Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008594.1 Hibiscus syriacus cultivar Beakdansim tig00111543_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: 1173925
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:498070 original size:18 final size:18
Alignment explanation
Indices: 498047--498090 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
498037 CGGATCAACT
498047 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
498065 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
498083 GGTCGGGT
1 GGTCGGGT
498091 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.20, G:0.52, T:0.18
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:501443 original size:20 final size:20
Alignment explanation
Indices: 501418--501531 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
501408 AATTGGGAAA
*
501418 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
501438 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
501458 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
501479 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
501499 TTCACAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
501519 TTCGCAACGCGAT
1 ATCGCAACGCGAT
501532 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:501480 original size:61 final size:61
Alignment explanation
Indices: 501415--501531 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
501405 ACAAATTGGG
* * * * * *
501415 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCACAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
501476 AAAATCGCAACGAGATACTGACTTTCACAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCACAACGCGATACTGACTATCGCAACGCGAT
501532 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCACAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:502132 original size:19 final size:19
Alignment explanation
Indices: 502110--502269 Score: 98
Period size: 19 Copynumber: 9.1 Consensus size: 19
502100 GAAACCAAAA
*
502110 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
502129 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
502143 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
502162 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
502176 TCTCGTTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
502195 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
502209 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
502228 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
502248 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
502268 TC
1 TC
502270 AACCAAAAGA
Statistics
Matches: 108, Mismatches: 16, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
14 29 0.27
16 7 0.06
17 8 0.07
19 32 0.30
20 31 0.29
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:502151 original size:14 final size:14
Alignment explanation
Indices: 502132--502220 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
502122 TTTCATTTCG
502132 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
502146 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
502165 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
502179 CGTTGTGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
502198 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
502212 CGTTGCGAT
1 CGTTGCGAT
502221 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 29 0.49
16 5 0.08
17 5 0.08
19 20 0.34
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:502157 original size:33 final size:33
Alignment explanation
Indices: 502115--502244 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
502105 CAAAATCGCA
**
502115 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
**
502148 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
*
502181 TTGTGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
502214 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
502245 ATTATCTCGT
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 77 0.84
34 15 0.16
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:504431 original size:21 final size:21
Alignment explanation
Indices: 504407--504557 Score: 65
Period size: 21 Copynumber: 7.2 Consensus size: 21
504397 TCATTCCTCG
504407 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
504428 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
504449 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** * *
504470 AGAGGCCCCTATCATTC-TTCG
1 AGAGTCCCCTCCCA-CCGTTCA
504491 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
504512 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
504533 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
504554 AGAG
1 AGAG
504558 CCCGATTCAC
Statistics
Matches: 88, Mismatches: 37, Indels: 11
0.65 0.27 0.08
Matches are distributed among these distances:
20 3 0.03
21 80 0.91
22 5 0.06
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:504431 original size:42 final size:42
Alignment explanation
Indices: 504385--504557 Score: 188
Period size: 42 Copynumber: 4.1 Consensus size: 42
504375 CCTATCATTG
*
504385 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
* * * * * * *
504427 AAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTATCGTTG
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
* *
504469 AAGAGGCCCCTATCATTCTTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
* * * *
504511 AAGAGGCCACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTC
1 AAGAGGCCACTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTC
504553 AAGAG
1 AAGAG
504558 CCCGATTCAC
Statistics
Matches: 107, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 4 0.04
42 101 0.94
43 2 0.02
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (42 bp):
AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
Found at i:504536 original size:84 final size:84
Alignment explanation
Indices: 504352--504527 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
504342 CCCGACTCGC
504352 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
504417 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* *
504436 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
504501 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
504520 CTGTCATC
1 CTGTCATC
504528 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:504557 original size:84 final size:84
Alignment explanation
Indices: 504352--504557 Score: 306
Period size: 84 Copynumber: 2.5 Consensus size: 84
504342 CCCGACTCGC
* *
504352 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
504417 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
504436 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
504501 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** * *
504520 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTGAAGAG
504558 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:506100 original size:19 final size:19
Alignment explanation
Indices: 506041--506107 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
506031 AAAAAGTACT
*
506041 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
506060 ACCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
506074 ATCACAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
506093 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
506108 TAAATTTGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
14 8 0.22
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.62
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:506158 original size:33 final size:32
Alignment explanation
Indices: 506116--506242 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
506106 ATTAAATTTG
506116 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
506149 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
506182 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
506215 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
506243 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:506205 original size:66 final size:66
Alignment explanation
Indices: 506109--506241 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
506099 ACGCGAAATT
*
506109 AAATTTGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
506174 G
66 G
*
506175 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
506240 G
66 G
506241 A
1 A
506242 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:508540 original size:12 final size:12
Alignment explanation
Indices: 508523--508547 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
508513 TCTTCGGGGA
508523 CTTTTTCTTCTT
1 CTTTTTCTTCTT
508535 CTTTTTCTTCTT
1 CTTTTTCTTCTT
508547 C
1 C
508548 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:508755 original size:24 final size:24
