.02
25 25 0.45
26 7 0.12
27 1 0.02
29 9 0.16
30 1 0.02
31 12 0.21
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.14
Consensus pattern (25 bp):
CAAAAAAAAAGTGAAAAAAAAAATT
Found at i:36186045 original size:42 final size:40
Alignment explanation
Indices: 36185987--36186077 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 40
36185977 TTGGAGTAAC
* *
36185987 AAAAAAAAATCAAAAAAAAATTCGAAAAAAAAAATTGATTGA
1 AAAAAAAAATCAAAAAAAAAGT-GAAAAAAAAAATTGAAT-A
36186029 AAAAAAAAATTCAAAAAAAAAGTGAAAAAAAAAATTGAATA
1 AAAAAAAAA-TCAAAAAAAAAGTGAAAAAAAAAATTGAATA
36186070 AAAAAAAA
1 AAAAAAAA
36186078 GGTGAGCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 9 0.20
42 25 0.54
43 12 0.26
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (40 bp):
AAAAAAAAATCAAAAAAAAAGTGAAAAAAAAAATTGAATA
Found at i:36186072 original size:12 final size:12
Alignment explanation
Indices: 36185987--36186075 Score: 63
Period size: 13 Copynumber: 6.8 Consensus size: 12
36185977 TTGGAGTAAC
*
36185987 AAAAAAAAA-TC
1 AAAAAAAAATTG
36185998 AAAAAAAAATTCG
1 AAAAAAAAATT-G
36186011 AAAAAAAAAATTGATTG
1 --AAAAAAAA---ATTG
*
36186028 AAAAAAAAAATTC
1 -AAAAAAAAATTG
*
36186041 AAAAAAAAAGTG
1 AAAAAAAAATTG
36186053 AAAAAAAAAATTG
1 -AAAAAAAAATTG
36186066 AATAAAAAAA
1 AA-AAAAAAA
36186076 AAGGTGAGCA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
11 9 0.14
12 13 0.20
13 21 0.33
15 8 0.12
16 9 0.14
17 1 0.02
18 3 0.05
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:36187174 original size:17 final size:18
Alignment explanation
Indices: 36187142--36187175 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36187132 AAAAGAGAGT
*
36187142 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
36187160 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
36187176 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:36197237 original size:12 final size:12
Alignment explanation
Indices: 36197222--36197254 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
36197212 ACTTTTCACT
36197222 TCTTTTTTTTGA
1 TCTTTTTTTTGA
*
36197234 TCTTTTTTTTTA
1 TCTTTTTTTTGA
36197246 -CTTTTTTTT
1 TCTTTTTTTT
36197255 CTTTTTTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (12 bp):
TCTTTTTTTTGA
Found at i:36198832 original size:20 final size:20
Alignment explanation
Indices: 36198809--36198854 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
36198799 GGGTTAAGAT
*
36198809 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
36198829 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
36198849 TGAGCT
1 TGAGCT
36198855 AGAAACGAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:36201448 original size:20 final size:20
Alignment explanation
Indices: 36201402--36201448 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36201392 AGCTCGTTTC
*
36201402 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
36201422 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
36201442 CAGCTCA
1 CAGCTCA
36201449 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:36204215 original size:13 final size:13
Alignment explanation
Indices: 36204197--36204221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36204187 AGAGAAGAAA
36204197 TTCAAAAAAAAAT
1 TTCAAAAAAAAAT
36204210 TTCAAAAAAAAA
1 TTCAAAAAAAAA
36204222 GGAAAAAAAA
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:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
TTCAAAAAAAAAT
Found at i:36205381 original size:48 final size:47
Alignment explanation
Indices: 36205304--36205407 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 47
36205294 GAGTGTATGG
*
36205304 AAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATCGA
1 AAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATCGA
* *
36205352 AAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATTGA
1 AAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATCGA
36205400 AAAAGAAA
1 AAAAGAAA
36205408 GAAAAGACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14
Consensus pattern (47 bp):
AAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATCGA
Found at i:36208565 original size:17 final size:18
Alignment explanation
Indices: 36208543--36208576 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36208533 ACAACACTCC
*
36208543 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
36208560 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
36208577 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:36209612 original size:10 final size:9
Alignment explanation
Indices: 36209599--36209633 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
