Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008726.1 Hibiscus syriacus cultivar Beakdansim tig00111792_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: 1298898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:93 original size:20 final size:19
Alignment explanation
Indices: 32--95 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
22 TTTTCCCAAT
32 TCGCAATGCG-ATAGTAAA
1 TCGCAATGCGAATAGTAAA
* * * *
50 TCGCAACGCGAATTGGGAAT
1 TCGCAATGCGAA-TAGTAAA
70 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAAT-AGTAAA
90 TCGCAA
1 TCGCAA
96 ATCGAATTGG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 9 0.26
19 2 0.06
20 24 0.69
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (19 bp):
TCGCAATGCGAATAGTAAA
Found at i:102 original size:40 final size:39
Alignment explanation
Indices: 29--120 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 39
19 TGATTTTCCC
*
29 AATTCGCAATGCGATAGTAAATCGCAACGCGAATTGGG-
1 AATTCGCAATGCGATAGTAAATCGCAAAGCGAATTGGGA
*
67 AATTCGCAATGCGAATAAGTAAATCGCAAATCGAATTGGGA
1 AATTCGCAATGCG-AT-AGTAAATCGCAAAGCGAATTGGGA
*
108 AAATCGCAATGCG
1 AATTCGCAATGCG
121 TACTGACTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
38 13 0.27
39 2 0.04
40 21 0.44
41 12 0.25
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (39 bp):
AATTCGCAATGCGATAGTAAATCGCAAAGCGAATTGGGA
Found at i:151 original size:19 final size:19
Alignment explanation
Indices: 106--154 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
96 ATCGAATTGG
*
106 GAAAATCGCAATGCGTACT
1 GAAAATCGCAATGCGTAAT
**
125 GACTATCGCAATGCGATAAT
1 GAAAATCGCAATGCG-TAAT
145 -AAAATCGCAA
1 GAAAATCGCAA
155 CGAGATACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (19 bp):
GAAAATCGCAATGCGTAAT
Found at i:181 original size:39 final size:38
Alignment explanation
Indices: 107--181 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 38
97 TCGAATTGGG
* * **
107 AAAATCGCAATGCGTACTGACTATCGCAATGCGATAAT
1 AAAATCGCAACGAGTACTGACTATCGCAACACGATAAT
* *
145 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAG-TACTGACTATCGCAACACGATA
182 CTACTTCGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
38 12 0.40
39 18 0.60
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (38 bp):
AAAATCGCAACGAGTACTGACTATCGCAACACGATAAT
Found at i:191 original size:18 final size:20
Alignment explanation
Indices: 149--198 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
139 GATAATAAAA
149 TCGCAACGA-GATACTTACTT
1 TCGCAAC-ACGATACTTACTT
169 TCGCAACACGATAC-TAC-T
1 TCGCAACACGATACTTACTT
*
187 TCGCAACGCGAT
1 TCGCAACACGAT
199 TTACTTAGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 12 0.43
19 4 0.14
20 12 0.43
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (20 bp):
TCGCAACACGATACTTACTT
Found at i:744 original size:19 final size:19
Alignment explanation
Indices: 720--764 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
710 GCAACGAGAT
* *
720 AATCGCAACGCGAAATAAA
1 AATCGCAACACGAAACAAA
*
739 AATCGCAACACGAAACCAA
1 AATCGCAACACGAAACAAA
758 AATCGCA
1 AATCGCA
765 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.27, G:0.13, T:0.09
Consensus pattern (19 bp):
AATCGCAACACGAAACAAA
Found at i:782 original size:19 final size:19
Alignment explanation
Indices: 760--929 Score: 172
Period size: 19 Copynumber: 9.1 Consensus size: 19
750 GAAACCAAAA
*
760 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
779 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
798 TTGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
817 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
837 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
853 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
870 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
889 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
909 ATCTCGTTGCGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
928 TC
1 TC
930 AAACAAAAGA
Statistics
Matches: 130, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 3 0.02
19 70 0.54
20 43 0.33
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:927 original size:39 final size:37
Alignment explanation
Indices: 760--929 Score: 161
Period size: 39 Copynumber: 4.5 Consensus size: 37
750 GAAACCAAAA
*
760 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATTTCGCGTTGCGATTTTCATT
* *
798 TTGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATTTCGC-GTTGCGATTTTCATT
* **
837 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATT-TCATTTCGCGTTGCGATTTTCATT
* *
870 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGAT-TTCATTT-CGCGTTGCGATTTTCATT
*
909 ATCTCGTTGCGATTTCATTTC
1 -TCGCGTTGCGATTTCATTTC
930 AAACAAAAGA
Statistics
Matches: 108, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
33 26 0.24
35 1 0.01
36 2 0.02
38 24 0.22
39 44 0.41
40 11 0.10
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (37 bp):
TCGCGTTGCGATTTCATTTCGCGTTGCGATTTTCATT
Found at i:2968 original size:21 final size:21
Alignment explanation
Indices: 2944--3010 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2934 TCATTCCTCG
2944 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2965 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2986 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3007 AGAG
1 AGAG
3011 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:4591 original size:19 final size:19
Alignment explanation
Indices: 4569--4686 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
4559 CGAAATTAAA
4569 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4588 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4603 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4621 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
4636 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
4654 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
4673 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4687 GGACATTAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4615 original size:33 final size:33
Alignment explanation
Indices: 4573--4666 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
4563 ATTAAATTCG
4573 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
4606 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
4639 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4667 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:6968 original size:12 final size:12
Alignment explanation
Indices: 6951--6975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6941 TCTTCGGGGA
6951 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6963 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6975 C
1 C
6976 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:8172 original size:20 final size:20
Alignment explanation
Indices: 8147--8197 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
8137 ATTCATTTGA
*
8147 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
8167 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
8187 TTATCGCAACG
1 CTATCGCAACG
8198 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:8276 original size:18 final size:18
Alignment explanation
Indices: 8249--8287 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
8239 TCGTTGCGAT
8249 TTTCAGTTCGCATTGTGA
1 TTTCAGTTCGCATTGTGA
*
8267 TTTCATTTCGCATTGTGA
1 TTTCAGTTCGCATTGTGA
8285 TTT
1 TTT
8288 TCTCGTTGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (18 bp):
TTTCAGTTCGCATTGTGA
Found at i:8423 original size:14 final size:14
Alignment explanation
Indices: 8404--8440 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
8394 CATCAATTAA
8404 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
8418 ACAAATCATCTTTT
1 ACAAATCAACATTT
8432 ACAAATCAA
1 ACAAATCAA
8441 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:10341 original size:20 final size:20
Alignment explanation
Indices: 10306--10373 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
10296 GAAACTTAAA
10306 ATCGCAACGC-GAAATGACT
1 ATCGCAACGCGGAAATGACT
*
10325 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* * **
10345 ATCGCAATGCGAAAATGAAA
1 ATCGCAACGCGGAAATGACT
10365 ATCGCAACG
1 ATCGCAACG
10374 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 10 0.24
20 31 0.76
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:10381 original size:14 final size:14
Alignment explanation
Indices: 10362--10419 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
10352 TGCGAAAATG
10362 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
10376 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
10392 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
10408 AAAATCGCAACG
1 AAAATCGCAACG
10420 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:10404 original size:32 final size:33
Alignment explanation
Indices: 10345--10424 Score: 135
Period size: 32 Copynumber: 2.4 Consensus size: 33
10335 GGAAATGGCT
*
10345 ATCGCAATGCGAAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCG-AAATGAAAATCGCAACGACAAA
10379 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
10411 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
10425 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 30 0.67
33 5 0.11
34 10 0.22
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:10453 original size:19 final size:19
