Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007490.1 Hibiscus syriacus cultivar Beakdansim tig00020682_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: 795028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:134626 original size:20 final size:20
Alignment explanation
Indices: 134595--134691 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
134585 TTTTGGTTGA
134595 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
134615 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
134635 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
134654 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
134669 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
134689 AAT
1 AAT
134692 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:134647 original size:21 final size:21
Alignment explanation
Indices: 134593--134657 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
134583 TCTTTTGGTT
134593 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
134614 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
134634 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
134655 GAA
1 GAA
134658 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:134661 original size:14 final size:14
Alignment explanation
Indices: 134642--134698 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
134632 GAGAAATGAA
134642 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
134656 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
134675 AATCGCAACGAGAG
1 AATCGCAACGAGAG
134689 AATCGCAACG
1 AATCGCAACG
134699 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:134674 original size:33 final size:33
Alignment explanation
Indices: 134593--134715 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
134583 TCTTTTGGTT
*
134593 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
134634 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
134667 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
134700 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
134716 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:134751 original size:14 final size:14
Alignment explanation
Indices: 134732--134769 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
134722 TTTGGTTTCG
134732 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
134746 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
134760 CGTTGCGATT
1 CGTTGCGATT
134770 TTCATTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.08, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:134810 original size:41 final size:41
Alignment explanation
Indices: 134753--134830 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
134743 TCTCGTTGCG
*
134753 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
134794 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
134831 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:134815 original size:20 final size:21
Alignment explanation
Indices: 134754--134829 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
134744 CTCGTTGCGA
134754 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
134775 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
134795 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
134816 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
134830 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:134951 original size:33 final size:33
Alignment explanation
Indices: 134909--134979 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
134899 AATACTAACT
*
134909 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
134942 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
134975 TGAAA
1 TGAAA
134980 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:135213 original size:22 final size:22
Alignment explanation
Indices: 135161--135215 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
135151 TGGTTGTGAG
**
135161 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
135183 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
135205 GGATTTCTTCG
1 GGATTTCTTCG
135216 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:135391 original size:20 final size:20
Alignment explanation
Indices: 135366--135579 Score: 252
Period size: 20 Copynumber: 10.7 Consensus size: 20
135356 CTTTAAATAT
135366 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
135386 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
135408 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
135427 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
135447 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
135467 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
135487 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
135507 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
135527 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
135547 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
135567 CGCGTTGCGATTT
1 CGCGTTGCGATTT
135580 TGGAAAATCG
Statistics
Matches: 167, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 148 0.89
21 15 0.09
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:135596 original size:21 final size:21
Alignment explanation
Indices: 135566--135648 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
135556 ATTTTCATAT
*
135566 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
135587 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
135608 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
135629 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
135649 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:135639 original size:42 final size:43
Alignment explanation
Indices: 135546--135644 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
135536 ATTTATGTGT
* *
135546 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
135587 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
135629 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
135645 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:136924 original size:43 final size:47
Alignment explanation
Indices: 136822--136927 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 47
136812 AGGATTAGAT
*
136822 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAATATTAGTTGTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAACATTAGTTGTAGTTA
*
136872 TTATTATTTTATTAGGAATT-A-GAGTTAAAACA-T-GTT-TAGTTTG
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACATTAGTTGTAG-TTA
136915 TTATTATTTTATT
1 TTATTATTTTATT
136928 CATTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
42 3 0.06
43 18 0.34
44 1 0.02
45 10 0.19
49 1 0.02
50 20 0.38
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (47 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACATTAGTTGTAGTTA
Found at i:137413 original size:40 final size:39
Alignment explanation
Indices: 137363--137439 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 39
137353 TCCTTAACTA
137363 GTTTTCAGCACCTAAAAGAAACACTAAATAATCCTAGTT
1 GTTTTCAGCACCTAAAAGAAACACTAAATAATCCTAGTT
137402 GTTTTCCAGCACCTAAAAGAAACACTAAATAATCCTAG
1 GTTTT-CAGCACCTAAAAGAAACACTAAATAATCCTAG
137440 CTGCTACTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 5 0.14
40 32 0.86
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (39 bp):
GTTTTCAGCACCTAAAAGAAACACTAAATAATCCTAGTT
Found at i:140224 original size:29 final size:31
Alignment explanation
Indices: 140155--140227 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
140145 GAAAATTACC
* *
140155 ACTTTGGTCCCT-AACTTTTAACAATTTTAT
1 ACTTTGGTCACTAAACTTTCAACAATTTTAT
*
140185 ACTTTGATCACTAAACTTTCAA-AA-TTTAT
1 ACTTTGGTCACTAAACTTTCAACAATTTTAT
*
140214 ATTTTGGTCACTAA
1 ACTTTGGTCACTAA
140228 CCAAAATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.46
30 12 0.32
31 8 0.22
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (31 bp):
ACTTTGGTCACTAAACTTTCAACAATTTTAT
Found at i:140411 original size:2 final size:2
Alignment explanation
Indices: 140404--140435 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
140394 CTACATATTC
140404 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
140436 TCCTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142067 original size:32 final size:32
Alignment explanation
Indices: 142027--142103 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
142017 CATTACGTTG
142027 AATAACCATAGCTGTTTGATTCACTCTATATA
1 AATAACCATAGCTGTTTGATTCACTCTATATA
*
142059 AATAACCATAGTTGTTTGATTCACTCTATATA
1 AATAACCATAGCTGTTTGATTCACTCTATATA
*
142091 AATAACTATAGCT
1 AATAACCATAGCT
142104 ATTTTGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (32 bp):
AATAACCATAGCTGTTTGATTCACTCTATATA
Found at i:142722 original size:24 final size:24
Alignment explanation
Indices: 142690--142737 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
142680 ATAAAAAAAT
142690 TAAACGAGCTTGTTCATGAACATA
1 TAAACGAGCTTGTTCATGAACATA
*
142714 TAAACGAGCTTGTTCGTGAACATA
1 TAAACGAGCTTGTTCATGAACATA
142738 AACGAACCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (24 bp):
TAAACGAGCTTGTTCATGAACATA
Found at i:145488 original size:2 final size:2
Alignment explanation
Indices: 145481--145512 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
145471 AAATTGAGAC
145481 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
145513 GAACAACCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146212 original size:18 final size:18
Alignment explanation
Indices: 146189--146235 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