36209589 CTTTTCACTT
36209599 TTTTTTGTTC
1 TTTTTT-TTC
*
36209609 TTTTTTTAC
1 TTTTTTTTC
36209618 TTTTTTTTC
1 TTTTTTTTC
36209627 TTTTTTT
1 TTTTTTT
36209634 GCTCACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:36209619 original size:21 final size:20
Alignment explanation
Indices: 36209590--36209648 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
36209580 CTCACAAGAC
*
36209590 TTTTCACTTTTTTTTGTTCTT
1 TTTTCACTTTTTTTTCTT-TT
*
36209611 TTTTTACTTTTTTTTCTTTT
1 TTTTCACTTTTTTTTCTTTT
36209631 TTTGCTCACTTCTTTTTT
1 TTT--TCACTT-TTTTTT
36209649 TTTGAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.16
21 16 0.50
22 5 0.16
23 6 0.19
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTCACTTTTTTTTCTTTT
Found at i:36212559 original size:20 final size:20
Alignment explanation
Indices: 36212513--36212559 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36212503 AGCTCGTTTC
*
36212513 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
36212533 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
36212553 CAGCTCA
1 CAGCTCA
36212560 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:36214232 original size:21 final size:21
Alignment explanation
Indices: 36214208--36214248 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36214198 ACATTCCATA
*
36214208 ACCAAACCTAAACCATATTCG
1 ACCAAACCTAAACCAAATTCG
* *
36214229 ACCAATCTTAAACCAAATTC
1 ACCAAACCTAAACCAAATTC
36214249 CTTCTATCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (21 bp):
ACCAAACCTAAACCAAATTCG
Found at i:36218586 original size:13 final size:13
Alignment explanation
Indices: 36218570--36218595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36218560 AAAAAAAAGG
36218570 AAAAAAAATTGCA
1 AAAAAAAATTGCA
36218583 AAAAAAAATTGCA
1 AAAAAAAATTGCA
36218596 TACGGTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTGCA
Found at i:36220886 original size:24 final size:25
Alignment explanation
Indices: 36220859--36220912 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
36220849 ATGAGTGATA
*
36220859 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
36220883 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
36220907 AAAAAA
1 AAAAAA
36220913 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:36233435 original size:17 final size:16
Alignment explanation
Indices: 36233409--36233451 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
36233399 ATTATATATA
36233409 TTTTTATTTTCTTTGTT
1 TTTTTATTTTCTTT-TT
* *
36233426 TTTTTGTTTTGTTTTT
1 TTTTTATTTTCTTTTT
*
36233442 TTTTTCTTTT
1 TTTTTATTTT
36233452 AGTGCAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (16 bp):
TTTTTATTTTCTTTTT
Found at i:36242591 original size:12 final size:13
Alignment explanation
Indices: 36242571--36242607 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
36242561 TATACTTCAA
36242571 AATTTTTTTTTTG
1 AATTTTTTTTTTG
36242584 AATTTTTTTTTTG
1 AATTTTTTTTTTG
36242597 AATTTTTTTTT
1 AATTTTTTTTT
36242608 CAAATTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:36242613 original size:13 final size:13
Alignment explanation
Indices: 36242570--36242614 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
36242560 TTATACTTCA
36242570 AAATTTTTTTTTT
1 AAATTTTTTTTTT
*
36242583 GAATTTTTTTTTT
1 AAATTTTTTTTTT
* *
36242596 GAATTTTTTTTTC
1 AAATTTTTTTTTT
36242609 AAATTT
1 AAATTT
36242615 CCTCTTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (13 bp):
AAATTTTTTTTTT
Found at i:36245346 original size:33 final size:34
Alignment explanation
Indices: 36245298--36245363 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
36245288 ATCACTCTCC
*
36245298 CTCATTTAAATGTCG-TCCATTGCATGTGGAACAT
1 CTCATTTAAATGTCGTTCCA-TGCATGTAGAACAT
*
36245332 CTCA-TTAATTGTCGTTCCATGCATGTAGAACA
1 CTCATTTAAATGTCGTTCCATGCATGTAGAACA
36245364 ACATCTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (34 bp):
CTCATTTAAATGTCGTTCCATGCATGTAGAACAT
Found at i:36245374 original size:34 final size:33
Alignment explanation
Indices: 36245302--36245374 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
36245292 CTCTCCCTCA
* * *
36245302 TTTAAATGTCGTCCATTGCATGTGGAACATCTC
1 TTTAATTGTCGTCCATTGCATGTAGAACAACTC
*
36245335 ATTAATTGTCGTTCCA-TGCATGTAGAACAACATC
1 TTTAATTGTCG-TCCATTGCATGTAGAACAAC-TC
36245369 TTTAAT
1 TTTAAT
36245375 GCATGTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (33 bp):
TTTAATTGTCGTCCATTGCATGTAGAACAACTC
Found at i:36246459 original size:20 final size:20
Alignment explanation
Indices: 36246436--36246482 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36246426 GGGTTAAGAT
36246436 TGAGCTGAATTGAGCAT-GAG