Alignment explanation
Indices: 10431--10494 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
10421 GAAACACAAA
10431 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
10450 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
10466 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
10483 TCGCATTGCGAT
1 TCGCATTGCGAT
10495 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 17 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:10513 original size:20 final size:19
Alignment explanation
Indices: 10479--10533 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
10469 TTGCGATTTT
*
10479 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
10498 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
10518 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
10534 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:11032 original size:18 final size:18
Alignment explanation
Indices: 11006--11050 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
10996 GTCGATCAGA
*
11006 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
11024 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
11042 TGATGGCTC
1 TGATGGCTC
11051 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:12706 original size:21 final size:22
Alignment explanation
Indices: 12670--12712 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12660 GATTTAGATA
12670 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
12692 GACGGA-TTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
12713 TGAGAGTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.19, C:0.16, G:0.47, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:12923 original size:20 final size:20
Alignment explanation
Indices: 12898--12991 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
12888 GATTATGTAT
12898 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12918 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
12938 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
12959 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12979 TATCGCATTGCGA
1 TATCGCGTTGCGA
12992 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:12992 original size:20 final size:20
Alignment explanation
Indices: 12878--12992 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
12868 CGCTTTGAAA
*
12878 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
12899 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
12919 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
12939 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
12960 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
12980 ATCGCATTGCGAT
1 ATCGCATTGCGAT
12993 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:13011 original size:41 final size:41
Alignment explanation
Indices: 12920--13054 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
12910 AAAGTCAGTA
* * * ** *
12920 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
12960 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
13002 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
13043 TCGCGTTGCGAT
1 TCGCGTTGCGAT
13055 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:13025 original size:20 final size:20
Alignment explanation
Indices: 12981--13073 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
12971 ATAGTCAGTA
* **
12981 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
13002 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
13022 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
13043 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
13063 TCGCATTGCGA
1 TCGCATTGCGA
13074 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:13055 original size:41 final size:41
Alignment explanation
Indices: 12981--13076 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
12971 ATAGTCAGTA
*
12981 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
13022 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
13063 TCGCATTGCGAATT
1 TCGCATTGCGAATT
13077 GGGAAAAATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:28562 original size:18 final size:18
Alignment explanation
Indices: 28525--28562 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28515 CTTCCTGGTG
*
28525 CCTTGGCTTGTTACGGTC
1 CCTTGGCTTGTTACGATC
*
28543 CCTTGGCTTGTTGCGATC
1 CCTTGGCTTGTTACGATC
28561 CC
1 CC
28563 CCCATATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.32, G:0.26, T:0.37
Consensus pattern (18 bp):
CCTTGGCTTGTTACGATC
Found at i:51026 original size:19 final size:19
Alignment explanation
Indices: 51002--51040 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
50992 TGTTTTAAGA
51002 GTGTTTTAAAATGATAAAT
1 GTGTTTTAAAATGATAAAT
51021 GTGTTTTAAAATGATAAAT
1 GTGTTTTAAAATGATAAAT
51040 G
1 G
51041 GGAGAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (19 bp):
GTGTTTTAAAATGATAAAT
Found at i:54734 original size:35 final size:34
Alignment explanation
Indices: 54649--54735 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
54639 ATTTGGTATT
*
54649 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
54683 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
54721 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
54736 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:55302 original size:27 final size:27
Alignment explanation
Indices: 55266--55334 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
55256 AGGTGAAGGC
*
55266 GGCGCTGGCGGCATCTGGTAATGGAAA
1 GGCGATGGCGGCATCTGGTAATGGAAA
*
55293 GGCGATGGCGGCATTTGGTAATGGAAA
1 GGCGATGGCGGCATCTGGTAATGGAAA
55320 GGCGATGGCGGCATC
1 GGCGATGGCGGCATC
55335 ATATATGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.22, C:0.17, G:0.42, T:0.19
Consensus pattern (27 bp):
GGCGATGGCGGCATCTGGTAATGGAAA
Found at i:56991 original size:111 final size:111
Alignment explanation
Indices: 56854--57186 Score: 621
Period size: 111 Copynumber: 3.0 Consensus size: 111
56844 ATTACAAAAA
56854 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
56919 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
56965 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
57030 ATTTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
57076 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
57141 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
57187 ATGATTTCCA
Statistics
Matches: 216, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 216 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:57291 original size:17 final size:18
Alignment explanation
Indices: 57248--57288 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
57238 GAATTATATT
57248 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
57265 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
57283 ATTAAA
1 AGTAAA
57289 TACATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:57944 original size:2 final size:2
Alignment explanation
Indices: 57937--57971 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
57927 GTGGCTTTGT
57937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57972 TTCATGTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:71285 original size:110 final size:111
Alignment explanation
Indices: 71015--71323 Score: 462
Period size: 111 Copynumber: 2.8 Consensus size: 111
71005 GTTCGATCCT
* * *
71015 AATGGATCAACTTTCCCAAATCTGATATTCCTTTCA-AAGAAGCGGAACAAATCCCTCTCTTCTA
1 AATGGATCAACTTTCCCAAATCTGATATTCCCTT-AGAAGAAGCGGAACATATCCCTCTCTTCCA
* *
71079 ATATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTACCCTGATTC
65 AGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTACCCTAATTC
**
71126 AATGGATCAACTTT-CCAATATCTGATATTCCCTTAGAAGAAGCAAAACATATCCCTCTCTTCCA
1 AATGGATCAACTTTCCCAA-ATCTGATATTCCCTTAGAAGAAGCGGAACATATCCCTCTCTTCCA
* * *
71190 AGATTTGATATTCCCTGAGTGACAGCGGAATAAGTCTATCC-AATTC
65 AGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTACCCTAATTC
* *
71236 AATGGATCAACTTTCCCAGATCTGATATTCCCTTAGAAGAAGCGGAACATATCCCTCTCTTTCAA
1 AATGGATCAACTTTCCCAAATCTGATATTCCCTTAGAAGAAGCGGAACATATCCCTCTCTTCCAA
*
71301 GATTTGATATTCCATGAGTGACA
66 GATTTGATATTCCCTGAGTGACA
71324 ATGGAACAAA
Statistics
Matches: 180, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
110 88 0.49
111 92 0.51
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (111 bp):
AATGGATCAACTTTCCCAAATCTGATATTCCCTTAGAAGAAGCGGAACATATCCCTCTCTTCCAA
GATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTACCCTAATTC
Found at i:73547 original size:3 final size:3
Alignment explanation
Indices: 73522--73617 Score: 137
Period size: 3 Copynumber: 33.3 Consensus size: 3
73512 AATTGTACAA
* * *
73522 AAT ACT AAT AAT ATT AAT GAT 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
73570 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT -AT AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
73614 AAT A
1 AAT A
73618 TTTGTGTATA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
2 8 0.10
3 75 0.90
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:74326 original size:30 final size:29
Alignment explanation
Indices: 74292--74380 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 29
74282 GACAAAATTC
*
74292 GTTTCAAGGGAAACAATCTCAAAGATGTTT
1 GTTTCAAGAGAAACAATCTCAAAGAT-TTT
*
74322 GTTTCATGAGAAAC-ATACTCAAAGACTTTT