146179 ATTTATCCCA
146189 AAGGACCACTTTGCCCCG
1 AAGGACCACTTTGCCCCG
146207 AAGGACCACTTTGCCCCG
1 AAGGACCACTTTGCCCCG
146225 AAGGACCACTT
1 AAGGACCACTT
146236 ATAATCCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17
Consensus pattern (18 bp):
AAGGACCACTTTGCCCCG
Found at i:150517 original size:18 final size:18
Alignment explanation
Indices: 150494--150585 Score: 130
Period size: 18 Copynumber: 5.1 Consensus size: 18
150484 GCACTGAAAA
* *
150494 TTTGTCCCAAAAGACCAC
1 TTTGTCCCGAAGGACCAC
150512 TTTGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
*
150530 TATGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
* *
150548 TTTTTCCCGAATGACCAC
1 TTTGTCCCGAAGGACCAC
*
150566 TATGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
150584 TT
1 TT
150586 ATAATCCCTC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (18 bp):
TTTGTCCCGAAGGACCAC
Found at i:150536 original size:36 final size:36
Alignment explanation
Indices: 150496--150585 Score: 144
Period size: 36 Copynumber: 2.5 Consensus size: 36
150486 ACTGAAAATT
* *
150496 TGTCCCAAAAGACCACTTTGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTTTGTCCCGAAGGACCACTA
* *
150532 TGTCCCGAAGGACCACTTTTTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTTTGTCCCGAAGGACCACTA
150568 TGTCCCGAAGGACCACTT
1 TGTCCCGAAGGACCACTT
150586 ATAATCCCTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (36 bp):
TGTCCCGAAGGACCACTTTGTCCCGAAGGACCACTA
Found at i:160784 original size:81 final size:81
Alignment explanation
Indices: 160689--160853 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 81
160679 ATAGCTTATT
*
160689 ACACAGACATGTATTCACATAACTCATTTAACATATATAGAATATCATGTAACATTCTAATAAAG
1 ACACACACATGTATTCACATAACTCATTTAACATATATAGAATATCATGTAACATTCTAATAAAG
160754 TCACATCATTTATCAC
66 TCACATCATTTATCAC
*
160770 ACACACACATGTATTCACATAACTCATTTAACATATATAGCATATCATGTAACATTCTAATAAAG
1 ACACACACATGTATTCACATAACTCATTTAACATATATAGAATATCATGTAACATTCTAATAAAG
160835 TCACATCATTTATCAC
66 TCACATCATTTATCAC
160851 ACA
1 ACA
160854 TACATACATT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (81 bp):
ACACACACATGTATTCACATAACTCATTTAACATATATAGAATATCATGTAACATTCTAATAAAG
TCACATCATTTATCAC
Found at i:161330 original size:53 final size:54
Alignment explanation
Indices: 161267--161390 Score: 146
Period size: 53 Copynumber: 2.3 Consensus size: 54
161257 GATACTACCC
* * * *
161267 TTCAAGGGTATCGATACTTTCC-CATGGTACCGATACCAAAATATCATTCAATG-
1 TTCAAGGGTATCGATAC-CTCCTCAAGGTACCGAAACCAAAATAGCATTCAATGT
* ** *
161320 TTCAAGGGTATTGATACCTCCTCAAGGTACCGAAACCAATCTAGCATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGAAACCAAAATAGCATTCAATGT
161374 TTCAA-GGTATCGATACC
1 TTCAAGGGTATCGATACC
161391 ATCCCATATA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
52 3 0.05
53 52 0.87
54 5 0.08
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCGAAACCAAAATAGCATTCAATGT
Found at i:167916 original size:31 final size:31
Alignment explanation
Indices: 167878--167955 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
167868 AGAGTCGAGG
*
167878 GTTTACCTATG-TCTTTCGAGACATATAGACA
1 GTTTACCTAGGTTCTTT-GAGACATATAGACA
* *
167909 GTTTACCTAGGTTCTTTGGGACCTATAGACA
1 GTTTACCTAGGTTCTTTGAGACATATAGACA
* *
167940 G-TTACCGAGGATCTTT
1 GTTTACCTAGGTTCTTT
167956 ATGACCTCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 13 0.32
31 23 0.56
32 5 0.12
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTTGAGACATATAGACA
Found at i:167955 original size:30 final size:30
Alignment explanation
Indices: 167901--168051 Score: 144
Period size: 30 Copynumber: 5.0 Consensus size: 30
167891 TTTCGAGACA
* * **
167901 TATAGACAGTTTACCTAGGTTCTTTGGGACC
1 TATAGACAG-TTACCGAGGATCTTTATGACC
167932 TATAGACAGTTACCGAGGATCTTTATGACC
1 TATAGACAGTTACCGAGGATCTTTATGACC
* *
167962 TCT-GCATAGTTACCGAGGATCTTTATGACC
1 TATAG-ACAGTTACCGAGGATCTTTATGACC
* * *
167992 TCTGGACAGTTACCGAGGATCTTTATAACC
1 TATAGACAGTTACCGAGGATCTTTATGACC
* * * * *
168022 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATAGACAGTTACCGAGGATCTTTATGACC
168051 T
1 T
168052 CTGGATAGGT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
29 13 0.12
30 83 0.78
31 10 0.09
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (30 bp):
TATAGACAGTTACCGAGGATCTTTATGACC
Found at i:167985 original size:60 final size:60
Alignment explanation
Indices: 167911--168051 Score: 194
Period size: 60 Copynumber: 2.4 Consensus size: 60
167901 TATAGACAGT
* * * *
167911 TTACCTAGGTTCTTTGGGACCTATAGACAGTTACCGAGGATCTTTATGACCTCTGCATAG
1 TTACCGAGGATCTTTGTGACCTATAGACAGTTACCGAGGATCTTTATAACCTCTGCATAG
* * * *
167971 TTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATAACCTCTGGATAG
1 TTACCGAGGATCTTTGTGACCTATAGACAGTTACCGAGGATCTTTATAACCTCTGCATAG
*
168031 TTACCG-GGGTCTTTGTGACCT
1 TTACCGAGGATCTTTGTGACCT
168052 CTGGATAGGT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 13 0.18
60 58 0.82
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (60 bp):
TTACCGAGGATCTTTGTGACCTATAGACAGTTACCGAGGATCTTTATAACCTCTGCATAG
Found at i:168078 original size:60 final size:60
Alignment explanation
Indices: 167936--168056 Score: 199
Period size: 60 Copynumber: 2.0 Consensus size: 60
167926 GGGACCTATA
*
167936 GACAGTTACCGAGGATCTTTATGACCTCTGCATAGTTACCGAGGATCTTTATGACCTCTG
1 GACAGTTACCGAGGATCTTTATAACCTCTGCATAGTTACCGAGGATCTTTATGACCTCTG
* * *
167996 GACAGTTACCGAGGATCTTTATAACCTCTGGATAGTTACCG-GGGTCTTTGTGACCTCTG
1 GACAGTTACCGAGGATCTTTATAACCTCTGCATAGTTACCGAGGATCTTTATGACCTCTG
168055 GA
1 GA
168057 TAGGTTCTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 18 0.32
60 39 0.68
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (60 bp):
GACAGTTACCGAGGATCTTTATAACCTCTGCATAGTTACCGAGGATCTTTATGACCTCTG
Found at i:173777 original size:30 final size:30
Alignment explanation
Indices: 173743--173874 Score: 194
Period size: 30 Copynumber: 4.4 Consensus size: 30
173733 GGTTCTTCGG
* *
173743 GACCTCTAGATAATTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
173773 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
173803 GACCTCTGGACAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
173833 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
173862 GACCTCTGGATAG
1 GACCTCTGGATAG
173875 GTCCTTTGGG
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
29 21 0.22
30 73 0.78
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:175119 original size:108 final size:110
Alignment explanation
Indices: 174991--175217 Score: 341
Period size: 112 Copynumber: 2.1 Consensus size: 110
174981 GTCATAGGTG
* * * *
174991 CATTTCAACATACTTTGTGTATGAAAGTTATCGAT-T-TTGCTTAATGCATAATGGTGCGTTTTC
1 CATTTCAACATACTTCGTGTATGAAAGTTATCGATATATTGCTTAATGCATAACGCTGCATTTTC
175054 GGCAAAAAAGGCACCACCCATGGTATTCATAATGAGGTGAATTAC
66 GGCAAAAAAGGCACCACCCATGGTATTCATAATGAGGTGAATTAC
*
175099 CATTTCAACATACTTCGTGTATGAATGTTATCGATCGATATTGCTTAATGCATAACGCTGCATTT
1 CATTTCAACATACTTCGTGTATGAAAGTTATCGAT--ATATTGCTTAATGCATAACGCTGCATTT
* ** *
175164 TCGGCATAAAAGGTGCCACCCATGTTATTCATAATGAGGTGAATTAC
64 TCGGCAAAAAAGGCACCACCCATGGTATTCATAATGAGGTGAATTAC
175211 CATTTCA
1 CATTTCA
175218 GCACTTCGGT
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
108 33 0.31
111 1 0.01
112 72 0.68
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (110 bp):
CATTTCAACATACTTCGTGTATGAAAGTTATCGATATATTGCTTAATGCATAACGCTGCATTTTC
GGCAAAAAAGGCACCACCCATGGTATTCATAATGAGGTGAATTAC
Found at i:183209 original size:22 final size:22
Alignment explanation
Indices: 183181--183242 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
183171 TACTGAAAGG
183181 AGTATCGATACCATAGTATAGA
1 AGTATCGATACCATAGTATAGA
183203 AGTATCGATACCATAGTATAGA
1 AGTATCGATACCATAGTATAGA
*
183225 AGTATCGATACAATAGTA
1 AGTATCGATACCATAGTA
183243 GGGGTATCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:183899 original size:112 final size:112
Alignment explanation
Indices: 183766--183999 Score: 387
Period size: 112 Copynumber: 2.1 Consensus size: 112
183756 ATCATAGGTG
* * * *
183766 CATTTCGACATACTTTGTGTATGAAAGTTATCGATCGATTTTGCTTAATGCATAACGGTGCGTTT
1 CATTTCAACATACTTCGTGTATGAAAATTATCGATCGATTTTGCTTAATGCATAACGGTGCATTT
183831 TCGGCAAAAAAGGCACCACCCATGGTATTCATAATGAGGTGAATTAC
66 TCGGCAAAAAAGGCACCACCCATGGTATTCATAATGAGGTGAATTAC
183878 CATTTCAACATACTTCGTGTATGAAAATTATCGATCGATTTTGCTTAATGCATAACGGTGCATTT
1 CATTTCAACATACTTCGTGTATGAAAATTATCGATCGATTTTGCTTAATGCATAACGGTGCATTT
* *** *
183943 TCGGCATAAAAGGTGTCACCCATGGTATTTATAATGAGGTGAATTAC
66 TCGGCAAAAAAGGCACCACCCATGGTATTCATAATGAGGTGAATTAC
183990 CATTTCAACA
1 CATTTCAACA
184000 CTTCGGTGCA
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (112 bp):
CATTTCAACATACTTCGTGTATGAAAATTATCGATCGATTTTGCTTAATGCATAACGGTGCATTT
TCGGCAAAAAAGGCACCACCCATGGTATTCATAATGAGGTGAATTAC
Found at i:193781 original size:189 final size:189
Alignment explanation
Indices: 193461--193838 Score: 720
Period size: 189 Copynumber: 2.0 Consensus size: 189
193451 CAAAGCTTCC
193461 CCTTTTCCATTTCATCGTTCATGCAAACTCCGAACGACTGAAGCTTTACTCCTGTTTCCTGAGAA
1 CCTTTTCCATTTCATCGTTCATGCAAACTCCGAACGACTGAAGCTTTACTCCTGTTTCCTGAGAA
193526 GAGCAAGACAGAGAGAAGCTACGAGTAAAGAAGTGAAACAAAAAAAAAACAGAAATTAAAAGTTG
66 GAGCAAGACAGAGAGAAGCTACGAGTAAAGAAGTGAAACAAAAAAAAAACAGAAATTAAAAGTTG
193591 TTATTTTTTGGTGTTGGGTTATAACTCACAAAGGATCTTTGGATTGCACACGAAAGCAA
131 TTATTTTTTGGTGTTGGGTTATAACTCACAAAGGATCTTTGGATTGCACACGAAAGCAA
193650 CCTTTTCCATTTCATCGTTCATGCAAACTCCGAACGACTGAAGCTTTACTCCTGTTTCCTGAGAA
1 CCTTTTCCATTTCATCGTTCATGCAAACTCCGAACGACTGAAGCTTTACTCCTGTTTCCTGAGAA
* * *
193715 GAGTATGACAGAGAGAAGCTATGAGTAAAGAAGTGAAACAAAAAAAAAACAGAAATTAAAAGTTG
