Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008506.1 Hibiscus syriacus cultivar Beakdansim tig00111358_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1253200
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 6
Found at i:225023 original size:15 final size:16
Alignment explanation
Indices: 225004--225051 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
224994 TTATATAGTT
225004 TTAATATTAAATATTA
1 TTAATATTAAATATTA
* *
225020 -TAATAGTATTAATAATA
1 TTAATA-T-TAAATATTA
225037 TTAATATTAAATATT
1 TTAATATTAAATATT
225052 TAGTATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
17 8 0.32
18 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TTAATATTAAATATTA
Found at i:225029 original size:18 final size:18
Alignment explanation
Indices: 225005--225051 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 18
224995 TATATAGTTT
225005 TAATATTAAATATTATAA
1 TAATATTAAATATTATAA
* *
225023 TAGTATT-AATA--ATAT
1 TAATATTAAATATTATAA
225038 TAATATTAAATATT
1 TAATATTAAATATT
225052 TAGTATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
15 9 0.39
16 4 0.17
17 4 0.17
18 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAATATTAAATATTATAA
Found at i:229098 original size:18 final size:16
Alignment explanation
Indices: 229075--229118 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 16
229065 TTAAAAAATT
229075 AAAAATTATTATTTATAA
1 AAAAATTATT-TTT-TAA
229093 AAAAATCTTATTTTTTAA
1 AAAAA--TTATTTTTTAA
229111 AAAAATTA
1 AAAAATTA
229119 AAAAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.12
18 13 0.54
19 3 0.12
20 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAAATTATTTTTTAA
Found at i:231316 original size:2 final size:2
Alignment explanation
Indices: 231309--231336 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
231299 TACTCTAATC
231309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
231337 TCTTTCCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:241491 original size:15 final size:15
Alignment explanation
Indices: 241458--241565 Score: 105
Period size: 14 Copynumber: 7.1 Consensus size: 15
241448 TTCCAAAAAT
241458 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
*
241473 -TAATTCAATTTCCA
1 GTAATTCATTTTCCA
241487 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
* *
241502 -AAATTCAATTTCCAAAAA
1 GTAATTCATTTTCC----A
241520 TGTAATTCATTTTCCA
1 -GTAATTCATTTTCCA
241536 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
* *
241551 -AAATTCAATTTCCA
1 GTAATTCATTTTCCA
241565 G
1 G
241566 AAAACCAATT
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
14 36 0.47
15 28 0.36
16 1 0.01
18 1 0.01
20 11 0.14
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:241500 original size:29 final size:29
Alignment explanation
Indices: 241458--241564 Score: 117
Period size: 29 Copynumber: 3.5 Consensus size: 29
241448 TTCCAAAAAT
241458 GTAATTCATTTTCCATAATTCAATTTCCA
1 GTAATTCATTTTCCATAATTCAATTTCCA
*
241487 GTAATTCATTTTCCAAAATTCAATTTCCAAAAA
1 GTAATTCATTTTCCATAATTCAATTTCC----A
*
241520 TGTAATTCATTTTCCAGTAATTCATTTTCCA
1 -GTAATTCATTTTCCA-TAATTCAATTTCCA
* *
241551 -AAATTCAATTTCCA
1 GTAATTCATTTTCCA
241565 GAAAACCAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
29 39 0.58
31 1 0.01
33 1 0.01
34 15 0.22
35 11 0.16
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.42
Consensus pattern (29 bp):
GTAATTCATTTTCCATAATTCAATTTCCA
Found at i:241526 original size:49 final size:50
Alignment explanation
Indices: 241473--241569 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 50
241463 TCATTTTCCA
241473 TAATTCAATTTCCAGTAATTCATTTTCCAAAATTCAATTTCCA-AAAATG
1 TAATTCAATTTCCAGTAATTCATTTTCCAAAATTCAATTTCCAGAAAATG
*
241522 TAATTCATTTTCCAGTAATTCATTTTCCAAAATTCAATTTCCAGAAAA
1 TAATTCAATTTCCAGTAATTCATTTTCCAAAATTCAATTTCCAGAAAA
241570 CCAATTACAG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 42 0.91
50 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (50 bp):
TAATTCAATTTCCAGTAATTCATTTTCCAAAATTCAATTTCCAGAAAATG
Found at i:242961 original size:16 final size:17
Alignment explanation
Indices: 242940--242987 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
242930 AATTAAATTT
242940 GGGTTG-TTTTCGGTTC
1 GGGTTGATTTTCGGTTC
*
242956 GGGTTGCTTTTCGGTTC
1 GGGTTGATTTTCGGTTC
*
242973 GAGTTGATTTT-GGTT
1 GGGTTGATTTTCGGTT
242988 AAAATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.04, C:0.10, G:0.35, T:0.50
Consensus pattern (17 bp):
GGGTTGATTTTCGGTTC
Found at i:244606 original size:318 final size:316
Alignment explanation
Indices: 243909--244543 Score: 873
Period size: 318 Copynumber: 2.0 Consensus size: 316
243899 TACATGCTCC
* * * * * * *
243909 TAAACCTTCGTAGAATACATATGTACTTTCAATTC-TTATTTTTGATAATATATTTTCTATTTTT
1 TAAACCATCGAAGAGTAAATATATACTTTCAATTCATCA-TTTTGATAATAAATTTTCTATTTTT
* * *
243973 CAATTTAGTCCCTTAATTTTTCATAATTTTCGTATTTATTCAATTCATTCTTTATTTTAAGTCTT
65 CAATTTAGTCCCTCAATTTTTCATAATTTTCGTATTTATTCAATTAATACTTTATTTTAAGTCTT
* * *
244038 TTTTTACCAAATTTAAATCACATGCTCATATACACAATAAAATGCCTATGTAACTTCAATTTTTT
130 TTTTTACCAAATTTAAACCACATGCTCATATACACAATAAAATACCTATGTAACTTCAATTTATT
* * *
244103 ACTTTTTTACAAAAAAATGTACTCTCTTTTTTATTTAGTCCCTTAACTTTGCATTTTACTCAATT
195 ACTTTTTTACAAAAAAATGTACTCTCTTTTTTAGTTAGTCACTTAACTTTGCATTTTACTCAATC
* * * *
244168 TGATATTTTGACTACAGTTGTTTACAAATTCTTTCTTCCCATCAGTTCCTTGACTCT
260 TGATATTTTGACTACAATTGTTTACAAATTCTTTCTTCCCAGCAATTCATTGACTCT
* * * * *
244225 TAAACCATCGTAGAGTACATATGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTC
1 TAAACCATCGAAGAGTAAATATATACTTTCAATTCATCATTTTGATAATAAATTTTCTATTTTTC
* * *
244290 AATTTAGTCCCTCAATTTTTCATAATTTTCTTATTTTTTCAATTAATACTTTCTTTTAAGTCTTT
66 AATTTAGTCCCTCAATTTTTCATAATTTTCGTATTTATTCAATTAATACTTTATTTTAAGTCTTT
* *
244355 TATTTACCAAATTTGAACCACATGCTCATATACCACAATAGAATACCTATGTAACTTCAA-TTAT
131 T-TTTACCAAATTTAAACCACATGCTCATATA-CACAATAAAATACCTATGTAACTTCAATTTAT
* *
244419 TACTTTTTTTTAC-TAAAATTGTACTCTCTTTTTTAGTTAG-CTACTTAACTTTGCATTTTACTC
194 TAC--TTTTTTACAAAAAAATGTACTCTCTTTTTTAGTTAGTC-ACTTAACTTTGCATTTTACTC
* * *
244482 AATCTGATCTTTTGACTACAATTGTTTGCTAATTCTTTCTTCCCAGCAATTCATTGACTCT
256 AATCTGATATTTTGACTACAATTGTTTACAAATTCTTTCTTCCCAGCAATTCATTGACTCT
244543 T
1 T
244544 TTATACTCTC
Statistics
Matches: 285, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
316 118 0.41
317 36 0.13
318 123 0.43
319 8 0.03
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (316 bp):
TAAACCATCGAAGAGTAAATATATACTTTCAATTCATCATTTTGATAATAAATTTTCTATTTTTC
AATTTAGTCCCTCAATTTTTCATAATTTTCGTATTTATTCAATTAATACTTTATTTTAAGTCTTT
TTTTACCAAATTTAAACCACATGCTCATATACACAATAAAATACCTATGTAACTTCAATTTATTA
CTTTTTTACAAAAAAATGTACTCTCTTTTTTAGTTAGTCACTTAACTTTGCATTTTACTCAATCT
GATATTTTGACTACAATTGTTTACAAATTCTTTCTTCCCAGCAATTCATTGACTCT
Found at i:249718 original size:41 final size:41
Alignment explanation
Indices: 249673--249763 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
249663 ACAAATAAGG
*
249673 GCAAAAATGTTTTTGGACCAAATTGAATTTGTTCAAACATT
1 GCAAAAATATTTTTGGACCAAATTGAATTTGTTCAAACATT
249714 GCAAAAATATTTTTGGACCAAATTGAATTTGTTCAAACATT
1 GCAAAAATATTTTTGGACCAAATTGAATTTGTTCAAACATT
249755 GCAAAAATA
1 GCAAAAATA
249764 ATTGAAAGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (41 bp):
GCAAAAATATTTTTGGACCAAATTGAATTTGTTCAAACATT
Found at i:251804 original size:3 final size:3
Alignment explanation
Indices: 251796--251857 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
251786 GTTTGTAGTA
251796 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
251843 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
251858 GGTTGAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:252641 original size:34 final size:34
Alignment explanation
Indices: 252580--252678 Score: 87
Period size: 34 Copynumber: 2.9 Consensus size: 34
252570 ATTAAAATAA
* * * *
252580 TATTTGTTTAAGTTTGAATAATAAAAAGAGT-GTA-
1 TATTTATTTAAATTTAAAT-ATTAAAAGA-TAGTAT
*
252614 TATTTATTTAATATTTTAAAT-TTAAAAGATATTAT
1 TATTTATTTAA-A-TTTAAATATTAAAAGATAGTAT
*
252649 TATTTATTTAAATTTAGATATTAAAAGATA
1 TATTTATTTAAATTTAAATATTAAAAGATA
252679 TTTGGTTGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
33 7 0.13
34 30 0.56
35 11 0.20
36 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.47
Consensus pattern (34 bp):
TATTTATTTAAATTTAAATATTAAAAGATAGTAT
Found at i:252679 original size:34 final size:35
Alignment explanation
Indices: 252614--252680 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
252604 AAAGAGTGTA
252614 TATTTATTTAATATTTTAAATTTAAAAGATATTAT
1 TATTTATTTAATATTTTAAATTTAAAAGATATTAT
*
252649 TATTTATTTAA-A-TTTAGATATTAAAAGATATT
1 TATTTATTTAATATTTTAAAT-TTAAAAGATATT
252681 TGGTTGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 6 0.20
34 13 0.43
35 11 0.37
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (35 bp):
TATTTATTTAATATTTTAAATTTAAAAGATATTAT
Found at i:252789 original size:20 final size:21
Alignment explanation
Indices: 252764--252814 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
252754 ATTCAAGAAC
252764 TTTTCTTCT-CTTAAAAAATA
1 TTTTCTTCTCCTTAAAAAATA
*
252784 TTTTC-TCTCCTTAGAAAATA
1 TTTTCTTCTCCTTAAAAAATA
*
252804 TTATCTT-TCCT
1 TTTTCTTCTCCT
252815 CCTTAGCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTCTTCTCCTTAAAAAATA
