Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003942.1 Hibiscus syriacus cultivar Beakdansim tig00008518_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: 365498
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:145048 original size:42 final size:42
Alignment explanation
Indices: 144972--145174 Score: 194
Period size: 42 Copynumber: 4.8 Consensus size: 42
144962 GACTCGCCTG
* * * * * * *
144972 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
145014 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * * * * * * *
145056 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
145098 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
145140 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
145175 CCCGATTCAC
Statistics
Matches: 130, Mismatches: 29, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 4 0.03
42 124 0.95
43 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:145132 original size:21 final size:21
Alignment explanation
Indices: 145108--145174 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
145098 TCATTCCTCG
145108 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
145129 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
145150 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
145171 AGAG
1 AGAG
145175 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:145153 original size:84 final size:84
Alignment explanation
Indices: 144969--145144 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
144959 CCCGACTCGC
*
144969 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
145034 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
145053 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
145118 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
145137 CTGTCATC
1 CTGTCATC
145145 GTTGAAGAGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:145174 original size:84 final size:84
Alignment explanation
Indices: 144969--145174 Score: 306
Period size: 84 Copynumber: 2.5 Consensus size: 84
144959 CCCGACTCGC
* * * *
144969 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
145034 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * *
145053 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
145118 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
145137 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
145175 CCCGATTCAC
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
84 110 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:146549 original size:14 final size:14
Alignment explanation
Indices: 146530--146565 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
146520 ATTGTTTAAT
146530 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
146544 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
146558 TGATTTGT
1 TGATTTGT
146566 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:146709 original size:14 final size:14
Alignment explanation
Indices: 146690--146746 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
146680 GCGAAATAAA
146690 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
146704 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
146723 AATCGCAACGAGAG
1 AATCGCAACGAGAG
146737 AATCGCAACG
1 AATCGCAACG
146747 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:146717 original size:33 final size:33
Alignment explanation
Indices: 146672--146761 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
146662 AAAAAGTACT
*
146672 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATAAAAATCGCAACGAGAGA
*
146705 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATAAAAATCGCAACGAGAGA
* *
146738 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATAAAAATCGC
146762 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATAAAAATCGCAACGAGAGA
Found at i:146728 original size:19 final size:19
Alignment explanation
Indices: 146672--146732 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
146662 AAAAAGTACT
* *
146672 ATCGCAATGCGAAATAAAA
1 ATCGCAACGCGAAATGAAA
*
146691 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
146705 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
146724 ATCGCAACG
1 ATCGCAACG
146733 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.56
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:146779 original size:19 final size:19
Alignment explanation
Indices: 146757--146907 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
146747 CGAAATTAAA
146757 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
146776 TTCGTATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
146791 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
146809 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
146823 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
146842 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
146857 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
146875 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
146894 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
146908 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:146803 original size:33 final size:32
Alignment explanation
Indices: 146761--146887 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
146751 ATTAAATTCG
*
146761 CGTTGCGATTTTCATTTCGTATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
146794 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
146827 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
146860 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
146888 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:146851 original size:66 final size:66
Alignment explanation
Indices: 146754--146886 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
146744 ACGCGAAATT
* *
146754 AAATTCGCGTTGCGATTTTCATTTCGTATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
146819 G
66 G
*
146820 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
146885 G
66 G
146886 A
1 A
146887 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:149202 original size:14 final size:15
Alignment explanation
Indices: 149170--149207 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
149160 TGGCATTTTC
*
149170 TTTTCTTTGGGGACT
1 TTTTCTTCGGGGACT
149185 TTTTCTTCGGGGACT
1 TTTTCTTCGGGGACT
149200 TTTTCTTC
1 TTTTCTTC