66 GAGCAAGACAGAGAGAAGCTACGAGTAAAGAAGTGAAACAAAAAAAAAACAGAAATTAAAAGTTG
*
193780 TTATTTTTTGGTGTTGGGTTATAACTCACAAAGGATCTTTGGGTTGCACACGAAAGCAA
131 TTATTTTTTGGTGTTGGGTTATAACTCACAAAGGATCTTTGGATTGCACACGAAAGCAA
193839 GAGATGAGAC
Statistics
Matches: 185, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 185 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (189 bp):
CCTTTTCCATTTCATCGTTCATGCAAACTCCGAACGACTGAAGCTTTACTCCTGTTTCCTGAGAA
GAGCAAGACAGAGAGAAGCTACGAGTAAAGAAGTGAAACAAAAAAAAAACAGAAATTAAAAGTTG
TTATTTTTTGGTGTTGGGTTATAACTCACAAAGGATCTTTGGATTGCACACGAAAGCAA
Found at i:194721 original size:177 final size:177
Alignment explanation
Indices: 194425--194783 Score: 623
Period size: 177 Copynumber: 2.0 Consensus size: 177
194415 AATATTAAAT
194425 ATATTATATATAACATATGAACTCAGTCCAAACCATTTAAAACTCAATTAATAATTTAAGATCCA
1 ATATTATATATAACATATGAACTCAGTCCAAACCATTTAAAACTCAATTAATAATTTAAGATCCA
* * *
194490 TTAGCTTTTAAAACTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTTTATTTTATAA
66 ATAACTTTTAAAACTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTTATAA
194555 TTATATATTATTTAAATTAATT-GTAAACTGTTTTTTTGAATTAAAAA
131 TTATATATTATTTAAATTAATTAG-AAACTGTTTTTTTGAATTAAAAA
*
194602 ATATTATATATAACATATGAGCTCA-TCCAAGACCATTTAAAACTCAATTAATAATTTAAGATCC
1 ATATTATATATAACATATGAACTCAGTCCAA-ACCATTTAAAACTCAATTAATAATTTAAGATCC
* * *
194666 AATAATTTTTATACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTTATA
65 AATAACTTTTAAAACTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTTATA
194731 ATTATATATTATTTAAATTAATTAGAAACTGTTTTTTTGAATTAAAAA
130 ATTATATATTATTTAAATTAATTAGAAACTGTTTTTTTGAATTAAAAA
194779 ATATT
1 ATATT
194784 TAATTTTTAT
Statistics
Matches: 173, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
176 5 0.03
177 167 0.97
178 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (177 bp):
ATATTATATATAACATATGAACTCAGTCCAAACCATTTAAAACTCAATTAATAATTTAAGATCCA
ATAACTTTTAAAACTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTTATAA
TTATATATTATTTAAATTAATTAGAAACTGTTTTTTTGAATTAAAAA
Found at i:201985 original size:42 final size:42
Alignment explanation
Indices: 201920--202016 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
201910 GTAAATAAAA
* * * * *
201920 AAACGCCGCAATAGGTTCGGACATTT-AGCGGCGTTTTTTTAG
1 AAACGCCACAATAAGTTCAGACATTTGA-CGCCGTTTTTTTAC
* *
201962 ACATGCCACAATAAGTTCAGACATTTGACGCCGTTTTTTTAC
1 AAACGCCACAATAAGTTCAGACATTTGACGCCGTTTTTTTAC
202004 AAACGCCACAATA
1 AAACGCCACAATA
202017 TGTTATGACA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (42 bp):
AAACGCCACAATAAGTTCAGACATTTGACGCCGTTTTTTTAC
Found at i:202027 original size:42 final size:41
Alignment explanation
Indices: 201920--202027 Score: 101
Period size: 42 Copynumber: 2.6 Consensus size: 41
201910 GTAAATAAAA
* * * * *
201920 AAACGCCGCAATAGGTTCGGACATTTAGCGGCGTTTTTTTAG
1 AAACGCCACAATAAGTT-AGACATTTAGCGCCGTTTTTTTAC
* *
201962 ACATGCCACAATAAGTTCAGACATTT-GACGCCGTTTTTTTAC
1 AAACGCCACAATAAGTT-AGACATTTAG-CGCCGTTTTTTTAC
*
202004 AAACGCCACAATATGTTATGACAT
1 AAACGCCACAATAAGTTA-GACAT
202028 GTAGTGACAT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.96
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (41 bp):
AAACGCCACAATAAGTTAGACATTTAGCGCCGTTTTTTTAC
Found at i:208795 original size:12 final size:12
Alignment explanation
Indices: 208778--208809 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
208768 GCAAGAAAGA
208778 AAAAAGAAGAAG
1 AAAAAGAAGAAG
208790 AAAAAGAAGAAG
1 AAAAAGAAGAAG
208802 AAGAAAGA
1 AA-AAAGA
208810 TAACAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:210587 original size:14 final size:14
Alignment explanation
Indices: 210568--210596 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
210558 GATGAACGCT
210568 GGTGTAAAGAAATA
1 GGTGTAAAGAAATA
210582 GGTGTAAAGAAATA
1 GGTGTAAAGAAATA
210596 G
1 G
210597 TGAAGACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (14 bp):
GGTGTAAAGAAATA
Found at i:211444 original size:101 final size:102
Alignment explanation
Indices: 211266--211487 Score: 288
Period size: 101 Copynumber: 2.2 Consensus size: 102
211256 GTTTGAGATA
*
211266 TTTCACTTGAAACAAAATTGATCTCAATTGAGACTATTTTCTTACAAATAAATTTCTTCTCGCTT
1 TTTCACTTGAAACAAAATTGATCTCAATTGAGACTATTTTCCTACAAATAAATTTCTTCTCGCTT
*
211331 GAGACAACTTTCCCTTGAAAT-ACAAATTTTTAAATTG
66 GAGACAACTTTCCCTTGAAATGA-AAATTTTGAAATTG
* * * * *
211368 TTTCACTTGAAAAAAAATTGAT-TCACTTGAGATTGTTTTCCTATAAATAAATTT-TGTCTCGCT
1 TTTCACTTGAAACAAAATTGATCTCAATTGAGACTATTTTCCTACAAATAAATTTCT-TCTCGCT
* ** *
211431 TGAGATAGTTTTCCCTTTAAATGAAAATTTTGAAATTG
65 TGAGACAACTTTCCCTTGAAATGAAAATTTTGAAATTG
* *
211469 TTTCCCTCGAAACAAAATT
1 TTTCACTTGAAACAAAATT
211488 TTATCTCACC
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
100 1 0.01
101 81 0.78
102 22 0.21
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (102 bp):
TTTCACTTGAAACAAAATTGATCTCAATTGAGACTATTTTCCTACAAATAAATTTCTTCTCGCTT
GAGACAACTTTCCCTTGAAATGAAAATTTTGAAATTG
Found at i:212085 original size:138 final size:137
Alignment explanation
Indices: 211924--212316 Score: 430
Period size: 138 Copynumber: 2.9 Consensus size: 137
211914 CCGTCCACTG
* * * *
211924 ACCAGATCTCCTCAACGTGAAGGAGCAGTGTCATCCTCAGAAAATCAAACTTTCTCAACACGAAG
1 ACCAGATCTCCTCAATGCGAAGGAGCAGTGTCATCCTCAGACAATCAAACTTCCTCAACACGAAG
211989 GAACCATGTTGTCTCCAAATTATCCAAATATGTCCAGACATCCTCAATGAGAAGAAAAAAATGTT
66 GAACCATGTTGTCTCCAAATTATCCAAATATGTCCAGACATCCTCAATGAGAAG-AAAAAATGTT
*
212054 ATCTACCA
130 ATCCACCA
* * * * * * *
212062 ATCAGATCTCCTGAATGCGAAGGATCAGTGTCATCATCAGACAATCAGACTTCCTCAACATGAAA
1 ACCAGATCTCCTCAATGCGAAGGAGCAGTGTCATCCTCAGACAATCAAACTTCCTCAACACGAAG
* * ** * * * * *
212127 GAACCGTGTTGTCTCCAAATTATCCAAATATTTTTAGACGTCATCAATGCGAAGAAACAATGTTT
66 GAACCATGTTGTCTCCAAATTATCCAAATATGTCCAGACATCCTCAATGAGAAGAAAAAATGTTA
*
212192 TCCACCG
131 TCCACCA
* * * * * *
212199 ACCATATCTCCTTAATGCGAAGGAGCATTTTCATACTCAGGCAAT-AAGACTTCCTCAACACGAA
1 ACCAGATCTCCTCAATGCGAAGGAGCAGTGTCATCCTCAGACAATCAA-ACTTCCTCAACACGAA
* ** * * * * *
212263 GGAACCATGTTATCTTTAAATTATCCAGAT-TGACCAAACTTTCTCAATGAGAAG
65 GGAACCATGTTGTCTCCAAATTATCCAAATATGTCCAGACATCCTCAATGAGAAG
212317 GAACAACGCC
Statistics
Matches: 206, Mismatches: 48, Indels: 4
0.80 0.19 0.02
Matches are distributed among these distances:
136 16 0.08
137 89 0.43
138 101 0.49
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (137 bp):
ACCAGATCTCCTCAATGCGAAGGAGCAGTGTCATCCTCAGACAATCAAACTTCCTCAACACGAAG
GAACCATGTTGTCTCCAAATTATCCAAATATGTCCAGACATCCTCAATGAGAAGAAAAAATGTTA
TCCACCA
Found at i:212466 original size:104 final size:104
Alignment explanation
Indices: 212286--212538 Score: 355
Period size: 104 Copynumber: 2.4 Consensus size: 104
212276 CTTTAAATTA
* * *
212286 TCCAGATTGAC-CAAACTTTCTCAATGAGAAGGAACAACGCCATCTGAAAGCAGCCATAACTCTT
1 TCCAGATTGACTC-AACTTTCTCAACGAGAAGGAACAACGCCATCTAAAAGCAGCCAGAACTCTT
* ** *
212350 CAACATGGATGAGTAGTATCGTCTTCAACACCAAATTATC
65 CAACATGGATGAGCAACATCATCTTCAACACCAAATTATC
* * *
212390 TCCAGATTGACTCAACTTTCTTAACAAGAAGGAACAACGCCATCTAAAAGTAGCCAGAACTCTTC
1 TCCAGATTGACTCAACTTTCTCAACGAGAAGGAACAACGCCATCTAAAAGCAGCCAGAACTCTTC
* *
212455 AACATGGATGAGCAACGTCATTTTCAACACCAAATTATC
66 AACATGGATGAGCAACATCATCTTCAACACCAAATTATC
* * *
212494 TCCAGATTGACTCGACTTCCTCAACGAGAAGAAACAACGCCATCT
1 TCCAGATTGACTCAACTTTCTCAACGAGAAGGAACAACGCCATCT
212539 TCAGTAAACA
Statistics
Matches: 131, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
104 130 0.99
105 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (104 bp):
TCCAGATTGACTCAACTTTCTCAACGAGAAGGAACAACGCCATCTAAAAGCAGCCAGAACTCTTC
AACATGGATGAGCAACATCATCTTCAACACCAAATTATC
Found at i:217276 original size:21 final size:22
Alignment explanation
Indices: 217252--217298 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
217242 ATAAAATGTC
*
217252 TTTTAACATATATTAAATAAT-
1 TTTTAACATATATTAAAGAATG
* *
217273 TTTTAATATATTTTAAAGAATG
1 TTTTAACATATATTAAAGAATG
217295 TTTT
1 TTTT
217299 TTGGATTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTTAACATATATTAAAGAATG
Found at i:219398 original size:13 final size:13
Alignment explanation
Indices: 219382--219416 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
219372 TAAGATTTTC
219382 TTTTTGAAAATCA
1 TTTTTGAAAATCA
219395 TTTTTG-AAATCA
1 TTTTTGAAAATCA
*
219407 ATTTTGAAAA
1 TTTTTGAAAA
219417 ATTACCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:221196 original size:12 final size:13
Alignment explanation
Indices: 221179--221211 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
221169 ATGGGCAAAA
*
221179 TTTGAAAACTAT-
1 TTTGAAAACAATG
221191 TTTGAAAACAATG
1 TTTGAAAACAATG
221204 TTTGAAAA
1 TTTGAAAA
221212 ATCAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:223793 original size:12 final size:12
Alignment explanation
Indices: 223776--223800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
223766 ATGATAGTTC
223776 TCCAACGTCATG
1 TCCAACGTCATG
223788 TCCAACGTCATG
1 TCCAACGTCATG
223800 T
1 T
223801 GTATTTATAA
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:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:237234 original size:60 final size:59
Alignment explanation
Indices: 237157--237309 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 59
237147 GTTCCTATAC
* * * *
237157 TTTTAAATATTTTAATTTCATCCCTAAACTATA-ATTATCATTCTAAATTAGTCCTCAAAC-
1 TTTTAAACATTTCAATTTCATCCC-AAACTATACA-T-TCATTCAAAATTAGTCCCCAAACT
* *
237217 TTTTGAGCATTTCAATTTCATCCCCAAACTATTACATTCATTCAAAATTAGTCCCCAAACT
1 TTTTAAACATTTCAATTTCAT-CCCAAACTA-TACATTCATTCAAAATTAGTCCCCAAACT
* *
237278 TTTTAAACATTCCAATTTCATCTCAAACTATA
1 TTTTAAACATTTCAATTTCATCCCAAACTATA