Found at i:261768 original size:17 final size:18
Alignment explanation
Indices: 261729--261768 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
261719 TTATTTTATT
261729 ATTTTTATTTTTTCATAC
1 ATTTTTATTTTTTCATAC
261747 A-TTTTATTTTGTTC-TA-
1 ATTTTTATTTT-TTCATAC
261763 ATTTTT
1 ATTTTT
261769 GTTATTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (18 bp):
ATTTTTATTTTTTCATAC
Found at i:266036 original size:7 final size:7
Alignment explanation
Indices: 266022--266071 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
266012 AAAAGAAAAG
266022 AAAA-GA
1 AAAATGA
266028 AAAATGA
1 AAAATGA
266035 AAAA-GA
1 AAAATGA
266041 AAAGATGA
1 AAA-ATGA
*
266049 AAGATGA
1 AAAATGA
*
266056 AAGATGA
1 AAAATGA
266063 AAAA-GA
1 AAAATGA
266069 AAA
1 AAA
266072 GAAAAAGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 14 0.36
7 21 0.54
8 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (7 bp):
AAAATGA
Found at i:266050 original size:14 final size:14
Alignment explanation
Indices: 266022--266073 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
266012 AAAAGAAAAG
266022 AAAAGAAAA-ATGA
1 AAAAGAAAAGATGA
266035 AAAAGAAAAGATGA
1 AAAAGAAAAGATGA
*
266049 AAGATG-AAAGATGA
1 AA-AAGAAAAGATGA
266063 AAAAGAAAAGA
1 AAAAGAAAAGA
266074 AAAAGAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 11 0.32
14 21 0.62
15 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (14 bp):
AAAAGAAAAGATGA
Found at i:266057 original size:28 final size:27
Alignment explanation
Indices: 266012--266086 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
266002 AACAGAATAA
*
266012 AAAAGAAAAGAAAAGAAAAATGAAAAAG
1 AAAAGAAAA-AGAAGAAAAATGAAAAAG
* * *
266040 AAAAGATGAAAGATGAAAGATGAAAAAG
1 AAAAGA-AAAAGAAGAAAAATGAAAAAG
266068 AAAAGAAAAAGAAGAAAAA
1 AAAAGAAAAAGAAGAAAAA
266087 AATTTGAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 10 0.26
28 27 0.69
29 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (27 bp):
AAAAGAAAAAGAAGAAAAATGAAAAAG
Found at i:266088 original size:11 final size:11
Alignment explanation
Indices: 266011--266080 Score: 61
Period size: 11 Copynumber: 5.7 Consensus size: 11
266001 CAACAGAATA
266011 AAAAAGAAAAG
1 AAAAAGAAAAG
266022 -AAAAGAAAAATG
1 AAAAAG-AAAA-G
266034 AAAAAGAAAAG
1 AAAAAGAAAAG
266045 ATGAAAGATGAAAGATG
1 A--AAA-A-GAAA-A-G
266062 AAAAAGAAAAG
1 AAAAAGAAAAG
266073 AAAAAGAA
1 AAAAAGAA
266081 GAAAAAAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
10 5 0.10
11 15 0.30
12 6 0.12
13 12 0.24
14 2 0.04
15 7 0.14
16 1 0.02
17 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:269277 original size:42 final size:42
Alignment explanation
Indices: 269170--269283 Score: 174
Period size: 42 Copynumber: 2.7 Consensus size: 42
269160 CCCGAATTTG
* *
269170 TAAATCTTTCGGGTCATCAATAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCT
* *
269212 TAAATCCTTCGGGTCATCAGTAAGTCTTTTGAGCATGATGGT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCT
* *
269254 TAAATCCTTCGGGTCATCTGTAAGCCTTTC
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTC
269284 AAGAAATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCT
Found at i:269505 original size:22 final size:21
Alignment explanation
Indices: 269477--269547 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
269467 CATCAGTAAG
269477 TCTTTCGAGCATGATGTTTAAA
1 TCTTTCGAGCATGATG-TTAAA
* * *
269499 TCTTTCGGGTCATCA-G-TAAG
1 TCTTTCGAG-CATGATGTTAAA
269519 TCTTTCGAGCATGATGCTTAAA
1 TCTTTCGAGCATGATG-TTAAA
*
269541 TCCTTCG
1 TCTTTCG
269548 GGTCATCTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
22 18 0.47
23 4 0.11
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (21 bp):
TCTTTCGAGCATGATGTTAAA
Found at i:269510 original size:42 final size:42
Alignment explanation
Indices: 269458--269569 Score: 181
Period size: 42 Copynumber: 2.7 Consensus size: 42
269448 ATTTGTAGGT
*
269458 TCTTT-GGGTCATCAGTAAGTCTTTCGAGCATGATGTTTAAA
1 TCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
269499 TCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
* * *
269541 TCCTTCGGGTCATCTGTAAGCCTTTCGAG
1 TCTTTCGGGTCATCAGTAAGTCTTTCGAG
269570 TAATATGATA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 5 0.08
42 61 0.92
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (42 bp):
TCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
Found at i:269524 original size:20 final size:20
Alignment explanation
Indices: 269458--269525 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
269448 ATTTGTAGGT
269458 TCTTT-GGGTCATCAGTAAG
1 TCTTTCGGGTCATCAGTAAG
* * *
269477 TCTTTCGAG-CATGATGTTTAAA
1 TCTTTCGGGTCATCA-G--TAAG
269499 TCTTTCGGGTCATCAGTAAG
1 TCTTTCGGGTCATCAGTAAG
269519 TCTTTCG
1 TCTTTCG
269526 AGCATGATGC
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 9 0.24
20 13 0.34
22 12 0.32
23 4 0.11
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
TCTTTCGGGTCATCAGTAAG
Found at i:269690 original size:303 final size:303
Alignment explanation
Indices: 269294--270156 Score: 1333
Period size: 304 Copynumber: 2.8 Consensus size: 303
269284 AAGAAATATA
*
269294 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAATTAAGCCTATTTTAGGGGTTT
1 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
* *
269359 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTT-CTTAACAACTAAT
66 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACTAAA
* *
269423 AAACTAAGTTTTCGAGGGTTTCTTGATTTGTAGGTTCTTTGGGTCATCAGTAAGTCTTTCGAGCA
131 AAACTAAGTTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGG-CATCAGTAAGTCTTTCGAGCA
269488 TGATGTTTAAATCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
195 TGATGTTTAAATCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
* *
269553 TCTGTAAGCCTTTCGAGTAATATGAT-AAGACCTTCGGGCCATCC
260 TCTGTAAGCCTTTCGAGCAAGATGATAAAG-CCTTCGGGCCATCC
*
269597 ATAAGACCTTCAGCGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
1 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
* *
269662 CTTAATTATCTCAAAAGAGTTATTAAAGGAAGCTATGCCTTTTAAGGGGTTCCTTGACAACTAAA
66 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACTAAA
*
269727 AAACTAAGCTTTT-GAGGGTTTCTTGATTTGTAAGTTCTTCGGGCTATCTGTAAGTCTTTCGAGC
131 AAACTAAG-TTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGGC-ATCAGTAAGTCTTTCGAGC
* * * **
269791 ATGATATTTAAATCCTTT-GGGTCATTAGTAAGTCTTTCAAGCATGATGCTTAAATTTTTCGGGT
194 ATGATGTTTAAAT-CTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
* *
269855 TATCTGTAAGCCTTTCGAGCAAGATGATAAAGCCTTCGGGTCATCC
258 CATCTGTAAGCCTTTCGAGCAAGATGATAAAGCCTTCGGGCCATCC
* *
269901 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGTCTGTTTTAGGGGTTT
1 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
*
269966 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGC-ATAGCCTTTTAAGGGGTTCCTTGACAATTAA
66 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTA-AGCCTTTTAAGGGGTTCCTTGACAACTAA
* * * * *
270030 GAAACTAAGCTTTCGAGGGTTTCTTGATTTGTAAATCCGTCGGGACATCAGTAAGTCTTTCGAGC
130 AAAACTAAGTTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGG-CATCAGTAAGTCTTTCGAGC
* * * * * *
270095 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG-ATAAGTCCTTCGGG
194 ATGATGTTTAAATCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
270157 CCATTCATAA
Statistics
Matches: 510, Mismatches: 41, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
303 130 0.25
304 368 0.72
305 12 0.02
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (303 bp):
ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTCCTTGACAACTAAA
AAACTAAGTTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGGCATCAGTAAGTCTTTCGAGCAT
GATGTTTAAATCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAT
CTGTAAGCCTTTCGAGCAAGATGATAAAGCCTTCGGGCCATCC
Found at i:269864 original size:42 final size:43
Alignment explanation
Indices: 269764--269880 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 43
269754 TTGTAAGTTC
* **
269764 TTCGGGCTATCTGTAAGTCTTTCGAGCATGATATTTAAATCCT
1 TTCGGGTTATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCT
* * *
269807 TT-GGGTCAT-TAGTAAGTCTTTCAAGCATGATGCTTAAAT-TT
1 TTCGGGTTATCT-GTAAGTCTTTCGAGCATGATGCTTAAATCCT
* *
269848 TTCGGGTTATCTGTAAGCCTTTCGAGCAAGATG
1 TTCGGGTTATCTGTAAGTCTTTCGAGCATGATG
269881 ATAAAGCCTT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
41 4 0.07
42 54 0.89
43 3 0.05
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.38
Consensus pattern (43 bp):
TTCGGGTTATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCT
Found at i:270126 original size:42 final size:41
Alignment explanation
Indices: 270061--270156 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 41
270051 TCTTGATTTG
* * *
270061 TAAATCCGTCGGGACATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGACATCAGTAAGTCTTTCGAGCAAGATG-A
* *
270103 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
1 TAAATCCTTCGGGACATCAGTAAGTCTTTCGAGCAAGATGA
*
270144 TAAGTCCTTCGGG
1 TAAATCCTTCGGG
270157 CCATTCATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 12 0.25
42 36 0.75
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (41 bp):
TAAATCCTTCGGGACATCAGTAAGTCTTTCGAGCAAGATGA
Found at i:270642 original size:3 final size:3
Alignment explanation
Indices: 270634--270677 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