149208 TTCTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.18, G:0.21, T:0.55
Consensus pattern (15 bp):
TTTTCTTCGGGGACT
Found at i:149215 original size:12 final size:12
Alignment explanation
Indices: 149198--149222 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
149188 TCTTCGGGGA
149198 CTTTTTCTTCTT
1 CTTTTTCTTCTT
149210 CTTTTTCTTCTT
1 CTTTTTCTTCTT
149222 C
1 C
149223 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:149431 original size:24 final size:24
Alignment explanation
Indices: 149397--149450 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
149387 CTGAAACATC
*
149397 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
149421 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
149445 ATCAAA
1 ATCAAA
149451 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:150222 original size:20 final size:20
Alignment explanation
Indices: 150197--150245 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
150187 TATTATCTCG
150197 TTGCGAAAGTCAGAATCGCA
1 TTGCGAAAGTCAGAATCGCA
*
150217 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGAATCGCA
150237 TTGCGAAAG
1 TTGCGAAAG
150246 GCAATCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (20 bp):
TTGCGAAAGTCAGAATCGCA
Found at i:150496 original size:19 final size:20
Alignment explanation
Indices: 150458--150507 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
150448 ATTCATTTGA
150458 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
150478 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
150497 CTATCGCAACG
1 CTATCGCAACG
150508 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:150574 original size:19 final size:19
Alignment explanation
Indices: 150533--150597 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
150523 GAAATGAAAA
150533 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
150549 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
150566 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
150585 TCGCATTGCGATT
1 TCGCATTGCGATT
150598 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:150628 original size:20 final size:20
Alignment explanation
Indices: 150603--150641 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
150593 CGATTCTCTC
150603 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
150623 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
150642 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:152647 original size:20 final size:20
Alignment explanation
Indices: 152624--152670 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
152614 GAAACTTAAA
152624 ATCGCAACACAAAAATGACT
1 ATCGCAACACAAAAATGACT
* ** *
152644 ATCGCAACGCGGAAATGGCT
1 ATCGCAACACAAAAATGACT
152664 ATCGCAA
1 ATCGCAA
152671 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (20 bp):
ATCGCAACACAAAAATGACT
Found at i:152679 original size:19 final size:20
Alignment explanation
Indices: 152636--152691 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
152626 CGCAACACAA
152636 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
152656 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
152675 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
152692 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:152699 original size:14 final size:14
Alignment explanation
Indices: 152680--152737 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
152670 ATGCGAAATG
152680 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
152694 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
152710 ATGAAATCGTAACGAC
1 A--AAATCGCAACGAC
152726 AAAATCGCAACG
1 AAAATCGCAACG
152738 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:152724 original size:32 final size:33
Alignment explanation
Indices: 152664--152742 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
152654 GGAAATGGCT
152664 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
152697 ATCGCAATGCGAAATG-AAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
152729 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
152743 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 28 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:152790 original size:14 final size:14
Alignment explanation
Indices: 152771--152828 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
152761 TTTCATTTCA
152771 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
152785 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
152801 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
152817 CGTTGCGATTTT
1 CGTTGCGATTTT
152829 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:152835 original size:33 final size:33
Alignment explanation
Indices: 152754--152844 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
152744 ACAAATCGCA
* * *
152754 TTGCAATTTTCATTTCACGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
152787 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
152819 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
152845 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:152843 original size:19 final size:19
Alignment explanation
Indices: 152749--152864 Score: 74
Period size: 19 Copynumber: 6.6 Consensus size: 19
152739 GAAACACAAA
*
152749 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
152768 TCACGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
152784 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
152800 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
152816 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
152833 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCATT
152852 TCCGCATTGCGAT
1 T-CGCATTGCGAT
152865 AGTCATTTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
14 15 0.20
15 3 0.04
16 11 0.14
17 4 0.05
18 12 0.16
19 20 0.26
20 11 0.14
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:152883 original size:20 final size:20
Alignment explanation
Indices: 152829--152872 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
152819 TTGCGATTTT
152829 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
152848 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
152868 CATTT
1 CATTT
152873 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:153388 original size:18 final size:18
Alignment explanation
Indices: 153365--153409 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