237310 TGCATATACT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
59 2 0.03
60 52 0.66
61 24 0.30
62 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (59 bp):
TTTTAAACATTTCAATTTCATCCCAAACTATACATTCATTCAAAATTAGTCCCCAAACT
Found at i:238802 original size:36 final size:36
Alignment explanation
Indices: 238755--238859 Score: 151
Period size: 36 Copynumber: 2.9 Consensus size: 36
238745 GATACAATAT
* *
238755 GTCCATCACCATTATCACGCCTATATCTTTACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
238791 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
238827 TTCCATCACCA-TATCACGCAC-ATATTATCACCA
1 GTCCATCACCATTATCACGC-CTATATCATCACCA
238860 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:239275 original size:17 final size:18
Alignment explanation
Indices: 239247--239285 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
239237 CAACAACAAA
239247 AAAACAACAAGA-AAGAAG
1 AAAACAACAAGAGAA-AAG
239265 AAAACAA-AAGAGAAAAG
1 AAAACAACAAGAGAAAAG
239282 AAAA
1 AAAA
239286 AGACTCCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAACAACAAGAGAAAAG
Found at i:239551 original size:24 final size:25
Alignment explanation
Indices: 239507--239556 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
239497 TTACTATTTC
*
239507 ATTTCATTTTCTTTCATCTTTTCTT
1 ATTTCATTTACTTTCATCTTTTCTT
239532 ATTTCA-TTACTTT-ATCCTTTTCTT
1 ATTTCATTTACTTTCAT-CTTTTCTT
239556 A
1 A
239557 ACCTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 15 0.65
25 6 0.26
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTCATTTACTTTCATCTTTTCTT
Found at i:243356 original size:22 final size:23
Alignment explanation
Indices: 243322--243374 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
243312 CACCATAGTC
*
243322 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACGCCCATAT
243345 CATCACCA-TATCACGCCCATAT
1 CATCACCATTATCACGCCCATAT
*
243367 TATCACCA
1 CATCACCA
243375 ACTTATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.32, C:0.38, G:0.04, T:0.26
Consensus pattern (23 bp):
CATCACCATTATCACGCCCATAT
Found at i:243372 original size:36 final size:36
Alignment explanation
Indices: 243283--243354 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
243273 GATACAATCT
*
243283 GTCCATCACCATTATCACGCCTATATCTTCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
243319 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
243355 TCACGCCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.36, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:244128 original size:10 final size:10
Alignment explanation
Indices: 244110--244163 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
244100 GATTCATTTG
*
244110 TACACATACA
1 TACATATACA
244120 TACATATACA
1 TACATATACA
*
244130 T--ATATATA
1 TACATATACA
*
244138 TACATATATA
1 TACATATACA
*
244148 TATATATA-A
1 TACATATACA
244157 TACATAT
1 TACATAT
244164 GTATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
8 7 0.18
9 7 0.18
10 24 0.63
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (10 bp):
TACATATACA
Found at i:244136 original size:2 final size:2
Alignment explanation
Indices: 244123--244203 Score: 92
Period size: 2 Copynumber: 41.0 Consensus size: 2
244113 ACATACATAC
* * *
244123 AT AT AC AT AT AT AT AT AC AT AT AT AT AT AT AT A- AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
244164 GT AT AT AT AT GT AT AT AT AT AT AT AT GT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244204 GTGTGTGTGT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:247293 original size:23 final size:23
Alignment explanation
Indices: 247241--247296 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
247231 TTTTCATGTA
* *
247241 ATATTTTTTACATTTTATGTATT
1 ATATTTTTTACATTTAATATATT
* *
247264 TTCTTTTTTAC-TTTAATATATAT
1 ATATTTTTTACATTTAATATAT-T
247287 ATATTTTTTA
1 ATATTTTTTA
247297 GATTACACAC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (23 bp):
ATATTTTTTACATTTAATATATT
Found at i:247360 original size:40 final size:39
Alignment explanation
Indices: 247314--247405 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 39
247304 CACACACATA
247314 TATATATATATATGTTA-ATTTTCATTATCTGTTTTATTAAT
1 TATATATATATAT-TTACATTTT-ATTATCT-TTTTATTAAT
* * *
247355 T-TATATATATATTTACTATTTTTTTATGTTTTTATTTAT
1 TATATATATATATTTAC-ATTTTATTATCTTTTTATTAAT
247394 TATATATATATA
1 TATATATATATA
247406 CATATTATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
39 13 0.29
40 26 0.58
41 6 0.13
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (39 bp):
TATATATATATATTTACATTTTATTATCTTTTTATTAAT
Found at i:251860 original size:195 final size:195
Alignment explanation
Indices: 251528--251889 Score: 625
Period size: 195 Copynumber: 1.9 Consensus size: 195
251518 ATTAAATCCG
*
251528 TAAAGCTGAGCTCTTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
* *
251593 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGTAATTCGGTGTTTGCTCCACTACTT
66 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
*
251658 TTGTCAGGCCAAAGACTTTGTGATGAAACGAACCCTTCAGTGATTATAATACTAAGTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAAACAAACCCTTCAGTGATTATAATACTAAGTTGTCCCTC
* * *
251723 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTTGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
* *
251788 ATATATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTATTT
66 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
* *
251853 TTGTCAGGTCAAAGACTTTGTGATGAGACAAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAAACAAACCCTT
251890 TAGTTAAACC
Statistics
Matches: 156, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
195 156 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (195 bp):
TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
TTGTCAGGCCAAAGACTTTGTGATGAAACAAACCCTTCAGTGATTATAATACTAAGTTGTCCCTC
Found at i:253072 original size:36 final size:36
Alignment explanation
Indices: 253032--253151 Score: 118
Period size: 36 Copynumber: 3.3 Consensus size: 36
253022 CAGATGATTA
*
253032 TCTCACTTGAGATTGTTTTTCTTAAAACATACTTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAGACTTTG
* * * *
253068 TCTCACTTGAGACTGTTTTACTCGAAAGA-AGA-TTTA
1 TCTCACTTGAGATTGTTTTTCT-TAAA-ACAGACTTTG
* ** * *
253104 TTTCACTCAAGTTTGCTTTTCTTAAAACAGACTTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAGACTTTG
253140 TCTCACTTGAGA
1 TCTCACTTGAGA
253152 CCGTTTTCAC
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
34 1 0.02
35 6 0.10
36 49 0.79
37 5 0.08
38 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (36 bp):
TCTCACTTGAGATTGTTTTTCTTAAAACAGACTTTG
Found at i:253127 original size:72 final size:76
Alignment explanation
Indices: 253048--253189 Score: 238
Period size: 72 Copynumber: 1.9 Consensus size: 76
253038 TTGAGATTGT
* *
253048 TTTTCTTAAAACATACTTTGTCTCACTTGAGACTGTTTT-ACTCGAAAGAA-G-ATTT-ATTTCA
1 TTTTCTTAAAACAGACTTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCA
253109 CTCAAGTTTGC
66 CTCAAGTTTGC
253120 TTTTCTTAAAACAGACTTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCA
1 TTTTCTTAAAACAGACTTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCA
253185 CTCAA
66 CTCAA
253190 TACTGTTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
72 37 0.58
73 11 0.17
74 1 0.02
75 4 0.06
76 11 0.17
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (76 bp):
TTTTCTTAAAACAGACTTTGTCTCACTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCA
CTCAAGTTTGC
Found at i:253377 original size:37 final size:37
Alignment explanation
Indices: 253317--253402 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
253307 TTGAAAAAAT
** *
253317 TTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAGG
1 TTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGG
* *
253353 TTCCCTTGAAACAAAATTTTGTCTCTCTTGATACAGT
1 TTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGG
*
253390 TTCTCTTGAAACA
1 TTCCCTTGAAACA
253403 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 11 0.26
37 32 0.74
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGG
Found at i:253395 original size:102 final size:103
Alignment explanation
Indices: 253271--253476 Score: 360
Period size: 102 Copynumber: 2.0 Consensus size: 103
253261 ACTAGGTTTC
*
253271 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATAAATTTT
253336 GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAAT-TTT
66 GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTT
* *
253373 GTCTCTCTTGATACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATAAATTTT
* *
253438 GTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTT
66 GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTT
253476 G
1 G
253477 AATCTGTTTC
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
102 94 0.96
103 4 0.04
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (103 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATAAATTTT
GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTT
Found at i:253458 original size:65 final size:65
Alignment explanation
Indices: 253353--253523 Score: 211
Period size: 65 Copynumber: 2.6 Consensus size: 65
253343 TTGAGATAGG
*
253353 TTCCCTTGAAACAAAATTTTGTCTCTCTTGATACAGTTTCTCTTGAAACATAAA-CATTGAAAAC
1 TTCCCTTGAAA-AAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAATCATTG-AAAC
253417 -AT
63 TAT
* * * * *
253419 TTCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGT
1 TTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCATTGAAACTAT
* * * *
253484 TTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCT
1 TTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCT
253524 TTTGGAACTA
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 6 0.07
65 75 0.82
66 11 0.12
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (65 bp):
TTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCATTGAAACTAT
Found at i:253489 original size:167 final size:167
Alignment explanation
Indices: 253271--253642 Score: 505
Period size: 167 Copynumber: 2.2 Consensus size: 167
253261 ACTAGGTTTC
* * **
253271 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAAATTTCCCTTGAAATGAATTT
1 GTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAAAAAATTTCCCTTGAAACAAATTT
* * * * *
253335 TGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATTTTGTCTCTCTTGATACAGTTTCTCTTGAA
65 CGTCTCCCTTGAGACAGGTTCCCTTGAAACAAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAA
253400 ACATAAACATTGAAAACATTTCCCTTGAAATAAATTTT
130 ACATAAACATTGAAAACATTTCCCTTGAAATAAATTTT
****
253438 GTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTC
1 GTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAAAAAATTTCCCTTGAAACAAATTTC
** ** * * * *
253503 GTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGATAGTTTCTCTTGAAA
66 GTCTCCCTTGAGACAGGTTCCCTTGAAACAAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAA
*
253568 CATAAACATTGAAAACATTTCCCTTGAAATGAATTTT
131 CATAAACATTGAAAACATTTCCCTTGAAATAAATTTT
* *
253605 GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAAT-TTTG
1 GTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTG
253643 TCTCCCTTGA
Statistics
Matches: 180, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
166 7 0.04
167 173 0.96
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (167 bp):
GTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAAAAAATTTCCCTTGAAACAAATTTC
GTCTCCCTTGAGACAGGTTCCCTTGAAACAAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAA
CATAAACATTGAAAACATTTCCCTTGAAATAAATTTT
Found at i:253545 original size:102 final size:101
Alignment explanation
Indices: 253418--253804 Score: 454
Period size: 102 Copynumber: 3.8 Consensus size: 101
253408 ATTGAAAACA
* * * * *
253418 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATC
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC
* * * * *
253481 TGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
65 -ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
* * * * *
253519 TTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
**
253584 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
* * * *
253621 GTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAAC
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
** * *
253686 ATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAG
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
** *
253723 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGACGCATAAACTTTGAAAACA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
253788 GTTTCCTTTGAAACAAA
66 -TTTCCCTTGAAACAAA
253805 ATCTTTGAAT
Statistics
Matches: 245, Mismatches: 37, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
101 56 0.23
102 183 0.75
103 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (101 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
Found at i:253574 original size:269 final size:269
Alignment explanation
Indices: 253219--253738 Score: 914
Period size: 269 Copynumber: 1.9 Consensus size: 269
253209 TTTTGTCTCT
* * *
253219 CTTGAAACAAATTTCGTCTCTCATGAGACATTTTCTTTTAGAACTAGGTTTCGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCCCATGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGA
253284 CAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
66 CAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
* * *
253349 TAGGTTCCCTTGAAACAAAATTTTGTCTCTCTTGATACAGTTTCTCTTGAAACATAAACATTGAA
131 TAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAA
* *
253414 AACATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAA
196 AACATTTCCCTTGAAATAAATTTTGTCACTCATGAGATAGTTTCTCTTGAAACAAAATCTTTGAA
253479 TCTGTTTCC
261 TCTGTTTCC
* * *
253488 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCCCATGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGA
* *
253553 TAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
66 CAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
253618 TAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAA
131 TAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAA
*
253683 AACATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAGTTTCTCTTGAAACAAA
196 AACATTTCCCTTGAAATAAATTTTGTCACTCATGAGATAGTTTCTCTTGAAACAAA
253739 TTTTGTCTCT
Statistics
Matches: 237, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
269 237 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (269 bp):
CTTGAAACAAATTTCGTCTCCCATGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGA
CAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
TAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAA
AACATTTCCCTTGAAATAAATTTTGTCACTCATGAGATAGTTTCTCTTGAAACAAAATCTTTGAA
TCTGTTTCC
Found at i:253667 original size:37 final size:37
Alignment explanation
Indices: 253599--253671 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
253589 CCTTGAAATG
* * *
253599 AATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGACAGGTTACCTTGAAACAA
* *
253636 AATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGGTTACCTTGAAACA
253672 TAAACATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGACAGGTTACCTTGAAACAA
Found at i:253721 original size:167 final size:161
Alignment explanation
Indices: 253353--253736 Score: 407
Period size: 167 Copynumber: 2.3 Consensus size: 161
253343 TTGAGATAGG
* * *
253353 TTCCCTTGAAACAAAATTTTGTCTCTCTTGATACAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTCCCTTG-AA-ATAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
253418 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTG
64 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTTG-ATC--
* * * *
253483 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATT
126 -TTCCCTTGAAACAAATTTCGACTACATTGAAACATT
** * *
253520 TTCTTTTGGAACTAAGTTTTATCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTCCCTT-GAAATAA-TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
*
253585 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAAT-TTTG-TC-TC
64 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTTGATCTTC
* **
253647 CCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAACA-T
129 CCTTGAAACAAATT-TC--G--AC-T--ACATTG-AAACATT
* *
253688 TTCCCTTGAAATGAATTTTGTCACTCATGAGATAGTTTCTCTTGAAACA
1 TTCCCTTGAAAT-AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
253737 AATTTTGTCT
Statistics
Matches: 182, Mismatches: 23, Indels: 24
0.79 0.10 0.10
Matches are distributed among these distances:
160 13 0.07
161 2 0.01
163 1 0.01
164 2 0.01
165 1 0.01
166 7 0.04
167 139 0.76
168 13 0.07
169 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (161 bp):
TTCCCTTGAAATAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATT
TCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATCTTTGATCTTCCC
TTGAAACAAATTTCGACTACATTGAAACATT
Found at i:253741 original size:36 final size:36
Alignment explanation
Indices: 253687--253768 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 36
253677 ATTGAAAACA
* ** *
253687 TTTCCCTTGAAATGAATTTTGTCACTCATGAGATAG
1 TTTCTCTTGAAACAAATTTTGTCACTCATGAGACAG
* *
253723 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCACTCATGAGACAG
253759 TTTCTCTTGA
1 TTTCTCTTGA
253769 CGCATAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCACTCATGAGACAG
Found at i:253882 original size:34 final size:34
Alignment explanation
Indices: 253829--253925 Score: 115
Period size: 34 Copynumber: 2.9 Consensus size: 34
253819 TTTAGGTTAA
* * *
253829 ACAAATCTCGTCTCCCTTGAGACAGTTTCT-TTC
1 ACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTC
* * *
253862 AGAAGTTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 ACAA-ATTTTGTCTCTCTTGAGACAGTTTCTCTTC
*
253897 ACAAATTTTGTCTCTCTTGAGACAATTTC
1 ACAAATTTTGTCTCTCTTGAGACAGTTTC
253926 CCTTGAAACT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
33 3 0.06
34 45 0.85
35 5 0.09
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (34 bp):
ACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTC
Found at i:255108 original size:2 final size:2
Alignment explanation
Indices: 255103--255156 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
255093 TTTTACTTTA
* * *
255103 AT AT AT AT AT AT AT AT AT AT AT AT -T TT AG AT -T AC 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
255143 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
255157 GTTAATTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:255190 original size:40 final size:39
Alignment explanation
Indices: 255144--255235 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 39
255134 TACATATATA
255144 TATATATATATATGTTA-ATTTTCATTATCTGTTTTATTAAT
1 TATATATATATAT-TTACATTTT-ATTATCT-TTTTATTAAT
* * *
255185 T-TATATATATATTTACTATTTTTTTATGTTTTTATTTAT
1 TATATATATATATTTAC-ATTTTATTATCTTTTTATTAAT
255224 TATATATATATA
1 TATATATATATA
255236 CATATTATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
39 13 0.29
40 26 0.58
41 6 0.13
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (39 bp):
TATATATATATATTTACATTTTATTATCTTTTTATTAAT
Found at i:255395 original size:17 final size:18
Alignment explanation
Indices: 255373--255414 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
255363 ATTTCATTTC
255373 TTTTTATGGATTTT-ATT