Alignment explanation
Indices: 508721--508774 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
508711 CTGAAACATC
*
508721 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
508745 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
508769 ATCAAA
1 ATCAAA
508775 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:509904 original size:19 final size:20
Alignment explanation
Indices: 509826--509908 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
509816 CGGGGAAATT
509826 GCAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGGCTATC
*
509846 ACAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGGCTATC
* ***
509866 GCAA-TCG-AAATGAAAAATC
1 GCAACGCGAAAATG-GCTATC
509885 GCAACGCGAAAAT-GCTATC
1 GCAACGCGAAAATGGCTATC
509904 GCAAC
1 GCAAC
509909 TGAAAATCGC
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
18 5 0.10
19 17 0.34
20 24 0.48
21 4 0.08
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAAATGGCTATC
Found at i:509973 original size:18 final size:18
Alignment explanation
Indices: 509934--509996 Score: 75
Period size: 19 Copynumber: 3.8 Consensus size: 18
509924 GAAATGAAAA
509934 TCGCATTGCGATTTC---
1 TCGCATTGCGATTTCATT
509949 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
509965 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
509984 TCGCA-TGCGATTT
1 TCGCATTGCGATTT
509997 TTCGTTGCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 10 0.24
15 3 0.07
16 3 0.07
17 3 0.07
18 11 0.26
19 12 0.29
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:509999 original size:19 final size:19
Alignment explanation
Indices: 509952--509997 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
509942 CGATTTCTCG
509952 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
509970 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
509989 -TGCGATTTT
1 TTGCGATTTT
509998 TCGTTGCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:510019 original size:18 final size:19
Alignment explanation
Indices: 509996--510035 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
509986 GCATGCGATT
509996 TTTCGT-TGCGATAGTCAG
1 TTTCGTGTGCGATAGTCAG
*
510014 TTTCGTGTGCGATAGTCTG
1 TTTCGTGTGCGATAGTCAG
510033 TTT
1 TTT
510036 TGCCTTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.12, C:0.15, G:0.28, T:0.45
Consensus pattern (19 bp):
TTTCGTGTGCGATAGTCAG
Found at i:511953 original size:19 final size:20
Alignment explanation
Indices: 511898--511944 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
511888 GAAACTTAAA
*
511898 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
511918 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
511938 ATCGCAA
1 ATCGCAA
511945 TGTGAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:511960 original size:19 final size:19
Alignment explanation
Indices: 511895--512060 Score: 87
Period size: 19 Copynumber: 9.5 Consensus size: 19
511885 CACGAAACTT
*
511895 AAAATCGCAACGCGAAAATG
1 AAAATCGCAATGCG-AAATG
** *
511915 ACTATCGCAACGCGGAAATG
1 AAAATCGCAATGC-GAAATG
*** *
511935 GCTATCGCAATGTGAAATG
1 AAAATCGCAATGCGAAATG
*
511954 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
511968 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
511987 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
512001 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
* *
512020 AAAATTGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
512034 AAAATCGCAATGCG-AATG
1 AAAATCGCAATGCGAAATG
512052 -AAATCGCAA
1 AAAATCGCAA
512061 CGACAAAATC
Statistics
Matches: 114, Mismatches: 17, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
14 29 0.25
15 3 0.03
16 6 0.05
17 15 0.13
18 2 0.02
19 32 0.28
20 26 0.23
21 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:511973 original size:14 final size:14
Alignment explanation
Indices: 511954--512076 Score: 86
Period size: 14 Copynumber: 7.9 Consensus size: 14
511944 ATGTGAAATG
511954 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
511968 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
511987 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
512001 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
512020 AAAATTGCAACGAC
1 AAAATCGCAACGAC
512034 AAAATCGCAATGCGA-
1 AAAATCGCAA--CGAC
512049 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
512065 AAAATCGCAACG
1 AAAATCGCAACG
512077 CGAAACACAA
Statistics
Matches: 88, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
14 40 0.45
15 6 0.07
16 8 0.09
17 13 0.15
18 2 0.02
19 19 0.22
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:511985 original size:33 final size:33
Alignment explanation
Indices: 511938--512081 Score: 247
Period size: 33 Copynumber: 4.4 Consensus size: 33
511928 GGAAATGGCT
*
511938 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
511971 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
512004 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
512037 ATCGCAATGCG-AATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
512068 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
512082 CACAAATCGT
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
31 25 0.24
32 6 0.06
33 75 0.71
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:512129 original size:14 final size:14
Alignment explanation
Indices: 512110--512167 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
512100 TTTCATTTCG
512110 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
512124 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
512140 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
512156 CGTTGCGATTTT
1 CGTTGCGATTTT
512168 CATTTCGCAT
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:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:512174 original size:33 final size:33
Alignment explanation
Indices: 512093--512183 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
512083 ACAAATCGTA
*
512093 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
512126 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
512158 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
512184 AGCTATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:512211 original size:20 final size:19
Alignment explanation
Indices: 512156--512222 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
512146 GCGATTTTGT
**
512156 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
512175 CATTGCGATAG-CTATTTCCG
1 CGTTGCGATAGTC-ATTT-CG
512195 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
512215 TGTTGCGA
1 CGTTGCGA
512223 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.03
19 12 0.31
20 22 0.56
21 4 0.10
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:512725 original size:18 final size:18
Alignment explanation
Indices: 512699--512743 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
512689 GTCGATCAGA
* *
512699 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTAGGCGAGG
*
512717 TGATAGCTCTAGGCGAGG
1 TGATGGCTCTAGGCGAGG
512735 TGATGGCTC
1 TGATGGCTC
512744 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:514104 original size:20 final size:20
Alignment explanation
Indices: 514056--514114 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
514046 AATAGTTTCT
** *
514056 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
514076 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
514096 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
514115 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:514395 original size:20 final size:21
Alignment explanation
Indices: 514370--514418 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
514360 TCTGAGAGAT
514370 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
514390 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
514412 AGAGATG
1 GGAGATG
514419 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:514404 original size:22 final size:22
Alignment explanation
Indices: 514377--514420 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
514367 GATGGAGATA
*
514377 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
514399 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
514421 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:514633 original size:20 final size:20
Alignment explanation
Indices: 514605--514699 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
514595 GATTATGTAT
*
514605 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
514625 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
514646 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
514666 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