153355 GTCGATCAGA
*
153365 TGATAGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
153383 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
*
153401 TGATGGCTC
1 TGATAGCTC
153410 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:154777 original size:20 final size:20
Alignment explanation
Indices: 154729--154787 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
154719 AATAGTTTCT
** *
154729 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
154749 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
154769 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
154788 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:155305 original size:20 final size:20
Alignment explanation
Indices: 155276--155328 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
155266 AATTATGTAT
*
155276 AATCGTGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
155296 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
155316 TATCTCGTTGCGA
1 AATCGCGTTGCGA
155329 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:155348 original size:41 final size:40
Alignment explanation
Indices: 155283--155389 Score: 106
Period size: 41 Copynumber: 2.6 Consensus size: 40
155273 TATAATCGTG
* * * * * * *
155283 TTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCG
1 TTGCGATAGTTAGTATCGCATTGCGAAAGTAAGTATCGCA
** * *
155323 TTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCA
1 TTGCGATAGT-TAGTATCGCATTGCGAAAGTAAGTATCGCA
155364 TTGCGATAGTTAGTATCGCATTGCGA
1 TTGCGATAGTTAGTATCGCATTGCGA
155390 TTTTCCCAAT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
40 22 0.42
41 30 0.58
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TTGCGATAGTTAGTATCGCATTGCGAAAGTAAGTATCGCA
Found at i:155362 original size:20 final size:20
Alignment explanation
Indices: 155337--155390 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
155327 GATTTTGTAT
155337 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
155357 TATCGCATTGCGATAGTTAG
1 TATCGCATTGCGATAGTAAG
155377 TATCGCATTGCGAT
1 TATCGCATTGCGAT
155391 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:156811 original size:16 final size:17
Alignment explanation
Indices: 156780--156812 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
156770 ATAAAAAGTC
*
156780 TATTATTAATCCTATTA
1 TATTATTAATCATATTA
156797 TATTA-TAATCATATTA
1 TATTATTAATCATATTA
156813 ATTTAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTATTAATCATATTA
Found at i:156871 original size:26 final size:26
Alignment explanation
Indices: 156842--156891 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
156832 ATAATAATCC
156842 TAATGT-ATAAATACTAATTAATTACA
1 TAATGTAATAAATACTAA-TAATTACA
* *
156868 TAATGTAATAATTATTAATAATTA
1 TAATGTAATAAATACTAATAATTA
156892 ATACATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (26 bp):
TAATGTAATAAATACTAATAATTACA
Found at i:158097 original size:12 final size:12
Alignment explanation
Indices: 158070--158114 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
158060 CATTTGTAAC
158070 AATAATAT-T-T
1 AATAATATATAT
158080 AATAATATATAT
1 AATAATATATAT
*
158092 ATTAATATATAT
1 AATAATATATAT
158104 AATAATATATA
1 AATAATATATA
158115 ATAACATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
12 22 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATAATATATAT
Found at i:158115 original size:10 final size:10
Alignment explanation
Indices: 158070--158118 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 10
158060 CATTTGTAAC
*
158070 AATAATATTT
1 AATAATATAT
158080 AATAATATAT
1 AATAATATAT
158090 ATATTAATATATAT
1 A-A-T-A-ATATAT
158104 AATAATATAT
1 AATAATATAT
158114 AATAA
1 AATAA
158119 CATAACATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 21 0.62
11 2 0.06
12 2 0.06
13 2 0.06
14 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AATAATATAT
Found at i:161182 original size:27 final size:29
Alignment explanation
Indices: 161151--161204 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
161141 TCTGGTAATT
161151 TTAAAAT-TTATTTA-ATTT-TAAAAAAAA
1 TTAAAATATT-TTTATATTTGTAAAAAAAA
161178 TTAAAATATTTTTATATTTGTAAAAAA
1 TTAAAATATTTTTATATTTGTAAAAAA
161205 TCATAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 11 0.46
28 6 0.25
29 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
TTAAAATATTTTTATATTTGTAAAAAAAA
Found at i:162754 original size:2 final size:2
Alignment explanation
Indices: 162747--162787 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
162737 TTGTTGTGTT
162747 TA TA TA 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 TA TA TA T
162788 TGTATTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:170436 original size:30 final size:33
Alignment explanation
Indices: 170395--170478 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 33
170385 GCAAATATTT
* *
170395 CAAATGCGTTAATATTCT-A-C-GAATTGCATC
1 CAAATGTGTTAATATTCTCACCAGAATTGCATA
170425 CAAATGTGTTAA-ATT-TCACCAAGAATTGCATA
1 CAAATGTGTTAATATTCTCACC-AGAATTGCATA
170457 CAAATGTGTTAAATATTC-CACC
1 CAAATGTGTT-AATATTCTCACC
170479 CCACGGATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
28 1 0.02
29 4 0.09
30 12 0.27
32 19 0.42
33 2 0.04
34 7 0.16
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (33 bp):
CAAATGTGTTAATATTCTCACCAGAATTGCATA
Found at i:170784 original size:14 final size:13
Alignment explanation
Indices: 170765--170794 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
170755 CATCCTTAAA
170765 AATAATTTATTGTT
1 AATAATTTATT-TT
170779 AATAATTTATTTT
1 AATAATTTATTTT
170792 AAT
1 AAT
170795 TACTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
AATAATTTATTTT
Found at i:171096 original size:14 final size:14
Alignment explanation
Indices: 171077--171104 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
171067 ATAAGTGTAA
171077 ATATATTTTTAATT
1 ATATATTTTTAATT
171091 ATATATTTTTAATT
1 ATATATTTTTAATT
171105 TACAACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATATTTTTAATT
Found at i:171477 original size:19 final size:19
Alignment explanation
Indices: 171438--171480 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
171428 ATATTATTAT
* * *
171438 AATGTAACATTATTGTTGG
1 AATGTAACATTACTATAGG
171457 AATGTAACATTACTATAGG
1 AATGTAACATTACTATAGG
171476 AATGT
1 AATGT
171481 TGTATTACCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (19 bp):