1 TTTTTATGGATTTTAATT
*
255390 TTTTTATGTATTTTAATT
1 TTTTTATGGATTTTAATT
*
255408 TATTTAT
1 TTTTTAT
255415 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (18 bp):
TTTTTATGGATTTTAATT
Found at i:255421 original size:18 final size:17
Alignment explanation
Indices: 255375--255432 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
255365 TTCATTTCTT
* *
255375 TTTATGGATTTTATTTT
1 TTTATGTATTTTATTTA
255392 TTTATGTATTTTAATTTA
1 TTTATGTATTTT-ATTTA
*
255410 TTTATTTATTTTTATTTAA
1 TTTATGTA-TTTTATTT-A
255429 TTTA
1 TTTA
255433 CTTGTTATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.31
18 15 0.43
19 9 0.26
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTATGTATTTTATTTA
Found at i:256215 original size:80 final size:81
Alignment explanation
Indices: 256078--256244 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 81
256068 TATTGAAGAG
256078 ATAGCTTGGATTACAGAGAGAGAGAGAGAGGGACTCAAAGCATGCTCATTTATCCACCTTCCAGG
1 ATAGCTTGGATTAC--A-AGAGAGAGAGAGGGACTCAAAGCATGCTCATTTATCCACCTTCCAGG
256143 GAATTTACTTCCATATCCA
63 GAATTTACTTCCATATCCA
256162 ATAGCTTGGATTAC-AGAGAGAGAGAGGGACTCAAAGCATGCTCATTTATCCACCTTCCAGGGAA
1 ATAGCTTGGATTACAAGAGAGAGAGAGGGACTCAAAGCATGCTCATTTATCCACCTTCCAGGGAA
256226 TTTACTTCCATATCCA
66 TTTACTTCCATATCCA
256242 ATA
1 ATA
256245 TCTTCAAAAC
Statistics
Matches: 83, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
80 69 0.83
84 14 0.17
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (81 bp):
ATAGCTTGGATTACAAGAGAGAGAGAGGGACTCAAAGCATGCTCATTTATCCACCTTCCAGGGAA
TTTACTTCCATATCCA
Found at i:257523 original size:2 final size:2
Alignment explanation
Indices: 257516--257552 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
257506 CTCTACCTCT
* *
257516 TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
257553 GAATGTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:257553 original size:14 final size:14
Alignment explanation
Indices: 257516--257558 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
257506 CTCTACCTCT
* *
257516 TATATATATATATA
1 TATATATATGTATG
257530 TATATATATGTATG
1 TATATATATGTATG
*
257544 TATATATATGAATG
1 TATATATATGTATG
257558 T
1 T
257559 GTATTTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:257581 original size:33 final size:33
Alignment explanation
Indices: 257539--257605 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
257529 ATATATATAT
257539 GTATGTATATATATGAATGTGTATTTTATGTTA
1 GTATGTATATATATGAATGTGTATTTTATGTTA
257572 GTATGTATATATATGAATGTGTATTTTATGTTA
1 GTATGTATATATATGAATGTGTATTTTATGTTA
257605 G
1 G
257606 GGTTGTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (33 bp):
GTATGTATATATATGAATGTGTATTTTATGTTA
Found at i:265758 original size:25 final size:25
Alignment explanation
Indices: 265730--265778 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
265720 AGTAATATAT
*
265730 ATAACAATATACGTAAAATAAATAC
1 ATAACAATATACATAAAATAAATAC
*
265755 ATAATAATATACATAAAATAAATA
1 ATAACAATATACATAAAATAAATA
265779 TGTAATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (25 bp):
ATAACAATATACATAAAATAAATAC
Found at i:265768 original size:12 final size:11
Alignment explanation
Indices: 265723--265774 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
265713 ATAATAGAGT
*
265723 AATATATATAA
1 AATATACATAA
*
265734 CAATATACGTAA
1 -AATATACATAA
265746 AATAAATACATAA
1 AAT--ATACATAA
265759 TAATATACATAA
1 -AATATACATAA
265771 AATA
1 AATA
265775 AATATGTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 7 0.21
12 17 0.50
13 7 0.21
14 3 0.09
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.29
Consensus pattern (11 bp):
AATATACATAA
Found at i:266303 original size:61 final size:61
Alignment explanation
Indices: 266201--266330 Score: 172
Period size: 61 Copynumber: 2.1 Consensus size: 61
266191 CTGGTATGCA
* * * * * * *
266201 ATTTACCCTTAGCTAGTAACTAAAACGTGAAATATACTAAACATA-GAGGACTTTATGCGTG
1 ATTTACCCTTAACTAATAACTAAAACGTAAAACATAATAAACA-AGGAGGACTTGATGCATG
*
266262 ATTTACCCTTAACTAATAACTAAAGCGTAAAACATAATAAACAAGGAGGACTTGATGCATG
1 ATTTACCCTTAACTAATAACTAAAACGTAAAACATAATAAACAAGGAGGACTTGATGCATG
266323 ATTTACCC
1 ATTTACCC
266331 AAAATCCTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 1 0.02
61 59 0.98
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (61 bp):
ATTTACCCTTAACTAATAACTAAAACGTAAAACATAATAAACAAGGAGGACTTGATGCATG
Found at i:267573 original size:21 final size:21
Alignment explanation
Indices: 267547--267596 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
267537 GGAAACTGTC
*
267547 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTATT
267568 TCAAGGGAGACAAAATTTATT
1 TCAAGGGAGACAAAATTTATT
267589 TCAAGGGA
1 TCAAGGGA
267597 AACCGTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTATT
Found at i:267610 original size:57 final size:57
Alignment explanation
Indices: 267518--267632 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
267508 ATCTCATGGA
* * *
267518 AGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
1 AGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGACAAAACTTGTTTCAAGGG
* *
267575 AGACAAAATTTATTTCAAGGGAAACCGTCTTAAGGGAGACAAAACTTGTTTCCAGGG
1 AGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGACAAAACTTGTTTCAAGGG
267632 A
1 A
267633 AACTGTTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.25
Consensus pattern (57 bp):
AGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGACAAAACTTGTTTCAAGGG
Found at i:276057 original size:16 final size:16
Alignment explanation
Indices: 276036--276069 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
276026 AAAAAGGGGG
276036 AGAAGTGTGTGTTTTA
1 AGAAGTGTGTGTTTTA
276052 AGAAGTGTGTGTTTTA
1 AGAAGTGTGTGTTTTA
276068 AG
1 AG
276070 TGTGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.41
Consensus pattern (16 bp):
AGAAGTGTGTGTTTTA
Found at i:277299 original size:36 final size:35
Alignment explanation
Indices: 277240--277395 Score: 155
Period size: 36 Copynumber: 4.5 Consensus size: 35
277230 AGAATCAAAG
*
277240 ATTTTGTTTCAAGGGAAACTGTCTCAAGGGAGACA
1 ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACA
*
277275 ATATTTGTTTCAAGAGAAATTGTCTCAAGGGAGACAA
1 AT-TTTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-A
* * * *
277312 AATTTGTTTAAAGGGAAACATAT-TCAA---AG---
1 ATTTTGTTTCAAGAGAAAC-TGTCTCAAGGGAGACA
*
277341 ATTTTGGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1 ATTTT-GTTTCAAGAGAAACTGTCTCAAGGGAGACA
*
277377 ATTTTGTTTCAAGTGAAAC
1 ATTTTGTTTCAAGAGAAAC
277396 AAATTCAAAG
Statistics
Matches: 98, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
29 6 0.06
30 16 0.16
33 4 0.04
35 15 0.15
36 53 0.54
37 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (35 bp):
ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACA
Found at i:277360 original size:30 final size:30
Alignment explanation
Indices: 277317--277425 Score: 96
Period size: 30 Copynumber: 3.5 Consensus size: 30
277307 GACAAAATTT
* *
277317 GTTTAAAGGGAAACATATTCAAAGATTTTG
1 GTTTCAAGAGAAACATATTCAAAGATTTTG
*
277347 GTTTCAAGAGAAAC-TGTCTCAAGAGAGACAATTTT-
1 GTTTCAAGAGAAACATAT-TC-A-A-AG---ATTTTG
* *
277382 GTTTCAAGTGAAACAAATTCAAAGATTTTG
1 GTTTCAAGAGAAACATATTCAAAGATTTTG
277412 GTTTCAAGAGAAAC
1 GTTTCAAGAGAAAC
277426 TGTCTTAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
29 7 0.11
30 27 0.43
31 1 0.02
32 3 0.05
33 3 0.05
34 1 0.02
35 15 0.24
36 6 0.10
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (30 bp):
GTTTCAAGAGAAACATATTCAAAGATTTTG
Found at i:277413 original size:65 final size:65
Alignment explanation
Indices: 277281--277443 Score: 254
Period size: 65 Copynumber: 2.5 Consensus size: 65
277271 GACAATATTT
* * *
277281 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACATATTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAATTTGTTTAAAGGGAAACAAATTCAAAGATTTT
277346 G
65 G
* * *
277347 GTTTCAAGAGAAACTGTCTCAAGAGAGACAATTTTGTTTCAAGTGAAACAAATTCAAAGATTTTG
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAATTTGTTTAAAGGGAAACAAATTCAAAGATTTTG
*
277412 GTTTCAAGAGAAACTGTCTTAAGAGAGACAAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
277444 AAATTTTCTG
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 62 0.70
66 27 0.30
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAATTTGTTTAAAGGGAAACAAATTCAAAGATTTTG
Found at i:280472 original size:14 final size:14
Alignment explanation
Indices: 280453--280480 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
280443 ACATAGCCAG
280453 TCATCCGACGATAA
1 TCATCCGACGATAA
280467 TCATCCGACGATAA
1 TCATCCGACGATAA
280481 CACATGGTGA
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:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
TCATCCGACGATAA
Found at i:285286 original size:14 final size:13
Alignment explanation
Indices: 285242--285312 Score: 58
Period size: 14 Copynumber: 5.5 Consensus size: 13
285232 AGTATTATAT
*
285242 AAATATATATAATA
1 AAATA-ATATACTA
*
285256 AAGTAATATA-TA
1 AAATAATATACTA
*
285268 TAATAATATACGTA
1 AAATAATATAC-TA
285282 AAATAA-ATAC-A
1 AAATAATATACTA
*
285293 TAATAATATACATA
1 AAATAATATAC-TA
285307 AAATAA
1 AAATAA
285313 ATAAGTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 6 0.13
12 14 0.30
13 9 0.20
14 17 0.37
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (13 bp):
AAATAATATACTA
Found at i:285295 original size:25 final size:25
Alignment explanation
Indices: 285243--285315 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
285233 GTATTATATA
* *
285243 AATATATATA-ATAAAGTAATATATAT
1 AATA-ATATACATAAAATAA-ATACAT
*
285269 AATAATATACGTAAAATAAATACAT