1 TGAGCTGAATTGAGC-TCGAG
* *
36246456 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
36246476 TGAGCTG
1 TGAGCTG
36246483 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:36249914 original size:20 final size:20
Alignment explanation
Indices: 36249889--36249935 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
36249879 AGATCGTTTC
36249889 CAGCTCACTCGAGCTC-ATGT
1 CAGCTCACTCGAGCTCAAT-T
*
36249909 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAATT
36249929 CAGCTCA
1 CAGCTCA
36249936 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAATT
Found at i:36252395 original size:14 final size:13
Alignment explanation
Indices: 36252377--36252410 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
36252367 ATAGTGAGTG
36252377 AAAAAGAAAATGA
1 AAAAAGAAAATGA
*
36252390 AGAAAAGAAAATTA
1 A-AAAAGAAAATGA
36252404 AAAAAGA
1 AAAAAGA
36252411 GAGTGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:36252491 original size:12 final size:12
Alignment explanation
Indices: 36252474--36252498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36252464 AAGAGAGAGG
36252474 GTTTGAAAAAGA
1 GTTTGAAAAAGA
36252486 GTTTGAAAAAGA
1 GTTTGAAAAAGA
36252498 G
1 G
36252499 AAGAGTGAAA
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:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (12 bp):
GTTTGAAAAAGA
Found at i:36254039 original size:20 final size:20
Alignment explanation
Indices: 36254014--36254060 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
36254004 AGATCGTTTC
36254014 CAGCTCACTCGAGCTC-ATGT
1 CAGCTCACTCGAGCTCAAT-T
*
36254034 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAATT
36254054 CAGCTCA
1 CAGCTCA
36254061 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAATT
Found at i:36254217 original size:20 final size:21
Alignment explanation
Indices: 36254182--36254220 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
36254172 CAGCTCGTTG
36254182 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
36254203 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
36254221 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:36254849 original size:13 final size:13
Alignment explanation
Indices: 36254831--36254855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36254821 GTATTGATCA
36254831 TGTGTTCACACCT
1 TGTGTTCACACCT
36254844 TGTGTTCACACC
1 TGTGTTCACACC
36254856 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:36258835 original size:16 final size:16
Alignment explanation
Indices: 36258814--36258851 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
36258804 AAAAAAAATC
36258814 AAAAAAAATTGATTGA
1 AAAAAAAATTGATTGA
36258830 AAAAAAAATTGATTGA
1 AAAAAAAATTGATTGA
36258846 AAAAAA
1 AAAAAA
36258852 TTCCAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (16 bp):
AAAAAAAATTGATTGA
Found at i:36263710 original size:28 final size:26
Alignment explanation
Indices: 36263653--36263710 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
36263643 TTGGAGTAAC
* **
36263653 AAAAAAAATCAAAAAAAAATTGATTGA
1 AAAAAAAATCAAAAAAAAAGTGA-AAA
*
36263680 AAAAAAATTCCAAAAAAAAAGTGAAAA
1 AAAAAAAAT-CAAAAAAAAAGTGAAAA
36263707 AAAA
1 AAAA
36263711 TCGAGCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.14
Consensus pattern (26 bp):
AAAAAAAATCAAAAAAAAAGTGAAAA
Found at i:36268878 original size:18 final size:17
Alignment explanation
Indices: 36268819--36268879 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
36268809 GCACTCTTTC
*
36268819 TTTTCTTTCTCCAATATTT
1 TTTTCTTT-TTCAAT-TTT
*
36268838 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
*
36268855 TGTTTCTTTTTCGATTTCT
1 T-TTTCTTTTTCAATTT-T
36268874 TTTTCT
1 TTTTCT
36268880 CTCGTCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 23 0.64
19 9 0.25
ACGTcount: A:0.10, C:0.18, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:36269827 original size:14 final size:14
Alignment explanation
Indices: 36269808--36269835 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36269798 TAGCTTCTTC
36269808 TTTTTTTTCACGAA
1 TTTTTTTTCACGAA
36269822 TTTTTTTTCACGAA
1 TTTTTTTTCACGAA
36269836 ATCTTTTTAA
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:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTTTTTCACGAA
Found at i:36269842 original size:15 final size:14
Alignment explanation
Indices: 36269810--36269843 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36269800 GCTTCTTCTT
*
36269810 TTTTTTCACGAATT
1 TTTTTTCACGAATC
36269824 TTTTTTCACGAAATC
1 TTTTTTCACG-AATC
36269839 TTTTT
1 TTTTT
36269844 AACTTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (14 bp):