AATGTAACATTACTATAGG
Found at i:172558 original size:15 final size:16
Alignment explanation
Indices: 172533--172575 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
172523 CTCAAAATTA
*
172533 AATATTATTTTA-AAT
1 AATAATATTTTACAAT
*
172548 AATTATATTTTTACAAT
1 AATAATA-TTTTACAAT
172565 AATAATATTTT
1 AATAATATTTT
172576 CACCTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AATAATATTTTACAAT
Found at i:172565 original size:17 final size:16
Alignment explanation
Indices: 172540--172575 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
172530 TTAAATATTA
*
172540 TTTTAAATAATTATAT
1 TTTTAAATAATAATAT
172556 TTTTACAATAATAATAT
1 TTTTA-AATAATAATAT
172573 TTT
1 TTT
172576 CACCTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAATAATAATAT
Found at i:173369 original size:5 final size:5
Alignment explanation
Indices: 173359--173770 Score: 146
Period size: 5 Copynumber: 80.6 Consensus size: 5
173349 TAATGAAAAC
* * * * * *
173359 AAATA AAATAA AGAAAA AAATA AAATG AAAT- AAAGA AAATA AGATG AAGTAA
1 AAATA AAAT-A A-AATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A
* * * * *
173411 AAAGA TAAAGA CAAAGA AAATA AAA-A ACAAAA CAAAGA AAAT- AAATA
1 AAATA -AAATA -AAATA AAATA AAATA A-AATA -AAATA AAATA AAATA
* * *
173458 CAAAGA AAATA AAAT- AAATA AAAT- AAATA CAAAGA AAATA AAAAA ATAATTA
1 -AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAATA A-AA-TA
173510 AAATA AAGATA AAA-A ATTAA-A AAATAA AAATAA AAATA AAATA AAGATA
1 AAATA AA-ATA AAATA A--AATA AAAT-A AAAT-A AAATA AAATA AA-ATA
* *
173559 ATAA-A TAGATA AAGAT- AAATA AAATT AAATA AAATA AAATA AAATA
1 A-AATA -AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA AAATA
*
173605 ATAA-A TAAAT- AAAT- AAATA AGAT- AAAT- AAATA AATATA AAATA
1 A-AATA -AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA
**
173648 AAAT- AAATAA AAATAA AAAGTAA AAAGTA AAATA AAGAT- AAAGG AAATA
1 AAATA AAAT-A AAAT-A AAA-T-A AAA-TA AAATA AA-ATA AAATA AAATA
** * * **
173697 AAA-A AAGGA AAATA AGATA AAGA-A GAA-A AAAT- AAATA ACCTA AAA-A
1 AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA
* * * *
173743 ATAGA AAACA AGATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
173771 AAATGGATTA
Statistics
Matches: 317, Mismatches: 48, Indels: 84
0.71 0.11 0.19
Matches are distributed among these distances:
4 57 0.18
5 161 0.51
6 85 0.27
7 14 0.04
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:173369 original size:18 final size:17
Alignment explanation
Indices: 173343--173773 Score: 140
Period size: 17 Copynumber: 23.8 Consensus size: 17
173333 ATGCTAGGAA
173343 AAAATATAATGAAAACAAAT
1 AAAATA-AA-GAAAA-AAAT
173363 AAAATAAAGAAAAAAAT
1 AAAATAAAGAAAAAAAT
*
173380 AAAATGAAATAAAGAAAAT
1 AAAAT-AAAGAAA-AAAAT
* * *
173399 AAGATGAAGTAAAAAGAT
1 AAAATAAAG-AAAAAAAT
*
173417 AAAGACAAAGAAAATAAA-
1 AAA-ATAAAGAAAA-AAAT
*
173435 AAACA-AAACAAAGAAAAT
1 AAA-ATAAAGAAA-AAAAT
*
173453 AAATACAAAGAAAATAAA-
1 AAA-ATAAAGAAAA-AAAT
* *
173471 ATAAATAAAATAAATACAAAG
1 A-AAAT-AAAGAAA-A-AAAT
*
173492 AAAATAAA-AAAATAATT
1 AAAATAAAGAAAA-AAAT
173509 AAAATAAAGATAAAAAATT
1 AAAATAAAGA-AAAAAA-T
173528 AAAAAATAAA-AATAAAAAT
1 --AAAATAAAGAA-AAAAAT
173547 AAAATAAAGATAATAAATAGAT
1 AAAATAAAG--AA-AAA-A-AT
*
173569 AAAGATAAATAAAATTAAAT
1 AAA-ATAAAGAAAA--AAAT
173589 AAAATAAA-ATAAAATAAT
1 AAAATAAAGA-AAAA-AAT
* *
173607 -AAATAAATAAATAAAT
1 AAAATAAAGAAAAAAAT
* *
173623 AAGATAAATAAATAAATAT
1 AAAATAAAGAAA-AAA-AT
173642 AAAATAAA-ATAAATAAA-
1 AAAATAAAGA-AAA-AAAT
* *
173659 AATAA-AAAGTAAAAAGT
1 AA-AATAAAGAAAAAAAT
173676 AAAATAAAGATAAAGGAAAT
1 AAAATAAAGA-AAA--AAAT
*
173696 AAAA-AAAG--GAAAAT
1 AAAATAAAGAAAAAAAT
*
173710 AAGATAAAGAAGAAAAA-
1 AAAATAAAGAA-AAAAAT
***
173727 ATAAATAACCTAAAAAAT
1 A-AAATAAAGAAAAAAAT
*
173745 AGAAA-ACAAG-ATAAAAT
1 A-AAATA-AAGAAAAAAAT
173762 AAAATAAA-AAAA
1 AAAATAAAGAAAA
173774 TGGATTACAA
Statistics
Matches: 319, Mismatches: 41, Indels: 106
0.68 0.09 0.23
Matches are distributed among these distances:
14 7 0.02
15 4 0.01
16 15 0.05
17 87 0.27
18 71 0.22
19 71 0.22
20 40 0.13
21 13 0.04
22 6 0.02
23 5 0.02
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (17 bp):
AAAATAAAGAAAAAAAT
Found at i:173402 original size:8 final size:9
Alignment explanation
Indices: 173343--173685 Score: 61
Period size: 9 Copynumber: 38.1 Consensus size: 9
173333 ATGCTAGGAA
173343 AAAATATAATG
1 AAAATA-AA-G
* *
173354 AAAACAAAT
1 AAAATAAAG
173363 AAAATAAAG
1 AAAATAAAG
*
173372 AAAA-AAAT
1 AAAATAAAG
173380 AAAAT---G
1 AAAATAAAG
173386 -AAATAAAG
1 AAAATAAAG
173394 AAAAT-AAG
1 AAAATAAAG
*
173402 ATGAAGTAAA-
1 A--AAATAAAG
*
173412 AAGATAAAG
1 AAAATAAAG
*
173421 ACAAAGAAA-
1 A-AAATAAAG
*
173430 ATAAA-AAAC
1 A-AAATAAAG
*
173439 AAAACAAAG
1 AAAATAAAG
173448 AAAAT--A-
1 AAAATAAAG
* *
173454 AATACAAAG
1 AAAATAAAG
173463 AAAATAAA-
1 AAAATAAAG
173471 ATAAATAAA-
1 A-AAATAAAG
173480 ATAAATACAAAG
1 A-AAAT--AAAG
173492 AAAATAAA-
1 AAAATAAAG
**
173500 AAAATAATT
1 AAAATAAAG
173509 AAAATAAAG
1 AAAATAAAG
* *
173518 ATAAAAAATTAA
1 A-AAATAA--AG
173530 AAAATAAA-
1 AAAATAAAG
*
173538 AATAA-AAAT
1 AA-AATAAAG
173547 AAAATAAAG
1 AAAATAAAG
*
173556 ATAATAAA-
1 AAAATAAAG
* *
173564 TAGATAAAG
1 AAAATAAAG
173573 ATAAATAAA-
1 A-AAATAAAG
*
173582 ATTAAATAAAAT
1 A--AAAT-AAAG
173594 AAAATAAA-
1 AAAATAAAG
*
173602 ATAATAAA-
1 AAAATAAAG
*
173610 TAAATAAA-
1 AAAATAAAG
*
173618 TAAAT-AAG
1 AAAATAAAG
*
173626 ATAAATAAAT
1 A-AAATAAAG
*
173636 AAATATAAAAT
1 AAA-AT-AAAG
*
173647 AAAATAAATA
1 AAAATAAA-G
173657 AAAATAAA-
1 AAAATAAAG
173665 AAGTAA-AAAG
1 AA--AATAAAG
173675 TAAAATAAAG
1 -AAAATAAAG
173685 A
1 A
173686 TAAAGGAAAT
Statistics
Matches: 253, Mismatches: 37, Indels: 86
0.67 0.10 0.23
Matches are distributed among these distances:
5 4 0.02
6 3 0.01
7 3 0.01
8 64 0.25
9 92 0.36
10 52 0.21
11 31 0.12
12 4 0.02
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (9 bp):
AAAATAAAG
Found at i:173466 original size:29 final size:29
Alignment explanation
Indices: 173434--173500 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
173424 AAGAAAATAA
*
173434 AAAACAAAACAAAGAAAATAAATACAAAG
1 AAAATAAAACAAAGAAAATAAATACAAAG
* *
173463 AAAATAAAATAAATAAAATAAATACAAAG
1 AAAATAAAACAAAGAAAATAAATACAAAG
173492 AAAATAAAA
1 AAAATAAAA
173501 AAATAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (29 bp):