270624 CATTTTTTAT
270634 TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
270678 ATAAATAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:279271 original size:2 final size:2
Alignment explanation
Indices: 279264--279303 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
279254 TTTTCAAATG
279264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
279304 GTTTGCTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:287931 original size:19 final size:18
Alignment explanation
Indices: 287903--287942 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
287893 TTGTTAAAAT
*
287903 TTATAAAATAATTTTTTTA
1 TTATAAAATAA-TGTTTTA
*
287922 TTATAGAATAATGTTTTA
1 TTATAAAATAATGTTTTA
287940 TTA
1 TTA
287943 AGTCCTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATAAAATAATGTTTTA
Found at i:289467 original size:32 final size:26
Alignment explanation
Indices: 289404--289470 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
289394 GTTCAAGCCT
289404 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
289430 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
*
289456 TTTCGAGTTCGAGTT
1 TTTCGAGTTCAAGTT
289471 GAACTTGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (26 bp):
TTTCGAGTTCAAGTTTCAATATTATA
Found at i:289658 original size:10 final size:10
Alignment explanation
Indices: 289626--289659 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
289616 AATTGGCGGT
289626 TTTTTTCCGG
1 TTTTTTCCGG
* *
289636 TTTTTCCCAG
1 TTTTTTCCGG
289646 TTTTTTCCGG
1 TTTTTTCCGG
289656 TTTT
1 TTTT
289660 CAGCCGGTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.03, C:0.21, G:0.15, T:0.62
Consensus pattern (10 bp):
TTTTTTCCGG
Found at i:291793 original size:102 final size:103
Alignment explanation
Indices: 291616--291818 Score: 295
Period size: 102 Copynumber: 2.0 Consensus size: 103
291606 AGAACATATT
* * * * * *
291616 AGCACACACAGTGCTATCATATCAGAATCATAATATGGATACAAAGTGCAATCACATCTGAATTA
1 AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCGGAAATA
*
291681 TACTAGTGTACCTACCGGTAACA-CTACAGTATATCATA
66 TACTAGTGTACCCACCGGTAACATC-ACAGTATATCATA
*
291719 AGCACACACAATGCTATCACATC-GAAATCAT-ATATGCACACAAAGTGCAATCATATCGGAAAT
1 AGCACACACAATGCTATCACATCAG-AATCATAATATGCACACAAAGTGCAATCACATCGGAAAT
291782 ATACTAGTGTACCCACCGGTAACATCACAGTATATCA
65 ATACTAGTGTACCCACCGGTAACATCACAGTATATCA
291819 ATCACTCAAC
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
102 62 0.69
103 28 0.31
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.24
Consensus pattern (103 bp):
AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCGGAAATA
TACTAGTGTACCCACCGGTAACATCACAGTATATCATA
Found at i:294610 original size:23 final size:23
Alignment explanation
Indices: 294584--294667 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
294574 CTCGTATAAA
*
294584 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
294607 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * * *
294630 TACACCGTAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
294653 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
294668 TATAATAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:295672 original size:21 final size:21
Alignment explanation
Indices: 295640--295682 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
295630 TGTTTATTTA
295640 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
*
295661 ATTGA-AGATGCATCTATGCAC
1 ATTGAGAG-TGCATCGATGCAC
295682 A
1 A
295683 CAACCCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:297514 original size:2 final size:2
Alignment explanation
Indices: 297507--297562 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
297497 ATCATCTGAG
297507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
297549 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
297563 TTTAATCCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:299239 original size:23 final size:23
Alignment explanation
Indices: 299213--299304 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
299203 CACCACAGCT
*
299213 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
299236 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * * *
299259 CGTAGAATTACACCGTAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
* * *
299282 CGTAGAATTGCACTGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
299305 TATAATAATG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:300310 original size:21 final size:21
Alignment explanation
Indices: 300278--300320 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
300268 TGTTTGTTTA
300278 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
300299 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
300320 A
1 A
300321 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:301626 original size:23 final size:24
Alignment explanation
Indices: 301600--301660 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
301590 GTTCTGTGAT
* *
301600 GTCCTTCGGGATAAAA-TTATGTG
1 GTCCTTCGGGACAAAACCTATGTG
301623 GTCCTTCGGGACAAAACCTATGTG
1 GTCCTTCGGGACAAAACCTATGTG
301647 GTCCTTCGGGACAA
1 GTCCTTCGGGACAA
301661 TTATGTGGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 15 0.43
24 20 0.57
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (24 bp):
GTCCTTCGGGACAAAACCTATGTG
Found at i:301857 original size:13 final size:13
Alignment explanation
Indices: 301839--301872 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
301829 TTGAAATCCT
301839 TATGAAATGTTTC
1 TATGAAATGTTTC
301852 TATGAAATGTTTC
1 TATGAAATGTTTC
301865 TATGAAAT
1 TATGAAAT
301873 AAATAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (13 bp):
TATGAAATGTTTC
Found at i:305752 original size:18 final size:18
Alignment explanation
Indices: 305725--305763 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
305715 TTGTTAAAAT
*
305725 TTATAAAATAATTTTTTA
1 TTATAAAATAATGTTTTA
*
305743 TTATAGAATAATGTTTTA
1 TTATAAAATAATGTTTTA
305761 TTA
1 TTA
305764 AGTCCTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTATAAAATAATGTTTTA
Found at i:307255 original size:26 final size:26
Alignment explanation
Indices: 307225--307291 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
307215 GTTCAAGCCT
307225 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
*
307251 TTTCGAGTTCAAGGTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
*
307277 TTTCGAGTTCGAGTT
1 TTTCGAGTTCAAGTT
307292 GAACTTGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (26 bp):
TTTCGAGTTCAAGTTTCAATATTATA
Found at i:310283 original size:102 final size:103
Alignment explanation
Indices: 310101--310301 Score: 273
Period size: 102 Copynumber: 2.0 Consensus size: 103
310091 AACATATTAA
* * * * * *
310101 CACACACAGTGCTATCATATCAGAATCATAATATGGATACAAAGTGCAATCACATCTGAATTATA
1 CACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCGGAAATATA
* *
310166 CTAGTGTACATACCGGTAACA-CTACAGTATATCATAAG
66 CTAGTGTACACACCGGTAACATC-ACAATATATCATAAG
*
310204 CACACACAATGCTATCACATC-GAAATCAT-ATATGCACACAAAGTGCAATCATATCGGAAATAT
1 CACACACAATGCTATCACATCAG-AATCATAATATGCACACAAAGTGCAATCACATCGGAAATAT
*
310267 ACTAGTGTACCCACCGGTAACATCACAATATATCA
65 ACTAGTGTACACACCGGTAACATCACAATATATCA
310302 ATCACTCAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
102 60 0.70
103 26 0.30
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.24
Consensus pattern (103 bp):
CACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCGGAAATATA
CTAGTGTACACACCGGTAACATCACAATATATCATAAG
Found at i:313082 original size:23 final size:23
Alignment explanation
Indices: 313056--313108 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
313046 CACCACAGCT
*
313056 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
313079 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
313102 CGTAGAA
1 CGTAGAA
313109 TTACACTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:313109 original size:23 final size:23
Alignment explanation
Indices: 313064--313147 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
313054 CTCGTATAAA
313064 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
313087 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * * * *
313110 TACACTGTAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
313133 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
313148 TATAATAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:314153 original size:21 final size:21
Alignment explanation
Indices: 314121--314163 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
314111 TGTTTATTTA
314121 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
314142 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
314163 A
1 A
314164 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:315987 original size:2 final size:2
Alignment explanation
Indices: 315980--316015 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
315970 ATCATCTGAG
315980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
316016 TTCTAATCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:317687 original size:23 final size:23
Alignment explanation
Indices: 317661--317718 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
317651 CACCACAGCT
* *
317661 CGTATAAATGTAACAAAGTGCCA
1 CGTAGAAATGCAACAAAGTGCCA