1 GTTTCAAGAGAAACAAT-CTCAAAGA-TTTT
74352 GTTTCAAGAGAAACAGA-CTCAAAGATTTT
1 GTTTCAAGAGAAACA-ATCTCAAAGATTTT
74381 CCTTCAAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
29 6 0.12
30 44 0.85
31 1 0.02
32 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (29 bp):
GTTTCAAGAGAAACAATCTCAAAGATTTT
Found at i:74392 original size:29 final size:30
Alignment explanation
Indices: 74330--74393 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
74320 TTGTTTCATG
* ** *
74330 AGAAACATACTCAAAGACTTTTGTTTCAAG
1 AGAAACAGACTCAAAGACTTTTCCTTCAAA
74360 AGAAACAGACTCAAAGA-TTTTCCTTCAAA
1 AGAAACAGACTCAAAGACTTTTCCTTCAAA
74389 AGAAA
1 AGAAA
74394 TTGTCTCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (30 bp):
AGAAACAGACTCAAAGACTTTTCCTTCAAA
Found at i:74551 original size:66 final size:66
Alignment explanation
Indices: 74348--74575 Score: 280
Period size: 66 Copynumber: 3.4 Consensus size: 66
74338 ACTCAAAGAC
* * *
74348 TTTTGTTTCAAGAGAAACAGACTCAAAGATTTTCCTTCAAAAGAAATTGTCTCAAGAGAGACAAA
1 TTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAAAGAGACAAA
74413 A
66 A
* * * * *
74414 TTTTGTTTCCAA-AGAAAGAGACTCAAAGGTTTTTTTCTTCAAAAGAAACTATATGAAAAGAGAC
1 TTTTGTTT-CAAGAGAAACAGACTCAAA-G-ATTTTTCTTCAAAAGAAACTGTCTCAAAAGAGAC
74478 AAAA
63 AAAA
* * * * * *
74482 TTTTATTTCCAGAGAAACATACTCAAAGATTTTTCTTCAAAATAAACCGTCTCAAAAGAAACAAA
1 TTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAAAGAGACAAA
74547 A
66 A
74548 TTTTGTTTCAAGAGAAACA-ACATCAAAG
1 TTTTGTTTCAAGAGAAACAGAC-TCAAAG
74576 GATACTGATA
Statistics
Matches: 136, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
65 2 0.01
66 76 0.56
67 7 0.05
68 51 0.38
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (66 bp):
TTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAAAGAGACAAA
A
Found at i:74686 original size:32 final size:32
Alignment explanation
Indices: 74645--74708 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
74635 TTTACATCAA
74645 GATGTTGAATCCCCAAAGATGCCCCAACATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
* * *
74677 GATGTTGAATCTCCAAAGATGTCCCATCATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
74709 ATTGTTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATGCCCCAACATTC
Found at i:75772 original size:12 final size:12
Alignment explanation
Indices: 75755--75784 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
75745 TTGTCATCTC
75755 TTTTTTCCTTTG
1 TTTTTTCCTTTG
*
75767 TTTTTTCTTTTG
1 TTTTTTCCTTTG
75779 TTTTTT
1 TTTTTT
75785 TTTTCTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTCCTTTG
Found at i:79595 original size:30 final size:29
Alignment explanation
Indices: 79561--79723 Score: 118
Period size: 29 Copynumber: 5.5 Consensus size: 29
79551 TCTTGAGAGG
* *
79561 CTAAAATAGTAAAAACATAAATTTAAAGGA
1 CTAAAATA-TAAAAATATAAACTTAAAGGA
* * *
79591 CTAAAATAAAAAAATAGAAAGTTAAAGGA
1 CTAAAATATAAAAATATAAACTTAAAGGA
*
79620 CTAAAATA-AAAAATATTGAAACTTAAAGGG
1 CTAAAATATAAAAATA-T-AAACTTAAAGGA
* *
79650 CT-AAATAATAAAAATAAAAACAT-AAGTGA
1 CTAAAAT-ATAAAAATATAAACTTAAAG-GA
* *
79679 CTAAAATA-ACAAAAAATAGACATTTAAAGGA
1 CTAAAATATA-AAAATATA-A-ACTTAAAGGA
* *
79710 TTAAAATATCAAAA
1 CTAAAATATAAAAA
79724 CAGAAGCATA
Statistics
Matches: 106, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
28 11 0.10
29 44 0.42
30 26 0.25
31 22 0.21
32 3 0.03
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (29 bp):
CTAAAATATAAAAATATAAACTTAAAGGA
Found at i:79615 original size:29 final size:29
Alignment explanation
Indices: 79583--79717 Score: 139
Period size: 29 Copynumber: 4.6 Consensus size: 29
79573 AAACATAAAT
*
79583 TTAAAGGACTAAAATAAAAAAATAGAAAG
1 TTAAAGGACTAAAATAAAAAAATAGAAAC
*
79612 TTAAAGGACTAAAATAAAAAATATTGAAAC
1 TTAAAGGACTAAAATAAAAAA-ATAGAAAC
* *
79642 TTAAAGGGCT-AAATAATAAAAATAAAAAC
1 TTAAAGGACTAAAATAA-AAAAATAGAAAC
* * *
79671 AT-AAGTGACTAAAATAACAAAAAATAGACAT
1 TTAAAG-GACTAAAAT-A-AAAAAATAGAAAC
*
79702 TTAAAGGATTAAAATA
1 TTAAAGGACTAAAATA
79718 TCAAAACAGA
Statistics
Matches: 87, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
28 3 0.03
29 37 0.43
30 24 0.28
31 19 0.22
32 4 0.05
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.21
Consensus pattern (29 bp):
TTAAAGGACTAAAATAAAAAAATAGAAAC
Found at i:79646 original size:59 final size:61
Alignment explanation
Indices: 79583--79743 Score: 152
Period size: 60 Copynumber: 2.7 Consensus size: 61
79573 AAACATAAAT
* ** * *
79583 TTAAAGGACTAAAATAA-AAAAATAGAAAGTTAAAG-GACTAAAATAA-AAAATATTGAAAC
1 TTAAAGGACTAAAATAATAAAAATAAAAACAT-AAGTGACTAAAATAACAAAAAATAGAAAC
* * *
79642 TTAAAGGGCT-AAATAATAAAAATAAAAACATAAGTGACTAAAATAACAAAAAATAGACAT
1 TTAAAGGACTAAAATAATAAAAATAAAAACATAAGTGACTAAAATAACAAAAAATAGAAAC
* * * * * *
79702 TTAAAGGATTAAAAT-ATCAAAACAGAAGCATAAGGGACTAAA
1 TTAAAGGACTAAAATAATAAAAATAAAAACATAAGTGACTAAA
79744 CAGTAATATG
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
58 9 0.11
59 31 0.37
60 39 0.47
61 4 0.05
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.20
Consensus pattern (61 bp):
TTAAAGGACTAAAATAATAAAAATAAAAACATAAGTGACTAAAATAACAAAAAATAGAAAC
Found at i:80261 original size:7 final size:7
Alignment explanation
Indices: 80249--80292 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
80239 TTTCTATCAT
80249 TCATTTC
1 TCATTTC
80256 TCATTTC
1 TCATTTC
80263 TCATTTC
1 TCATTTC
80270 TCATTTC
1 TCATTTC
80277 TCATTTC
1 TCATTTC
80284 TCATTTC
1 TCATTTC
80291 TC
1 TC
80293 TTTGTTTCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.57
Consensus pattern (7 bp):
TCATTTC
Found at i:80957 original size:21 final size:22
Alignment explanation
Indices: 80915--80963 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
80905 GGGCTCTGAT
*
80915 CGGCTCGGGAAGCACTCGGCGG
1 CGGCTCGGGAAGCACACGGCGG
*
80937 CGGCTTGGGAAGCA-ACGGCGG
1 CGGCTCGGGAAGCACACGGCGG
*
80958 CAGCTC
1 CGGCTC
80964 ACGGGACGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.16, C:0.31, G:0.43, T:0.10
Consensus pattern (22 bp):
CGGCTCGGGAAGCACACGGCGG
Found at i:83005 original size:54 final size:54
Alignment explanation
Indices: 82957--83090 Score: 180
Period size: 54 Copynumber: 2.5 Consensus size: 54
82947 TTGATTTTGA
* * *
82957 TCTAGAAATTTGATTTCCAGTAATGGCGCCACTAGATGCCGAA-TTTGATTCCCT
1 TCTAGAAATTTGATTTCCAGTAATGACGACACTAGATGCC-AAGTTTGATTCTCT
* * *
83011 TCTAGAAAATTGATTTCCAGTAATGACGACGCTAGATGCCAAGTCTGATTCTCT
1 TCTAGAAATTTGATTTCCAGTAATGACGACACTAGATGCCAAGTTTGATTCTCT
* *
83065 TCTAGAAATTTGCTTTCCAATAATGA
1 TCTAGAAATTTGATTTCCAGTAATGA
83091 TCCTCTCAGG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
53 2 0.03
54 68 0.97
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (54 bp):
TCTAGAAATTTGATTTCCAGTAATGACGACACTAGATGCCAAGTTTGATTCTCT
Found at i:83195 original size:54 final size:54
Alignment explanation
Indices: 83058--83195 Score: 127
Period size: 54 Copynumber: 2.6 Consensus size: 54
83048 GCCAAGTCTG
* * ** * * *
83058 ATTCTCTTCTAGAAATTTGCTTTCCAATAATGATCCTCTCAGGAGTGATGGTTG
1 ATTCTCCTCTAGAAATTTGATTTCCGGTAATGATCCTATCAGGAGTGAAGGTTA
* * * * *
83112 A-TC-CCTGTCTATAAGTTTGGTTTCTGGTAATGATCCTATCAGGGGTGAAGGTTA
1 ATTCTCC--TCTAGAAATTTGATTTCCGGTAATGATCCTATCAGGAGTGAAGGTTA
*
83166 ATTCTCCTCTAGAAATTTGATCTCCGGTAA
1 ATTCTCCTCTAGAAATTTGATTTCCGGTAA
83196 AGAGCCCATC
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
52 1 0.02
53 2 0.03
54 57 0.89
55 2 0.03
56 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (54 bp):
ATTCTCCTCTAGAAATTTGATTTCCGGTAATGATCCTATCAGGAGTGAAGGTTA
Found at i:88728 original size:20 final size:21
Alignment explanation
Indices: 88677--88730 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
88667 ACAGGTAACG
*
88677 AATTTGACAAAA-CTGATTGA
1 AATTTGAAAAAACCTGATTGA
* *
88697 AAATTAAAAAAACCTG-TTGA
1 AATTTGAAAAAACCTGATTGA
*
88717 AATTTGAGAAAACC
1 AATTTGAAAAAACC
88731 GGTAAAAAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (21 bp):
AATTTGAAAAAACCTGATTGA
Found at i:89888 original size:228 final size:228
Alignment explanation
Indices: 89463--89922 Score: 751
Period size: 228 Copynumber: 2.0 Consensus size: 228
89453 AAGTATTGTT
*
89463 GAAACCCTAGTTTTTTAGTATTACAATAATCAGAAATATGGATTAGGTTTATGGGTTTGAGGTTT
1 GAAACCCTAGTTTTTTAGTATTACAATAATCAGAAATAGGGATTAGGTTTATGGGTTTGAGGTTT
* *
89528 TCGAAGTAAAGAAGCATTTGAGACCGATTACAGGTAGAAAGTGATATTCTACGTATAAAATAAAT
66 TCGAAGTAAAGAAGCATTTGAGACCGATTACAAGTAGAAAGTGATATTCTACGTAGAAAATAAAT
* **
89593 ATCGATACTTTTATATAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAAGGTATTGATA
131 ATCGATACTTTTATATAATATTATAGGTAGAAAATGATATTATAGGTTGTATAAAGGTACCGATA
89658 CTTGTAGTAGAGAGTATTCTCATTCCTTTGAAG
196 CTTGTAGTAGAGAGTATTCTCATTCCTTTGAAG
* * ** *
89691 GAAACCCTAGTTTTTTAGTATTACAGTATTTGGAAATAGGGATTAGGTTTATGGGTTTGGGGTTT
1 GAAACCCTAGTTTTTTAGTATTACAATAATCAGAAATAGGGATTAGGTTTATGGGTTTGAGGTTT
* * * * *
89756 TCGAAGTAAAGAAGGATTTGAGACCGATTATAATTAGAAAGTGATATTCTAGGTAGCAAATAAAA
66 TCGAAGTAAAGAAGCATTTGAGACCGATTACAAGTAGAAAGTGATATTCTACGTAGAAAAT-AAA
*
89821 TATTGATACTTTTATATAATATTATAGGTAGAAAATGATATTATAGGTTGTATAAA-GTACCGAT
130 TATCGATACTTTTATATAATATTATAGGTAGAAAATGATATTATAGGTTGTATAAAGGTACCGAT
89885 ACTTGTAGTAGAGAGTATTCTCATTCCTTTGAAG
195 ACTTGTAGTAGAGAGTATTCTCATTCCTTTGAAG
89919 GAAA
1 GAAA
89923 ACTGATTACT
Statistics
Matches: 214, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
228 157 0.73
229 57 0.27