514686 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
514700 TTTCCCAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.05
20 46 0.72
21 13 0.20
22 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:514648 original size:41 final size:41
Alignment explanation
Indices: 514585--514679 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
514575 CGCTTTGAAA
514585 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
514626 ATCTCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
514667 ATCGCATTGCGAT
1 ATCGCATTGCGAT
514680 AGTCAGTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:514713 original size:61 final size:61
Alignment explanation
Indices: 514605--514720 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
514595 GATTATGTAT
* * * ** *
514605 TATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 TATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAG
*
514666 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 TATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
514721 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 45 0.96
62 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (61 bp):
TATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAG
Found at i:514810 original size:21 final size:21
Alignment explanation
Indices: 514770--514810 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
514760 ACTGTAGACC
** *
514770 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
514791 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
514811 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:523488 original size:21 final size:20
Alignment explanation
Indices: 523442--523495 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
523432 GATTCTGACT
*
523442 ATCGCATTGCGATTTTTCAA
1 ATCGCATTGCGATTTTCCAA
* *
523462 ATTCGCGTTGTGATTTTCCTAA
1 A-TCGCATTGCGATTTTCC-AA
*
523484 ATCGCAATGCGA
1 ATCGCATTGCGA
523496 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATTTTCCAA
Found at i:523506 original size:20 final size:20
Alignment explanation
Indices: 523481--523557 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
523471 GTGATTTTCC
523481 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
523501 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
* *
523521 TAAATCACAATGCGAATATG
1 TAAATCGCAATGCGAATACG
*
523541 TAAATCGCAACGCGAAT
1 TAAATCGCAATGCGAAT
523558 CTGACTATCG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:523567 original size:20 final size:20
Alignment explanation
Indices: 523544--523609 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
523534 GAATATGTAA
*
523544 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
523564 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
523584 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
523604 ATCGCA
1 ATCGCA
523610 TTACTGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:524479 original size:24 final size:24
Alignment explanation
Indices: 524452--524505 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
524442 GTATTCGAAA
524452 TTTGATCTTAGTCAATACCCGGAC
1 TTTGATCTTAGTCAATACCCGGAC
* * *
524476 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTAGTCAATACCCGGAC
524500 TTTGAT
1 TTTGAT
524506 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCCGGAC
Found at i:527022 original size:19 final size:19
Alignment explanation
Indices: 527000--527137 Score: 116
Period size: 19 Copynumber: 7.7 Consensus size: 19
526990 CTTAATGTCT
527000 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
527019 ATCGCAA--CG---TGAAA
1 ATCGCAATGCGAAATGAAA
*
527033 ATCGCAATGCGAATATGAAT
1 ATCGCAATGCGAA-ATGAAA
* * **
527053 ATCGCAACGTAGAAATGACT
1 ATCGCAATG-CGAAATGAAA
527073 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
527092 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
527106 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
527125 ATCGCAACGCGAA
1 ATCGCAATGCGAA
527138 TTTAGTTTCG
Statistics
Matches: 96, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 36 0.38
20 25 0.26
21 3 0.03
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:527042 original size:33 final size:33
Alignment explanation
Indices: 527000--527133 Score: 169
Period size: 33 Copynumber: 3.8 Consensus size: 33
526990 CTTAATGTCT
527000 ATCGCAATGCGAAATGAAAATCGCAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGTGAAA
*
527033 ATCGCAATGCGAATATGAATATCGCAACGTAGAAATGA
1 ATCGCAATGCGAA-ATGAAAATCGCAACGT-G-AA--A
* *
527071 CTATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGTGAAA
*
527106 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
527134 CGAATTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
33 40 0.45
34 15 0.17
35 2 0.02
36 2 0.02
37 1 0.01
38 2 0.02
39 14 0.16
40 13 0.15
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGTGAAA
Found at i:527083 original size:73 final size:72
Alignment explanation
Indices: 526993--527133 Score: 228
Period size: 73 Copynumber: 1.9 Consensus size: 72
526983 CAATCATCTT
* * * *
526993 AATGTCTATCGCAATGCGAAATGAAAATCGCAACGTGAAAATCGCAATGCGAATATGAATATCGC
1 AATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAAAGCGAA-ATGAAAATCGC
527058 AACGTAGA
65 AACGTAGA
*
527066 AATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCA
1 AATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAAAGCGAAATGAAAATCGCA
527131 ACG
66 ACG
527134 CGAATTTAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 14 0.22
73 49 0.78
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.17
Consensus pattern (72 bp):
AATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAAAGCGAAATGAAAATCGCA
ACGTAGA
Found at i:527168 original size:19 final size:19
Alignment explanation
Indices: 527133--527175 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
527123 AAATCGCAAC
*
527133 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
527152 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
527171 GCGAT
1 GCGAT
527176 AGTCATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.16, G:0.28, T:0.42
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:529277 original size:19 final size:19
Alignment explanation
Indices: 529255--529298 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
529245 AAATCGCAAC
529255 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
529274 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
529293 GCGATT
1 GCGATT
529299 TTGTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:529299 original size:19 final size:19
Alignment explanation
Indices: 529264--529301 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
529254 CGCGATTATA
529264 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
529283 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
529302 TCGTTGCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.16, G:0.32, T:0.47
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:529308 original size:14 final size:14
Alignment explanation
Indices: 529284--529329 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
529274 GCGATTTTGG
*
529284 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
*
529298 TTTGTCGTTGCGAT
1 TTTCTCGTTGCGAT
*
529312 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
529326 TTTC
1 TTTC
529330 ATTTCGCGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.07, C:0.22, G:0.24, T:0.48
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:529578 original size:94 final size:94
Alignment explanation
Indices: 529432--529811 Score: 674
Period size: 94 Copynumber: 4.1 Consensus size: 94
529422 ATGGATTGCA
* *
529432 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
529496 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
529525 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
529590 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
529619 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
529684 TTAGCAGAATTGGCAGTAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
529713 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
529777 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
529807 TTACT
1 TTACT
529812 AAGCAATCTA
Statistics
Matches: 277, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
93 23 0.08
94 254 0.92
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:531571 original size:19 final size:19
Alignment explanation
Indices: 531516--531583 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
531506 TGAAATGAAA
*
531516 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
531536 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
**
531556 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
531575 ATCGCAACG