* * *
317684 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCAACAAAGTGCCA
*
317707 CGTAGAATTGCA
1 CGTAGAAATGCA
317719 CCGTAGTGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (23 bp):
CGTAGAAATGCAACAAAGTGCCA
Found at i:317719 original size:23 final size:23
Alignment explanation
Indices: 317676--317729 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
317666 AAATGTAACA
317676 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
317699 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
*
317722 TAGTGCCA
1 AAGTGCCA
317730 TATAATAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:318724 original size:21 final size:21
Alignment explanation
Indices: 318692--318734 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
318682 TGTTTGTTTA
318692 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
318713 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
318734 A
1 A
318735 CAACCCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:321950 original size:24 final size:23
Alignment explanation
Indices: 321893--321982 Score: 110
Period size: 23 Copynumber: 3.9 Consensus size: 23
321883 GTCGAGGGTT
* *
321893 TTATGTGGTTCTTCGAGACAAAA
1 TTATGTGGTCCTTCGGGACAAAA
*
321916 TTATGTAGTCCTTCGGGACAAAA
1 TTATGTGGTCCTTCGGGACAAAA
*
321939 CCTATGTGGTCCTTCGGGAC-AAA
1 -TTATGTGGTCCTTCGGGACAAAA
* *
321962 TTATGTGGTCATTTGGGACAA
1 TTATGTGGTCCTTCGGGACAA
321983 TAATGTGATA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
22 16 0.28
23 24 0.42
24 17 0.30
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (23 bp):
TTATGTGGTCCTTCGGGACAAAA
Found at i:324300 original size:26 final size:26
Alignment explanation
Indices: 324264--324314 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
324254 AAAGATGAAG
*
324264 AAATTACTTTTTCATGTCTTTCTCTA
1 AAATTACTTTTTCATGTATTTCTCTA
324290 AAATTACTTTTTCATGTATTTCTCT
1 AAATTACTTTTTCATGTATTTCTCT
324315 CATTCTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.55
Consensus pattern (26 bp):
AAATTACTTTTTCATGTATTTCTCTA
Found at i:330599 original size:30 final size:29
Alignment explanation
Indices: 330563--330643 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
330553 TAAAATATAT
330563 AACTTTTCAAAATTACATTTTTAGACCCT-A
1 AACTTTT-AAAATTACATTTTTA-ACCCTCA
** *
330593 AACTTTTATAAATTTTATACTTTAACCCTCA
1 AACTTTTA-AAATTACAT-TTTTAACCCTCA
330624 AACTTTTAAAACTTACATTT
1 AACTTTTAAAA-TTACATTT
330644 AGTCACTAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
29 1 0.02
30 23 0.56
31 17 0.41
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (29 bp):
AACTTTTAAAATTACATTTTTAACCCTCA
Found at i:331282 original size:23 final size:20
Alignment explanation
Indices: 331233--331286 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
331223 TTGTAATTGC
*
331233 TTGGAAATGATGCTTGAAAG
1 TTGGAAATCATGCTTGAAAG
*
331253 -TGCAAATCATGCTTGAATCAAG
1 TTGGAAATCATGCTTG-A--AAG
331275 TTGGAAATCATG
1 TTGGAAATCATG
331287 TCTACAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 13 0.48
20 1 0.04
22 3 0.11
23 10 0.37
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (20 bp):
TTGGAAATCATGCTTGAAAG
Found at i:332652 original size:20 final size:20
Alignment explanation
Indices: 332627--332702 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
332617 TTTTTGGCTC
*
332627 AAAGGATCGATCTCTTAGCA
1 AAAGGATCGATCCCTTAGCA
* *
332647 AAAGGATTGATCCCTT-GACC
1 AAAGGATCGATCCCTTAG-CA
* *
332667 AAAGGATCGATCCCCTAGAA
1 AAAGGATCGATCCCTTAGCA
*
332687 AAATGATCGATCCCTT
1 AAAGGATCGATCCCTT
332703 GGATTCCAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.96
21 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
AAAGGATCGATCCCTTAGCA
Found at i:332699 original size:40 final size:40
Alignment explanation
Indices: 332626--332703 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
332616 ATTTTTGGCT
* * * *
332626 CAAAGGATCGATCTCTTAGCAAAAGGATTGATCCCTTGAC
1 CAAAGGATCGATCCCCTAGAAAAAGGATCGATCCCTTGAC
*
332666 CAAAGGATCGATCCCCTAGAAAAATGATCGATCCCTTG
1 CAAAGGATCGATCCCCTAGAAAAAGGATCGATCCCTTG
332704 GATTCCAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (40 bp):
CAAAGGATCGATCCCCTAGAAAAAGGATCGATCCCTTGAC
Found at i:332781 original size:21 final size:21
Alignment explanation
Indices: 332736--332815 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
332726 ATCAATTTAC
**
332736 AAAAGGATCGAT-CCTTCGAGG
1 AAAAGGATCGATCCCTTC-ACA
* *
332757 AAAAGGATTGATCCCTTTACA
1 AAAAGGATCGATCCCTTCACA
* * *
332778 AAAATGATCGATCCCTTCCCC
1 AAAAGGATCGATCCCTTCACA
332799 AAAAGGATCGATCCCTT
1 AAAAGGATCGATCCCTT
332816 ATGTATTAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 44 0.92
22 4 0.08
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTCACA
Found at i:337546 original size:23 final size:23
Alignment explanation
Indices: 337488--337548 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
337478 AAAGTCAACT
* *
337488 GTCAACGATTTGACTCGGGCAAC
1 GTCAACGAGTTGACTCGGGCAAA
* * *
337511 GATCAACGGGTTGATTCGGTCAAA
1 G-TCAACGAGTTGACTCGGGCAAA
337535 GTCAACGAGTTGAC
1 GTCAACGAGTTGAC
337549 CCGATGAGTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (23 bp):
GTCAACGAGTTGACTCGGGCAAA
Found at i:343733 original size:3 final size:3
Alignment explanation
Indices: 343725--343794 Score: 52
Period size: 3 Copynumber: 23.3 Consensus size: 3
343715 AATTAATTAA
* ** * * * *
343725 ATT ATT ATT TTT AAA ATT ACT ATT ATT ATT -TA AAT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
343772 ATT ATA ATT ATT AATT ATT ATT A
1 ATT ATT ATT ATT -ATT ATT ATT A
343795 AATAATTACA
Statistics
Matches: 49, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
2 1 0.02
3 45 0.92
4 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:351759 original size:32 final size:32
Alignment explanation
Indices: 351717--351783 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
351707 AGATTCTGGA
* *
351717 AACAATAAGTATCTCTACGAGATGAGCATAAC
1 AACAAAAAGTATCTCTACAAGATGAGCATAAC
351749 AACAAAAAGTATCTCTACAAGATGAGCATAAC
1 AACAAAAAGTATCTCTACAAGATGAGCATAAC
351781 AAC
1 AAC
351784 CATTTCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (32 bp):
AACAAAAAGTATCTCTACAAGATGAGCATAAC
Found at i:355998 original size:45 final size:45
Alignment explanation
Indices: 355602--355994 Score: 597
Period size: 45 Copynumber: 8.7 Consensus size: 45
355592 GGGAGCTTTT
* *
355602 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
355647 GGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
355692 GGATATTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * *
355737 GGATGTTTTCAAAACCTTTGGGTCATCTGTAATCCCTTCAGCGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
**
355782 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAACGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
355827 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
355872 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * * * *
355917 AGATGTTTTCAAAGCTTTCGAGTCATCTCTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
355962 TGATGTTTTCAAACCCTTCGGGTCATCTGTAAG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
355995 ACCTACAATG
Statistics
Matches: 320, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 320 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:356213 original size:20 final size:19
Alignment explanation
Indices: 356174--356237 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
356164 ACTTAAACTG
356174 TTATT-TTTAAA-ATTACTA
1 TTATTATTTAAATATTA-TA
356192 TTATTATTTAAATATTAGTA
1 TTATTATTTAAATATTA-TA
*
356212 TTAATTA-TTAATTATTATAA
1 TT-ATTATTTAAATATTAT-A
356232 TTATTA
1 TTATTA
356238 AATAATTACA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.12
19 11 0.28
20 20 0.50
21 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTATTTAAATATTATA
Found at i:357867 original size:17 final size:18
Alignment explanation
Indices: 357840--357874 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
357830 AAAAAAATCC
357840 TTATATTATTTTTAATAT
1 TTATATTATTTTTAATAT
357858 TTAT-TTATTTTTAATAT
1 TTATATTATTTTTAATAT
357875 CAAAGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTATTTTTAATAT
Found at i:360934 original size:32 final size:32
Alignment explanation
Indices: 360888--361010 Score: 147
Period size: 32 Copynumber: 3.8 Consensus size: 32
360878 TAGATACTAC
*
360888 TCAGTGTTGCATTTAGATAATACACAATAGAG
1 TCAGTGTTGCATTTAGATAATGCACAATAGAG
* * * *
360920 TCAGTGTTGTATTTATATAATTCACAGTAGAG
1 TCAGTGTTGCATTTAGATAATGCACAATAGAG
* * * *
360952 TCAGTGTTGCATTCAGATATTGCACAAGAGTG
1 TCAGTGTTGCATTTAGATAATGCACAATAGAG
**
360984 TCAGTGTCACATTTAGATAATGCACAA
1 TCAGTGTTGCATTTAGATAATGCACAA
361011 CAGTTACAGT
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 75 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (32 bp):
TCAGTGTTGCATTTAGATAATGCACAATAGAG
Found at i:363012 original size:40 final size:40
Alignment explanation
Indices: 362968--363116 Score: 184
Period size: 40 Copynumber: 3.8 Consensus size: 40
362958 ACATATATAG
*
362968 TATATAATATATAGTTTTTTTATAAA-ATTTTGAAAAAATA
1 TATATAATATATAGTTTTTTTAAAAACATTTTG-AAAAATA
* *
363008 TATATAATATATAGTTTTTTAAAAAAACATTTT-AAAAACA
1 TATATAATATATAGTTTTTT-TAAAAACATTTTGAAAAATA
* *
363048 TATATAATATATAG-TTTCTTAAAAATATTTTG-AAAATA