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (228 bp):
GAAACCCTAGTTTTTTAGTATTACAATAATCAGAAATAGGGATTAGGTTTATGGGTTTGAGGTTT
TCGAAGTAAAGAAGCATTTGAGACCGATTACAAGTAGAAAGTGATATTCTACGTAGAAAATAAAT
ATCGATACTTTTATATAATATTATAGGTAGAAAATGATATTATAGGTTGTATAAAGGTACCGATA
CTTGTAGTAGAGAGTATTCTCATTCCTTTGAAG
Found at i:90718 original size:18 final size:18
Alignment explanation
Indices: 90695--90737 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
90685 TTGATTGAAG
*
90695 TGAGGGATCAACCGATTC
1 TGAGGGATCAACAGATTC
90713 TGAGGGATCAACAGATTC
1 TGAGGGATCAACAGATTC
*
90731 GGAGGGA
1 TGAGGGA
90738 ATTGTGTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.35, T:0.19
Consensus pattern (18 bp):
TGAGGGATCAACAGATTC
Found at i:95412 original size:650 final size:647
Alignment explanation
Indices: 94126--95421 Score: 2170
Period size: 646 Copynumber: 2.0 Consensus size: 647
94116 TTAAGTTTAG
* *
94126 GTGTGTTTGGTTGGGAGAATCTGAGATTCTCATGGGAATGGAATCCACATTCCTCCGTTTGGTTG
1 GTGTGTTTGGTTGGGAGAATCTGAGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTG
*
94191 GCCGGGAATGTCATTCCTGGTAATCTTACATGACCAATAGTGAATTTTTTGGGGTATATTATCGG
66 GCCGGGAATGTCATCCCTGGTAATCTTACATGACCAATAGTGAATTTTTTGGGGTATATTATCGG
* * *
94256 GAATGTCATTTCCTCCCTTTCCTTAGGTATTGTTGGATTACCGACATTTTGGACTAATATGCCCT
131 GAATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACCGACATTTTGAACTAAAATGCCCT
94321 TAATTTTTTTTCTTTCAAAAATATCATTATTCTATCATTGAATAATAAAAATTATACGAAGGTTA
196 TAATTTTTTTTCTTTCAAAAATATCATTATTCTATCATTGAATAATAAAAATTATACGAAGGTTA
* * *
94386 AATTATAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAATCTATAATTAAAATTATATGA
261 AATTAAAAATGTATCCTTAAACTATTTTAGATTTACAAAAAAAATCTATAATTAAAATTATATAA
* *
94451 AGTTCAGGGTTAAAATAAAATTTTAGCTTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAA
326 AGTTCAGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAA
* *
94516 AATTATAAAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTTTAACTTGTTA
391 AATTATAAAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTTCAACTTATTA
94581 AAAAACAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTA
456 AAAAACAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTA
*
94646 ACCAAACACGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCTAGTAAT
521 ACCAAACACGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAAT
* * *
94711 CCTATTCCCTGGTAATCTTTTATTCTCATTGGTAATCTTACATTCCGTGAACCAAACGCACA
586 CCTATTCCCTGATAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACA
* *
94773 GTGTGTTTGGTTGGGGGAATGTGAGA-TCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTG
1 GTGTGTTTGGTTGGGAGAATCTGAGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTG
* *
94837 GCCGGGAATGTCATCCCTGGTAATCTTACATTACCAATAGTGGATTTTTTGGGGTATATTA-CTG
66 GCCGGGAATGTCATCCCTGGTAATCTTACATGACCAATAGTGAATTTTTTGGGGTATATTATC-G
* * *
94901 GG-ATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTATCGGCGTTTTGAACTAAAATGCCC
130 GGAATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACCGACATTTTGAACTAAAATGCCC
* *
94965 TTAATTTTTTTTTCTTTCAAAAATATCATTATTCTGTCATTGAATAATAAAAATTCTACGAAGGT
195 TTAA-TTTTTTTTCTTTCAAAAATATCATTATTCTATCATTGAATAATAAAAATTATACGAAGGT
**
95030 TAAATTAAAAATGTATCCTTAAACTATTTTAGATTTACTAAAAAATGTCTATAATTAAAATTTTA
259 TAAATTAAAAATGTATCCTTAAACTATTTTAGATTTAC-AAAAAAAATCTATAATTAAAA--TTA
95095 TATAAAGTTCAGAGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTT
321 TATAAAGTTCAG-GGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTT
*
95160 GTAAAAAAATTATATAAATTTTATGAATTT-AATTTTTTAAAGAAAATATATAAATA-TTTTCAA
385 GT-AAAAAATTATAAAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTTCAA
* * *
95223 CTTATTAAAAAACAAATATATAATAAGGACAATTTGGTTAAATATACATTCTAATAATTTTTTAT
449 CTTATTAAAAAACAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTAT
*
95288 TCCTTTAACCAAACACGGTAATCTTATATTCCTGCTAAACCAACCAAACACAAAATACAACATTC
514 TCCTTTAACCAAACAC-GTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTC
* *
95353 CCAGTAATCCTATTCTCTGATAATCTTTTATTCCCACTGGTAATCTTACATTTCGTGAACCAAAC
578 CCAGTAATCCTATTCCCTGATAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAAC
95418 GCAC
643 GCAC
95422 CGTAAGGGTA
Statistics
Matches: 606, Mismatches: 35, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
645 61 0.10
646 191 0.32
647 43 0.07
649 97 0.16
650 188 0.31
651 26 0.04
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (647 bp):
GTGTGTTTGGTTGGGAGAATCTGAGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTG
GCCGGGAATGTCATCCCTGGTAATCTTACATGACCAATAGTGAATTTTTTGGGGTATATTATCGG
GAATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACCGACATTTTGAACTAAAATGCCCT
TAATTTTTTTTCTTTCAAAAATATCATTATTCTATCATTGAATAATAAAAATTATACGAAGGTTA
AATTAAAAATGTATCCTTAAACTATTTTAGATTTACAAAAAAAATCTATAATTAAAATTATATAA
AGTTCAGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAA
AATTATAAAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTTCAACTTATTA
AAAAACAAATATATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTA
ACCAAACACGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAAT
CCTATTCCCTGATAATCTTTTATTCCCACTGGTAATCTTACATTCCGTGAACCAAACGCACA
Found at i:96136 original size:17 final size:17
Alignment explanation
Indices: 96114--96147 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
96104 GAATGCAAAA
96114 AGGGTA-CCAATACCCCC
1 AGGGTATCC-ATACCCCC
96131 AGGGTATCCATACCCCC
1 AGGGTATCCATACCCCC
96148 TGGCTGCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.26, C:0.41, G:0.18, T:0.15
Consensus pattern (17 bp):
AGGGTATCCATACCCCC
Found at i:96216 original size:21 final size:21
Alignment explanation
Indices: 96190--96229 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
96180 TTTAATTTAA
*
96190 TGAAGGAGTACCGATACCCTG
1 TGAAGGAGTACCAATACCCTG
*
96211 TGAAGGGGTACCAATACCC
1 TGAAGGAGTACCAATACCC
96230 CCTATTATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (21 bp):
TGAAGGAGTACCAATACCCTG
Found at i:96295 original size:20 final size:22
Alignment explanation
Indices: 96257--96296 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
96247 TGTTTTGCAA
96257 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
96279 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
96297 ATATACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:96667 original size:18 final size:18
Alignment explanation
Indices: 96644--96702 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
96634 GTTGCAGTCA
96644 GGGGGTATGGATACCCCT
1 GGGGGTATGGATACCCCT
96662 GGGGGTATCGG-TA-CCC-
1 GGGGGTAT-GGATACCCCT
96678 --GGGTATGGATACCCCT
1 GGGGGTATGGATACCCCT
96694 CGGGGGTAT
1 -GGGGGTAT
96703 TGGTACCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
13 2 0.06
14 8 0.24
15 3 0.09
17 3 0.09
18 10 0.29
19 8 0.24
ACGTcount: A:0.15, C:0.22, G:0.41, T:0.22
Consensus pattern (18 bp):
GGGGGTATGGATACCCCT
Found at i:96687 original size:32 final size:33
Alignment explanation
Indices: 96646--96710 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
96636 TGCAGTCAGG
96646 GGGTATGGATACCCCT-GGGGGTATCGGTACCC
1 GGGTATGGATACCCCTCGGGGGTATCGGTACCC
*
96678 GGGTATGGATACCCCTCGGGGGTATTGGTACCC
1 GGGTATGGATACCCCTCGGGGGTATCGGTACCC
96711 ATTTTGCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.15, C:0.25, G:0.37, T:0.23
Consensus pattern (33 bp):
GGGTATGGATACCCCTCGGGGGTATCGGTACCC
Found at i:100174 original size:23 final size:22
Alignment explanation
Indices: 100146--100222 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
100136 ACATTGTAGA
100146 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
100168 CGTGCATC-AGTGCACCTTCATA--
1 -GTGCATCGA-TGCACATTCA-AGG
*
100190 GTGAATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
100212 GATGCATCGAT
1 G-TGCATCGAT
100223 ACACTAGGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 1 0.02
21 15 0.34
22 3 0.07
23 24 0.55
24 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:107795 original size:3 final size:3
Alignment explanation
Indices: 107774--107824 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
107764 TAAAGAAAGG
* * * *
107774 GAA G-A GAA GAA AAA CAA GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
107821 GAA G
1 GAA G
107825 GAGGAGGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.04, G:0.27, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:107795 original size:12 final size:12
Alignment explanation
Indices: 107778--107820 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
107768 GAAAGGGAAG
107778 AGAAGAAAAACA
1 AGAAGAAAAACA
107790 AGAAGAAAAACA
1 AGAAGAAAAACA
* *
107802 AGAAGAAGAAGA
1 AGAAGAAAAACA
107814 AGAAGAA
1 AGAAGAA
107821 GAAGGAGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAACA
Found at i:109513 original size:21 final size:19
Alignment explanation
Indices: 109470--109527 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
109460 GAACAATTGA
109470 TAACAATTGGTATC-TTTT
1 TAACAATTGGTATCTTTTT
109488 TAACAATTGGTATCCTTTTT
1 TAACAATTGGTAT-CTTTTT
*
109508 TAAACAATTGATATCTTTTT
1 T-AACAATTGGTATCTTTTT
109528 CATTAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 13 0.36
19 1 0.03
20 11 0.31
21 11 0.31
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (19 bp):
TAACAATTGGTATCTTTTT
Found at i:109785 original size:15 final size:16
Alignment explanation
Indices: 109746--109793 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