TTTTTTCACGAATC
Found at i:36272996 original size:30 final size:30
Alignment explanation
Indices: 36272962--36273058 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
36272952 AGCTCACTCC
36272962 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
36272992 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
36273022 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
36273052 TAGCTCA
1 TAGCTCA
36273059 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:36278296 original size:20 final size:20
Alignment explanation
Indices: 36278273--36278318 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
36278263 GGGTTAAGAT
*
36278273 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
36278293 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
36278313 TGAGCT
1 TGAGCT
36278319 AGAAACAAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:36283573 original size:31 final size:31
Alignment explanation
Indices: 36283530--36283618 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 31
36283520 ATTGGGTAGT
* *
36283530 TTTATGTGTGAACAATCAGCAATGAAGAGTC
1 TTTAGGTGTGAACAATCAGCAATGAAGAGCC
*
36283561 TTTAGGTGTGAACAATTAGCAATGAAGAGCC
1 TTTAGGTGTGAACAATCAGCAATGAAGAGCC
* *
36283592 TCTAGGTGTTAACAATCAGCAATGAAG
1 TTTAGGTGTGAACAATCAGCAATGAAG
36283619 GGACTTGGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (31 bp):
TTTAGGTGTGAACAATCAGCAATGAAGAGCC
Found at i:36284024 original size:46 final size:46
Alignment explanation
Indices: 36283949--36284056 Score: 153
Period size: 46 Copynumber: 2.3 Consensus size: 46
36283939 CTATAAACAA
* * * *
36283949 ACAAATTAAATGAATTTAAGACAACTTAAATTGCTATAATAATTTAG
1 ACAAATTAAATG-ACTAAAGACAACTTAAATTACTATAATAAATTAG
* *
36283996 ACAAATTAAATGACTAAAGACAACTTAAATTACTGTAGTAAATTAG
1 ACAAATTAAATGACTAAAGACAACTTAAATTACTATAATAAATTAG
36284042 ACAAATTAAATGACT
1 ACAAATTAAATGACT
36284057 TAACTTATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
46 43 0.78
47 12 0.22
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (46 bp):
ACAAATTAAATGACTAAAGACAACTTAAATTACTATAATAAATTAG
Found at i:36288892 original size:27 final size:27
Alignment explanation
Indices: 36288862--36289039 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
36288852 ATATTGAGCC
* *
36288862 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
36288889 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
36288916 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
36288944 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
36288971 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
36288998 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
36289025 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
36289040 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:36288974 original size:55 final size:54
Alignment explanation
Indices: 36288862--36289039 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
36288852 ATATTGAGCC
* * * * *
36288862 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
36288916 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
36288971 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
36289025 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
36289040 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:36312102 original size:29 final size:29
Alignment explanation
Indices: 36312039--36312106 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
36312029 TAATCAACCG
*
36312039 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
36312068 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
36312097 CGCACACTTA
1 CGCACACTTA
36312107 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:36312276 original size:29 final size:29
Alignment explanation
Indices: 36312213--36312280 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
36312203 TAATCAACCG
36312213 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
36312242 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
36312271 CGCACACTTA
1 CGCACACTTA
36312281 CCATTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:36312450 original size:29 final size:29
Alignment explanation
Indices: 36312387--36312454 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
36312377 TAATCAACCG
36312387 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
36312416 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
36312445 CGCACACTTA
1 CGCACACTTA
36312455 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:36312595 original size:29 final size:30
Alignment explanation