1 TATATAATATATAGTTTTTTTAAAAACATTTTGAAAAATA
*
363086 TATATAATATATAG--TTTTTGAAAACATTTTG
1 TATATAATATATAGTTTTTTTAAAAACATTTTG
363117 TTGAGTTAAT
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
37 14 0.15
38 29 0.30
39 4 0.04
40 40 0.42
41 4 0.04
42 5 0.05
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (40 bp):
TATATAATATATAGTTTTTTTAAAAACATTTTGAAAAATA
Found at i:366602 original size:23 final size:22
Alignment explanation
Indices: 366524--366594 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
366514 CGTGGGGAGT
366524 ATCGATTCCCCT--AA-GGGGA
1 ATCGATTCCCCTGCAAGGGGGA
** * *
366543 ATCGGCTCCCTTTCAAAGGGGGA
1 ATCGATTCCCCTGC-AAGGGGGA
* *
366566 ATTGATTCCCCTGCAAGGGGGT
1 ATCGATTCCCCTGCAAGGGGGA
366588 ATCGATT
1 ATCGATT
366595 ACCTCTGCCC
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
19 9 0.24
22 15 0.39
23 14 0.37
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (22 bp):
ATCGATTCCCCTGCAAGGGGGA
Found at i:368984 original size:3 final size:3
Alignment explanation
Indices: 368976--369003 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
368966 TAAGTCCGCA
368976 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
369004 CTTTCCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:370858 original size:28 final size:27
Alignment explanation
Indices: 370822--370884 Score: 101
Period size: 26 Copynumber: 2.3 Consensus size: 27
370812 TTTCAACACA
*
370822 TTTTAAAAACATATATATAATATATAGT
1 TTTTGAAAA-ATATATATAATATATAGT
370850 TTTTG-AAAATATATATAATATATAGT
1 TTTTGAAAAATATATATAATATATAGT
370876 TTTTGAAAA
1 TTTTGAAAA
370885 TATTTTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 23 0.70
27 6 0.18
28 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (27 bp):
TTTTGAAAAATATATATAATATATAGT
Found at i:370868 original size:26 final size:26
Alignment explanation
Indices: 370832--370887 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
370822 TTTTAAAAAC
370832 ATATATATAATATATAGTTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAA
370858 ATATATATAATATATAGTTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAA
370884 ATAT
1 ATAT
370888 TTTGAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (26 bp):
ATATATATAATATATAGTTTTTGAAA
Found at i:370890 original size:11 final size:11
Alignment explanation
Indices: 370876--370935 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
370866 AATATATAGT
370876 TTTTGAAAATA
1 TTTTGAAAATA
370887 TTTTGAAAATA
1 TTTTGAAAATA
*
370898 TATAT-AATATATA
1 T-TTTGAA-A-ATA
370911 GTTTTTGAAAATA
1 --TTTTGAAAATA
*
370924 TTTTAAAAATA
1 TTTTGAAAATA
370935 T
1 T
370936 ATATATTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
11 25 0.62
12 3 0.08
13 6 0.15
14 3 0.08
15 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:370891 original size:37 final size:37
Alignment explanation
Indices: 370850--370953 Score: 190
Period size: 37 Copynumber: 2.8 Consensus size: 37
370840 AATATATAGT
370850 TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
370887 TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
* *
370924 TTTTAAAAATATATATATTATATAGTTTTT
1 TTTTGAAAATATATATAATATATAGTTTTT
370954 TTAAAACTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
Found at i:370965 original size:27 final size:28
Alignment explanation
Indices: 370924--370976 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
370914 TTTGAAAATA
370924 TTTTAAAAATATATATATTATATAGTTT
1 TTTTAAAAATATATATATTATATAGTTT
*
370952 TTTTAAAACT-TATATATTATATAGT
1 TTTTAAAAATATATATATTATATAGT
370977 ATTATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (28 bp):
TTTTAAAAATATATATATTATATAGTTT
Found at i:372290 original size:15 final size:15
Alignment explanation
Indices: 372255--372304 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
372245 TTTGATCCAA
*
372255 CATTTTATTTAT-TT
1 CATTTTATTTTTATT
*
372269 C-TTTTATTTTTCTT
1 CATTTTATTTTTATT
*
372283 TATTTTATTTTTATT
1 CATTTTATTTTTATT
372298 CATTTTA
1 CATTTTA
372305 CTTTCTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
15 18 0.60
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (15 bp):
CATTTTATTTTTATT
Found at i:396410 original size:39 final size:36
Alignment explanation
Indices: 396367--396584 Score: 278
Period size: 37 Copynumber: 5.7 Consensus size: 36
396357 ACATATATAG
396367 TATATAATATATAGTTCTTTATAAA-ATTTTGAAAACATA
1 TATATAATATATAGTT-TTTA-AAATATTTTG-AAA-ATA
*
396406 TATATAATATATAGTTTTTTTAAAAAATGTTTTGAAAA-A
1 TATATAATATATAG--TTTTT--AAAATATTTTGAAAATA
396445 TATATAATATATAGTTTTTAAAAATATTTTGAAAATA
1 TATATAATATATAGTTTTT-AAAATATTTTGAAAATA
*
396482 TATATAATATATAGTTTTTGAAAACATTTTGAAAAAATA
1 TATATAATATATAGTTTTT-AAAATATTTTG--AAAATA
396521 TATATAATATATAGTTTTTGAAAATATTTTGAAAATA
1 TATATAATATATAGTTTTT-AAAATATTTTGAAAATA
396558 TATATAATATATAGTTTTTGAAAATAT
1 TATATAATATATAGTTTTT-AAAATAT
396585 ATACTATATA
Statistics
Matches: 166, Mismatches: 5, Indels: 18
0.88 0.03 0.10
Matches are distributed among these distances:
36 15 0.09
37 68 0.41
39 65 0.39
40 4 0.02
41 8 0.05
42 6 0.04
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAATATTTTGAAAATA
Found at i:396469 original size:76 final size:76
Alignment explanation
Indices: 396367--396581 Score: 305
Period size: 76 Copynumber: 2.8 Consensus size: 76
396357 ACATATATAG
* *
396367 TATATAATATATAGTTCTTTATAAA-ATTTTGAAAACATATATATAATATATAGTTTTTTTAAAA
1 TATATAATATATAGTT-TTTAAAAATATTTTG-AAA-ATATATATAATATATAGTTTTTTGAAAA
396431 AATGTTTTG-AAAA-A
63 AA--TTTTGAAAAATA
*
396445 TATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAG-TTTTTGAAAACAT
1 TATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTTTGAAAAAAT
396509 TTTGAAAAAATA
66 TTTG-AAAAATA
*
396521 TATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAG-TTTTTGAAAA
1 TATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTTTGAAAA
396582 TATATACTAT
Statistics
Matches: 129, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
73 5 0.04
75 14 0.11
76 78 0.60
77 10 0.08
78 22 0.17
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (76 bp):
TATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTTTGAAAAAAT
TTTGAAAAATA
Found at i:396602 original size:26 final size:26
Alignment explanation
Indices: 396547--396600 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 26
396537 TTTGAAAATA
396547 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
*
396573 TTTTG-AAA-ATATATACTATATAGT
1 TTTTGAAAATATATATAATATATAGT
396597 TTTT
1 TTTT
396601 TTAAAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 19 0.70
25 3 0.11
26 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (26 bp):
TTTTGAAAATATATATAATATATAGT
Found at i:396643 original size:14 final size:14
Alignment explanation
Indices: 396624--396671 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
396614 TATTATACAA
396624 TATTATATATTATT
1 TATTATATATTATT
*
396638 TATTATATCTTATT
1 TATTATATATTATT
* * *
396652 CATTTTTTATTATT
1 TATTATATATTATT
*
396666 TTTTAT
1 TATTAT
396672 GTCTTTATTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTATATATTATT
Found at i:397275 original size:18 final size:18
Alignment explanation
Indices: 397252--397288 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
397242 ATAAAAAAAT
397252 GTATTTGTTATCTTGCTC
1 GTATTTGTTATCTTGCTC
*
397270 GTATTTTTTATCTTGCTC
1 GTATTTGTTATCTTGCTC
397288 G
1 G
397289 CCTTTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (18 bp):
GTATTTGTTATCTTGCTC
Found at i:397294 original size:18 final size:18
Alignment explanation
Indices: 397254--397296 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
397244 AAAAAAATGT
* *
397254 ATTTGTTATCTTGCTCGT
1 ATTTTTTATCTTGCTCGC
397272 ATTTTTTATCTTGCTCGC
1 ATTTTTTATCTTGCTCGC
*
397290 CTTTTTT
1 ATTTTTT
397297 CATTTGCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.12, T:0.60
Consensus pattern (18 bp):
ATTTTTTATCTTGCTCGC
Found at i:398581 original size:17 final size:17
Alignment explanation
Indices: 398559--398591 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
398549 CTATATTTTC
398559 AAATAATAAAAAGTTAA
1 AAATAATAAAAAGTTAA
398576 AAATAATAAAAAGTTA
1 AAATAATAAAAAGTTA
398592 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
AAATAATAAAAAGTTAA
Found at i:401156 original size:53 final size:53
Alignment explanation
Indices: 401076--401183 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
401066 TAGTTCCGCT
*
401076 CGATCAGTCTCTGTAATGTTTTGTTCAAGATTGTCTTGAAGATGCCAACATAG
1 CGATCAGTCTCTGTAATGTTTTGTTCAAAATTGTCTTGAAGATGCCAACATAG
*
401129 CGATCTGTCTCTGTAATGTTTTGTTCAAAATTGTCTTGAAGATGCCAACATAG
1 CGATCAGTCTCTGTAATGTTTTGTTCAAAATTGTCTTGAAGATGCCAACATAG
401182 CG
1 CG
401184 TATGCAGCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (53 bp):
CGATCAGTCTCTGTAATGTTTTGTTCAAAATTGTCTTGAAGATGCCAACATAG
Found at i:402777 original size:33 final size:32
Alignment explanation
Indices: 402739--402803 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
402729 AATTTCAAAG
*
402739 AGTTCTAA-AGTTTAGGGACTAAATCTAAAAGAA
1 AGTTCTAATAG-TTAAGGACTAAAT-TAAAAGAA
402772 AGTTCTAATAGTTAAGGACTAAATTAAAAGAA
1 AGTTCTAATAGTTAAGGACTAAATTAAAAGAA
402804 TCTAAACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 8 0.27
33 20 0.67
34 2 0.07
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.28