1 AATAATATACATAAAATAAATACAT
285294 AATAATATACATAAAATAAATA
1 AATAATATACATAAAATAAATA
285316 AGTAATACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 31 0.74
26 11 0.26
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (25 bp):
AATAATATACATAAAATAAATACAT
Found at i:285297 original size:11 final size:11
Alignment explanation
Indices: 285283--285339 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
285273 ATATACGTAA
285283 AATAAATACAT
1 AATAAATACAT
285294 AATAATATACAT
1 AATAA-ATACAT
*
285306 -A-AAATAAAT
1 AATAAATACAT
285315 AAGT-AATACAT
1 AA-TAAATACAT
285326 AA-AACATACAT
1 AATAA-ATACAT
285337 AAT
1 AAT
285340 GGTACAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
9 5 0.14
10 4 0.11
11 22 0.59
12 6 0.16
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (11 bp):
AATAAATACAT
Found at i:285841 original size:61 final size:61
Alignment explanation
Indices: 285739--285866 Score: 186
Period size: 61 Copynumber: 2.1 Consensus size: 61
285729 CTTGTTTGCA
* * * * * *
285739 ATTTACCCTTAACTAGTAACTAAAACGTGAAATATACTAAAC-AGAGAGGACTTTATGCGTG
1 ATTTACCCTTAACTAATAACTAAAACGTAAAACATAATAAACAAG-GAGGACTTGATGCATG
285800 ATTTACCCTTAACTAATAACTAAAACGTAAAACATAATAAACAAGGAGGACTTGATGCATG
1 ATTTACCCTTAACTAATAACTAAAACGTAAAACATAATAAACAAGGAGGACTTGATGCATG
285861 ATTTAC
1 ATTTAC
285867 TCAAAATCCT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.27
Consensus pattern (61 bp):
ATTTACCCTTAACTAATAACTAAAACGTAAAACATAATAAACAAGGAGGACTTGATGCATG
Found at i:286726 original size:37 final size:36
Alignment explanation
Indices: 286685--286881 Score: 161
Period size: 37 Copynumber: 5.2 Consensus size: 36
286675 ATATATATTT
*
286685 TAATATAGTATAGTTTTCAAAAATATTTTTGAAAATA
1 TAATATA-TATAGTTTTGAAAAATATTTTTGAAAATA
* ** *
286722 TAATATATAGTTGTTTTTTAAAATCGGTTTTTG-AAA-A
1 TAATATATA-TAGTTTTGAAAAAT--ATTTTTGAAAATA
**
286759 T-ATATATATAGTTTTGAAAAGGATTTTTGAAAATA
1 TAATATATATAGTTTTGAAAAATATTTTTGAAAATA
286794 TATATATTATATAGTTTTGAAAACA-ATTTTTTGAAAATA
1 TA-ATA-TATATAGTTTTGAAAA-ATA-TTTTTGAAAATA
* *
286833 T-ATATTATATAGTTTTGAAAATACTTTTTTTTAAAACGTA
1 TAATA-TATATAGTTTTGAAAA-A-TATTTTTGAAAA--TA
286873 TAATATATA
1 TAATATATA
286882 GTTTCTTTTT
Statistics
Matches: 131, Mismatches: 14, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
33 6 0.05
34 3 0.02
35 11 0.08
36 9 0.07
37 44 0.34
38 29 0.22
39 19 0.15
40 7 0.05
41 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (36 bp):
TAATATATATAGTTTTGAAAAATATTTTTGAAAATA
Found at i:286880 original size:38 final size:37
Alignment explanation
Indices: 286749--286885 Score: 138
Period size: 38 Copynumber: 3.7 Consensus size: 37
286739 TTAAAATCGG
**
286749 TTTTTG-AAA-ATATA-TATATAGTTTTGAAAAGGA-
1 TTTTTGAAAACATATATTATATAGTTTTGAAAACAAT
*
286782 TTTTTGAAAATATATATATTATATAGTTTTGAAAACAAT
1 TTTTTG-AAA-ACATATATTATATAGTTTTGAAAACAAT
* * *
286821 TTTTTGAAAATATATATTATATAGTTTTGAAAATACTT
1 TTTTTGAAAACATATATTATATAGTTTTGAAAACA-AT
* * *
286859 TTTTTTAAAACGTATAATATATAGTTT
1 TTTTTGAAAACATATATTATATAGTTT
286886 CTTTTTCAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
33 6 0.07
35 2 0.02
36 1 0.01
37 30 0.34
38 44 0.49
39 6 0.07
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.47
Consensus pattern (37 bp):
TTTTTGAAAACATATATTATATAGTTTTGAAAACAAT
Found at i:288122 original size:28 final size:29
Alignment explanation
Indices: 288091--288145 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
288081 ATTTACTCCC
* * *
288091 AAAATTTAAC-TTTTTTTCTTTTTTTAAA
1 AAAAATTAACATTTATTTATTTTTTTAAA
288119 AAAAATTAACATTTATTTATTTTTTTA
1 AAAAATTAACATTTATTTATTTTTTTA
288146 GTTATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.58
Consensus pattern (29 bp):
AAAAATTAACATTTATTTATTTTTTTAAA
Found at i:295638 original size:35 final size:35
Alignment explanation
Indices: 295528--295646 Score: 100
Period size: 35 Copynumber: 3.4 Consensus size: 35
295518 TCGATCAAGC
* * *
295528 TGGTAATTCCTTATATTGGTTTAGACCGATCGA-A
1 TGGTAATTCCTTATATAGGTTCAAACCGATCGATA
*** * **
295562 CTGGTAATTCCTTACGGCAGGTTC-AACTCAGTTAAAT-
1 -TGGTAATTCCTTA-TATAGGTTCAAAC-C-GATCGATA
295599 TGGTAATTCCTTATATAGGTTCAAACCGATCGATA
1 TGGTAATTCCTTATATAGGTTCAAACCGATCGATA
295634 TGGTAATTCCTTA
1 TGGTAATTCCTTA
295647 CGGATCTAAG
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
34 4 0.06
35 35 0.56
36 21 0.33
37 3 0.05
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (35 bp):
TGGTAATTCCTTATATAGGTTCAAACCGATCGATA
Found at i:298281 original size:18 final size:17
Alignment explanation
Indices: 298250--298285 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
298240 GATTTGATGA
298250 TTAGAATTTCAAAGAGT
1 TTAGAATTTCAAAGAGT
*
298267 TTAGTAATTTTAAAGAGT
1 TTAG-AATTTCAAAGAGT
298285 T
1 T
298286 GTTGAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.42
Consensus pattern (17 bp):
TTAGAATTTCAAAGAGT
Found at i:302876 original size:25 final size:25
Alignment explanation
Indices: 302848--302896 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
302838 TTATTATTAT
302848 TATTATTAC-ATTATTATAATAATAA
1 TATTA-TACTATTATTATAATAATAA
* *
302873 TATTATACTTTTATTTTAATAATA
1 TATTATACTATTATTATAATAATA
302897 TATAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTATACTATTATTATAATAATAA
Found at i:302886 original size:22 final size:22
Alignment explanation
Indices: 302805--302897 Score: 57
Period size: 22 Copynumber: 4.1 Consensus size: 22
302795 AAATTATATT
*
302805 TATTGATAATTTTAATAATAA-AA
1 TATT-ATACTTTT-ATAATAATAA
* * * *
302828 TATAATA-TTTT-TATTATTAT
1 TATTATACTTTTATAATAATAA
302848 TATTATTACATTATTATAATAATAA
1 TATTA-TAC-TT-TTATAATAATAA
**
302873 TATTATACTTTTATTTTAATAA
1 TATTATACTTTTATAATAATAA
302895 TAT
1 TAT
302898 ATAATAAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.07
20 5 0.09
21 6 0.11
22 16 0.30
23 7 0.13
24 5 0.09
25 11 0.20
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (22 bp):
TATTATACTTTTATAATAATAA
Found at i:303316 original size:14 final size:13
Alignment explanation
Indices: 303297--303342 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
303287 CAAACACCAC
303297 AAAATAAATTTTAA
1 AAAAT-AATTTTAA
*
303311 AAAATATTTTTAA
1 AAAATAATTTTAA
*
303324 AAAATATTTTTAA
1 AAAATAATTTTAA
303337 AAAATA
1 AAAATA
303343 TAATTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 26 0.84
14 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:303321 original size:13 final size:13
Alignment explanation
Indices: 303305--303343 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
303295 ACAAAATAAA
303305 TTTTAAAAAATAT
1 TTTTAAAAAATAT
303318 TTTTAAAAAATAT
1 TTTTAAAAAATAT
303331 TTTTAAAAAATAT
1 TTTTAAAAAATAT
303344 AATTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:303349 original size:14 final size:13
Alignment explanation
Indices: 303306--303349 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
303296 CAAAATAAAT
*
303306 TTTAAAAAATATT
1 TTTAAAAAATATA
*
303319 TTTAAAAAATATT
1 TTTAAAAAATATA
303332 TTTAAAAAATATAA
1 TTTAAAAAATAT-A
303346 TTTA
1 TTTA
303350 TTTTTCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 25 0.86
14 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTAAAAAATATA
Found at i:308237 original size:21 final size:20
Alignment explanation
Indices: 308211--308264 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
308201 CAATTCAAAA
308211 TATAATATTATGAATATATTT
1 TATAATATTA-GAATATATTT
* * *
308232 TATAATTTTAGATTGTATTT
1 TATAATATTAGAATATATTT
308252 TAT-ATATTA-AATA
1 TATAATATTAGAATA
308265 ACATTATAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 2 0.07
19 5 0.19
20 11 0.41
21 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
TATAATATTAGAATATATTT
Found at i:311700 original size:28 final size:28
Alignment explanation
Indices: 311668--311734 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
311658 TATCAATAAC
*
311668 CATATATTTAAC-TAAACTCAAATTCTTA
1 CATATATTTAACTTAAA-TCAAATTCATA
311696 CATATATTTAACTTAAATCAAATTCATA
1 CATATATTTAACTTAAATCAAATTCATA
311724 CATATATTTAA
1 CATATATTTAA
311735 AACATTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 33 0.89
29 4 0.11
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (28 bp):
CATATATTTAACTTAAATCAAATTCATA
Found at i:311831 original size:6 final size:6
Alignment explanation
Indices: 311822--311871 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
311812 GTCTTCATTC
*
311822 TTCTTG TTCTTG TTC--- TTCTTG TTCTTG TTCTTG CTCTTG TTCTTG
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG
311867 TTCTT
1 TTCTT
311872 CTTCATCATC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
6 36 0.92
ACGTcount: A:0.00, C:0.20, G:0.14, T:0.66
Consensus pattern (6 bp):
TTCTTG
Found at i:311839 original size:15 final size:15
Alignment explanation
Indices: 311819--311874 Score: 85
Period size: 15 Copynumber: 3.5 Consensus size: 15
311809 TTAGTCTTCA
311819 TTCTTCTTGTTCTTG
1 TTCTTCTTGTTCTTG
311834 TTCTTCTTGTTCTTG
1 TTCTTCTTGTTCTTG
311849 TTCTTGCTCTTGTTCTTG
1 TTC-T--TCTTGTTCTTG
311867 TTCTTCTT
1 TTCTTCTT
311875 CATCATCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 22 0.58
16 1 0.03
17 1 0.03
18 14 0.37
ACGTcount: A:0.00, C:0.21, G:0.12, T:0.66
Consensus pattern (15 bp):
TTCTTCTTGTTCTTG
Found at i:314596 original size:51 final size:51
Alignment explanation
Indices: 314532--314714 Score: 222
Period size: 51 Copynumber: 3.4 Consensus size: 51
314522 GATTCAGTGC
* * * **
314532 AAGTATGTATTAAGTGTTACACTTTTTTGCTTTATTCACTTACACCAATGT
1 AAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTCACTTACACCAATGT
*