109736 TTAAAAAGGC
109746 ACCGATACCCCCAGGGT
1 ACCGATA-CCCCAGGGT
109763 ATCC-ATACCCC-GGGT
1 A-CCGATACCCCAGGGT
109778 ACCGATACCCCCAGGG
1 ACCGATA-CCCCAGGG
109794 GTATTCATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.07
15 8 0.30
16 8 0.30
17 7 0.26
18 2 0.07
ACGTcount: A:0.23, C:0.42, G:0.23, T:0.12
Consensus pattern (16 bp):
ACCGATACCCCAGGGT
Found at i:110713 original size:54 final size:53
Alignment explanation
Indices: 110623--110882 Score: 324
Period size: 54 Copynumber: 4.8 Consensus size: 53
110613 ATACTATCAG
110623 CACTAAGTGTGCAACCCACGAAATT-AGTAATATGTTTATGAACGACCGTATCGA
1 CACTAAGTGTGCAACCCACG-AATTCA-TAATATGTTTATGAACGACCGTATCGA
* * *
110677 CACTAAGTGTGTAACCCACAGAATTCATAATGTGTTTATGAACGACCGTATCGG
1 CACTAAGTGTGCAACCCAC-GAATTCATAATATGTTTATGAACGACCGTATCGA
* * * * * *
110731 CAATAAGTGTGCAACCCACGGAATTCATAATGTGTTTATAAACGATCGCATCGG
1 CACTAAGTGTGCAACCCAC-GAATTCATAATATGTTTATGAACGACCGTATCGA
* * * ** *
110785 CATTATGTGTGCAACCCACGAAATTCATAATATGTTTATCAACGACATTATCAA
1 CACTAAGTGTGCAACCCACG-AATTCATAATATGTTTATGAACGACCGTATCGA
110839 CACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACG
1 CACTAAGTGTGCAACCCAC-GAATTCATAATATGTTTATGAACG
110883 TCCTGTTGAG
Statistics
Matches: 180, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 176 0.98
55 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (53 bp):
CACTAAGTGTGCAACCCACGAATTCATAATATGTTTATGAACGACCGTATCGA
Found at i:113875 original size:22 final size:21
Alignment explanation
Indices: 113829--113908 Score: 101
Period size: 20 Copynumber: 3.7 Consensus size: 21
113819 CAGAACCCGT
113829 GGGGGTATCGATTCCC-TCAA
1 GGGGGTATCGATTCCCTTCAA
113849 GGGGGTATCGATTCCCATTCAAA
1 GGGGGTATCGATTCCC-TTC-AA
*
113872 GGGGGAATC-AGTTCCCCTTCAA
1 GGGGGTATCGA-TT-CCCTTCAA
113894 GGGGGTATCGATTCC
1 GGGGGTATCGATTCC
113909 TCCAGCACTA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
20 16 0.31
21 2 0.04
22 15 0.29
23 16 0.31
24 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCTTCAA
Found at i:113886 original size:23 final size:22
Alignment explanation
Indices: 113829--113908 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
113819 CAGAACCCGT
*
113829 GGGGGTATCGATTCCC--TCAA
1 GGGGGAATCGATTCCCATTCAA
*
113849 GGGGGTATCGATTCCCATTCAAA
1 GGGGGAATCGATTCCCATTC-AA
*
113872 GGGGGAATC-AGTTCCCCTTCAA
1 GGGGGAATCGA-TTCCCATTCAA
*
113894 GGGGGTATCGATTCC
1 GGGGGAATCGATTCC
113909 TCCAGCACTA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
20 16 0.31
22 17 0.33
23 19 0.37
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCATTCAA
Found at i:118005 original size:117 final size:117
Alignment explanation
Indices: 117785--118005 Score: 286
Period size: 117 Copynumber: 1.9 Consensus size: 117
117775 CTTTTAAATC
* * *
117785 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAATCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
117850 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * *
117902 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTTTCTT-AACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCC-TTCTTCAACAT
* * *
117965 TTCATTTTGATTTTCCAAGTCTATTTTAGCTTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
118006 TATCATTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 1 0.01
117 79 0.89
118 9 0.10
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:119724 original size:54 final size:54
Alignment explanation
Indices: 119642--119882 Score: 315
Period size: 54 Copynumber: 4.5 Consensus size: 54
119632 TGTTTTCAAC
* *
119642 ACGACTGTATCGGCACTAAGTGTGCAACCCACGTAATTCATAATATATTTATGA
1 ACGACCGTATCGGCACTAAGTGTGCAACCCACATAATTCATAATATATTTATGA
* * * *
119696 ACGACCATATCGGCACTAAGTGTGCAACCTACATAATACATAATATGTTTATGA
1 ACGACCGTATCGGCACTAAGTGTGCAACCCACATAATTCATAATATATTTATGA
* * * * *
119750 ACGACCGTATAGGCACTAAGT-TGTAACCCACAAAATTCATAATGTGTTTATGA
1 ACGACCGTATCGGCACTAAGTGTGCAACCCACATAATTCATAATATATTTATGA
** *
119803 ACGACCGTATCGGCACTAAGTGTGCAACCCACGGAATTCACAATATGA-TTATGA
1 ACGACCGTATCGGCACTAAGTGTGCAACCCACATAATTCATAATAT-ATTTATGA
* *
119857 ATGACCGTATCGGCACTACGTGTGCA
1 ACGACCGTATCGGCACTAAGTGTGCA
119883 CCTCATAGAA
Statistics
Matches: 163, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 47 0.29
54 116 0.71
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (54 bp):
ACGACCGTATCGGCACTAAGTGTGCAACCCACATAATTCATAATATATTTATGA
Found at i:119829 original size:107 final size:108
Alignment explanation
Indices: 119642--119882 Score: 331
Period size: 107 Copynumber: 2.2 Consensus size: 108
119632 TGTTTTCAAC
* **
119642 ACGACTGTATCGGCACTAAGTGTGCAACCCACGTAATTCATAATATATTTATGAACGACCATATC
1 ACGACCGTATCGGCACTAAGTGTGCAACCCACAAAATTCATAATATATTTATGAACGACCATATC
* * * *
119707 GGCACTAAGTGTGCAACCTACATAATACATAATATGTTTATGA
66 GGCACTAAGTGTGCAACCCACAGAATACACAATATGATTATGA
* * * * *
119750 ACGACCGTATAGGCACTAAGT-TGTAACCCACAAAATTCATAATGTGTTTATGAACGACCGTATC
1 ACGACCGTATCGGCACTAAGTGTGCAACCCACAAAATTCATAATATATTTATGAACGACCATATC
* *
119814 GGCACTAAGTGTGCAACCCACGGAATTCACAATATGATTATGA
66 GGCACTAAGTGTGCAACCCACAGAATACACAATATGATTATGA
* *
119857 ATGACCGTATCGGCACTACGTGTGCA
1 ACGACCGTATCGGCACTAAGTGTGCA
119883 CCTCATAGAA
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
107 92 0.81
108 22 0.19
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (108 bp):
ACGACCGTATCGGCACTAAGTGTGCAACCCACAAAATTCATAATATATTTATGAACGACCATATC
GGCACTAAGTGTGCAACCCACAGAATACACAATATGATTATGA
Found at i:125676 original size:21 final size:21
Alignment explanation
Indices: 125652--125710 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
125642 TTCTATGTGG
*
125652 TCCTTTGGGACATATATGTAA
1 TCCTTTGGGACATATATGCAA
* *
125673 TCCTTTGGAACATATATGCAT
1 TCCTTTGGGACATATATGCAA
* *
125694 TTCTTTGGGACACATAT
1 TCCTTTGGGACATATAT
125711 TTGGTCCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
TCCTTTGGGACATATATGCAA
Found at i:125779 original size:21 final size:21
Alignment explanation
Indices: 125753--125812 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
125743 AGAGAATTAT
125753 ATGTGGTCCTTCGGGACATAG
1 ATGTGGTCCTTCGGGACATAG
*
125774 ATGTGGTCCTTCGGGACATAT
1 ATGTGGTCCTTCGGGACATAG
* *
125795 ATGAGGTCCTTAGGGACA
1 ATGTGGTCCTTCGGGACA
125813 ACTTTATATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (21 bp):
ATGTGGTCCTTCGGGACATAG
Found at i:135260 original size:46 final size:46
Alignment explanation
Indices: 135207--135294 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
135197 ACCGCTATGT
*
135207 ATTTTCATTTGTGACATCCTTTCATGCCAATTATGCACTGTTATAC
1 ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTTATAC
* *
135253 ATTTTCATTTATGACATCCTTTCATTCCAATTATGCATTGTT
1 ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTT
135295 CTTCATCTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (46 bp):
ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTTATAC
Found at i:135763 original size:54 final size:53
Alignment explanation
Indices: 135582--136020 Score: 490
Period size: 54 Copynumber: 8.2 Consensus size: 53
135572 ATTAAAATGA
* *
135582 ACACGTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGTGTTGC
1 ACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTT-GTGAGTTGC
** * * *
135636 ACACATAGTGTTTGTAC-GTTGTTCATCAACATATGATG-ATATGTGGGTTGC
1 ACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTGTGAGTTGC
* * * * *
135687 ACACATAGTGCATGTACAGTTGTTCATCAACATATGATGAATTATGTGGGTTAC
1 ACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-TGTGAGTTGC
135741 ACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGC
1 ACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTT-GTGAGTTGC
* * * * **
135795 ACACATATTG-CTGAAATGGTTGTTCATCGACATATGATGAATTCCATGAGTTGC
1 ACACATAGTGCCT-ATACGGTTGTTCATCAACATATGATGAATT-TGTGAGTTGC
* * * *
135849 ACACATAGTGCCGAAACGGTTGTTTATCAACATATGATGAATTCCGTGAGTTGC
1 ACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-TGTGAGTTGC
* * * * * *
135903 ACACATAGTGTCGAAATGGTTGTTCATCAATATATGATGAATTTCGTGAGTTGT
1 ACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTT-GTGAGTTGC
* * *
135957 ACACATAGTGCCGA-AGCGGTTGTTCATCAACATATGATAAATTTCCTGAGTTGC
1 ACACATAGTGCCTATA-CGGTTGTTCATCAACATATGATGAATTT-GTGAGTTGC
136011 ACACATAGTG
1 ACACATAGTG
136021 TCGTTTAGTA
Statistics
Matches: 337, Mismatches: 39, Indels: 18
0.86 0.10 0.05
Matches are distributed among these distances:
51 23 0.07
52 24 0.07
53 27 0.08
54 262 0.78
55 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (53 bp):
ACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTGTGAGTTGC
Found at i:135834 original size:108 final size:108
Alignment explanation
Indices: 135599--136020 Score: 547
Period size: 108 Copynumber: 3.9 Consensus size: 108
135589 GTGCCTATAC
* **
135599 GGTTGTTCATCAACATATGATGAATTTCGTGTGTTGCACACATAGTGTTTG-TAC-GTTGTTCAT
1 GGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTG-CCGATACGGTTGTTCAT
* * *
135662 CAACATATGATG-ATAT-GTGGGTTGCACACATAGTGCATGTACA-
65 CAACATATGATGAATTTCGTGAGTTGCACACATAGTGC-TG-AAAT
* * *
135705 -GTTGTTCATCAACATATGATGAATTAT-GTGGGTTACACACATAGTGCCTATACGGTTGTTCAT
1 GGTTGTTCATCAACATATGATGAATT-TCGTGAGTTGCACACATAGTGCCGATACGGTTGTTCAT
*
135768 CAACATATGATGAATTTCGTGAGTTGCACACATATTGCTGAAAT
65 CAACATATGATGAATTTCGTGAGTTGCACACATAGTGCTGAAAT
* * * * *
135812 GGTTGTTCATCGACATATGATGAATTCCATGAGTTGCACACATAGTGCCGAAACGGTTGTTTATC