Consensus pattern (32 bp):
AGTTCTAATAGTTAAGGACTAAATTAAAAGAA
Found at i:403202 original size:11 final size:11
Alignment explanation
Indices: 403186--403239 Score: 99
Period size: 11 Copynumber: 4.8 Consensus size: 11
403176 ACATAGCAAC
403186 GAATTAAAAAT
1 GAATTAAAAAT
403197 GAATTAAAAAT
1 GAATTAAAAAT
403208 GAATTAAAAAT
1 GAATTAAAAAT
403219 GAATTAAAAAT
1 GAATTAAAAAT
403230 GAATTGAAAA
1 GAATT-AAAA
403240 CGAAGAGTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
11 38 0.90
12 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (11 bp):
GAATTAAAAAT
Found at i:404170 original size:239 final size:238
Alignment explanation
Indices: 403729--404205 Score: 690
Period size: 239 Copynumber: 2.0 Consensus size: 238
403719 TCGGTCTGAA
* *
403729 ACTCTTCAAAAAGGGGCCGAAAACCCTTGGACTTCCGCCTCATCGATCACCTCCGTTAGTCTTTG
1 ACTCTTCAAAAAGGGGCCGAAAACCCTTCGACTTCCGCCTCATCGATCACCTCCGTCAGTCTTTG
** * ** *
403794 GATCGAGCTAGCTCTGAAGTATATTGTTCACGCCATCCACGGGCTTCACTTCACTGTCAGGGTCT
66 GATCGAGCTAGCTCCAAAGTATATTGTTCACGCCATCCACGGGCTTCACTTCACCGTCAGAATAT
* *
403859 GCCAGTGGAAGCCACAAAAGCCGGTGTAGCTTCAGCCAAGAGGTACGATCTCCTTCTCTGTACTT
131 GCAAGTGGAAGCCACAAAAGCCGGTGTAGCTTCAACCAAGAGGTACGATCTCCTTCTCTGTACTT
403924 ATTAATTTTGTTTGTTTGTTTCGAATGGGTTGGGTTTCTTCTCTT
196 ATTAA-TTT-TTTGTTTGTTTCGAATGGGTTGGGTTTCTTCTCTT
* * * *
403969 ACTCTTCAAAAA-GGGCCGAGAACCCTTCGACTTTCGCCTCGTCGATCGCCTCCGTCAG-CTATT
1 ACTCTTCAAAAAGGGGCCGAAAACCCTTCGACTTCCGCCTCATCGATCACCTCCGTCAGTCT-TT
* *
404032 GGATCGAGCTAGCTCCAAAGTATGTTGTTCATGCCATCCACGGGCTTCACTTCACCGTCTA-AAT
65 GGATCGAGCTAGCTCCAAAGTATATTGTTCACGCCATCCACGGGCTTCACTTCACCGTC-AGAAT
* * * * *
404096 ATGCAAGTGGAAGCCCCAAACGCTGGTGTAGCTTCAACCGAGAGGTACGATCTCCTTCTCTTTAC
129 ATGCAAGTGGAAGCCACAAAAGCCGGTGTAGCTTCAACCAAGAGGTACGATCTCCTTCTCTGTAC
* *
404161 TTTTTAATTTTTTGTTTGTTTCGAATGGGTTGGTTTTCTTCTCTT
194 TTATTAATTTTTTGTTTGTTTCGAATGGGTTGGGTTTCTTCTCTT
404206 GCTTCTTTTT
Statistics
Matches: 212, Mismatches: 23, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
237 34 0.16
238 5 0.02
239 160 0.75
240 13 0.06
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (238 bp):
ACTCTTCAAAAAGGGGCCGAAAACCCTTCGACTTCCGCCTCATCGATCACCTCCGTCAGTCTTTG
GATCGAGCTAGCTCCAAAGTATATTGTTCACGCCATCCACGGGCTTCACTTCACCGTCAGAATAT
GCAAGTGGAAGCCACAAAAGCCGGTGTAGCTTCAACCAAGAGGTACGATCTCCTTCTCTGTACTT
ATTAATTTTTTGTTTGTTTCGAATGGGTTGGGTTTCTTCTCTT
Found at i:407838 original size:20 final size:20
Alignment explanation
Indices: 407815--407867 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
407805 AACTGGTCTA
*
407815 AGTTAACTTGAACTGTTATG
1 AGTTAACTTGAACTGATATG
* * *
407835 AGTTAACCTAAATTGATATG
1 AGTTAACTTGAACTGATATG
*
407855 AGTTAACTCGAAC
1 AGTTAACTTGAAC
407868 CGGATCAAGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (20 bp):
AGTTAACTTGAACTGATATG
Found at i:417268 original size:41 final size:42
Alignment explanation
Indices: 417172--417273 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 42
417162 TGAGCCTTCA
* * * *
417172 AAATGAACTTTCAAAATGCCCCCACATGAATCATTTTTTGTCTG
1 AAATGGACCTTCAAAATGCCCCAACAT--ATCATTTCTTGTCTG
*
417216 AAATGGGCCTTCAAAATGCCCCAACAT-TCTATTTCTTGT-TG
1 AAATGGACCTTCAAAATGCCCCAACATATC-ATTTCTTGTCTG
417257 AAATGGACCTTCAAAAT
1 AAATGGACCTTCAAAAT
417274 ATCCCAACCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
41 20 0.39
42 8 0.16
44 23 0.45
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (42 bp):
AAATGGACCTTCAAAATGCCCCAACATATCATTTCTTGTCTG
Found at i:426242 original size:21 final size:21
Alignment explanation
Indices: 426213--426265 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
426203 ATTCTGACTA
426213 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
426234 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
426255 TCGCAATGCGA
1 TCGCATTGCGA
426266 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:426280 original size:20 final size:20
Alignment explanation
Indices: 426255--426363 Score: 127
Period size: 20 Copynumber: 5.7 Consensus size: 20
426245 TTTTCCTAAT
*
426255 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
426275 TCGCAACGTGAATATGTAAA
1 TCGCAACGCGAATACGTAAA
*
426295 TCGCAATGCG---ACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
426312 TCGTAATGCGAATACGT-AA
1 TCGCAACGCGAATACGTAAA
*
426331 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATACGTAAA
426351 TCGCAACGCGAAT
1 TCGCAACGCGAAT
426364 CTGACTATCG
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
17 15 0.20
19 16 0.21
20 44 0.59
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:426312 original size:17 final size:17
Alignment explanation
Indices: 426290--426322 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
426280 ACGTGAATAT
426290 GTAAATCGCAATGCGAC
1 GTAAATCGCAATGCGAC
*
426307 GTAAATCGTAATGCGA
1 GTAAATCGCAATGCGA
426323 ATACGTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (17 bp):
GTAAATCGCAATGCGAC
Found at i:426325 original size:37 final size:36
Alignment explanation
Indices: 426268--426363 Score: 102
Period size: 37 Copynumber: 2.6 Consensus size: 36
426258 CAATGCGAAT
* * *
426268 ACGTAAATCGCAACGTGAATATGTAAATCGCAATGCG
1 ACGTAAATCGCAACGCGAATACGT-AATCGCAACGCG
* *
426305 ACGTAAATCGTAATGCGAATACGTAATCGCAACGCG
1 ACGTAAATCGCAACGCGAATACGTAATCGCAACGCG
*
426341 AATATGTAAATCGCAACGCGAAT
1 ---ACGTAAATCGCAACGCGAAT
426364 CTGACTATCG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 11 0.23
37 20 0.42
39 17 0.35
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (36 bp):
ACGTAAATCGCAACGCGAATACGTAATCGCAACGCG
Found at i:426457 original size:20 final size:20
Alignment explanation
Indices: 426350--426456 Score: 160
Period size: 20 Copynumber: 5.3 Consensus size: 20
426340 GAATATGTAA
*
426350 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
* *
426370 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
426390 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
426410 ATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
426430 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
426450 ATCGCAA
1 ATCGCAA
426457 TACTGAATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:426633 original size:20 final size:20
Alignment explanation
Indices: 426608--426645 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
426598 ATCTCTCTGG
*
426608 CGACATCCGTTCCTATCCAA
1 CGACATCCGTTCCCATCCAA
*
426628 CGACATCCTTTCCCATCC
1 CGACATCCGTTCCCATCC
426646 GGCAACAGGT
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:0.21, C:0.45, G:0.08, T:0.26
Consensus pattern (20 bp):
CGACATCCGTTCCCATCCAA
Found at i:429825 original size:20 final size:20
Alignment explanation
Indices: 429757--429824 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
429747 CAACGCAGAA
429757 ATCGCAACAC-GAATATGACT
1 ATCGCAACACGGAA-ATGACT
429777 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
*
429797 ATCGCAACGCGGAAATGACT
1 ATCGCAACACGGAAATGACT
429817 ATCGCAAC
1 ATCGCAAC
429825 GAGAGAATCG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGGAAATGACT
Found at i:429959 original size:33 final size:34
Alignment explanation
Indices: 429907--429982 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
429897 TTTAGTTTCG
*
429907 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCAATTTCGCATTGCGATTCTCT
* *
429941 CGTTGTGA-TTTCAATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCAATTTCGCATTGCGATTCTCT
429974 CGTTGCGAT
1 CGTTGCGAT
429983 AGTCATTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 30 0.81
34 7 0.19
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCAATTTCGCATTGCGATTCTCT
Found at i:429991 original size:33 final size:32
Alignment explanation
Indices: 429907--430002 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 32
429897 TTTAGTTTCG
429907 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGA-TTTCA-TTTCGCATTGCGATTCTCT
* *
429941 CGTTGTGATTTCAATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTC-ATTTCGCATTGCGATTCTCT
* *
429974 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGAT-TTCATTT-CGCATTGCGAT
430003 AGTCTGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
33 34 0.64
34 19 0.36
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTCATTTCGCATTGCGATTCTCT
Found at i:430129 original size:14 final size:14
Alignment explanation
Indices: 430110--430144 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
430100 TCAAATAAAA
430110 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
430124 AAATCATCTTTTAC
1 AAATCAACATTTAC
430138 AAATCAA
1 AAATCAA
430145 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:431508 original size:21 final size:22
Alignment explanation
Indices: 431475--431530 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
431465 CGTGAGGGTG
** *
431475 CTCTTGAGGGATGATAGG-GGC
1 CTCTTGAACGATGAGAGGAGGC
*
431496 CTCTTGAACGATG-GGGGAGGC
1 CTCTTGAACGATGAGAGGAGGC
431517 CTCTTGAACGATGA
1 CTCTTGAACGATGA
431531 CAGGTGAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.21, C:0.18, G:0.38, T:0.23
Consensus pattern (22 bp):
CTCTTGAACGATGAGAGGAGGC
Found at i:432035 original size:20 final size:20
Alignment explanation
Indices: 432012--432100 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 20
432002 GAAACTTAAA