AAAATAAAACAAAGAAAATAAATACAAAG
Found at i:173476 original size:4 final size:4
Alignment explanation
Indices: 173464--173658 Score: 107
Period size: 4 Copynumber: 45.8 Consensus size: 4
173454 AATACAAAGA
* * *
173464 AAAT AAAAT AAAT AAAAT AAAT ACAA- AGA- AAAT AAAA AAAT AATT AAAAT
1 AAAT -AAAT AAAT -AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT -AAAT
* *
173514 AAAGAT AAA- AAATT AAA- AAAT AAA- AATAA AAAT AAAAT AAAG ATAAT
1 -AA-AT AAAT AAA-T AAAT AAAT AAAT AA-AT AAAT -AAAT AAAT A-AAT
*
173561 AAAT AGAT AAAGAT AAAT AAAATT AAAT AAAAT AAAAT AAA- ATAAT AAAT
1 AAAT AAAT -AA-AT AAAT -AAA-T AAAT -AAAT -AAAT AAAT A-AAT AAAT
*
173611 AAAT AAAT AAAT AAGAT AAAT AAAT AAAT ATA- AAAT AAAAT AAAT AAA
1 AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAA
173659 AATAAAAAGT
Statistics
Matches: 155, Mismatches: 13, Indels: 45
0.73 0.06 0.21
Matches are distributed among these distances:
3 14 0.09
4 79 0.51
5 57 0.37
6 5 0.03
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:173531 original size:6 final size:6
Alignment explanation
Indices: 173463--173689 Score: 96
Period size: 6 Copynumber: 36.3 Consensus size: 6
173453 AAATACAAAG
* * * *
173463 AAAAT- AAAATA AATAA-A ATAAATA CAAA-G AAAATA AAAA-A ATAATT
1 AAAATA AAAATA AA-AATA A-AAATA AAAATA AAAATA AAAATA AAAATA
* *
173509 AAAATA AAGATAA AAAATTAA AAAATA AAAATA AAAAT- AAAATA AAGATA
1 AAAATA AAAAT-A AAAA-T-A AAAATA AAAATA AAAATA AAAATA AAAATA
* * * *
173559 ATAAATA GATAAAGA TAAATA AAATTA AATAAAA TAAAAT- AAAATA ATAAATAA
1 A-AAATA -A-AAATA AAAATA AAAATA AA-AATA -AAAATA AAAATA A-AAAT-A
* *
173613 ATAAATA AATAAGA TAAATAA ATAAATA TAAAAT- AAAAT- -AAATA AAAATA
1 A-AAATA AA-AATA AAAAT-A A-AAATA -AAAATA AAAATA AAAATA AAAATA
*
173663 AAAAGTA AAAAGT- AAAATA AAGATA AA
1 AAAA-TA AAAA-TA AAAATA AAAATA AA
173690 GGAAATAAAA
Statistics
Matches: 173, Mismatches: 25, Indels: 47
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.02
5 28 0.16
6 73 0.42
7 41 0.24
8 27 0.16
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:173534 original size:38 final size:37
Alignment explanation
Indices: 173463--173679 Score: 161
Period size: 38 Copynumber: 5.8 Consensus size: 37
173453 AAATACAAAG
*
173463 AAAATAAA-ATAAATAAA-ATAAATACAA-AGAAAATAAA
1 AAAATAAATA-AAATAAAGATAAA-A-AATAAAAAATAAA
*
173500 AAAATAATTAAAATAAAGATAAAAAATTAAAAAATAAA
1 AAAATAAATAAAATAAAGATAAAAAA-TAAAAAATAAA
*
173538 AATAA-AAATAAAATAAAGATAATAAATAGATAAAGATAAA
1 AA-AATAAATAAAATAAAGATAAAAAATA-A-AAA-ATAAA
*
173578 TAAAATTAAATAAAATAAA-AT--AAAATAATAAATAAA
1 -AAAA-TAAATAAAATAAAGATAAAAAATAAAAAATAAA
* * *
173614 TAAATAAATAAGAT-AA-ATAAATAAATATAAAATAAA
1 AAAATAAATAAAATAAAGATAAA-AAATAAAAAATAAA
*
173650 ATAAATAAA-AATAA-AAAG-TAAAAAGTAAAA
1 A-AAATAAATAA-AATAAAGATAAAAAATAAAA
173680 TAAAGATAAA
Statistics
Matches: 148, Mismatches: 14, Indels: 37
0.74 0.07 0.19
Matches are distributed among these distances:
33 4 0.03
34 9 0.06
35 4 0.03
36 27 0.18
37 33 0.22
38 38 0.26
39 10 0.07
40 7 0.05
41 4 0.03
42 12 0.08
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (37 bp):
AAAATAAATAAAATAAAGATAAAAAATAAAAAATAAA
Found at i:173620 original size:84 final size:79
Alignment explanation
Indices: 173449--173689 Score: 217
Period size: 84 Copynumber: 2.9 Consensus size: 79
173439 AAAACAAAGA
* * * *
173449 AAATAAATACAAAGAAAATAAAATAAATAAAATAAATACAAAGAAAATAAAAAAATAATTAAAAT
1 AAATAAATAAAAAAAAAATAAAATAAATATAATAAATACAAAGAAAATAAAAAAATAAATAAAAT
173514 AAAGATAAAAAATT
66 AAAGATAAAAAATT
* *
173528 AAA-AAATAAAAATAAAAATAAAATAAAGATAATAAATAGATAAAGATAAATAAAATTAAATAAA
1 AAATAAATAAAAA-AAAAATAAAATAAATATAATAAAT--ACAAAGA-AAATAAAA--AAAT-AA
*
173592 ATAAAATAAA-ATAATAAA-T
59 ATAAAATAAAGATAAAAAATT
*
173611 AAATAAATAAATAAGATAAAT-AAATAAATATAAAATAAAATA-AATA-AAAATAAAAAGTAA-A
1 AAATAAATAAA-AA-AAAAATAAAATAAATAT--AAT-AAATACAA-AGAAAATAAAAA--AATA
173672 AAGTAAAATAAAGATAAA
58 AA-TAAAATAAAGATAAA
173690 GGAAATAAAA
Statistics
Matches: 134, Mismatches: 11, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
78 8 0.06
79 24 0.18
81 10 0.07
82 17 0.13
83 18 0.13
84 30 0.22
85 20 0.15
86 3 0.02
87 4 0.03
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (79 bp):
AAATAAATAAAAAAAAAATAAAATAAATATAATAAATACAAAGAAAATAAAAAAATAAATAAAAT
AAAGATAAAAAATT
Found at i:173683 original size:53 final size:51
Alignment explanation
Indices: 173453--173683 Score: 171
Period size: 48 Copynumber: 4.5 Consensus size: 51
173443 CAAAGAAAAT
* * * *
173453 AAATACAAAGAAAATAAAATAAATAAAATAAATA-CAAAGAAAATAAA-AAA
1 AAATAAAAATAAAATAAAATAAAT-AAATAAATATAAAATAAAATAAATAAA
* *
173503 ATAATTAAAATAAAGATAAAA-AATTAAA-AAATA-AAAATAAAAATAAAATAAA
1 A-AATAAAAATAAA-ATAAAATAAATAAATAAATATAAAAT-AAAAT-AAATAAA
173555 GATAATAAATAGATAAAGAT-AAATAAAATTAAATAAA-ATAAAATAAAAT-AATAAA
1 -A-AATAAA-A-ATAAA-ATAAAAT-AAA-TAAATAAATATAAAATAAAATAAATAAA
*
173610 TAAAT--AAAT-AAATAAGATAAATAAATAAATATAAAATAAAATAAAT-AA
1 -AAATAAAAATAAAATAAAATAAATAAATAAATATAAAATAAAATAAATAAA
173658 AAATAAAAAGTAAAAAGTAAAATAAA
1 AAATAAAAA-T-AAAA-TAAAATAAA
173684 GATAAAGGAA
Statistics
Matches: 148, Mismatches: 11, Indels: 41
0.74 0.05 0.20
Matches are distributed among these distances:
47 12 0.08
48 19 0.13
49 19 0.13
50 12 0.08
51 16 0.11
52 13 0.09
53 15 0.10
54 7 0.05
55 15 0.10
56 2 0.01
57 10 0.07
58 8 0.05
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (51 bp):
AAATAAAAATAAAATAAAATAAATAAATAAATATAAAATAAAATAAATAAA
Found at i:173701 original size:29 final size:28
Alignment explanation
Indices: 173523--173718 Score: 108
Period size: 29 Copynumber: 7.0 Consensus size: 28
173513 TAAAGATAAA
* * *
173523 AAATTAAAAAATAAAAATAAAAATAAAAT
1 AAATAAAAAAAT-AAAATAAAGATAAAGT
* * *
173552 AAAGATAATAAAT-AGATAAAGATAAA-T
1 AAATA-AAAAAATAAAATAAAGATAAAGT
173579 AAAATTAAATAAAATAAAATAAA-AT-AA-T
1 -AAA-TAAA-AAAATAAAATAAAGATAAAGT
*
173607 AAATAAATAAAT-AAAT-AAGATAAA-T
1 AAATAAAAAAATAAAATAAAGATAAAGT
* *
173632 AAATAAATATAAAATAAAATAAATA-AAAAT
1 AAAT-AA-A-AAAATAAAATAAAGATAAAGT
*
173662 AAA-AAGTAAAAAGTAAAATAAAGATAAAGG
1 AAATAA--AAAAA-TAAAATAAAGATAAAGT
*
173692 AAATAAAAAAAGGAAAAT-AAGATAAAG
1 AAATAAAAAAA-TAAAATAAAGATAAAG
173719 AAGAAAAAAT
Statistics
Matches: 135, Mismatches: 15, Indels: 35
0.73 0.08 0.19
Matches are distributed among these distances:
23 2 0.01
24 6 0.04
25 11 0.08
26 6 0.04
27 5 0.04
28 38 0.28
29 40 0.30
30 25 0.19
31 2 0.01