1 ATCGCAACG
531584 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.36
20 26 0.59
21 2 0.05
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:531598 original size:33 final size:33
Alignment explanation
Indices: 531556--531647 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
531546 GGAAATGACT
*
531556 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACAAGAGA
* * *
531589 ATCGCAACGCAAAATTAAAATCGCAACAAGATA
1 ATCGCAACGCGAAATGAAAATCGCAACAAGAGA
531622 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
531648 TGCGATTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAAGAGA
Found at i:531652 original size:19 final size:19
Alignment explanation
Indices: 531507--531652 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
531497 TCTTTTGGTT
*
531507 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
531526 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
531546 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
531566 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
531583 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
531599 AAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
531616 --AA-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
531632 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
531651 GA
1 GA
531653 TTTTGGTTTC
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.19
15 3 0.03
16 2 0.02
17 3 0.03
18 3 0.03
19 39 0.38
20 31 0.30
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:531698 original size:21 final size:20
Alignment explanation
Indices: 531679--531749 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
531669 CGATTCTCTC
*
531679 GTTGCGATTTTTATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
531699 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
531720 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
531740 GTTGCGATTT
1 GTTGCGATTT
531750 GAAGTTTAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:532375 original size:40 final size:40
Alignment explanation
Indices: 532331--532522 Score: 192
Period size: 40 Copynumber: 4.8 Consensus size: 40
532321 TACATATTGT
532331 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
* * *
532371 CGTTGCGATTTATGTATTCTCGTTGCTATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
* * *
532411 CGTTGCGATTTTACGTATTGTCGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATTCTCGTTGCGA-TTTACAGATACG
* * * * *
532453 CGTTGCGATAGT-CAG-AATCGCGTTGCGATTTATATG-TTCG
1 CGTTGCGAT-TTAC-GTATTCTCGTTGCGATTTACA-GATACG
* * *
532493 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGTATTCTCGTTGCGATT
532523 CTGGAAAATC
Statistics
Matches: 127, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.01
40 75 0.59
41 30 0.24
42 21 0.17
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
Found at i:532402 original size:60 final size:61
Alignment explanation
Indices: 532308--532522 Score: 183
Period size: 60 Copynumber: 3.5 Consensus size: 61
532298 CTTTAAAAAT
* * * *
532308 CGCGTTGCGATTTTACATATTGTCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTTACATATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATA
** *
532369 CGCGTTGCGA-TTTATGTATTCTCGTTGCTATTTACGGATACGCGTTGCGATTTTAC-G-TA
1 CGCGTTGCGATTTTACATATTCTCGTTGCGATTTACGGATACGCGTTGCGA-TTTACAGATA
* ** * * * *
532428 TTGTCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATG-T
1 -CG-CGTTGCGATTTTACATATTCTCGTTGCGAT-TTACGGATA-CGCGTTGCGATTTACA-GAT
*
532490 T
61 A
*
532491 CGCGTTGCGATTTT-CATATTCGCGTTGCGATT
1 CGCGTTGCGATTTTACATATTCTCGTTGCGATT
532523 CTGGAAAATC
Statistics
Matches: 124, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
59 2 0.02
60 48 0.39
61 40 0.32
62 31 0.25
63 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (61 bp):
CGCGTTGCGATTTTACATATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATA
Found at i:532446 original size:21 final size:20
Alignment explanation
Indices: 532310--532461 Score: 130
Period size: 20 Copynumber: 7.5 Consensus size: 20
532300 TTAAAAATCG
*
532310 CGTTGCGATTTTACATATTGT
1 CGTTGCGA-TTTACGTATTGT
*
532331 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTGT
*
532351 CGTTGCGATTTACAG-ATACG-
1 CGTTGCGATTTAC-GTAT-TGT
* *
532371 CGTTGCGATTTATGTATTCT
1 CGTTGCGATTTACGTATTGT
* * *
532391 CGTTGCTATTTACGGATACG-
1 CGTTGCGATTTACGTAT-TGT
532411 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTGT
* **
532432 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATTGT
532453 CGTTGCGAT
1 CGTTGCGAT
532462 AGTCAGAATC
Statistics
Matches: 106, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.01
20 62 0.58
21 43 0.41
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTGT
Found at i:532493 original size:20 final size:20
Alignment explanation
Indices: 532470--532522 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
532460 ATAGTCAGAA
*
532470 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
532490 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
532510 TCGCGTTGCGATT
1 TCGCGTTGCGATT
532523 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:532893 original size:21 final size:21
Alignment explanation
Indices: 532867--532941 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
532857 TATATATATA
532867 TATTAAAATATATTATTTAAT
1 TATTAAAATATATTATTTAAT
**
532888 TATTAAAATATAAAAATTT-AT
1 TATTAAAATAT-ATTATTTAAT
* *
532909 TA-TAAAGTATATTAATTTAACC
1 TATTAAAATATATT-ATTTAA-T
532931 T-TTAAAATATA
1 TATTAAAATATA
532942 AAAAATAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
19 1 0.02
20 11 0.26
21 16 0.38
22 14 0.33
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (21 bp):
TATTAAAATATATTATTTAAT
Found at i:532920 original size:41 final size:40
Alignment explanation
Indices: 532867--532965 Score: 130
Period size: 42 Copynumber: 2.5 Consensus size: 40
532857 TATATATATA
* *
532867 TATTA-AAATATATTATTTAA-TTATTAAAATATAAAAATT
1 TATTATAAATATATTATTTAACCT-TTAAAATATAAAAAAT
532906 TATTATAAAGTATATTAATTTAACCTTTAAAATATAAAAAAT
1 TATTATAAA-TATATT-ATTTAACCTTTAAAATATAAAAAAT
*
532948 AATTATAAATATATTATT
1 TATTATAAATATATTATT
532966 ATAGAATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
39 5 0.09
40 6 0.11
41 12 0.23
42 29 0.55
43 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (40 bp):
TATTATAAATATATTATTTAACCTTTAAAATATAAAAAAT
Found at i:532956 original size:20 final size:20
Alignment explanation
Indices: 532883--532960 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 20
532873 AATATATTAT
532883 TTAATTATTAAAATATAAAAA
1 TTAATTA-TAAAATATAAAAA
* * * *
532904 TTTATTATAAAGTATATTAAT
1 TTAATTATAAAATATA-AAAA
532925 TTAACCTT-TAAAATATAAAAA
1 TTAA--TTATAAAATATAAAAA
*
532946 ATAATTAT-AAATATA
1 TTAATTATAAAATATA
532961 TTATTATAGA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
19 9 0.20
20 9 0.20
21 16 0.36
22 8 0.18
23 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (20 bp):
TTAATTATAAAATATAAAAA
Found at i:532975 original size:15 final size:14
Alignment explanation
Indices: 532949--532985 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
532939 ATAAAAAATA
532949 ATTATAAATATATT
1 ATTATAAATATATT
532963 ATTATAGAATATATT
1 ATTATA-AATATATT
*
532978 ATTTTAAA
1 ATTATAAA
532986 AATAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:534808 original size:57 final size:59
Alignment explanation
Indices: 534746--534859 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
534736 AGGGTAAAGG
* *
534746 ATATTACTTTA-TTAGTCAT-T-GACTATTAAAAGTTATAAAGTATCA-TTCGACTATAGA
1 ATATTACTTTATTTAGTC-TCTCAACTATTAAAAGTTATAAAATAT-AGTTCGACTATAGA
*
534803 ATATTACTTTATTTAGTCTCTCAACTATTTAAAGTTATAAAATATAGTTCGACTATA
1 ATATTACTTTATTTAGTCTCTCAACTATTAAAAGTTATAAAATATAGTTCGACTATA
534860 AAATGTTGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
57 12 0.24
58 8 0.16
59 30 0.60
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (59 bp):
ATATTACTTTATTTAGTCTCTCAACTATTAAAAGTTATAAAATATAGTTCGACTATAGA
Found at i:535080 original size:29 final size:30
Alignment explanation
Indices: 534990--535081 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 30
534980 AACAATAAAG
*
534990 TGAC-CATTTTGTAACTTGTAATAGTCAAA
1 TGACTCATTTTGTAACTTCTAATAGTCAAA
**** **
535019 TGACTCAACAAAGTAACATTCT-ATAGTTGAA
1 TGACTC-ATTTTGTAAC-TTCTAATAGTCAAA
*
535050 TGA-TCATTTTGTAACTTTTAATAGTCAAA
1 TGACTCATTTTGTAACTTCTAATAGTCAAA
535079 TGA
1 TGA
535082 ATTAATAAGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
28 3 0.07
29 20 0.44
30 3 0.07
31 16 0.36
32 3 0.07
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (30 bp):
TGACTCATTTTGTAACTTCTAATAGTCAAA
Found at i:536934 original size:2 final size:2
Alignment explanation
Indices: 536927--536961 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