Indices: 36312556--36312634 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
36312546 CTTAATAATC
36312556 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
36312586 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
36312615 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
36312635 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:36312628 original size:174 final size:174
Alignment explanation
Indices: 36311928--36312603 Score: 1262
Period size: 174 Copynumber: 3.9 Consensus size: 174
36311918 AACTCAAGGT
* *
36311928 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* * *
36311993 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
36312058 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
36312102 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
36312167 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
36312232 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
36312276 ACTTACCATTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
36312341 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
36312406 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
36312450 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAGTAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
36312515 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
*
36312580 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
36312604 TGTACAATTT
Statistics
Matches: 491, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 491 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:36320076 original size:29 final size:29
Alignment explanation
Indices: 36320013--36320080 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
36320003 TAATCAACCG
*
36320013 CGCACACTTAGTGCCACGTCCTTTAAACT
1 CGCACACTTAGTGCCACGTCATTTAAACT
* * **
36320042 CACACACTTAGTGCCATG-CATTTCAAGTT
1 CGCACACTTAGTGCCACGTCATTT-AAACT
36320071 CGCACACTTA
1 CGCACACTTA
36320081 CCTTTTCCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCACGTCATTTAAACT
Found at i:36320250 original size:29 final size:29
Alignment explanation
Indices: 36320187--36320254 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
36320177 TAATCAACCG
36320187 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
36320216 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
36320245 CGCACACTTA
1 CGCACACTTA
36320255 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:36320424 original size:29 final size:29
Alignment explanation
Indices: 36320361--36320428 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
36320351 TAATCAACCG
36320361 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
36320390 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
36320419 CGCACACTTA
1 CGCACACTTA
36320429 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:36320569 original size:29 final size:30
Alignment explanation
Indices: 36320530--36320608 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
36320520 CTTAATAATC
36320530 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
36320560 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
36320589 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
36320609 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:36320602 original size:174 final size:174
Alignment explanation
Indices: 36319903--36320577 Score: 1246
Period size: 174 Copynumber: 3.9 Consensus size: 174
36319893 AACTCAAGGT
* *
36319903 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* * *
36319968 G-AAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCACGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATG-
36320032 C-CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
130 CACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
36320076 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
36320141 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
36320206 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
36320250 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
36320315 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
36320380 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
36320424 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAGTAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
36320489 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
*
36320554 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
36320578 TGTACAATTT
Statistics
Matches: 491, Mismatches: 9, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
173 65 0.13
174 426 0.87
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:36327397 original size:131 final size:131