432012 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
432032 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
432052 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* **
432072 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
432092 ATCGCAACG
1 ATCGCAACG
432101 AGAGAATCGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:432165 original size:20 final size:20
Alignment explanation
Indices: 432137--432313 Score: 157
Period size: 20 Copynumber: 9.5 Consensus size: 20
432127 GATTCTTTCG
* **
432137 TTGCCATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
432157 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
432177 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
432197 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
432217 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
432231 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
432250 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* *
432264 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
*
432284 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
432304 TTGCGATAGT
1 TTGCGATAGT
432314 AAACTATTCT
Statistics
Matches: 135, Mismatches: 8, Indels: 28
0.79 0.05 0.16
Matches are distributed among these distances:
14 14 0.10
16 12 0.09
17 6 0.04
18 4 0.03
19 7 0.05
20 92 0.68
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:432277 original size:33 final size:34
Alignment explanation
Indices: 432157--432290 Score: 126
Period size: 33 Copynumber: 3.8 Consensus size: 34
432147 CAAATTCGCA
*
432157 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCGCATTGCGAT--TC--TCTCG
* * * *
432195 CATTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 --TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
**
432231 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
* *
432264 TTGCGATAGTCATTTTTGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
432291 AGTCATTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
33 27 0.34
34 22 0.28
36 3 0.04
38 1 0.01
40 26 0.33
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:434215 original size:20 final size:20
Alignment explanation
Indices: 434192--434354 Score: 135
Period size: 20 Copynumber: 8.6 Consensus size: 20
434182 TCTGAAACTT
434192 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
434212 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
434232 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
**
434252 ACTATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
434271 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
434291 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
434311 ACTATCGC-A-ACG-CAA-G
1 AAAATCGCAACACGAAAATG
434327 --AATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
434344 AAAATCGCAAC
1 AAAATCGCAAC
434355 GACAGAATCG
Statistics
Matches: 116, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
14 5 0.04
15 1 0.01
16 6 0.05
17 1 0.01
18 2 0.02
19 25 0.22
20 76 0.66
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:434288 original size:59 final size:60
Alignment explanation
Indices: 434195--434321 Score: 247
Period size: 59 Copynumber: 2.1 Consensus size: 60
434185 GAAACTTAAA
434195 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACT
434255 ATCGCAACACG-AAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACT
434314 ATCGCAAC
1 ATCGCAAC
434322 GCAAGAATCG
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
59 56 0.84
60 11 0.16
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.17
Consensus pattern (60 bp):
ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACT
Found at i:434323 original size:79 final size:73
Alignment explanation
Indices: 434192--434354 Score: 227
Period size: 79 Copynumber: 2.2 Consensus size: 73
434182 TCTGAAACTT
434192 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTAT
1 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGC-AA---GA--AT
434257 CGCAACACGAAATG
60 CGCAACACGAAATG
** * **
434271 AAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCAAGAATCGCAAC
1 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCAAGAATCGCAAC
434336 ACGAAATG
66 ACGAAATG
434344 AAAATCGCAAC
1 AAAATCGCAAC
434355 GACAGAATCG
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
73 27 0.34
75 2 0.03
78 2 0.03
79 48 0.61
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.15
Consensus pattern (73 bp):
AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCAAGAATCGCAAC
ACGAAATG
Found at i:434739 original size:22 final size:22
Alignment explanation
Indices: 434689--434742 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
434679 ATTTCGCCGA
*
434689 AGATGGAGACTGATATCGTCGG
1 AGATGGGGACTGATATCGTCGG
* **
434711 AGATGGGGACTGATTTTTTCGG
1 AGATGGGGACTGATATCGTCGG
434733 AGATGGGGAC
1 AGATGGGGAC
434743 GGATGTCGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.39, T:0.26
Consensus pattern (22 bp):
AGATGGGGACTGATATCGTCGG
Found at i:434963 original size:20 final size:20
Alignment explanation
Indices: 434940--435012 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
434930 CGATAGTCAG
* *
434940 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
* *
434960 ATTCGCATTGCGATGTATGT
1 ATTCGCATTGCGATTTACGT
434980 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
435000 ATTCGCATTGCGA
1 ATTCGCATTGCGA
435013 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:434984 original size:40 final size:40
Alignment explanation
Indices: 434922--435012 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
434912 GCTATGTAAA
*
434922 TCGCATTGCGATAGTCAGATTCGCGTTGCGATTTACATAT
1 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACATAT
*
434962 TCGCATTGCGAT-GT-ATGTATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATAGTCA-G-ATTCGCATTGCGATTTACATAT
435002 TCGCATTGCGA
1 TCGCATTGCGA
435013 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
38 1 0.02
39 3 0.06
40 43 0.91
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACATAT
Found at i:435033 original size:21 final size:21
Alignment explanation
Indices: 435009--435054 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
434999 TATTCGCATT
435009 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
435030 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
435051 GCGA
1 GCGA
435055 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:439935 original size:2 final size:2
Alignment explanation
Indices: 439928--440003 Score: 138
Period size: 2 Copynumber: 39.0 Consensus size: 2
439918 TTTTTAATGA
439928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
439969 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
440004 TTCATGGTAT
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 70 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:441274 original size:599 final size:595
Alignment explanation
Indices: 440512--441709 Score: 2308
Period size: 600 Copynumber: 2.0 Consensus size: 595
440502 AAATTGAATT
440512 ATTTTAGCCATTATCTCCATGTTGTCTTTGTGTCTTCCTAGAATATATGTCATACTTTTAGCGTC
1 ATTTTAGCCATTATCTCCATGTTGTCTTTGTGTCTTCCTAGAATATATGTCATACTTTTAGCGTC
*
440577 TTGATATTGATATTATTCATGTAGCCTAATTTAAAAAATAGTTTTTGAAACGCTTTATGTGAGAA
66 TTGATATTGATATTATTCATGTAGCCTAATTTAAAAAATAGTTTTTGAAACGCGTTATGTGAGAA
440642 ATTTTATATTTGATATTAAATTTGATATAATTAAAGGGGTGAATGTTATTTCTTGAGGTTTCGAT
131 ATTTTATATTTGATATTAAATTTGATATAATTAAAGGGGTGAATGTTATTTCTTGAGGTTTCGAT
440707 TCGAGCACCATCGATTGTAGGATATTTGGGCGATCATTATCAAATGGTTGAGAGTCTTTGGAATA
196 TCGAGCACCATCGATTGTAGGATATTTGGGCGATCATTATCAAATGGTTGAGAGTCTTTGGAATA
440772 TATACTACCATTTGTAATCACTCTAGATT-AAAAAATTAAATTAAATTTTTAATTTAAGTTAGTA
261 TATACTACCATTTGTAATCACTCTAGATTAAAAAAATTAAATTAAATTTTTAATTTAAGTTAGTA
440836 TCCAAACTTTGTTACTTAATTCAAATGATTTATCTGAACCAAATTAAACAATAGAGCTAAGTTCA
326 TCCAAACTTTGTTACTTAATTCAAATGATTTATCTGAACCAAATTAAACAATAGAGCTAAGTTCA
440901 TGTAACATTAAATTAAAGCTTGAAAATAATTTGAAACAAAAAATATTTATATTAAAGTTGAGAGT
391 TGTAACATTAAATTAAAGCTTGAAAATAATTTGAAACAAAAAATATTTATATTAAAGTTGAGAGT
*
440966 AAATTACAATGGTAGTCACTAAACTTTTAGAGTGTTCTCACTTTTATCATTGAGCTTTTAAAACT
456 AAAATACAATGGTAGTCACTAAACTTTTAGAGTGTTCTCACTTTTATCATTGAGCTTTTAAAACT
441031 TGCATTATAATCACTACTTTTTTATTAATCTAAGGTGATTATAAGTGGTAGTATTTGTTATAAAG
521 TGCATTATAATCACTACTTTTTTATTAATCTAAGGTGATTATAAGTGGTAGTATTTGTTATAAAG
441096 ACTATCAACC
586 ACTATCAACC
441106 ATTTTAGCCATTATCTCCATGTTGTCTTTGTGTCTTCCTAGAATATATATGTCATATACTTTTAG
1 ATTTTAGCCATTATCTCCATGTTGTCTTTGTGTCTTCCTAG-A-ATATATGTC--ATACTTTTAG
*
441171 CGTCTTGATATTGATATTATTCATGTAGCCTAGTTTTAAAAAATAGTTTTTGAAACGCGTTATGT
62 CGTCTTGATATTGATATTATTCATGTAGCCTA-ATTTAAAAAATAGTTTTTGAAACGCGTTATGT
441236 GAGAAATTTTATATTTGATATTAAATTTGATATAATTAAAGGGGTGAATGTTATTTCTTGAGGTT
126 GAGAAATTTTATATTTGATATTAAATTTGATATAATTAAAGGGGTGAATGTTATTTCTTGAGGTT
441301 TCGATTCGAGCACCATCGATTGTAGGATATTTGGGCGATCATTATCAAATGGTTGAGAGTCTTTG
191 TCGATTCGAGCACCATCGATTGTAGGATATTTGGGCGATCATTATCAAATGGTTGAGAGTCTTTG
441366 GAATATATACTACCATTTGTAATCACTCTAGATTAAAAAAATTAAATTAAATTTTTAATTTAAGT
256 GAATATATACTACCATTTGTAATCACTCTAGATTAAAAAAATTAAATTAAATTTTTAATTTAAGT
441431 TAGTATCCAAACTTTGTTACTTAATTCAAATGATTTATCTGAACCAAATTAAACAATAGAGCTAA
321 TAGTATCCAAACTTTGTTACTTAATTCAAATGATTTATCTGAACCAAATTAAACAATAGAGCTAA