536917 TAATTAGCAA
536927 AT AT AT AT AT 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 AT AT AT AT AT A
536962 GAATTTCTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:545465 original size:14 final size:15
Alignment explanation
Indices: 545435--545476 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
545425 CAAAATGTAA
**
545435 AAGAAAAACAATGAT
1 AAGAAAAACAAAAAT
545450 AA-AAAAACAAAAAT
1 AAGAAAAACAAAAAT
*
545464 AAGAAAAATAAAA
1 AAGAAAAACAAAA
545477 TCAACATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.10
Consensus pattern (15 bp):
AAGAAAAACAAAAAT
Found at i:547158 original size:9 final size:9
Alignment explanation
Indices: 547144--547169 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
547134 CTAAATGTAT
547144 AATTTTATA
1 AATTTTATA
547153 AATTTTATA
1 AATTTTATA
547162 AATTTTAT
1 AATTTTAT
547170 TAACTGTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATTTTATA
Found at i:547774 original size:21 final size:21
Alignment explanation
Indices: 547750--547789 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
547740 GGTTATGAAG
* *
547750 TTATGTTTTAGGGTTTAAGAT
1 TTATATTTTAGGATTTAAGAT
*
547771 TTATATTTTATGATTTAAG
1 TTATATTTTAGGATTTAAG
547790 TTAGGGGTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (21 bp):
TTATATTTTAGGATTTAAGAT
Found at i:548616 original size:32 final size:32
Alignment explanation
Indices: 548549--548617 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
548539 AAACACTCAC
* *
548549 TTTTATTAATGAGTTTGCCTTTTGAATTCTAA
1 TTTTATTAATGAGTTCGCCTTTTGAATTCAAA
*
548581 TTTTATTAATGAGTTCGCCTTTTGGATT-AAGA
1 TTTTATTAATGAGTTCGCCTTTTGAATTCAA-A
548613 TTTTA
1 TTTTA
548618 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (32 bp):
TTTTATTAATGAGTTCGCCTTTTGAATTCAAA
Found at i:548865 original size:29 final size:31
Alignment explanation
Indices: 548832--548898 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
548822 TCAAAAAGTA
*
548832 ACAAAATGA-TATTAACTTTAAT-AAACTATT
1 ACAAAATGATTATTAAATTT-ATCAAACTATT
*
548862 -C-AAATAATTATTAAATTTATCAAACTATT
1 ACAAAATGATTATTAAATTTATCAAACTATT
548891 ACAAAATG
1 ACAAAATG
548899 GTTCACAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
28 7 0.23
29 18 0.60
30 1 0.03
31 4 0.13
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (31 bp):
ACAAAATGATTATTAAATTTATCAAACTATT
Found at i:549137 original size:32 final size:32
Alignment explanation
Indices: 549070--549138 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
549060 AAACACTCGC
* ***
549070 TTTTATTAACGAGTTTGCCTTTTGAATTCTTA
1 TTTTATTAACGAGTTCGCCTTTTGAATTAAGA
* *
549102 TTTTATTAATGAGTTCGCCTTTTGGATTAAGA
1 TTTTATTAACGAGTTCGCCTTTTGAATTAAGA
549134 TTTTA
1 TTTTA
549139 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.52
Consensus pattern (32 bp):
TTTTATTAACGAGTTCGCCTTTTGAATTAAGA
Found at i:549395 original size:30 final size:30
Alignment explanation
Indices: 549352--549418 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
549342 TCAAAAAGTA
* *
549352 ACAAAATGATATTAACTTTAAT-AAACTATT
1 ACAAAATAATATTAAATTT-ATCAAACTATT
*
549382 -CAAAATAATTATTAAATTTATCAATCTATT
1 ACAAAATAA-TATTAAATTTATCAAACTATT
549412 ACAAAAT
1 ACAAAAT
549419 GGTTCACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 9 0.29
30 16 0.52
31 6 0.19
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.37
Consensus pattern (30 bp):
ACAAAATAATATTAAATTTATCAAACTATT
Found at i:549434 original size:521 final size:521
Alignment explanation
Indices: 548453--549501 Score: 1893
Period size: 521 Copynumber: 2.0 Consensus size: 521
548443 ATAATATGAT
* * * **
548453 TAATTATAAGATAGAATCAGTTCAAAAGATTTTTCAATTATTAATGTACACATATTTTATAGATG
1 TAATTATAAGATAGAATCAATTCAAAAGATTTTTCAACTACTAATGTACACATATTTTATAGACA
* *
548518 TAATTATTTAAAATTAAAAAAAAACACTCACTTTTATTAATGAGTTTGCCTTTTGAATTCTAATT
66 TAATTATGTAAAATTAAAAAAAAACACTCACTTTTATTAACGAGTTTGCCTTTTGAATTCTAATT
548583 TTATTAATGAGTTCGCCTTTTGGATTAAGATTTTAAAATTTTAAAATTATTAGATTAAATTAATT
131 TTATTAATGAGTTCGCCTTTTGGATTAAGATTTTAAAATTTTAAAATTATTAGATTAAATTAATT
548648 AGATTAGGGATTAACCTCGCAATTTATGCATGGCATACAAGCTTATAGGAAAATTTGATAATCAA
196 AGATTAGGGATTAACCTCGCAATTTATGCATGGCATACAAGCTTATAGGAAAATTTGATAATCAA
548713 TGTAAACAAAATTATTAGGGTAAATTACACAAATAGTCTATAAACTATGTTGAAATGTTGTTTTT
261 TGTAAACAAAATTATTAGGGTAAATTACACAAATAGTCTATAAACTATGTTGAAATGTTGTTTTT
548778 GGTCATTGAAAATTATAAAAGTTAGAGAATGATCATTAAACTTCTCAAAAAGTAACAAAATGATA
326 GGTCATTGAAAATTATAAAAGTTAGAGAATGATCATTAAACTTCTCAAAAAGTAACAAAATGATA
548843 TTAACTTTAATAAACTATTCAAATAATTATTAAATTTATCAAACTATTACAAAATGGTTCACAAA
391 TTAACTTTAATAAACTATTCAAATAATTATTAAATTTATCAAACTATTACAAAATGGTTCACAAA
*
548908 CATATCCAATTTTATCGTTATTTTATAACGTGTAAAGGGTACTTTGCAATAGTTCATTAAATTTA
456 CATATCCAATTTTATCGTTATTTTATAACGTGTAAAGGGTACTTTGCAATAGTTCAATAAATTTA
548973 A
521 A
*
548974 TAATTATAAGATATAATCAATTCAAAAGATTTTTCAACTACTAATGTACACATATTTTATAGACA
1 TAATTATAAGATAGAATCAATTCAAAAGATTTTTCAACTACTAATGTACACATATTTTATAGACA
* *** * * *
549039 TAGTTATGTAAAATTTCTAGAAAACACTCGCTTTTATTAACGAGTTTGCCTTTTGAATTCTTATT
66 TAATTATGTAAAATTAAAAAAAAACACTCACTTTTATTAACGAGTTTGCCTTTTGAATTCTAATT
*
549104 TTATTAATGAGTTCGCCTTTTGGATTAAGATTTTAAATTTTTAAAATTATTAGATT-AATTAATT
131 TTATTAATGAGTTCGCCTTTTGGATTAAGATTTTAAAATTTTAAAATTATTAGATTAAATTAATT
*
549168 AGATTAGGGATTAACCTCGCAATTTATGCATGGCATACAAGCTTATAGGAAATTTTGATAATCAA
196 AGATTAGGGATTAACCTCGCAATTTATGCATGGCATACAAGCTTATAGGAAAATTTGATAATCAA
*
549233 TGTAAACAAAATTATTAGGGTAAATTACACAAATAGTCTTTAAACTATGTTGAAATGTTGTTTTT
261 TGTAAACAAAATTATTAGGGTAAATTACACAAATAGTCTATAAACTATGTTGAAATGTTGTTTTT
549298 GGTCATTGAAAATTATAAAAGTTAGAGAATGATCATTAAACTTCTCAAAAAGTAACAAAATGATA
326 GGTCATTGAAAATTATAAAAGTTAGAGAATGATCATTAAACTTCTCAAAAAGTAACAAAATGATA
*
549363 TTAACTTTAATAAACTATTCAAAATAATTATTAAATTTATCAATCTATTACAAAATGGTTCACAA
391 TTAACTTTAATAAACTATTC-AAATAATTATTAAATTTATCAAACTATTACAAAATGGTTCACAA
*
549428 ACATATCCAATTTTATCGTTTTTTTATAACGTGTAAAGGGTACTTTGCAATAGTTCAATAAATTT
455 ACATATCCAATTTTATCGTTATTTTATAACGTGTAAAGGGTACTTTGCAATAGTTCAATAAATTT
549493 AA
520 AA
549495 TAATTAT
1 TAATTAT
549502 TTTATGATTT
Statistics
Matches: 506, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
520 221 0.44
521 285 0.56
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (521 bp):
TAATTATAAGATAGAATCAATTCAAAAGATTTTTCAACTACTAATGTACACATATTTTATAGACA
TAATTATGTAAAATTAAAAAAAAACACTCACTTTTATTAACGAGTTTGCCTTTTGAATTCTAATT
TTATTAATGAGTTCGCCTTTTGGATTAAGATTTTAAAATTTTAAAATTATTAGATTAAATTAATT
AGATTAGGGATTAACCTCGCAATTTATGCATGGCATACAAGCTTATAGGAAAATTTGATAATCAA
TGTAAACAAAATTATTAGGGTAAATTACACAAATAGTCTATAAACTATGTTGAAATGTTGTTTTT
GGTCATTGAAAATTATAAAAGTTAGAGAATGATCATTAAACTTCTCAAAAAGTAACAAAATGATA
TTAACTTTAATAAACTATTCAAATAATTATTAAATTTATCAAACTATTACAAAATGGTTCACAAA
CATATCCAATTTTATCGTTATTTTATAACGTGTAAAGGGTACTTTGCAATAGTTCAATAAATTTA
A
Found at i:549865 original size:6 final size:6
Alignment explanation
Indices: 549856--549893 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
549846 CTAATTAAGT
549856 ATATTA ATATTA ATATTA ATATTA ATATTA ATGATTA A
1 ATATTA ATATTA ATATTA ATATTA ATATTA AT-ATTA A
549894 GACAAGGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
ATATTA
Found at i:553715 original size:60 final size:59
Alignment explanation
Indices: 553643--553779 Score: 220
Period size: 60 Copynumber: 2.3 Consensus size: 59
553633 AGTAAACTGC
*
553643 TCAATGACCAAAATAAGAAATATAAAAAATAAAAGTGATCAAAATGTAACTTTTTCAAAA
1 TCAATGACCAAAATAAGAAAGATAAAAAATAAAAGTGATC-AAATGTAACTTTTTCAAAA
* *
553703 TCAATGAACAAAAAAAGAAAGATAAAAAATAAAAGTGATCAAATGTAACTTTTTCAAAA
1 TCAATGACCAAAATAAGAAAGATAAAAAATAAAAGTGATCAAATGTAACTTTTTCAAAA
* *
553762 TCAGTGACCGAAATAAGA
1 TCAATGACCAAAATAAGA
553780 TAGACGGAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 33 0.47
60 37 0.53
ACGTcount: A:0.56, C:0.10, G:0.11, T:0.23
Consensus pattern (59 bp):
TCAATGACCAAAATAAGAAAGATAAAAAATAAAAGTGATCAAATGTAACTTTTTCAAAA
Found at i:556076 original size:21 final size:21
Alignment explanation
Indices: 556046--556095 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
556036 AACTAGCCTG
556046 AGATGCATGGTAATAATCTTC
1 AGATGCATGGTAATAATCTTC
*
556067 AGATGTATGGTAATAATCTTC
1 AGATGCATGGTAATAATCTTC
556088 AGATGCAT
1 AGATGCAT
556096 ATGTTGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (21 bp):
AGATGCATGGTAATAATCTTC
Found at i:559159 original size:36 final size:35
Alignment explanation
Indices: 559082--559179 Score: 115
Period size: 36 Copynumber: 2.8 Consensus size: 35
559072 AACACAGTCA
* *
559082 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
1 TCAATTACATTATAAACCCCAAATTCAAAAATACT
* *
559117 TCAATTATATTATAAACCTCAAATTTCAAAAATACT
1 TCAATTACATTATAAACCCCAAA-TTCAAAAATACT
* * **