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (28 bp):
AAATAAAAAAATAAAATAAAGATAAAGT
Found at i:173727 original size:28 final size:29
Alignment explanation
Indices: 173669--173727 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
173659 AATAAAAAGT
* *
173669 AAAAAGTAAAATAAAGATAAAGGAAATAA
1 AAAAAGGAAAATAAAGATAAAGGAAAAAA
*
173698 AAAAAGGAAAAT-AAGATAAA-GAAGAAA
1 AAAAAGGAAAATAAAGATAAAGGAAAAAA
173725 AAA
1 AAA
173728 TAAATAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 8 0.30
28 8 0.30
29 11 0.41
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (29 bp):
AAAAAGGAAAATAAAGATAAAGGAAAAAA
Found at i:175681 original size:85 final size:85
Alignment explanation
Indices: 175538--175855 Score: 415
Period size: 85 Copynumber: 3.7 Consensus size: 85
175528 ACACATCCTC
* * * ** * *
175538 GAGCTGAATGGAATCGAACTCGACAGTGT-TT-GTTGATAGATAGGCCTCCTCGTCTTGAGCTAT
1 GAGCTGAATGTAATCAAACTCGA-AG-GTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
*
175601 GCTGTAAATTTGATATGTCTTT
64 GCTGTAAATTTGATATGCCTTT
* * * * *
175623 GAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGAGAGATAACCCTTCTTGCCTTGAGTTATGT
1 GAGCTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
175688 TGTGAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* *
175708 GAGCTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATATCCCTTCTCGCCTTGAGCTATAC
1 GAGCTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
175773 TGTAAATTTGATGTGCCTTT
66 TGTAAATTTGATATGCCTTT
* ** *
175793 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAAACTTCTCACCTTGAGCTAT
1 GAGCTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
175856 ATAATCGAAC
Statistics
Matches: 205, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
83 2 0.01
84 4 0.02
85 199 0.97
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTTT
Found at i:176048 original size:85 final size:85
Alignment explanation
Indices: 175902--176079 Score: 223
Period size: 85 Copynumber: 2.1 Consensus size: 85
175892 ATTCTTGCCT
* * * * * *
175902 TGTTGTAAATTTGATATGCCTTTGAGCGAAATGTAATCGAATTCGAAGGTCTTTATTGACAGATA
1 TGTTGTAAATTTGACATACCTTTAAGCGAAATGTAATCGAACTCGAAGGTCTTGATAGACAGATA
*
175967 ACCCTTCTCGCCTTGAGTTA
66 ACCCTTCTCGCCTTGAGCTA
* *
175987 TGTTGTAAATTTGACATACCTTTAAGATG-AATGTAATCGAACTCGAAGGTCTTGGTAGACAGAT
1 TGTTGTAAATTTGACATACCTTTAAG-CGAAATGTAATCGAACTCGAAGGTCTTGATAGACAGAT
* * *
176051 AGCCTTTCTCGCTTTGAGCTA
65 AACCCTTCTCGCCTTGAGCTA
*
176072 TGCTGTAA
1 TGTTGTAA
176080 TAGGTTGGGA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 78 0.99
86 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (85 bp):
TGTTGTAAATTTGACATACCTTTAAGCGAAATGTAATCGAACTCGAAGGTCTTGATAGACAGATA
ACCCTTCTCGCCTTGAGCTA
Found at i:176713 original size:64 final size:64
Alignment explanation
Indices: 176612--176970 Score: 551
Period size: 64 Copynumber: 5.6 Consensus size: 64
176602 GCATTGTTTC
*** * *
176612 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
176676 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTTAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
176740 GAGTCCAATATCCTTTGA-TGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTT
1 GAGTCCAATATCC-TTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * *
176804 GAGTCTAATATCCTTCATTGTGAAGTTGAAATTGACTTTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
176868 GAGTCCAATATCCATCACTATGAAGTTGAAATTGACTCTGAATGAAA-TGGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACT-GGAAAGTTGTTTGTT
*
176932 GAGTCCAATATCCTTCACTATGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCT
176971 AAAAGCTGCA
Statistics
Matches: 273, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
63 4 0.01
64 267 0.98
65 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (64 bp):
GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:182012 original size:21 final size:20
Alignment explanation
Indices: 181976--182389 Score: 189
Period size: 22 Copynumber: 20.8 Consensus size: 20
181966 TAATAAAAAC
*
181976 AAATAATATAAAG-AAAATA
1 AAATAAAATAAAGAAAAATA
*
181995 AAATAAAATAAAGGGAAAAATG
1 AAATAAAATAAA--GAAAAATA
*
182017 AAAT-AAATAAA-ATAAGATA
1 AAATAAAATAAAGA-AAAATA
* * *
182036 AAGTAAAAAGATAAAGACAAAGA
1 AA--ATAAA-ATAAAGAAAAATA
* *
182059 AAATAAAACAAATAAAAAT-
1 AAATAAAATAAAGAAAAATA
*
182078 AAAGAAAATAAAGAAAAAATAA
1 AAATAAAATAAAG-AAAAAT-A
*
182100 AAATAAAATAAA-TAAAATA
1 AAATAAAATAAAGAAAAATA
* *
182119 AAGATAAAGATAAATACAAATA
1 AA-ATAAA-ATAAAGAAAAATA
182141 AAA-AATAAGTAAA-ATAAAGATA
1 AAATAA-AA-TAAAGA-AAA-ATA
*
182163 AAA-AATAA-AAATAAAAATA
1 AAATAA-AATAAAGAAAAATA
*
182182 AAGATAAATATAAAGATAAAT-
1 AA-ATAAA-ATAAAGAAAAATA
*
182203 AAAT-AAAT-AA-ATAAAT-
1 AAATAAAATAAAGAAAAATA
182219 AAATAAAGAT-AA-AAAAATA
1 AAATAAA-ATAAAGAAAAATA
182238 AAA-AAAATAAAGATAAAAATA
1 AAATAAAATAAAG--AAAAATA
*
182259 AAA-ATAAAT-AAGTAAAAT-
1 AAATA-AAATAAAGAAAAATA
** *
182277 AAA-AAAATAAAGTTAAAGA
1 AAATAAAATAAAGAAAAATA
*
182296 AAATAAAA-AAA-ATAAATA
1 AAATAAAATAAAGAAAAATA
* *
182314 AGATAAAAATAAATAAAAATAA
1 AAAT-AAAATAAAGAAAAAT-A
182336 AAAGTAAAATAAAGATAAAGAT-
1 AAA-TAAAATAAAGA-AAA-ATA
*
182358 AAAGAAAAT-AA-AAAAA-A
1 AAATAAAATAAAGAAAAATA
*
182375 AAATAAGATAAAGAA
1 AAATAAAATAAAGAA
182390 TAAGAAAAAC
Statistics
Matches: 314, Mismatches: 36, Indels: 90
0.71 0.08 0.20
Matches are distributed among these distances:
16 10 0.03
17 18 0.06
18 41 0.13
19 58 0.18
20 47 0.15
21 56 0.18
22 67 0.21
23 14 0.04
24 3 0.01
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (20 bp):
AAATAAAATAAAGAAAAATA
Found at i:182077 original size:6 final size:6
Alignment explanation
Indices: 182068--182380 Score: 150
Period size: 6 Copynumber: 51.0 Consensus size: 6
182058 AAAATAAAAC
* *
182068 AAATAA AAATAA AGAA-AA TAAAGAAA AAATAA AAATAA AATAAATA AAATAA
1 AAATAA AAATAA A-AATAA -AAA-TAA AAATAA AAATAA AA-ATA-A AAATAA
* * * * * *
182120 AGATAA AGAT-- AAATAC AAATAA AAA-AT AAGT-A AAATAA AGATAAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAAT-AA
* * * *
182165 AAATAA AAATAA AAATAA AGATAA ATATAA AGATAA ATAA-AT AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A-AATAA AAATAA
* * *
182213 ATAA-AT AAATAA AGATAA AAA-AA TAAA-AA AAATAA AGATAA AAATAA
1 A-AATAA AAATAA AAATAA AAATAA -AAATAA AAATAA AAATAA AAATAA
* *
182260 AAATAA ATAAGTAA AATAAAA AAATAA AGTTAA-AGA AAATAA AAAAAA