1 GGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCGATACGGTTGTTCATC
*
135877 AACATATGATGAATTCCGTGAGTTGCACACATAGTG-TCGAAAT
66 AACATATGATGAATTTCGTGAGTTGCACACATAGTGCT-GAAAT
* *
135920 GGTTGTTCATCAATATATGATGAATTTCGTGAGTTGTACACATAGTGCCGA-AGCGGTTGTTCAT
1 GGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCGATA-CGGTTGTTCAT
* *
135984 CAACATATGATAAATTTCCTGAGTTGCACACATAGTG
65 CAACATATGATGAATTTCGTGAGTTGCACACATAGTG
136021 TCGTTTAGTA
Statistics
Matches: 278, Mismatches: 28, Indels: 18
0.86 0.09 0.06
Matches are distributed among these distances:
105 45 0.16
106 24 0.09
107 7 0.03
108 202 0.73
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (108 bp):
GGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCGATACGGTTGTTCATC
AACATATGATGAATTTCGTGAGTTGCACACATAGTGCTGAAAT
Found at i:135908 original size:27 final size:27
Alignment explanation
Indices: 135770--135909 Score: 76
Period size: 27 Copynumber: 5.2 Consensus size: 27
135760 TTGTTCATCA
*
135770 ACATATGATGAATTTCGTGAGTTGCAC
1 ACATATGATGAATTCCGTGAGTTGCAC
* * * *
135797 ACATATTGCTGAAAT-GGT-TGTT-CATC
1 ACATA-TGATGAATTCCGTGAGTTGCA-C
*
135823 GACATATGATGAATTCCATGAGTTGCAC
1 -ACATATGATGAATTCCGTGAGTTGCAC
** * * * *
135851 ACATAGTGCCGAA-ACGGT-TGTT-TATC
1 ACATA-TGATGAATTCCGTGAGTTGCA-C
135877 AACATATGATGAATTCCGTGAGTTGCAC
1 -ACATATGATGAATTCCGTGAGTTGCAC
135905 ACATA
1 ACATA
135910 GTGTCGAAAT
Statistics
Matches: 79, Mismatches: 22, Indels: 24
0.63 0.18 0.19
Matches are distributed among these distances:
25 3 0.04
26 20 0.25
27 33 0.42
28 20 0.25
29 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (27 bp):
ACATATGATGAATTCCGTGAGTTGCAC
Found at i:136463 original size:20 final size:20
Alignment explanation
Indices: 136438--136510 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
136428 TGGATTCATG
136438 GTATCGATACTTCTCTCCTT
1 GTATCGATACTTCTCTCCTT
* *
136458 GTATCGATATTTCTCTCCTA
1 GTATCGATACTTCTCTCCTT
* *
136478 GTATCGATACTTCTATACTAT
1 GTATCGATACTTCTCTCCT-T
136499 GGTATCGATACT
1 -GTATCGATACT
136511 CCATTATAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 34 0.76
22 11 0.24
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.42
Consensus pattern (20 bp):
GTATCGATACTTCTCTCCTT
Found at i:136524 original size:19 final size:21
Alignment explanation
Indices: 136476--136528 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
136466 ATTTCTCTCC
*
136476 TAGTATCGATACTTCTATACTA
1 TAGTATCGATACTTCCATA-TA
*
136498 TGGTATCGATAC-TCCAT-TA
1 TAGTATCGATACTTCCATATA
136517 TAGTATCGATAC
1 TAGTATCGATAC
136529 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.46
21 4 0.14
22 11 0.39
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (21 bp):
TAGTATCGATACTTCCATATA
Found at i:138551 original size:2 final size:2
Alignment explanation
Indices: 138544--138576 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
138534 GTTAGGGGTT
138544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
138577 GTATGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:142412 original size:4 final size:4
Alignment explanation
Indices: 142403--142451 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
142393 ATTTTATTCA
** * *
142403 ATTT ATTT ATTT ATTT CAAAT ATTT ATTC ATTT ATTT ATTT AGTT ATTT
1 ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
142452 CAAATTTGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
4 34 0.94
5 2 0.06
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:142494 original size:23 final size:23
Alignment explanation
Indices: 142434--142494 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
142424 ATTTATTCAT
* * *
142434 TTATTTATTTAGTTATTTCAAAT
1 TTATTTATTTATTTGTTTCAAAA
* * *
142457 TTGTTTGTTTGTTTGTTTCAAAA
1 TTATTTATTTATTTGTTTCAAAA
*
142480 TTATTTTTTTATTTG
1 TTATTTATTTATTTG
142495 AAGTGATATG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (23 bp):
TTATTTATTTATTTGTTTCAAAA
Found at i:144362 original size:15 final size:15
Alignment explanation
Indices: 144342--144380 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
144332 TGTAGATGAG
*
144342 GGTGATGATGGTGGT
1 GGTGATGATAGTGGT
144357 GGTGATGATAGTGGT
1 GGTGATGATAGTGGT
*
144372 GGTGGTGAT
1 GGTGATGAT
144381 TAGAGTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.51, T:0.33
Consensus pattern (15 bp):
GGTGATGATAGTGGT
Found at i:144387 original size:18 final size:18
Alignment explanation
Indices: 144350--144387 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
144340 AGGGTGATGA
*
144350 TGGTGGTGGTGATGATAG
1 TGGTGGTGGTGATGAGAG
*
144368 TGGTGGTGGTGATTAGAG
1 TGGTGGTGGTGATGAGAG
144386 TG
1 TG
144388 ATAATGATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (18 bp):
TGGTGGTGGTGATGAGAG
Found at i:159050 original size:16 final size:16
Alignment explanation
Indices: 159031--159064 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
159021 GTTCATTACC
159031 TAATAGAATCATCAGT
1 TAATAGAATCATCAGT
159047 TAATAGAATCATCAGT
1 TAATAGAATCATCAGT
159063 TA
1 TA
159065 TTCATAACAT
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:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (16 bp):
TAATAGAATCATCAGT
Found at i:160521 original size:9 final size:9
Alignment explanation
Indices: 160507--160555 Score: 53
Period size: 9 Copynumber: 5.0 Consensus size: 9
160497 TCGGTCTAAC
160507 GGCTCGGTT
1 GGCTCGGTT
160516 GGCTCGGTTAGGT
1 GGCTCGG-T---T
*
160529 GGCTCGGTC
1 GGCTCGGTT
160538 GGCTCGGTT
1 GGCTCGGTT
160547 GGCTCGGTT
1 GGCTCGGTT
160556 ATTAAACTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 24 0.71
10 1 0.03
12 1 0.03
13 8 0.24
ACGTcount: A:0.02, C:0.22, G:0.45, T:0.31
Consensus pattern (9 bp):
GGCTCGGTT
Found at i:160521 original size:22 final size:22
Alignment explanation
Indices: 160496--160546 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
160486 GTCAACTCGA
*
160496 CTCGGTCTA-ACGGCTCGGTTGG
1 CTCGGT-TAGACGGCTCGGTCGG
**
160518 CTCGGTTAGGTGGCTCGGTCGG
1 CTCGGTTAGACGGCTCGGTCGG
160540 CTCGGTT
1 CTCGGTT
160547 GGCTCGGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.06, C:0.25, G:0.39, T:0.29
Consensus pattern (22 bp):
CTCGGTTAGACGGCTCGGTCGG
Found at i:166403 original size:21 final size:21
Alignment explanation
Indices: 166379--166420 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
166369 TTTATCAAAT
*
166379 TCATACTTATGGTATCGATAC
1 TCATACATATGGTATCGATAC
*
166400 TCATTCATATGGTATCGATAC
1 TCATACATATGGTATCGATAC
166421 CCCTATACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
TCATACATATGGTATCGATAC
Found at i:167864 original size:2 final size:2
Alignment explanation
Indices: 167857--167889 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
167847 TCTATTAATT
167857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
167890 TAATAAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:169736 original size:3 final size:3
Alignment explanation
Indices: 169723--169783 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
169713 GTAATTATTT
169723 ATA ATA A-A ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
169769 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
169784 GGATGAAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:170101 original size:22 final size:21
Alignment explanation
Indices: 170048--170102 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
170038 AACATCCTGT
170048 ACTGTAGGTCTTATAGATGGC
1 ACTGTAGGTCTTATAGATGGC
* ** *
170069 CCTG-AGGTCTTATCATCTTGC
1 ACTGTAGGTCTTAT-AGATGGC
170090 ACTGTAGGTCTTA
1 ACTGTAGGTCTTA
170103 CAAATGACCC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 9 0.33
21 10 0.37
22 8 0.30
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
ACTGTAGGTCTTATAGATGGC
Found at i:170176 original size:74 final size:74
Alignment explanation
Indices: 170082--170328 Score: 440
Period size: 74 Copynumber: 3.3 Consensus size: 74
170072 GAGGTCTTAT
* * *
170082 CATCTTGCACTGTAGGTCTTACAAATGACCCTGAGGCTTTAAATATAAAAAAGCTCCCGAAGGCT
1 CATCCTGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
170147 TTTTGAAAA
66 TTTTGAAAA
* *
170156 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCTGAAGGCT
1 CATCCTGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
170221 TTTTGAAAA
66 TTTTGAAAA
*
170230 CATCCTGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAATCTCCCGAAGGCT
1 CATCCTGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
170295 TTTTGAAAA
66 TTTTGAAAA
170304 CATCCTGCACTGTAGGTCTTACAGA
1 CATCCTGCACTGTAGGTCTTACAGA
170329 CGTGGGAAAT
Statistics
Matches: 166, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 166 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (74 bp):
CATCCTGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
TTTTGAAAA
Found at i:170978 original size:22 final size:22
Alignment explanation
Indices: 170950--171028 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
170940 AATAAGGTTT
* *
170950 TCATCTTTGAAAAAAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
170972 TCATCTTTGAGGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
170994 TCATCTTTGATGGGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
171016 TCATTTTTGAAGA
1 TCATCTTTGAAGA
171029 ATGTAGATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:172481 original size:75 final size:75
Alignment explanation