441496 GTTCATGTAACATTAAATTAAAGCTTGAAAATAATTTGAAACAAAAAATATTTATATTAAAGTTG
386 GTTCATGTAACATTAAATTAAAGCTTGAAAATAATTTGAAACAAAAAATATTTATATTAAAGTTG
*
441561 AGAGTAAAATACAATGGTAGTCACTAAACTTTTAGAGTGTTCTCACTTTTATCATTGAGGTTTTA
451 AGAGTAAAATACAATGGTAGTCACTAAACTTTTAGAGTGTTCTCACTTTTATCATTGAGCTTTTA
441626 AAACTTGCATTATAATCACTACTTTTTTATTAATCTAAGGTGATTATAAGTGGTAGTATTTGTTA
516 AAACTTGCATTATAATCACTACTTTTTTATTAATCTAAGGTGATTATAAGTGGTAGTATTTGTTA
441691 TAAAGACTATCAACC
581 TAAAGACTATCAACC
441706 ATTT
1 ATTT
441710 GACAATAAAC
Statistics
Matches: 594, Mismatches: 4, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
594 41 0.07
595 1 0.00
596 9 0.02
598 42 0.07
599 194 0.33
600 307 0.52
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (595 bp):
ATTTTAGCCATTATCTCCATGTTGTCTTTGTGTCTTCCTAGAATATATGTCATACTTTTAGCGTC
TTGATATTGATATTATTCATGTAGCCTAATTTAAAAAATAGTTTTTGAAACGCGTTATGTGAGAA
ATTTTATATTTGATATTAAATTTGATATAATTAAAGGGGTGAATGTTATTTCTTGAGGTTTCGAT
TCGAGCACCATCGATTGTAGGATATTTGGGCGATCATTATCAAATGGTTGAGAGTCTTTGGAATA
TATACTACCATTTGTAATCACTCTAGATTAAAAAAATTAAATTAAATTTTTAATTTAAGTTAGTA
TCCAAACTTTGTTACTTAATTCAAATGATTTATCTGAACCAAATTAAACAATAGAGCTAAGTTCA
TGTAACATTAAATTAAAGCTTGAAAATAATTTGAAACAAAAAATATTTATATTAAAGTTGAGAGT
AAAATACAATGGTAGTCACTAAACTTTTAGAGTGTTCTCACTTTTATCATTGAGCTTTTAAAACT
TGCATTATAATCACTACTTTTTTATTAATCTAAGGTGATTATAAGTGGTAGTATTTGTTATAAAG
ACTATCAACC
Found at i:443724 original size:31 final size:32
Alignment explanation
Indices: 443668--443760 Score: 93
Period size: 31 Copynumber: 2.9 Consensus size: 32
443658 TTTAATAAAT
*
443668 TAAG-ATAAAATATATACTTTCAAAAGCTAAAAC
1 TAAGAATAAAATATATA-TTTTAAAAG-TAAAAC
* **
443701 -AATAATAAAATATAT-TTTTAAAAGTTTAAC
1 TAAGAATAAAATATATATTTTAAAAGTAAAAC
* *
443731 TAAGAATAAAATATATATTTTTAAATTAAA
1 TAAGAATAAAATATATATTTTAAAAGTAAA
443761 TTATCTTTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
30 4 0.08
31 22 0.46
32 11 0.23
33 11 0.23
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (32 bp):
TAAGAATAAAATATATATTTTAAAAGTAAAAC
Found at i:443826 original size:24 final size:26
Alignment explanation
Indices: 443777--443844 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
443767 TTAAATTAAA
443777 TTAAT-TATAAAATATATTTAATAAG
1 TTAATATATAAAATATATTTAATAAG
*
443802 TTAATATA-AAAATATTTTTAA-AAG
1 TTAATATATAAAATATATTTAATAAG
443826 TTAATATATATAAAATATA
1 TT-A-ATATATAAAATATA
443845 ATGAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 5 0.14
25 18 0.49
26 7 0.19
27 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
TTAATATATAAAATATATTTAATAAG
Found at i:444528 original size:20 final size:19
Alignment explanation
Indices: 444482--444529 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
444472 ATGACCAACA
* *
444482 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCC
*
444501 AAATCGCAACGCGGTCTCC
1 AAATCGCAACGCGATCTCC
444520 AATATCGCAA
1 AA-ATCGCAA
444530 ATCAGTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCC
Found at i:444590 original size:21 final size:22
Alignment explanation
Indices: 444564--444607 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
444554 ATTTTGACTA
444564 TCGCATTGCGATTTTCCA-AAT
1 TCGCATTGCGATTTTCCAGAAT
444585 TCGCATTGCGATTTTCCAGAAT
1 TCGCATTGCGATTTTCCAGAAT
444607 T
1 T
444608 TTAGAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCAGAAT
Found at i:444738 original size:20 final size:20
Alignment explanation
Indices: 444615--444747 Score: 67
Period size: 20 Copynumber: 6.7 Consensus size: 20
444605 ATTTTAGAAA
*
444615 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * *
444635 ATCGCAACTCGA-TCTCCAGT
1 ATCGCAACGCGATTCT-GACT
** * *
444655 ATCGCAAATCAGTTTCCAGA-T
1 ATCGCAACGC-GATT-CTGACT
* *
444676 -TCGCAACGCGATTTTAACT
1 ATCGCAACGCGATTCTGACT
* * * * *
444695 ATCGTAATGCGAATATGTA-G
1 ATCGCAACGCGATTCTG-ACT
444715 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
444735 ATCGCAACGCGAT
1 ATCGCAACGCGAT
444748 AATACAAAAT
Statistics
Matches: 80, Mismatches: 25, Indels: 16
0.66 0.21 0.13
Matches are distributed among these distances:
18 1 0.01
19 8 0.10
20 65 0.81
21 3 0.04
22 2 0.03
23 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:445158 original size:19 final size:19
Alignment explanation
Indices: 445134--445214 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 19
445124 TTATTTTGGA
445134 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
*
445153 TTTTTCACTATCACAACAACAC
1 TTTTTCACTAT--C-GCAACAC
*
445175 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
445197 ATTTTAACTATCGCAACA
1 TTTTTCACTATCGCAACA
445215 TATTTTTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
19 22 0.44
21 5 0.10
22 12 0.24
23 7 0.14
25 4 0.08
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:445194 original size:22 final size:21
Alignment explanation
Indices: 445140--445225 Score: 63
Period size: 19 Copynumber: 4.0 Consensus size: 21
445130 TGGATTTTTC
445140 ACTATCGCAACACTTTTTC--
1 ACTATCGCAACACTTTTTCAA
*
445159 ACTATCACAACAACACGTTTTTCAA
1 ACTAT--C-GCAACAC-TTTTTCAA
* *
445184 ACTCTCGCAACACATTTT--A
1 ACTATCGCAACACTTTTTCAA
*
445203 ACTATCGCAACATATTTTTCAA
1 ACTATCGCAACA-CTTTTTCAA
445225 A
1 A
445226 ATCGCGTTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
19 17 0.33
20 4 0.08
21 5 0.10
22 14 0.27
23 7 0.14
25 4 0.08
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (21 bp):
ACTATCGCAACACTTTTTCAA
Found at i:446735 original size:35 final size:34
Alignment explanation
Indices: 446689--446801 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
446679 AAAACAATCC
*
446689 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
446724 TCAATTTCATTCTAAACTCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAAC-CCAAATTCCAAAATAAT
* * *
446759 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
446794 TCAATTTC
1 TCAATTTC
446802 TGTCTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 64 0.93
36 5 0.07
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:448019 original size:19 final size:19
Alignment explanation
Indices: 447995--448050 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
447985 ATGACCAACA
447995 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
**
448014 AAATCGCAACACGATCTCT
1 AAATCGCAATGCGATCTCT
448033 AAATCGC-ATCGCGATCTC
1 AAATCGCAAT-GCGATCTC
448051 CAGTATCGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 1 0.03
19 31 0.97
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.23
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:448180 original size:20 final size:20
Alignment explanation
Indices: 448157--448393 Score: 117
Period size: 20 Copynumber: 11.7 Consensus size: 20
448147 GAATATGTAA
448157 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
448177 ATCGCAACGC-AATCTCGAGT
1 ATCGCAACGCGATTCT-GACT
** * *
448197 ATCGCAAATCAGTTTCCAGA-T
1 ATCGCAACGC-GATT-CTGACT
*
448218 -TCGCAACGCGATTTTGACT
1 ATCGCAACGCGATTCTGACT
** * **
448237 ATCGCATTGCGATTTTAGAAA
1 ATCGCAACGCGATTCT-GACT
* * * *
448258 ATCGCAATGCGAATATGTA-A
1 ATCGCAACGCGATTCTG-ACT
*
448278 ATCGCAACACGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
448298 ATCGCAACACGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
448318 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
* ** *
448339 ATCGCAACACGATAAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
*
448360 ATCGCAACGCGATTCTAACT
1 ATCGCAACGCGATTCTGACT
*
448380 ATCGCAATGCGATT
1 ATCGCAACGCGATT
448394 TTCCAAATTT
Statistics
Matches: 164, Mismatches: 38, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
18 2 0.01
19 13 0.08
20 97 0.59
21 44 0.27
22 7 0.04
23 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:448322 original size:41 final size:41
Alignment explanation
Indices: 448276--448386 Score: 195
Period size: 41 Copynumber: 2.7 Consensus size: 41
448266 GCGAATATGT
*
448276 AAATCGCAACACGATTCTGACTATCGCAACACGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACACGATAATACA
*
448317 TAATCGCAACGCGATTCTGACTATCGCAACACGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACACGATAATACA
*
448358 AAATCGCAACGCGATTCTAACTATCGCAA
1 AAATCGCAACGCGATTCTGACTATCGCAA
448387 TGCGATTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.21
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACACGATAATACA
Found at i:448322 original size:61 final size:60
Alignment explanation
Indices: 448136--448330 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
448126 GATTTTAGAA
* * *
448136 AATCGCAATGAGAATATGTAAATCGCAACGCGATTCTGACTATCGCAACGCAATCT-CGAGT
1 AATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCGCAACGCGATATAC-A-T
* * ** * * ** * * *
448197 -ATCGCAAAT-C-AGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTGCGATTTTAGAA
1 AATCGC-AATGCGAATATGTA-AATCGCAACGCGATTCTGACTATCGCAACGCGA-TATACAT
* *
448257 AATCGCAATGCGAATATGTAAATCGCAACACGATTCTGACTATCGCAACACGATAATACAT
1 AATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCGCAACGCGAT-ATACAT
*
448318 AATCGCAACGCGA
1 AATCGCAATGCGA
448331 TTCTGACTAT
Statistics
Matches: 99, Mismatches: 27, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
59 4 0.04
60 37 0.37
61 54 0.55
62 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (60 bp):
AATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCGCAACGCGATATACAT
Done.