1 AAATAA A-AA-TAA AA-ATAA AAATAA A---AATA-A AAATAA AAATAA
* *
182308 TAAAT-A AGATAA AAAT-- AAATAA AAATAA AAAGT-A AAATAA AGATAA
1 -AAATAA AAATAA AAATAA AAATAA AAATAA AAA-TAA AAATAA AAATAA
* *
182354 AGATAAAGA AAATAA AAAAAA AAATAA
1 A-A-ATA-A AAATAA AAATAA AAATAA
182381 GATAAAGAAT
Statistics
Matches: 237, Mismatches: 36, Indels: 68
0.70 0.11 0.20
Matches are distributed among these distances:
4 7 0.03
5 19 0.08
6 159 0.67
7 32 0.14
8 14 0.06
9 6 0.03
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:182245 original size:159 final size:161
Alignment explanation
Indices: 182072--182398 Score: 429
Period size: 159 Copynumber: 2.0 Consensus size: 161
182062 TAAAACAAAT
* * *
182072 AAAAATAAAGAAAATAAAGA-AAAAATAAAAATAAAATAAATAAAAT-AAAGATAAAGATAAATA
1 AAAAATAAAAAAAATAAAGATAAAAATAAAAAT-AAATAAATAAAATAAAAAATAAAGATAAAGA
*
182135 CAAATAAAAAATAAGTAAAATAAAGAT-AAA-AAATAAAAATAAAAA-TAAAGATAAATATAAAG
65 -AAATAAAAAA-AA-T-AAAT-AAGATAAAATAAATAAAAATAAAAAGTAAA-ATAAAGATAAAG
* * *
182197 ATAAA-TAAATAAATAAATAAATAA-ATAAAG-ATAA-
124 ATAAAGAAAATAAAAAAAAAAATAAGATAAAGAATAAG
* *
182231 AAAAATAAAAAAAATAAAGATAAAAATAAAAATAAATAAGTAAAATAAAAAAATAAAGTTAAAGA
1 AAAAATAAAAAAAATAAAGATAAAAATAAAAATAAATAAATAAAAT-AAAAAATAAAGATAAAGA
182296 AAATAAAAAAAATAAATAAGATAAAAATAAATAAAAATAAAAAGTAAAATAAAGATAAAGATAAA
65 AAATAAAAAAAATAAATAAGAT-AAAATAAATAAAAATAAAAAGTAAAATAAAGATAAAGATAAA
182361 GAAAATAAAAAAAAAAATAAGATAAAGAATAAG
129 GAAAATAAAAAAAAAAATAAGATAAAGAATAAG
182394 AAAAA
1 AAAAA
182399 CAACCTAAAA
Statistics
Matches: 148, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
156 5 0.03
157 4 0.03
158 4 0.03
159 64 0.43
160 42 0.28
161 20 0.14
162 4 0.03
163 5 0.03
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.17
Consensus pattern (161 bp):
AAAAATAAAAAAAATAAAGATAAAAATAAAAATAAATAAATAAAATAAAAAATAAAGATAAAGAA
AATAAAAAAAATAAATAAGATAAAATAAATAAAAATAAAAAGTAAAATAAAGATAAAGATAAAGA
AAATAAAAAAAAAAATAAGATAAAGAATAAG
Found at i:182392 original size:67 final size:62
Alignment explanation
Indices: 182061--182398 Score: 215
Period size: 67 Copynumber: 5.2 Consensus size: 62
182051 GACAAAGAAA
* * *
182061 ATAAAACAAATAAAAATAAAGA-AA-ATAAAGAAAAAATAAAAATAAAATAAATAAAATAAAGAT
1 ATAAAAAAAATAAAAA-AAAAATAAGATAAAG-ATAAA-AAAAATAAAA-AAA-AAAAT-AA-AT
182124 AAAG
59 AAAG
* * * * *
182128 ATAAATACAAATAAAAAATAAGTAAAATAAAGATAAAAAATAAAAATAAAAATAAAGATAAATAT
1 ATAAA-AAAAATAAAAAAAAAATAAGATAAAGATAAAAAA-AATAA-AAAAA-AAA-AT-AA-AT
182193 AAAG
59 AAAG
* * * * *
182197 AT-AAATAAATAAATAAATAAATAA-ATAAAGAT-AAAAAAATAAAAAAAATAA-AGATAAAA
1 ATAAAAAAAATAAA-AAAAAAATAAGATAAAGATAAAAAAAATAAAAAAAAAAATAAATAAAG
* *
182256 ATAAAAATAAATAAGTAAAATAAAA-AA-ATAAAGTTAAAGAAAATAAAAAAAATAAATAAGATA
1 ATAAAAA-AAATAA--AAAA-AAAATAAGATAAAGATAAAAAAAATAAAAAAAA-AAATAA-ATA
*
182319 AAA
60 AAG
* *
182322 ATAAATAAAAATAAAAAGTAAAATAAAGATAAAGATAAAGAAAATAAAAAAAAAAATAAGATAAA
1 ATAAA-AAAAATAAAAA-AAAAAT-AAGATAAAGATAAAAAAAATAAAAAAAAAAATAA-ATAAA
182387 G
62 G
*
182388 AATAAGAAAAA
1 -ATAAAAAAAA
182399 CAACCTAAAA
Statistics
Matches: 227, Mismatches: 22, Indels: 45
0.77 0.07 0.15
Matches are distributed among these distances:
59 7 0.03
60 4 0.02
61 6 0.03
62 13 0.06
63 21 0.09
64 14 0.06
65 5 0.02
66 41 0.18
67 56 0.25
68 39 0.17
69 21 0.09
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (62 bp):
ATAAAAAAAATAAAAAAAAAATAAGATAAAGATAAAAAAAATAAAAAAAAAAATAAATAAAG
Found at i:183310 original size:12 final size:13
Alignment explanation
Indices: 183293--183325 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
183283 AATGGTTCCA
*
183293 TATTTTTC-TGTG
1 TATTTTTCATATG
183305 TATTTTTCATATG
1 TATTTTTCATATG
183318 TATTTTTC
1 TATTTTTC
183326 GAGTTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.15, C:0.09, G:0.09, T:0.67
Consensus pattern (13 bp):
TATTTTTCATATG
Found at i:184535 original size:2 final size:2
Alignment explanation
Indices: 184528--184562 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
184518 GTTAGTCAGC
184528 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
184563 GAAAGAGAGA
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:186264 original size:28 final size:28
Alignment explanation
Indices: 186204--186300 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
186194 ATCATAAAAC
* *
186204 TTAATATTA-TTATTTTTAAAATATTAAA
1 TTAAT-TTATTTATTATTAAAATATTATA
*
186232 ATAATTTATTTATTATTAAAATATTATA
1 TTAATTTATTTATTATTAAAATATTATA
* *
186260 TTAA-TAATTTTATTAATAAAAATATTAATA
1 TTAATTTA-TTTATT-ATTAAAATATT-ATA
* *
186290 TTGATATATTT
1 TTAATTTATTT
186301 TATTGAAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
27 5 0.09
28 30 0.55
29 10 0.18
30 9 0.16
31 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TTAATTTATTTATTATTAAAATATTATA
Found at i:186315 original size:33 final size:30
Alignment explanation
Indices: 186240--186319 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 30
186230 AAATAATTTA
*
186240 TTTATT-ATTAAAATATT-ATATTAATAAT
1 TTTATTAATAAAAATATTAATATTAATAAT
*
186268 TTTATTAATAAAAATATTAATATTGATATAT
1 TTTATTAATAAAAATATTAATATTAATA-AT
186299 TTTATTGAAATAAAAATATTA
1 TTTATT--AATAAAAATATTA
186320 TAAATTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
28 6 0.13
29 10 0.22
30 8 0.18
31 8 0.18
33 13 0.29
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTATTAATAAAAATATTAATATTAATAAT
Found at i:186337 original size:33 final size:33
Alignment explanation
Indices: 186274--186337 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
186264 TAATTTTATT
* *
186274 AATAAAAATATTAATATTGATATATTTTATTGA
1 AATAAAAATATTAAAATTGATATATATTATTGA
186307 AATAAAAATATTATAAATT-ATAT-TAATTATT
1 AATAAAAATATTA-AAATTGATATAT-ATTATT
186338 TATAAAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 22 0.81
34 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (33 bp):
AATAAAAATATTAAAATTGATATATATTATTGA
Found at i:186343 original size:31 final size:30
Alignment explanation
Indices: 186308--186378 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
186298 TTTTATTGAA
186308 ATAAAAATATTATA-AATTATATTAATTATTT
1 ATAAAAATATTATAGAATTATATT-A-TATTT
*
186339 ATAAAAAGTA--ATAGTATTATATTATATTT
1 ATAAAAA-TATTATAGAATTATATTATATTT
186368 -TAAAAATATTA
1 ATAAAAATATTA
186379 ATTAGTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
27 2 0.06
28 6 0.17
29 6 0.17
30 4 0.11
31 15 0.43
32 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