Indices: 172397--172536 Score: 199
Period size: 75 Copynumber: 1.9 Consensus size: 75
172387 GATATGAATA
* * * *
172397 TTCAAAATACATTAACATTCCTGATTTTGATTGAAATGGGCTTTCAACATGTCCCAACATTTGCT
1 TTCAAAATACATCAACATTCCTCATTTTGATAGAAATGGGCTTTCAACATGCCCCAACATTTGCT
172462 GATACAAACG
66 GATACAAACG
* * * * *
172472 TTCAAAATACGTCAACATTCTTCTTTTTGATAGAAATGGGCTTTCAGCATGCCCCAATATTTGCT
1 TTCAAAATACATCAACATTCCTCATTTTGATAGAAATGGGCTTTCAACATGCCCCAACATTTGCT
172537 TCTTGTTGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 56 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (75 bp):
TTCAAAATACATCAACATTCCTCATTTTGATAGAAATGGGCTTTCAACATGCCCCAACATTTGCT
GATACAAACG
Found at i:175194 original size:32 final size:32
Alignment explanation
Indices: 175153--175214 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
175143 GAAGAAATGA
175153 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
175185 TTGTTATGCTCATCTTGTAGAGATACTTCT
1 TTGTTATGCTCATCTTGTAGAGATACTTCT
175215 TGTTTCCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (32 bp):
TTGTTATGCTCATCTTGTAGAGATACTTCTCG
Found at i:178699 original size:43 final size:44
Alignment explanation
Indices: 178635--178719 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 44
178625 TTGTGCATCA
* *
178635 AACAAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTAC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTAC
* *
178679 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACT
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACT
178720 TCTCTAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 29 0.78
44 8 0.22
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTAC
Found at i:181222 original size:2 final size:2
Alignment explanation
Indices: 181215--181247 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
181205 TCTATTAATT
181215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
181248 TAATAAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:181582 original size:2 final size:2
Alignment explanation
Indices: 181575--181618 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
181565 TCACACGCAC
181575 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
181617 AT
1 AT
181619 TTGTTTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:183129 original size:3 final size:3
Alignment explanation
Indices: 183121--183164 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
183111 GTAATTATTT
183121 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
183165 GGATGAAAAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:194905 original size:18 final size:18
Alignment explanation
Indices: 194859--194899 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
194849 TGTCAAAATA
*
194859 GTATCGATACTGAAGTGG
1 GTATCGATACCGAAGTGG
194877 GTATCGATACCGAAGTGG
1 GTATCGATACCGAAGTGG
194895 GTATC
1 GTATC
194900 AGTACCATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.27
Consensus pattern (18 bp):
GTATCGATACCGAAGTGG
Found at i:202223 original size:73 final size:73
Alignment explanation
Indices: 202139--202295 Score: 269
Period size: 73 Copynumber: 2.2 Consensus size: 73
202129 TTAAAGAAGT
*
202139 AGAAGAAAAGGGTCAGGTGATCTAACATAACCTTAAAGTAGCAACAGACAGATAAAAGTCTTACG
1 AGAAGAAAAGGGTCAGGTGATCCAACATAACCTTAAAGTAGCAACAGACAGATAAAAGTCTTACG
202204 CGTATTTA
66 CGTATTTA
* * *
202212 AGAAGAAAAGGGTCAGGTGATCCAATATAACCTTAAAGTGGCAACAGACAGATAAAAGTCTTATG
1 AGAAGAAAAGGGTCAGGTGATCCAACATAACCTTAAAGTAGCAACAGACAGATAAAAGTCTTACG
202277 CGTATTTA
66 CGTATTTA
*
202285 AAAAGAAAAGG
1 AGAAGAAAAGG
202296 TTGAGTATCA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (73 bp):
AGAAGAAAAGGGTCAGGTGATCCAACATAACCTTAAAGTAGCAACAGACAGATAAAAGTCTTACG
CGTATTTA
Found at i:204312 original size:23 final size:22
Alignment explanation
Indices: 204282--204327 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
204272 TTACGCAGTC
* *
204282 CTTTGGGATAAATCTATGTGGT
1 CTTTGGGACAAATCTACGTGGT
*
204304 CTTTCGGGACAATTCTACGTGGT
1 CTTT-GGGACAAATCTACGTGGT
204327 C
1 C
204328 GTTCAAGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (22 bp):
CTTTGGGACAAATCTACGTGGT
Found at i:204346 original size:24 final size:24
Alignment explanation
Indices: 204306--204393 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
204296 TATGTGGTCT
* ** *
204306 TTCGGGAC-AATTCTACGTGGTCG
1 TTCGAGACAAATTCTACGCAGTCC
*
204329 TTCAAGACAAATTCTACGCAGTCC
1 TTCGAGACAAATTCTACGCAGTCC
*
204353 TTCGAGACAAATTCTATGCAGTCC
1 TTCGAGACAAATTCTACGCAGTCC
204377 TTCGAGACAAATTCTAC
1 TTCGAGACAAATTCTAC
204394 ATGGCACTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 6 0.11
24 50 0.89
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (24 bp):
TTCGAGACAAATTCTACGCAGTCC
Found at i:204403 original size:24 final size:23
Alignment explanation
Indices: 204333--204405 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 23
204323 TGGTCGTTCA
*
204333 AGACAAATTCTACGCAGTCCTTCG
1 AGACAAATTCTA-GCAGGCCTTCG
*
204357 AGACAAATTCTATGCAGTCCTTCG
1 AGACAAATTCTA-GCAGGCCTTCG
204381 AGACAAATTCTA-CATGGCACTTCG
1 AGACAAATTCTAGCA-GGC-CTTCG
204405 A
1 A
204406 TGTAAATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.04
23 2 0.04
24 41 0.91
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (23 bp):
AGACAAATTCTAGCAGGCCTTCG
Found at i:205283 original size:18 final size:18
Alignment explanation
Indices: 205241--205283 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
205231 TTTCACTTGG
205241 GAGATGAAGAAGAAAAGA
1 GAGATGAAGAAGAAAAGA
* *
205259 GAAATGATGAAGAAAA-A
1 GAGATGAAGAAGAAAAGA
205276 GAGGATGA
1 GA-GATGA
205284 GTGTTTGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (18 bp):
GAGATGAAGAAGAAAAGA
Found at i:208718 original size:23 final size:23
Alignment explanation
Indices: 208692--208736 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
208682 CACCACAGCT
*
208692 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
208715 CGTAGAATTGCATCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
208737 ATATAAGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:209005 original size:31 final size:30
Alignment explanation
Indices: 208960--209019 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
208950 TATTGTATAG
208960 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
208990 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
209020 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:211342 original size:22 final size:22
Alignment explanation
Indices: 211317--211372 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
211307 CAATGGTAAA
211317 ATTATACTCT-AGGTCAACCTAT
1 ATTAT-CTCTAAGGTCAACCTAT
* *
211339 ATTATTTCTAAGGTCATCCTAT
1 ATTATCTCTAAGGTCAACCTAT
*
211361 ATTATTTCTAAG
1 ATTATCTCTAAG
211373 CTTAAAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (22 bp):
ATTATCTCTAAGGTCAACCTAT
Found at i:214502 original size:2 final size:2
Alignment explanation
Indices: 214495--214520 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
214485 TTATGTTCAC
214495 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
214521 CAATGGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220336 original size:2 final size:2
Alignment explanation
Indices: 220329--220356 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
220319 ACCAAATTGA
220329 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
220357 TGCATTAAAA
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:223429 original size:102 final size:102
Alignment explanation
Indices: 223250--223450 Score: 332
Period size: 102 Copynumber: 2.0 Consensus size: 102
223240 TCATTCGTTG
* **
223250 AGTATCGATACCAGGGCAGGACTATTGATACTCCCCATAGGGGTATCGATACTAGCTAATTTTTG
1 AGTATCGATACCAGGGAAGGACTATCAATACTCCCCATAGGGGTATCGATACTAGCTAATTTTTG
*
223315 AAACATCGAACCTCATTTTGGTATTGATACTCAATCA
66 AAACATCAAACCTCATTTTGGTATTGATACTCAATCA
* *
223352 AGTATCGATACCAGGGAAGGAGTATCAATACTCCCCATAGGGGTATCGATATTGAGCTAATTTTT
1 AGTATCGATACCAGGGAAGGACTATCAATACTCCCCATAGGGGTATCGATACT-AGCTAATTTTT
223417 -AAACATCAAACCTCATTTTGGTATTGATACTCAA
65 GAAACATCAAACCTCATTTTGGTATTGATACTCAA
223451 CCTAGAGTAT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 81 0.88
103 11 0.12
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (102 bp):
AGTATCGATACCAGGGAAGGACTATCAATACTCCCCATAGGGGTATCGATACTAGCTAATTTTTG
AAACATCAAACCTCATTTTGGTATTGATACTCAATCA
Found at i:224772 original size:2 final size:2
Alignment explanation
Indices: 224765--224819 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
224755 ACTCAAAAAG
224765 TA 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 TA
224807 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
224820 CATTCAAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:227694 original size:19 final size:20
Alignment explanation
Indices: 227653--227694 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
227643 AAACAATTCT
* **
227653 AAAGTTTTTAATATTTTGCA
1 AAAGTTTTTAATAATTTAAA
227673 AAAGTTTTT-ATAATTTAAA
1 AAAGTTTTTAATAATTTAAA
227692 AAA
1 AAA
227695 AAAATCCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (20 bp):
AAAGTTTTTAATAATTTAAA
Found at i:233502 original size:16 final size:16
Alignment explanation
Indices: 233478--233510 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
233468 TATCGCCGAC
*