559153 TTAATTACATGACCAACCCCAAATTCA
1 TCAATTACATTATAAACCCCAAATTCA
559180 TAATCCATTC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 24 0.46
36 28 0.54
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (35 bp):
TCAATTACATTATAAACCCCAAATTCAAAAATACT
Found at i:560106 original size:19 final size:19
Alignment explanation
Indices: 560082--560123 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
560072 TATGACAAAT
560082 TTTGAGGATAGATTATGAA
1 TTTGAGGATAGATTATGAA
560101 TTTGAGGATAGATTATGAA
1 TTTGAGGATAGATTATGAA
560120 TTTG
1 TTTG
560124 GGGTTGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (19 bp):
TTTGAGGATAGATTATGAA
Found at i:572842 original size:14 final size:14
Alignment explanation
Indices: 572823--572851 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
572813 TTCTCAAGTA
572823 TTTAAATATAAAAT
1 TTTAAATATAAAAT
572837 TTTAAATATAAAAT
1 TTTAAATATAAAAT
572851 T
1 T
572852 ATTTTACGAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATATAAAAT
Found at i:575537 original size:25 final size:24
Alignment explanation
Indices: 575508--575554 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
575498 TTGTTTCATT
575508 TTAATACCCCGTTAAGTTTTGCACC
1 TTAATA-CCCGTTAAGTTTTGCACC
* *
575533 TTAATATCCTTTAAGTTTTGCA
1 TTAATACCCGTTAAGTTTTGCA
575555 AAAATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (24 bp):
TTAATACCCGTTAAGTTTTGCACC
Found at i:578609 original size:5 final size:5
Alignment explanation
Indices: 578599--578628 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
578589 ATAAAAGCTT
578599 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC
1 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC
578629 ATGATCAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TCTCC
Found at i:583194 original size:31 final size:31
Alignment explanation
Indices: 583171--583281 Score: 186
Period size: 31 Copynumber: 3.6 Consensus size: 31
583161 AATTTTCAAG
*
583171 CTCGACTCGAACTCGAAAGAAAATATTGAAC
1 CTCGACTCGAACTCGAAAGAAAATATTGAAA
* * *
583202 CTCGACTCAAACTCGAAAGTAAAGATTGAAA
1 CTCGACTCGAACTCGAAAGAAAATATTGAAA
583233 CTCGACTCGAACTCGAAAGAAAATATTGAAA
1 CTCGACTCGAACTCGAAAGAAAATATTGAAA
583264 CTCGACTCGAACTCGAAA
1 CTCGACTCGAACTCGAAA
583282 AGGCTCGAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (31 bp):
CTCGACTCGAACTCGAAAGAAAATATTGAAA
Found at i:583361 original size:12 final size:12
Alignment explanation
Indices: 583344--583368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
583334 GCTTGATTGA
583344 AGCTCGATTTTG
1 AGCTCGATTTTG
583356 AGCTCGATTTTG
1 AGCTCGATTTTG
583368 A
1 A
583369 ACCTACAAAA
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:585704 original size:7 final size:7
Alignment explanation
Indices: 585692--585768 Score: 52
Period size: 7 Copynumber: 11.3 Consensus size: 7
585682 AATCGGATTA
585692 AGGGTTT
1 AGGGTTT
585699 AGGGTTT
1 AGGGTTT
*
585706 CTGGG-TT
1 -AGGGTTT
585713 -GGGTTT
1 AGGGTTT
*
585719 AGGATTT
1 AGGGTTT
585726 AGGGTTT
1 AGGGTTT
* *
585733 ATGTTTT
1 AGGGTTT
**
585740 A-ATTTT
1 AGGGTTT
585746 AGGGTTT
1 AGGGTTT
**
585753 ATAGTTT
1 AGGGTTT
585760 AGGGTTT
1 AGGGTTT
585767 AG
1 AG
585769 AGTGTAATCT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
5 3 0.06
6 7 0.13
7 41 0.76
8 3 0.06
ACGTcount: A:0.17, C:0.01, G:0.34, T:0.48
Consensus pattern (7 bp):
AGGGTTT
Found at i:585738 original size:20 final size:21
Alignment explanation
Indices: 585715--585768 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
585705 TCTGGGTTGG
585715 GTTTAGGATTTAGGGTTTAT-
1 GTTTAGGATTTAGGGTTTATA
585735 GTTTTA--ATTTTAGGGTTTATA
1 G-TTTAGGA-TTTAGGGTTTATA
*
585756 GTTTAGGGTTTAG
1 GTTTAGGATTTAG
585769 AGTGTAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
19 1 0.04
20 17 0.61
21 10 0.36
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (21 bp):
GTTTAGGATTTAGGGTTTATA
Found at i:586907 original size:12 final size:12
Alignment explanation
Indices: 586892--586917 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
586882 ATGATCCTTT
586892 ATATTAAAATTG
1 ATATTAAAATTG
586904 ATATTAAAATTG
1 ATATTAAAATTG
586916 AT
1 AT
586918 GAGTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATATTAAAATTG
Found at i:595970 original size:21 final size:21
Alignment explanation
Indices: 595940--595999 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
595930 AATAAATTAG
*
595940 AGTAGAGGTTTCAAAACCCCA
1 AGTAGTGGTTTCAAAACCCCA
595961 AGTAGTGGTTTCAAAACCCCA
1 AGTAGTGGTTTCAAAACCCCA
595982 AGTAGTGGTTTCAAAACC
1 AGTAGTGGTTTCAAAACC
596000 ATTTCGACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTAGTGGTTTCAAAACCCCA
Found at i:597386 original size:22 final size:21
Alignment explanation
Indices: 597361--597444 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
597351 TAATTAAATG
*
597361 ATTATTTGTATATATTTATAAA
1 ATTATTT-TAAATATTTATAAA
*
597383 ATTATATTAAATTATTCTA-AAA
1 ATTATTTTAAA-TATT-TATAAA
*
597405 ATTATATTTATAATA-TTATGAA
1 ATTAT-TTTA-AATATTTATAAA
597427 ATTATTTTTAAATATTTA
1 ATTA-TTTTAAATATTTA
597445 ATTTTTAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
21 9 0.18
22 32 0.63
23 8 0.16
24 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATTTTAAATATTTATAAA
Found at i:597483 original size:23 final size:22
Alignment explanation
Indices: 597439--597488 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
597429 TATTTTTAAA
*
597439 TATTTAATTTTTAAAATCATAT
1 TATTTAATTTTTAAAATAATAT
* *
597461 TATTTATTTATTTGAAATAATAT
1 TATTTAATT-TTTAAAATAATAT
597484 TATTT
1 TATTT
597489 TTAAATTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTTAATTTTTAAAATAATAT
Found at i:597676 original size:24 final size:22
Alignment explanation
Indices: 597647--597709 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
597637 TTAAATAAAT
597647 ATTTTTATAATATTATAACTATAA
1 ATTTTTATAATATTATAA-TAT-A
*
597671 ATTTTT-TGAATTATT-TGATATA
1 ATTTTTAT-AA-TATTATAATATA
*
597693 ATTTTTATAAAATTATA
1 ATTTTTATAATATTATA
597710 TAAATCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
21 3 0.09
22 10 0.31
23 5 0.16
24 10 0.31
25 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (22 bp):
ATTTTTATAATATTATAATATA
Found at i:598809 original size:20 final size:21
Alignment explanation
Indices: 598763--598820 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
598753 ATTATCCAAT
* *
598763 AAACTTGACATCTATAACAAC
1 AAACTTGAAATCCATAACAAC
598784 AAACTTGAAATCCATAACAA-
1 AAACTTGAAATCCATAACAAC
*
598804 AAACTTAAAATCCATAA
1 AAACTTGAAATCCATAA
598821 TAATAAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:599382 original size:113 final size:113
Alignment explanation
Indices: 599209--599434 Score: 452
Period size: 113 Copynumber: 2.0 Consensus size: 113
599199 ACTCACAACC
599209 AATATATCAAATAATTATCAAATAAATTATGACAAAACCTAATTCTTTATCTTGGCTTAAAATTA
1 AATATATCAAATAATTATCAAATAAATTATGACAAAACCTAATTCTTTATCTTGGCTTAAAATTA
599274 AATGTGTTGTGATAAATGAAACACAAAATAAAATTATAATATTGGTCT
66 AATGTGTTGTGATAAATGAAACACAAAATAAAATTATAATATTGGTCT
599322 AATATATCAAATAATTATCAAATAAATTATGACAAAACCTAATTCTTTATCTTGGCTTAAAATTA
1 AATATATCAAATAATTATCAAATAAATTATGACAAAACCTAATTCTTTATCTTGGCTTAAAATTA
599387 AATGTGTTGTGATAAATGAAACACAAAATAAAATTATAATATTGGTCT
66 AATGTGTTGTGATAAATGAAACACAAAATAAAATTATAATATTGGTCT
599435 GTTGTGTGTA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (113 bp):
AATATATCAAATAATTATCAAATAAATTATGACAAAACCTAATTCTTTATCTTGGCTTAAAATTA
AATGTGTTGTGATAAATGAAACACAAAATAAAATTATAATATTGGTCT
Found at i:601599 original size:2 final size:2
Alignment explanation
Indices: 601547--601583 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
601537 ACACACACAC
601547 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
601584 CTTTGCCCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:609669 original size:41 final size:41
Alignment explanation
Indices: 609619--609712 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
609609 AAAACGTCTA
*
609619 TAAAGTATGAGTT-TATAGCAGCGTTTGTATAAAAACGCCAC
1 TAAAATATGA-TTCTATAGCAGCGTTTGTATAAAAACGCCAC
* * * *
609660 TAAAATATGATTCTTTAGCGGTGTTTGTATACAAACGCCAC
1 TAAAATATGATTCTATAGCAGCGTTTGTATAAAAACGCCAC
*
609701 TAATATACTGAT
1 TAAAATA-TGAT
609713 AATTTCTGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 2 0.04
41 39 0.87
42 4 0.09
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (41 bp):
TAAAATATGATTCTATAGCAGCGTTTGTATAAAAACGCCAC
Found at i:610834 original size:27 final size:27
Alignment explanation
Indices: 610800--610863 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
610790 GATAATGGCT
610800 CTGAATCATTTAGAATATACTTCTGTG
1 CTGAATCATTTAGAATATACTTCTGTG
*
610827 CTGAATCATTTAGAATATATTTCTGTG
1 CTGAATCATTTAGAATATACTTCTGTG
610854 CTGAATCATT