Alignment explanation
Indices: 36327163--36327425 Score: 517
Period size: 131 Copynumber: 2.0 Consensus size: 131
36327153 AAACAAAGGT
36327163 ATCAATAATTATTTTGTGGTATCGATATTTTATGAGAAAGTATCGATACTTAAATAAAAATCAAT
1 ATCAATAATTATTTTGTGGTATCGATATTTTATGAGAAAGTATCGATACTTAAATAAAAATCAAT
*
36327228 ACCATTTTGATATTCTATTTATTTTAAGACTGTACATAATAACAAGTATCAATACCAATGCCAAA
66 ACCATTTTGATATTCTATTTATTTTAAGACTATACATAATAACAAGTATCAATACCAATGCCAAA
36327293 A
131 A
36327294 ATCAATAATTATTTTGTGGTATCGATATTTTATGAGAAAGTATCGATACTTAAATAAAAATCAAT
1 ATCAATAATTATTTTGTGGTATCGATATTTTATGAGAAAGTATCGATACTTAAATAAAAATCAAT
36327359 ACCATTTTGATATTCTATTTATTTTAAGACTATACATAATAACAAGTATCAATACCAATGCCAAA
66 ACCATTTTGATATTCTATTTATTTTAAGACTATACATAATAACAAGTATCAATACCAATGCCAAA
36327424 A
131 A
36327425 A
1 A
36327426 CATCGATACA
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 131 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (131 bp):
ATCAATAATTATTTTGTGGTATCGATATTTTATGAGAAAGTATCGATACTTAAATAAAAATCAAT
ACCATTTTGATATTCTATTTATTTTAAGACTATACATAATAACAAGTATCAATACCAATGCCAAA
A
Found at i:36333378 original size:19 final size:18
Alignment explanation
Indices: 36333342--36333389 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
36333332 AATTCACATC
**
36333342 TCATTTCATCATTTCATATT
1 TCATTTC-TCATCCCATA-T
36333362 TCATTTCTCATCCCATAT
1 TCATTTCTCATCCCATAT
36333380 TCATTTCTCA
1 TCATTTCTCA
36333390 ACTTTGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
19 8 0.31
20 7 0.27
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (18 bp):
TCATTTCTCATCCCATAT
Found at i:36334134 original size:20 final size:20
Alignment explanation
Indices: 36334096--36334134 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36334086 TTACACAATT
*
36334096 CAATTTTCACATTAAATTTC
1 CAATTTTCACACTAAATTTC
* *
36334116 CAATTTTTACACTATATTT
1 CAATTTTCACACTAAATTT
36334135 GCATAAACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (20 bp):
CAATTTTCACACTAAATTTC
Found at i:36336303 original size:43 final size:43
Alignment explanation
Indices: 36336256--36336497 Score: 281
Period size: 43 Copynumber: 5.6 Consensus size: 43
36336246 AATTAAACTA
** *
36336256 GCACACACAGTGCATCATCAAATAATACTAAAGCAACATACTG
1 GCACACACAGTGCATCATCGGATAATACTGAAGCAACATACTG
* * *
36336299 GCACACATAGTGCATCATCGGATAA-AATCGAAGCAACATACTA
1 GCACACACAGTGCATCATCGGATAATACT-GAAGCAACATACTG
* * * * * * *
36336342 CCACACATAGTGCATCATCGAATAA-AATCAAAGAAACATACTA
1 GCACACACAGTGCATCATCGGATAATACT-GAAGCAACATACTG
* *
36336385 GCACACACAGTGTATCATCGGATAATACCGAAGCAACATACTG
1 GCACACACAGTGCATCATCGGATAATACTGAAGCAACATACTG
* *
36336428 GCACACACAGTGCATCATCGGATAATACCGAAGCGACATACTG
1 GCACACACAGTGCATCATCGGATAATACTGAAGCAACATACTG
* *
36336471 GCAGACATAGTGCATCATCGGATAATA
1 GCACACACAGTGCATCATCGGATAATA
36336498 TCAAAGTATA
Statistics
Matches: 174, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
42 2 0.01
43 171 0.98
44 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (43 bp):
GCACACACAGTGCATCATCGGATAATACTGAAGCAACATACTG
Found at i:36336410 original size:129 final size:129
Alignment explanation
Indices: 36336252--36336503 Score: 378
Period size: 129 Copynumber: 2.0 Consensus size: 129
36336242 ACGCAATTAA
* *
36336252 ACTAGCACACACAGTGCATCATCAAATAATACTAAAGCAACATACTGGCACACATAGTGCATCAT
1 ACTAGCACACACAGTGCATCATCAAATAATACCAAAGCAACATACTGGCACACACAGTGCATCAT
*
36336317 CGGATAAAATCGAAGCAACATACTACCACACATAGTGCATCATCGAATAAAATCAAAGAAACAT
66 CGGATAAAACCGAAGCAACATACTACCACACATAGTGCATCATCGAATAAAATCAAAGAAACAT
* ** *
36336381 ACTAGCACACACAGTGTATCATCGGATAATACCGAAGCAACATACTGGCACACACAGTGCATCAT
1 ACTAGCACACACAGTGCATCATCAAATAATACCAAAGCAACATACTGGCACACACAGTGCATCAT
* * ** * * *
36336446 CGGATAATACCGAAGCGACATACTGGCAGACATAGTGCATCATCGGATAATATCAAAG
66 CGGATAAAACCGAAGCAACATACTACCACACATAGTGCATCATCGAATAAAATCAAAG
36336504 TATAACTTGC
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
129 109 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (129 bp):
ACTAGCACACACAGTGCATCATCAAATAATACCAAAGCAACATACTGGCACACACAGTGCATCAT
CGGATAAAACCGAAGCAACATACTACCACACATAGTGCATCATCGAATAAAATCAAAGAAACAT
Found at i:36336496 original size:86 final size:86
Alignment explanation
Indices: 36336252--36336497 Score: 339
Period size: 86 Copynumber: 2.9 Consensus size: 86
36336242 ACGCAATTAA
* *
36336252 ACTAGCACACACAGTGCATCATCAAATAATACTAAAGCAACATACTGGCACACATAGTGCATCAT
1 ACTAGCACACACAGTGCATCATCGAATAATACCAAAGCAACATACTGGCACACATAGTGCATCAT
* *
36336317 CGGATAAAATCGAAGCAACAT
66 CGGATAATACCGAAGCAACAT
* * * * * * * *
36336338 ACTACCACACATAGTGCATCATCGAATAAAATCAAAGAAACATACTAGCACACACAGTGTATCAT