233478 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
233494 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
233510 C
1 C
233511 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:238370 original size:23 final size:23
Alignment explanation
Indices: 238340--238389 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
238330 TTTTTAAGTG
238340 AATGAAGTTTACTCAATATGACC
1 AATGAAGTTTACTCAATATGACC
238363 AATGAAGTTTACTCAATATGACC
1 AATGAAGTTTACTCAATATGACC
238386 AATG
1 AATG
238390 GAGGTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (23 bp):
AATGAAGTTTACTCAATATGACC
Found at i:244586 original size:36 final size:36
Alignment explanation
Indices: 244493--244841 Score: 325
Period size: 36 Copynumber: 9.8 Consensus size: 36
244483 TTTTCAGTTA
* * ***
244493 CACCACCACCTCCTCCAGGAACAGCATCAACAATGC
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
* * *
244529 CATCACCT--T-GTCCTGGAACAGCATCGTTAATGA
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
* *
244562 CACCACCTCCTCCTCCTGGAACAGCATCGATAATTC
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
* * * *
244598 CACCACCTCTTTCTCTTGGAACAACATCGTTAATGC
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
*
244634 CACCACCTCCCCCTCCTGGAACAGCATCGTTAATGC
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
* * *
244670 CTCCA---ACTCCTCCTGGAACAACATCGTTAATGC
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
* * *
244703 CACCTCCTTCTCCTCCTGGAACAACATCGTTAATGC
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
* * ***
244739 CACCACCACCTCCTCCTGGAATAGCATCCACAATGCCAC
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATG---C
* ***
244778 CACCACCTCCTCCTCCAGGAACAGCATCCACAATGC
1 CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
**
244814 CACCAATTCCTCCTCACT-GAACAGCATC
1 CACCACCTCCTCCTC-CTGGAACAGCATC
244842 CACAATGCCG
Statistics
Matches: 258, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
33 53 0.21
34 1 0.00
35 1 0.00
36 169 0.66
37 1 0.00
39 33 0.13
ACGTcount: A:0.27, C:0.40, G:0.12, T:0.21
Consensus pattern (36 bp):
CACCACCTCCTCCTCCTGGAACAGCATCGTTAATGC
Found at i:244633 original size:105 final size:105
Alignment explanation
Indices: 244524--244818 Score: 301
Period size: 105 Copynumber: 2.8 Consensus size: 105
244514 CAGCATCAAC
* **
244524 AATGCCATCACCTTGTCCTGGAACAGCATCGTTAATGACACCACCTCCTCCTCCTGGAACAGCAT
1 AATGCCACCACCTCCTCCTGGAACAGCATCGTTAATGACACCACCTCCTCCTCCTGGAACAGCAT
* * *
244589 CGATAATTCCACCACC-TCTTTCTCTTGGAACAACATCGTT
66 CGATAATGCCACCACCTTC-TCCTCCTGGAACAACATCGTT
* ** *
244629 AATGCCACCACCTCCCCCTCCTGGAACAGCATCGTTAATG---CCTCCAACTCCTCCTGGAACAA
1 AATGCCACCACCT---CCTCCTGGAACAGCATCGTTAATGACACCACCTCCTCCTCCTGGAACAG
* *
244691 CATCGTTAATGCCACCTCCTTCTCCTCCTGGAACAACATCGTT
63 CATCGATAATGCCACCACCTTCTCCTCCTGGAACAACATCGTT
* *** *
244734 AATGCCACCACCACCTCCTCCTGGAATAGCATCCACAATGCCACCACCACCTCCTCCTCCAGGAA
1 AATG---CCACCACCTCCTCCTGGAACAGCATCGTTAATG--A-CACCACCTCCTCCTCCTGGAA
* *
244799 CAGCATCCACAATGCCACCA
60 CAGCATCGATAATGCCACCA
244819 ATTCCTCCTC
Statistics
Matches: 152, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
105 89 0.59
106 2 0.01
108 31 0.20
111 30 0.20
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.22
Consensus pattern (105 bp):
AATGCCACCACCTCCTCCTGGAACAGCATCGTTAATGACACCACCTCCTCCTCCTGGAACAGCAT
CGATAATGCCACCACCTTCTCCTCCTGGAACAACATCGTT
Found at i:244638 original size:72 final size:72
Alignment explanation
Indices: 244493--244818 Score: 322
Period size: 69 Copynumber: 4.6 Consensus size: 72
244483 TTTTCAGTTA
* * * * * * *
244493 CACCACCACCTCCTCCAGGAACAGCATCAACAATGCCATCA-C-C-TTGTCCTGGAACAGCATCG
1 CACCACCTCCTCCTCCTGGAACAGCATCGATAATGCCACCACCTCTTTCTCCTGGAACAACATCG
*
244555 TTAATGA
66 TTAATGC
* *
244562 CACCACCTCCTCCTCCTGGAACAGCATCGATAATTCCACCACCTCTTTCTCTTGGAACAACATCG
1 CACCACCTCCTCCTCCTGGAACAGCATCGATAATGCCACCACCTCTTTCTCCTGGAACAACATCG
244627 TTAATGC
66 TTAATGC
* * * *
244634 CACCACCTCCCCCTCCTGGAACAGCATCGTTAATGCCTCCAACTC---CTCCTGGAACAACATCG
1 CACCACCTCCTCCTCCTGGAACAGCATCGATAATGCCACCACCTCTTTCTCCTGGAACAACATCG
244696 TTAATGC
66 TTAATGC
* * * * * * * * * *
244703 CACCTCCTTCTCCTCCTGGAACAACATCGTTAATGCCACCACCACCTCCTCCTGGAATAGCATCC
1 CACCACCTCCTCCTCCTGGAACAGCATCGATAATGCCACCACCTCTTTCTCCTGGAACAACATCG
**
244768 ACAATGCCAC
66 TTAATG---C
* * *
244778 CACCACCTCCTCCTCCAGGAACAGCATCCACAATGCCACCA
1 CACCACCTCCTCCTCCTGGAACAGCATCGATAATGCCACCA
244819 ATTCCTCCTC
Statistics
Matches: 213, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
69 96 0.45
70 1 0.00
71 1 0.00
72 80 0.38
75 35 0.16
ACGTcount: A:0.27, C:0.40, G:0.12, T:0.21
Consensus pattern (72 bp):
CACCACCTCCTCCTCCTGGAACAGCATCGATAATGCCACCACCTCTTTCTCCTGGAACAACATCG
TTAATGC
Found at i:247637 original size:23 final size:22
Alignment explanation
Indices: 247605--247648 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
247595 GATTTTATGT
*
247605 TTATAAAATTTCAGGGGCAAAC
1 TTATAAAATTTAAGGGGCAAAC
*
247627 TTATAGAAATTTAAGTGGCAAA
1 TTATA-AAATTTAAGGGGCAAA
247649 AACTGAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (22 bp):
TTATAAAATTTAAGGGGCAAAC
Found at i:250067 original size:22 final size:22
Alignment explanation
Indices: 250038--250090 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
250028 TCTCTTTCAA
*
250038 ATAC-TGGAGTTAGGAGAATCG
1 ATACTTGGAGATAGGAGAATCG
*
250059 GTACTTGGAGATAGGAGAATCG
1 ATACTTGGAGATAGGAGAATCG
250081 ATACTTGGAG
1 ATACTTGGAG
250091 GTACGATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.32, C:0.09, G:0.34, T:0.25
Consensus pattern (22 bp):
ATACTTGGAGATAGGAGAATCG
Found at i:251769 original size:15 final size:15
Alignment explanation
Indices: 251749--251797 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
251739 TCATATCAGA
*
251749 ATTCGAATATATGAT
1 ATTCGAATATATGTT
* *
251764 ATTCGAGTATGTGTT
1 ATTCGAATATATGTT
*
251779 ATTCGGATATATGTT
1 ATTCGAATATATGTT
251794 ATTC
1 ATTC
251798 TCATCGAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (15 bp):
ATTCGAATATATGTT
Found at i:252662 original size:38 final size:39
Alignment explanation
Indices: 252588--252686 Score: 139
Period size: 38 Copynumber: 2.6 Consensus size: 39
252578 GTGTTGGCGG
*
252588 CGCTGCTCGATATCTTGAGCCGCTTGTTCTTCTGGCCTC
1 CGCTGCTCGATGTCTTGAGCCGCTTGTTCTTCTGGCCTC
* *
252627 CGCTGCTTGATGTCTTGAGCC-CTTGTTCTTTTGGCCTC
1 CGCTGCTCGATGTCTTGAGCCGCTTGTTCTTCTGGCCTC
* *
252665 CACT-CTCGATGTCATGAGCCGC
1 CGCTGCTCGATGTCTTGAGCCGC
252687 CCGCTTGTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.26
38 20 0.38
39 19 0.36
ACGTcount: A:0.09, C:0.32, G:0.23, T:0.35
Consensus pattern (39 bp):
CGCTGCTCGATGTCTTGAGCCGCTTGTTCTTCTGGCCTC
Found at i:254451 original size:183 final size:183
Alignment explanation
Indices: 254128--254982 Score: 1130
Period size: 183 Copynumber: 4.7 Consensus size: 183
254118 ATGTCAGTAT
* * * * *
254128 GTGTTGATACTTTATAAAAATGTATCGATCTATAACAATATAATAGGTAAAAATATGAAAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAA-C
* * * * * * *
254193 -GGTTTAATTATGACAAAACCGGTGAAGT-GCTACCGTATATGTTGAAAGTATCGATTA-GATTG
65 AGGTATCATTATGACAAAACCGGT-AAATCGCTACAGAATATGTTGAAAGTGTCGA-TACCATTG
* * * * *
254255 TAATTAGTATCGACATTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCAATAAA
128 AAATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAA
** * *
254311 GTGTCGATAC-AAATAAAAAATGTATCGACCCATAACAATATAACATGTAAAAATATGATAAAAT
1 GTGTCGATACTTTAT-AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAA-
* * ** *
254375 C-GGTTTCATTATGACAAAACCGGTAAATCGCTACTAG-ATATATTGAGTGTGTTGATACCATTG
64 CAGGTATCATTATGACAAAACCGGTAAATCGCTAC-AGAATATGTTGAAAGTGTCGATACCATTG
254438 AAATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAA
128 AAATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAA
* * * *
254494 GTGTCAATACTTTATAAAAATGTATCGATCTATAACAATATAACATATAAAAATATAACAAAACA
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACA
* * * * *
254559 TGTATCATTATGACAAAACCGGTAAAGCGCTATATG-ATATGTTGAAAGTGTCGATTCTATTGAA
66 GGTATCATTATGACAAAACCGGTAAATCGCTACA-GAATATGTTGAAAGTGTCGATACCATTGAA
254623 ATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAA
130 ATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAA
*
254677 GTGTCGATACTTTATAAAAATTTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACA
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACA
* * * *
254742 GATATCATTATGACAAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATTCCATTGAAA
66 GGTATCATTATGACAAAACCGGTAAATCGCTACAGAATATGTTGAAAGTGTCGATACCATTGAAA
* * *
254807 TAAGTATCGAAACTTTTGGAATTTAAAAGAGAAGTAGTAATAACGCCTATAAA
131 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAA
* * * *
254860 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGAAAAAAATATTACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG-TAAAAATATGACAAAAC
* * * *
254925 AGGTATCACTATGACAAAACCGGTAAATCGCTACCGAATATATTGAAAGCGTCGATAC
65 AGGTATCATTATGACAAAACCGGTAAATCGCTACAGAATATGTTGAAAGTGTCGATAC
254983 TTTAATAAGT
Statistics
Matches: 599, Mismatches: 64, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
182 10 0.02
183 519 0.87
184 70 0.12
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (183 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACA
GGTATCATTATGACAAAACCGGTAAATCGCTACAGAATATGTTGAAAGTGTCGATACCATTGAAA
TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAA
Done.