1 CTGAATCATT
610864 CAGCATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (27 bp):
CTGAATCATTTAGAATATACTTCTGTG
Found at i:618501 original size:16 final size:16
Alignment explanation
Indices: 618476--618506 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
618466 ATCCTAAAAA
*
618476 TTCTATTTCTATTTTT
1 TTCTAATTCTATTTTT
618492 TTCTAATTCTATTTT
1 TTCTAATTCTATTTT
618507 CTTAAGACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTAATTCTATTTTT
Found at i:619629 original size:2 final size:2
Alignment explanation
Indices: 619622--619664 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
619612 TGTTATTTCA
619622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
619663 AT
1 AT
619665 TTTCTAGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:621385 original size:49 final size:49
Alignment explanation
Indices: 621308--621406 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
621298 CAATACATTT
* *
621308 GCTGTGAACTTAAAGGAATGAGGGAAAGGGATAGATAAAAGAAGAAGAA
1 GCTGTGAACTTAAAGGAATGAGGAAAAGGAATAGATAAAAGAAGAAGAA
*
621357 GCTGTGAACTTAAAGGAATGAGGAAAAGGAATAGATAGAAGAAGAAGAA
1 GCTGTGAACTTAAAGGAATGAGGAAAAGGAATAGATAAAAGAAGAAGAA
621406 G
1 G
621407 AAGAAGATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.49, C:0.04, G:0.32, T:0.14
Consensus pattern (49 bp):
GCTGTGAACTTAAAGGAATGAGGAAAAGGAATAGATAAAAGAAGAAGAA
Found at i:621563 original size:23 final size:23
Alignment explanation
Indices: 621506--621564 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
621496 AACTACGGAC
*
621506 TAAAATCGAATAGCGTTATGGAT
1 TAAAATCGAATGGCGTTATGGAT
621529 TAAAATCGAATGGCGTTATGGAT
1 TAAAATCGAATGGCGTTATGGAT
621552 TAAAATCGAATGG
1 TAAAATCGAATGG
621565 ACCGATAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (23 bp):
TAAAATCGAATGGCGTTATGGAT
Found at i:624322 original size:20 final size:21
Alignment explanation
Indices: 624293--624367 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
624283 AAATGACCAA
624293 CAAATTCGCAACGCCAA-TT-
1 CAAATTCGCAACGCCAAGTTC
624312 CAAATTTCGCAAC-CCAAGTTC
1 CAAA-TTCGCAACGCCAAGTTC
*
624333 CAAATTCGCAACGCGATAG-TC
1 CAAATTCGCAACGCCA-AGTTC
*
624354 GAAATTCGCAACGC
1 CAAATTCGCAACGC
624368 GATACTCCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
19 8 0.16
20 18 0.37
21 21 0.43
22 2 0.04
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.20
Consensus pattern (21 bp):
CAAATTCGCAACGCCAAGTTC
Found at i:624358 original size:21 final size:21
Alignment explanation
Indices: 624331--624385 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
624321 CAACCCAAGT
*
624331 TCCAAATTCGCAACGCGATAG
1 TCCAAATTCGCAACGCGATAC
*
624352 TCGAAATTCGCAACGCGATAC
1 TCCAAATTCGCAACGCGATAC
*
624373 TCCAAAATCGCAA
1 TCCAAATTCGCAA
624386 TGCATTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.18
Consensus pattern (21 bp):
TCCAAATTCGCAACGCGATAC
Found at i:624507 original size:15 final size:15
Alignment explanation
Indices: 624481--624521 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
624471 GACCACGATG
624481 GGACGG-GACGGGAC
1 GGACGGCGACGGGAC
**
624495 GGGGGGCGACGGGAC
1 GGACGGCGACGGGAC
624510 GGACGGCGACGG
1 GGACGGCGACGG
624522 CGGTGCGCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.17, C:0.22, G:0.61, T:0.00
Consensus pattern (15 bp):
GGACGGCGACGGGAC
Found at i:630759 original size:15 final size:15
Alignment explanation
Indices: 630739--630769 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
630729 CATGATATGT
630739 GTTGTCGTGACTGCA
1 GTTGTCGTGACTGCA
630754 GTTGTCGTGACTGCA
1 GTTGTCGTGACTGCA
630769 G
1 G
630770 CAACCACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.35, T:0.32
Consensus pattern (15 bp):
GTTGTCGTGACTGCA
Found at i:638196 original size:9 final size:9
Alignment explanation
Indices: 638184--638240 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
638174 TAATGTTTTG
638184 TATTTAATT
1 TATTTAATT
*
638193 TATTTAA-G
1 TATTTAATT
638201 TATTTAATT
1 TATTTAATT
638210 TATTTAA--
1 TATTTAATT
* *
638217 TATTTTACT
1 TATTTAATT
638226 TATTTAATT
1 TATTTAATT
*
638235 TTTTTA
1 TATTTA
638241 CAGATATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 6 0.15
8 7 0.18
9 26 0.67
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:638205 original size:17 final size:17
Alignment explanation
Indices: 638183--638232 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
638173 TTAATGTTTT
638183 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
638200 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
638217 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
638233 TTTTTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:638228 original size:16 final size:16
Alignment explanation
Indices: 638192--638237 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
638182 TGTATTTAAT
* *
638192 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
638209 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
638225 TTATTTAAT-TTTT
1 TTATTTAATATTTT
638238 TTACAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:642512 original size:15 final size:15
Alignment explanation
Indices: 642492--642527 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
642482 TAAGAGTCTA
642492 AGTTGAGATGATCTT
1 AGTTGAGATGATCTT
642507 AGTTGAGATGATCTT
1 AGTTGAGATGATCTT
*
642522 GGTTGA
1 AGTTGA
642528 CTCCTCCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.39
Consensus pattern (15 bp):
AGTTGAGATGATCTT
Found at i:646406 original size:3 final size:3
Alignment explanation
Indices: 646398--646423 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
646388 GTTGTTTTTG
646398 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
646424 GTTTTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:646805 original size:31 final size:31
Alignment explanation
Indices: 646770--646835 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
646760 ATTTGCACAT
646770 TTTTTGTCACTTATGTTATCGTTTTATTAAG
1 TTTTTGTCACTTATGTTATCGTTTTATTAAG
646801 TTTTTGTCACTTATGTTATCGTTTTATTAAG
1 TTTTTGTCACTTATGTTATCGTTTTATTAAG
646832 TTTT
1 TTTT
646836 GTTCGCTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (31 bp):
TTTTTGTCACTTATGTTATCGTTTTATTAAG
Found at i:648655 original size:23 final size:23
Alignment explanation
Indices: 648622--648672 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
648612 AACTTTCATT
*
648622 AAAATAACAAT-GAAATAATTTAC
1 AAAATAACAATCAAAATAA-TTAC
648645 ATAAAT-ACAATCAAAATAATTAC
1 A-AAATAACAATCAAAATAATTAC
648668 AAAAT
1 AAAAT
648673 CGATCATAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 4 0.16
23 11 0.44
24 10 0.40
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAATAACAATCAAAATAATTAC
Found at i:649203 original size:21 final size:21
Alignment explanation
Indices: 649145--649205 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
649135 ATATAAAATT
*
649145 TGTCCCGAAGGACCTCATATA
1 TGTCCCGAAGGACCTCGTATA
*
649166 TGTCCCAAAGGACCTCGTATA
1 TGTCCCGAAGGACCTCGTATA
649187 TGTCCCGAAGGACCTCGTA
1 TGTCCCGAAGGACCTCGTA
649206 GAACCCTCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCGTATA
Found at i:649319 original size:28 final size:28
Alignment explanation
Indices: 649266--649319 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
649256 TTACATGTTT
* *
649266 CATATGTCATATAATCACTAATTCATCA
1 CATATGTCATATAATCAATAACTCATCA
*
649294 CATAT-TCATATACTCATATAACTCAT
1 CATATGTCATATAATCA-ATAACTCAT
649320 ATCATTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (28 bp):
CATATGTCATATAATCAATAACTCATCA
Found at i:651129 original size:82 final size:82
Alignment explanation
Indices: 650992--651160 Score: 284
Period size: 82 Copynumber: 2.1 Consensus size: 82
650982 CAAGAAGAAA
* * * * *
650992 AATCAATGGATCCAAATAACCTGATAATCGGATATCACTCTATGTGGTATTTTTGCTTGAGAAAG
1 AATCAATGGATCCAAACAACCCGATAATCAGATATCACTCTACGTGATATTTTTGCTTGAGAAAG
651057 CACCTCCGGTGAAACAT
66 CACCTCCGGTGAAACAT
651074 AATCAATGGATCCAAACAACCCGATAATCAGATATCACTCTACGTGATATTTTTGCTTGAGAAAG
1 AATCAATGGATCCAAACAACCCGATAATCAGATATCACTCTACGTGATATTTTTGCTTGAGAAAG
*
651139 CACCTCCTGTGAAACAT
66 CACCTCCGGTGAAACAT
651156 AATCA
1 AATCA
651161 GTGAATTCAT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (82 bp):
AATCAATGGATCCAAACAACCCGATAATCAGATATCACTCTACGTGATATTTTTGCTTGAGAAAG
CACCTCCGGTGAAACAT
Found at i:652473 original size:17 final size:17
Alignment explanation
Indices: 652415--652481 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
652405 AAAAAAACTT
*
652415 AATATTATTATTTTTAA
1 AATATTATTATTATTAA
** *
652432 AATA-TAGAATAATTAA
1 AATATTATTATTATTAA
652448 TACATTATTATTATTATTAA
1 -A-A-TATTATTATTATTAA
*
652468 AATATTATTTTTAT
1 AATATTATTATTAT
652482 AATTTTATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