1 ACTAGCACACACAGTGCATCATCGAATAATACCAAAGCAACATACTGGCACACATAGTGCATCAT
36336403 CGGATAATACCGAAGCAACAT
66 CGGATAATACCGAAGCAACAT
* * * * *
36336424 ACTGGCACACACAGTGCATCATCGGATAATACCGAAGCGACATACTGGCAGACATAGTGCATCAT
1 ACTAGCACACACAGTGCATCATCGAATAATACCAAAGCAACATACTGGCACACATAGTGCATCAT
36336489 CGGATAATA
66 CGGATAATA
36336498 TCAAAGTATA
Statistics
Matches: 135, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 135 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (86 bp):
ACTAGCACACACAGTGCATCATCGAATAATACCAAAGCAACATACTGGCACACATAGTGCATCAT
CGGATAATACCGAAGCAACAT
Found at i:36340776 original size:27 final size:27
Alignment explanation
Indices: 36340746--36340923 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
36340736 ATATTGAGTC
* * * *
36340746 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
36340773 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
36340800 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
36340828 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
36340855 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
36340882 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
36340909 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
36340924 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:36340885 original size:82 final size:81
Alignment explanation
Indices: 36340767--36340922 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
36340757 TGCTATATAA
* *
36340767 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
36340832 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
36340849 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
36340913 CACTTAGTGC
65 CACTTAGTGC
36340923 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:36348966 original size:27 final size:27
Alignment explanation
Indices: 36348936--36349113 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
36348926 ATATTGAGTC
* * * *
36348936 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
36348963 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
36348990 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
36349018 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
36349045 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
36349072 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
36349099 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
36349114 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:36349075 original size:82 final size:81
Alignment explanation
Indices: 36348957--36349112 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
36348947 TGCTATATAA
* *
36348957 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
36349022 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
36349039 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
36349103 CACTTAGTGC
65 CACTTAGTGC
36349113 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:36362334 original size:20 final size:20
Alignment explanation
Indices: 36362311--36362364 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
36362301 AGTTTTTCCC
*
36362311 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
36362331 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
36362351 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
36362365 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:36362346 original size:30 final size:30
Alignment explanation
Indices: 36362311--36362384 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
36362301 AGTTTTTCCC
36362311 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
36362341 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
36362371 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
36362385 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:36362374 original size:20 final size:20
Alignment explanation
Indices: 36362311--36362375 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
36362301 AGTTTTTCCC
* * * *
36362311 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
36362331 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
36362350 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
36362371 AGCTC
1 AGCTC
36362376 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:36364022 original size:13 final size:13
Alignment explanation
Indices: 36364006--36364039 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
36363996 AAATTGATTG
*
36364006 AAAAAAAAATTCA
1 AAAAAAAAAGTCA
*
36364019 AAAAAAAAAGTGA
1 AAAAAAAAAGTCA
36364032 AAAAAAAA
1 AAAAAAAA
36364040 TCGAGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAGTCA
Done.