314583 AAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTAACTTACACCAGTGTAAGCAGTGT
1 AAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTCACTTACACC------A--A-TGT
*
314643 AAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTCACTTACACCAGTGT
1 AAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTCACTTACACCAATGT
314694 AAGTATGTGTTAAGTGCTACA
1 AAGTATGTGTTAAGTGCTACA
314715 TTTTATTTTA
Statistics
Matches: 115, Mismatches: 8, Indels: 18
0.82 0.06 0.13
Matches are distributed among these distances:
51 64 0.56
54 1 0.01
57 1 0.01
59 1 0.01
60 48 0.42
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (51 bp):
AAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTCACTTACACCAATGT
Found at i:314673 original size:60 final size:60
Alignment explanation
Indices: 314580--314696 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
314570 CTTACACCAA
314580 TGTAAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTAACTTACACCAGTGTAAGCAG
1 TGTAAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTAACTTACACCAGTGTAAGCAG
*
314640 TGTAAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTCACTTACACCAGTGTAAG
1 TGTAAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTAACTTACACCAGTGTAAG
314697 TATGTGTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.41
Consensus pattern (60 bp):
TGTAAGTATGTGTTAAGTGCTACACTTCTTTATTTTATTAACTTACACCAGTGTAAGCAG
Found at i:330006 original size:2 final size:2
Alignment explanation
Indices: 329999--330023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
329989 TTTATAAATG
329999 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
330024 AAATATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:330871 original size:14 final size:15
Alignment explanation
Indices: 330840--330889 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
330830 TTGTTTGAAC
330840 TAAAATTGAACTAAAAT
1 TAAAATT-AA-TAAAAT
330857 TAAAA-T-ATAAAAAT
1 TAAAATTAAT-AAAAT
*
330871 TGAAATTAATAAAAT
1 TAAAATTAATAAAAT
330886 TAAA
1 TAAA
330890 TTGCATCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.04
14 10 0.36
15 9 0.32
16 3 0.11
17 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (15 bp):
TAAAATTAATAAAAT
Found at i:331806 original size:31 final size:31
Alignment explanation
Indices: 331760--331834 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
331750 TTTGATAATA
* *
331760 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAATAATTTTATAATCATTTA-ATAAATT
* *
331791 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAATAATTTTATAATCATTTAATAAATT
331822 TAATAAGTAATTT
1 TAATAA-TAATTT
331835 AAATTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 27 0.73
32 10 0.27
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (31 bp):
TAATAATAATTTTATAATCATTTAATAAATT
Found at i:332594 original size:11 final size:10
Alignment explanation
Indices: 332574--332653 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 10
332564 AGTTTAAAAA
*
332574 ATTATAAAAT
1 ATTATTAAAT
332584 ACTTATTAAAT
1 A-TTATTAAAT
332595 -TTATTAAAAT
1 ATTATT-AAAT
*
332605 ATTATAAAATT
1 ATTATTAAA-T
*
332616 ATTAATAAAT
1 ATTATTAAAT
332626 -TTATCTAAAT
1 ATTAT-TAAAT
* *
332636 ACTATAAAAT
1 ATTATTAAAT
332646 AATTATTA
1 -ATTATTA
332654 TATTATCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.15
10 18 0.33
11 28 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:332602 original size:31 final size:30
Alignment explanation
Indices: 332567--332653 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
332557 TCAATAAAGT
*
332567 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAATATTATAAAATA-TTATTAAATTTA
*
332598 TTAAAATATTATAAAATTATTAATAAATTTA
1 TTAAAATATTATAAAA-TATTATTAAATTTA
*
332629 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATATTATAAAAT-ATTATTA
332654 TATTATCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAAATATTATAAAATATTATTAAATTTA
Found at i:332612 original size:19 final size:21
Alignment explanation
Indices: 332571--332620 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
332561 TAAAGTTTAA
332571 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAATACTTATT
*
332591 AAATTTATTAAAATA-TTA-T
1 AAAATTATTAAAATACTTATT
332610 AAAATTATTAA
1 AAAATTATTAA
332621 TAAATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTATTAAAATACTTATT
Found at i:332921 original size:40 final size:39
Alignment explanation
Indices: 332866--332991 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 39
332856 AAATGACCAA
* *
332866 CAAATTCGCAACGCGAATTCCAATTTCGCAACACAGTTTC
1 CAAAATCGCAACGCGAATTCCAA-ATCGCAACACAGTTTC
**
332906 CAAATAT-GCAACGCGAATATGTAAATCGCAACACAGTTTC
1 CAAA-ATCGCAACGCGAAT-TCCAAATCGCAACACAGTTTC
** *
332946 CAAAATCGCAACGCGAATTTGTAAATCACAACACAGTTTC
1 CAAAATCGCAACGCGAA-TTCCAAATCGCAACACAGTTTC
332986 CAAAAT
1 CAAAAT
332992 TGCGTTGCGA
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
39 2 0.03
40 70 0.91
41 5 0.06
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (39 bp):
CAAAATCGCAACGCGAATTCCAAATCGCAACACAGTTTC
Found at i:332936 original size:20 final size:20
Alignment explanation
Indices: 332913--332977 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
332903 TTCCAAATAT
*
332913 GCAACGCGAATATGTAAATC
1 GCAACGCGAATTTGTAAATC
* * **
332933 GCAACAC-AGTTTCCAAAATC
1 GCAACGCGAATTT-GTAAATC
332953 GCAACGCGAATTTGTAAATC
1 GCAACGCGAATTTGTAAATC
*
332973 ACAAC
1 GCAAC
332978 ACAGTTTCCA
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.79
21 4 0.12
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (20 bp):
GCAACGCGAATTTGTAAATC
Found at i:332991 original size:20 final size:20
Alignment explanation
Indices: 332928--332991 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
332918 GCGAATATGT
332928 AAATCGCAACACAGTTTCCA
1 AAATCGCAACACAGTTTCCA
* * **
332948 AAATCGCAACGCGAATTT-GT
1 AAATCGCAACAC-AGTTTCCA
*
332968 AAATCACAACACAGTTTCCA
1 AAATCGCAACACAGTTTCCA
332988 AAAT
1 AAAT
332992 TGCGTTGCGA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
19 4 0.12
20 25 0.76
21 4 0.12
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (20 bp):
AAATCGCAACACAGTTTCCA
Found at i:333085 original size:57 final size:57
Alignment explanation
Indices: 333004--333114 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 57
332994 CGTTGCGATA
*
333004 GTACTGTTTACCTACATCGATAATTCA-TGATGCGAATTTGAAAATCGCTTTGCGGTT
1 GTACTGTTTACCTACATCGATAATT-AGCGATGCGAATTTGAAAATCGCTTTGCGGTT
* * * *
333061 GTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCTCTTTGCG
1 GTACTGTTTACCTACATCGATAATTAGCGATGCGAATTTGAAAATCGCTTTGCG
333115 AATTTGGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
56 1 0.02
57 47 0.98
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (57 bp):
GTACTGTTTACCTACATCGATAATTAGCGATGCGAATTTGAAAATCGCTTTGCGGTT
Found at i:333134 original size:21 final size:20
Alignment explanation
Indices: 333088--333136 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
333078 CGGTAATTAG
333088 CGTTGCGAATTTGAAAATCT
1 CGTTGCGAATTTGAAAATCT
*
333108 CTTTGCGAATTTGGAAAATCGT
1 CGTTGCGAATTT-GAAAATC-T
333130 -GTTGCGA
1 CGTTGCGA
333137 TAACACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.44
21 13 0.52
22 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCT
Found at i:333233 original size:20 final size:20
Alignment explanation
Indices: 333208--333274 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
333198 GGTAATTAGC
333208 TTGCGAATTTGAAAATCGCG
1 TTGCGAATTTGAAAATCGCG
*** * *
333228 TTGCG-ATAACACTATTCGCG
1 TTGCGAATTTGA-AAATCGCG
*
333248 TTGCGAATTTGGAAAATCGGG
1 TTGCGAATTT-GAAAATCGCG
333269 TTGCGA
1 TTGCGA
333275 TAACACTGTT
Statistics
Matches: 33, Mismatches: 11, Indels: 5
0.67 0.22 0.10
Matches are distributed among these distances:
19 3 0.09
20 16 0.48
21 13 0.39
22 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGCG
Found at i:333239 original size:97 final size:98
Alignment explanation
Indices: 333110--333333 Score: 360
Period size: 97 Copynumber: 2.3 Consensus size: 98
333100 GAAAATCTCT
*
333110 TTGCGAATTTGGAAAATCGTGTTGCGATAACACTATTCGCGTTGCGAATTTGGAATATCGCGTTG
1 TTGCGAATTT-GAAAATCGTGTTGCGATAACACTATTCGCGTTGCGAATTTGGAAAATCGCGTTG
* *
333175 CGATAACAATGTTTACCTATGTTGGTAATTAG-C
65 CGATAACAATGTTTACCTATATCGGTAATTAGTC
* *
333208 TTGCGAATTTGAAAATCGCGTTGCGATAACACTATTCGCGTTGCGAATTTGGAAAATCGGGTTGC
1 TTGCGAATTTGAAAATCGTGTTGCGATAACACTATTCGCGTTGCGAATTTGGAAAATCGCGTTGC
* *
333273 GATAACACTGTTTACCTATATCGGTAATTAGTG
66 GATAACAATGTTTACCTATATCGGTAATTAGTC
*
333306 TTGCGAATTTGTAAATCGTGTTGCGATA
1 TTGCGAATTTGAAAATCGTGTTGCGATA
333334 GTACTATTAA
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 80 0.69
98 36 0.31
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (98 bp):
TTGCGAATTTGAAAATCGTGTTGCGATAACACTATTCGCGTTGCGAATTTGGAAAATCGCGTTGC
GATAACAATGTTTACCTATATCGGTAATTAGTC
Found at i:333330 original size:57 final size:58
Alignment explanation
Indices: 333245--333389 Score: 211
Period size: 57 Copynumber: 2.5 Consensus size: 58
333235 AACACTATTC
* * *
333245 GCGTTGCGAATTTGGAAAATCGGGTTGCGATAACACTGTTTACCTATATCGGTAATTA
1 GCGTTGCGAATTTGGAAAATCGCGTTGCGATAACACTATTAACCTATATCGGTAATTA
* * * **
333303 GTGTTGCGAATTT-GTAAATCGTGTTGCGATAGTACTATTAACCTATATCGGTAATTA
1 GCGTTGCGAATTTGGAAAATCGCGTTGCGATAACACTATTAACCTATATCGGTAATTA
333360 GCGTTGCGAATTTGGAAAATCGCGTTGCGA
1 GCGTTGCGAATTTGGAAAATCGCGTTGCGA
333390 ATTTAGAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
57 50 0.66
58 26 0.34
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (58 bp):
GCGTTGCGAATTTGGAAAATCGCGTTGCGATAACACTATTAACCTATATCGGTAATTA
Done.