16 8 0.21
17 16 0.42
18 2 0.05
19 3 0.08
20 9 0.24
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
AATATTATTATTATTAA
Found at i:652827 original size:22 final size:22
Alignment explanation
Indices: 652797--652848 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
652787 TATAATTGAG
*
652797 TATATTATTATAATATTAAAAA
1 TATAATATTATAATATTAAAAA
*
652819 TATAATATTATATTATTAAAAA
1 TATAATATTATAATATTAAAAA
652841 TATTAATA
1 TA-TAATA
652849 AATATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATAATATTATAATATTAAAAA
Found at i:652853 original size:22 final size:22
Alignment explanation
Indices: 652810--652853 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
652800 ATTATTATAA
*
652810 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
652832 TATTAAAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
652854 AGTTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:652860 original size:23 final size:22
Alignment explanation
Indices: 652805--652861 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
652795 AGTATATTAT
* *
652805 TATAATATTAAAAATATAATAT
1 TATAGTATTAAAAATATAATAA
*
652827 TATATTATTAAAAATATTAATAAA
1 TATAGTATTAAAAATA-TAAT-AA
652851 TATAGT-TTAAA
1 TATAGTATTAAA
652862 TAGTTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.50
23 9 0.30
24 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TATAGTATTAAAAATATAATAA
Found at i:653591 original size:185 final size:186
Alignment explanation
Indices: 653159--653808 Score: 590
Period size: 185 Copynumber: 3.5 Consensus size: 186
653149 TAGGTTGCAT
* * * * * * *
653159 CTAAAATATTACGAGAGTTTAAGATGAT-GAGACCTTAAACATTCACACTATAACAAAATAATTT
1 CTAAAATGTTACCAGAGTTT-AGCTGATGGAG-CCTTAGACATTCTCACAATAACAAAATAAGTT
* * *
653223 AAAAGGTAAAAATGTTATGAATATCTATAAGAAAT-TCGATTACACCCAAGAATGTTATGATTCA
64 AAAAGCTGAAAATGTTATGAATATCTATAAGAAATCTCG-TTACACCCAAGAATGTTATAATTCA
* * * * * * *
653287 CTAAG-AAGTAGGTTGCGATTTAGGATGTTAACTTTATTTGTAATAAAATTAGTTGTGC
128 CTAAGAAAGTAGGTTGCGATTGAGAATATTAACTTTATTTATAATAAAATGAGTTATGA
* * * * * **
653345 CTACAATGTCATCAAAGTTTATGCTGATGGAGCCTTAGGCATTCTCATGATAACAAAATAAGTTA
1 CTAAAATGTTACCAGAGTTTA-GCTGATGGAGCCTTAGACATTCTCACAATAACAAAATAAGTTA
* * * * * * *
653410 AAAGCTGGAAGTTTTATGAATATCTATAAGAAATCTTGTTACGCCCAAGAATTTTATAATTCGCT
65 AAAGCTGAAAATGTTATGAATATCTATAAGAAATCTCGTTACACCCAAGAATGTTATAATTCACT
*
653475 AAGAAAGTAGGTTGCGATATGA-AATATTGA-TTT-TTTATAATAAAATCGA-TTATGA
130 AAGAAAGTAGGTTGCGAT-TGAGAATATTAACTTTATTTATAATAAAAT-GAGTTATGA
653530 CTAAAATGTTACCAGAGTTTGAGCTGATGGAGCCTTAGACATTCTCACAATAACAAAATAAGTTA
1 CTAAAATGTTACCAGAGTTT-AGCTGATGGAGCCTTAGACATTCTCACAATAACAAAATAAGTTA
** *
653595 AAAGCTGAAAATGTTATGAATATCTATAAGAAATC-CGGTTGTACCCAAGAATGTTATAGTTCAC
65 AAAGCTGAAAATGTTATGAATATCTATAAGAAATCTC-GTTACACCCAAGAATGTTATAATTCAC
** * * * * *
653659 TAAGAAAGTAGGTTGTTATCTG-GAATGTTAATTTTCTTTGTAATAAAATCGA--T-CGCA
129 TAAGAAAGTAGGTTGCGAT-TGAGAATATTAACTTTATTTATAATAAAAT-GAGTTATG-A
* ** * * * * * * *
653716 CCTGAAATGTTATTAGAGTTTTAGTTGGTGG-GCCCTAGATATTCTCGCGATAATAAAATAAGTT
1 -CTAAAATGTTACCAGAG-TTTAGCTGATGGAGCCTTAGACATTCTCACAATAACAAAATAAGTT
* * *
653780 GAAAGCT-AAAATGTTATAAATATTTATAA
64 AAAAGCTGAAAATGTTATGAATATCTATAA
653809 AAAAAATTAG
Statistics
Matches: 382, Mismatches: 68, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
185 172 0.45
186 145 0.38
187 60 0.16
188 5 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (186 bp):
CTAAAATGTTACCAGAGTTTAGCTGATGGAGCCTTAGACATTCTCACAATAACAAAATAAGTTAA
AAGCTGAAAATGTTATGAATATCTATAAGAAATCTCGTTACACCCAAGAATGTTATAATTCACTA
AGAAAGTAGGTTGCGATTGAGAATATTAACTTTATTTATAATAAAATGAGTTATGA
Found at i:654145 original size:73 final size:70
Alignment explanation
Indices: 654068--654300 Score: 200
Period size: 73 Copynumber: 3.2 Consensus size: 70
654058 TCGAATTTTT
*
654068 AATATTGATACTTAATATGTGATGATCGATAATTTTAAATATTGAAAAAGTTGA-AGATAAGATC
1 AATATTGATACTT-ATATGTGATGATCGATACTTTTAAATATT-AAAAAGTTGATA-A-AAGATC
654132 AAAAGTTAA
62 AAAAGTTAA
* ** * ** *
654141 AATATTAATACTTATGCGGTAATGATTAATACTTTTAAATATTAAAAAGTTGATAAAATATCAAA
1 AATATTGATACTTAT-ATGTGATGATCGATACTTTTAAATATTAAAAAGTTGATAAAAGATCAAA
*
654206 ATTTAA
65 AGTTAA
* * * * * * *
654212 AATATCG-TACTTATGTGATGATGGTCGATACTTTTATATATTAAAAAATTGATGAAGATGATCG
1 AATATTGATACTTATATG-TGATGATCGATACTTTTAAATATTAAAAAGTTGAT-AA-AAGATCA
**
654276 ACGGTTAA
63 AAAGTTAA
* *
654284 AATATTAATACATATAT
1 AATATTGATACTTATAT
654301 TATGATGTTT
Statistics
Matches: 125, Mismatches: 29, Indels: 12
0.75 0.17 0.07
Matches are distributed among these distances:
69 1 0.01
70 36 0.29
71 20 0.16
72 27 0.22
73 41 0.33
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.36
Consensus pattern (70 bp):
AATATTGATACTTATATGTGATGATCGATACTTTTAAATATTAAAAAGTTGATAAAAGATCAAAA
GTTAA
Found at i:654246 original size:70 final size:73
Alignment explanation
Indices: 654087--654294 Score: 203
Period size: 70 Copynumber: 2.9 Consensus size: 73
654077 ACTTAATATG
*
654087 TGATGATCGATAATTTTAAATATTGAAAAAGTTGA-AGATAAGATCAAAAGTTAAAATATTAATA
1 TGATGATCGATACTTTTAAATATT-AAAAAGTTGATAGATAAGATCAAAAGTTAAAATATTAATA
*
654151 CTTATGCGG
65 CTTATGCGA
* ** * * **
654160 TAATGATTAATACTTTTAAATATTAAAAAGTTGATA-A-AATATCAAAATTTAAAATA-TCGTAC
1 TGATGATCGATACTTTTAAATATTAAAAAGTTGATAGATAAGATCAAAAGTTAAAATATTAATAC
*
654222 TTATGTGA
66 TTATGCGA
* * * * **
654230 TGATGGTCGATACTTTTATATATTAAAAAATTGAT-GA-AGATGATCGACGGTTAAAATATTAAT
1 TGATGATCGATACTTTTAAATATTAAAAAGTTGATAGATA-A-GATCAAAAGTTAAAATATTAAT
654293 AC
64 AC
654295 ATATATTATG
Statistics
Matches: 107, Mismatches: 23, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
70 41 0.38
71 18 0.17
72 23 0.21
73 25 0.23
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (73 bp):
TGATGATCGATACTTTTAAATATTAAAAAGTTGATAGATAAGATCAAAAGTTAAAATATTAATAC
TTATGCGA
Found at i:657366 original size:38 final size:37
Alignment explanation
Indices: 657071--657403 Score: 345
Period size: 38 Copynumber: 8.9 Consensus size: 37
657061 TTTAGAATAT
* *
657071 ATATATATATTATATAATTTTGAAAACA-TTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
*
657107 A-ATATATAGTATATAGTTTTTAAAACATTTTTGAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTG-AAA
657144 CATATATATATTATATAG-TTTTAAAACA-TTTTGAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
*
657180 ACAATATATATTATATAGTTTTTAAAACA-TTTTGAAAA
1 A-TATATATATTATATAGTTTTTAAAACATTTTTG-AAA
* **
657218 TATATATATATTATATAATTTTTAAAACATTTTCAAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * *
657256 CATATATATGTTATATAATTTTTAAAACGTTTTTGAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
657294 ATATAAATATAATATATGGTTTTTAAAACAATTTTTGAAA
1 ATAT--ATATATTATATAGTTTTTAAAAC-ATTTTTGAAA
* * * **
657334 ATATATATAATATATAGTTTTAAAAATTATTTTT-TTA
1 ATATATATATTATATAGTTTTTAAAA-CATTTTTGAAA
* * * *
657371 ACATATATATTAAATAGTTTTAAAAATATTTTT
1 ATATATATATTATATAGTTTTTAAAACATTTTT
657404 CATTGTATTT
Statistics
Matches: 257, Mismatches: 27, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
35 24 0.09
36 31 0.12
37 51 0.20
38 101 0.39
39 37 0.14
40 13 0.05
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (37 bp):
ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
Found at i:659642 original size:10 final size:11
Alignment explanation
Indices: 659616--659649 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
659606 TCACTAACTC
659616 TTTTCATTTTCA
1 TTTT-ATTTTCA
659628 TTTTATTTT-A
1 TTTTATTTTCA
659638 TTTTATTTTCA
1 TTTTATTTTCA
659649 T
1 T
659650 CAATTGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 7 0.33
12 4 0.19
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:662869 original size:24 final size:24
Alignment explanation
Indices: 662842--662887 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
662832 AATGGAACAT
662842 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
662866 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
662888 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:663154 original size:53 final size:54
Alignment explanation
Indices: 663064--663192 Score: 224
Period size: 53 Copynumber: 2.4 Consensus size: 54
663054 CTAAGACATG
*
663064 TTAAACAAATATATATATATATATATGAACAAAAAAAATCAGTTTCCAAGACACA
1 TTAAATAAATATATATATATATATATGAAC-AAAAAAATCAGTTTCCAAGACACA
663119 TTAAATAAATATATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACA
1 TTAAATAAATATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACA
*
663172 TTAAATAAAAATATATATATA
1 TTAAATAAATATATATATATA
663193 CGTTTAACAA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
53 43 0.60
55 29 0.40
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (54 bp):
TTAAATAAATATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACA
Done.