ATAAAAATATTATAGAATTATATTATATTT
Found at i:186411 original size:23 final size:23
Alignment explanation
Indices: 186362--186412 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
186352 GTATTATATT
**
186362 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
186385 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
186408 ATATT
1 ATATT
186413 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:186614 original size:22 final size:23
Alignment explanation
Indices: 186586--186632 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
186576 TTGATTATTT
186586 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
186608 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
186631 TA
1 TA
186633 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:186637 original size:22 final size:22
Alignment explanation
Indices: 186594--186637 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
186584 TTTATTATAA
*
186594 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
186616 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
186638 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:188400 original size:3 final size:3
Alignment explanation
Indices: 188392--188446 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
188382 CAGAAAAGAA
188392 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
188440 AAT AAT A
1 AAT AAT A
188447 GAGTAAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:188535 original size:12 final size:12
Alignment explanation
Indices: 188528--188559 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
188518 GAAAAAATAT
188528 AAATAAAAATGA
1 AAATAAAAATGA
188540 AAATAAAAATGA
1 AAATAAAAATGA
*
188552 AACTAAAA
1 AAATAAAA
188560 TAAAACAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (12 bp):
AAATAAAAATGA
Found at i:188588 original size:17 final size:16
Alignment explanation
Indices: 188510--188589 Score: 56
Period size: 17 Copynumber: 4.8 Consensus size: 16
188500 GTCAAAGAAA
188510 AAAAGAAAGAAAAAATAT
1 AAAA-AAAGAAAAAA-AT
**
188528 AAATAAAA-ATGAAAAT
1 AAA-AAAAGAAAAAAAT
*
188544 -AAAAATGAAACTAAAAT
1 AAAAAAAGAAA--AAAAT
*
188561 AAAACAAGAAAAAAAT
1 AAAAAAAGAAAAAAAT
188577 AACAAAAAGAAAA
1 AA-AAAAAGAAAA
188590 TTATATATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
14 3 0.06
15 3 0.06
16 9 0.19
17 18 0.38
18 14 0.29
19 1 0.02
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAT
Found at i:188764 original size:9 final size:9
Alignment explanation
Indices: 188752--188795 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
188742 TGATATTAAT
188752 AATAAAAAA
1 AATAAAAAA
*
188761 AATAAAAGA
1 AATAAAAAA
*
188770 AATAAATAA
1 AATAAAAAA
*
188779 AGTAAAAAA
1 AATAAAAAA
188788 AATAAAAA
1 AATAAAAA
188796 GGACCAGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (9 bp):
AATAAAAAA
Found at i:188765 original size:27 final size:26
Alignment explanation
Indices: 188725--188794 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
188715 AATAAGTAGG
* *
188725 ATAAAAAAAGATAATAATGATATTAAT-A
1 ATAAAAAAA-ATAA-AA-GAAATAAATAA
188753 ATAAAAAAAATAAAAGAAATAAATAA
1 ATAAAAAAAATAAAAGAAATAAATAA
188779 AGTAAAAAAAATAAAA
1 A-TAAAAAAAATAAAA
188795 AGGACCAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
25 7 0.18
26 4 0.11
27 18 0.47
28 9 0.24
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (26 bp):
ATAAAAAAAATAAAAGAAATAAATAA
Found at i:191186 original size:110 final size:110
Alignment explanation
Indices: 190984--191391 Score: 618
Period size: 110 Copynumber: 3.7 Consensus size: 110
190974 TTTTGTCGCT
* * * * *
190984 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATAAAAATTGAAAAGTTGTTTG
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAAT-GAAACTGAAAAGTTGTTTG
* * * *
191049 TTGATAGTCAGTCACCCCTTCGTTGTGAAGTTGAGCCTGTGTTGTC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * * *
191095 TCGAGTCCAATATCTTTCACTGTGAAATTAAAATTGACTCTGAATGAAACTGAAAATTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
191160 TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* *
191205 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
191270 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGCC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* *
191315 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTTTGACTCTGAATGAAATTGAAAAGTTGTTT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTT-AAA-ATTGACTCTGAATGAAACTGAAAAGTTGTTT
191380 GTTGACAGTCAG
64 GTTGACAGTCAG
191392 CTTTTCTCGA
Statistics
Matches: 269, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
110 187 0.70
111 41 0.15
112 41 0.15
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:193067 original size:7 final size:7
Alignment explanation
Indices: 193050--193155 Score: 76
Period size: 7 Copynumber: 15.0 Consensus size: 7
193040 TGCATATGCA
193050 TCTTGTTT
1 TCTT-TTT
193058 TCTTTTT
1 TCTTTTT
193065 TCTTTATT
1 TCTTT-TT
*
193073 T-TTAATT
1 TCTT-TTT
*
193080 TGTTTTT
1 TCTTTTT
*
193087 GCTTTTT
1 TCTTTTT
*
193094 GCTTTTT
1 TCTTTTT
193101 TCTTTTT
1 TCTTTTT
193108 TCTTTTT
1 TCTTTTT
*
193115 GC--TTT
1 TCTTTTT
193120 T-TTTTT
1 TCTTTTT
193126 TCTTTTT
1 TCTTTTT
*
193133 GCTTTTTT
1 TC-TTTTT
*
193141 TCTTCTTC
1 TCTT-TTT
193149 TCTTTTT
1 TCTTTTT
193156 GTTCTTTATT
Statistics
Matches: 79, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
5 3 0.04
6 4 0.05
7 51 0.65
8 21 0.27
ACGTcount: A:0.03, C:0.13, G:0.06, T:0.78
Consensus pattern (7 bp):
TCTTTTT
Found at i:193125 original size:39 final size:42
Alignment explanation
Indices: 193055--193156 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 42
193045 ATGCATCTTG
**
193055 TTTTCTTTTTTCTTTATTTTTAATTTGTTTTTGCTTTTTGC-TT
1 TTTTCTTTTTTCTTT-TTGCT-ATTTGTTTTTGCTTTTTGCTTT
*
193098 TTTTCTTTTTTCTTTTTGCT-TTT-TTTTTTCTTTTTGCTTT
1 TTTTCTTTTTTCTTTTTGCTATTTGTTTTTGCTTTTTGCTTT
*
193138 TTTTCTTCTTCTCTTTTTG
1 TTTTCTT-TTTTCTTTTTG
193157 TTCTTTATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
39 13 0.25
40 12 0.23
41 10 0.19
42 3 0.06
43 15 0.28
ACGTcount: A:0.03, C:0.13, G:0.06, T:0.78
Consensus pattern (42 bp):
TTTTCTTTTTTCTTTTTGCTATTTGTTTTTGCTTTTTGCTTT
Found at i:193126 original size:18 final size:18
Alignment explanation
Indices: 193055--193147 Score: 89
Period size: 18 Copynumber: 5.1 Consensus size: 18
193045 ATGCATCTTG
* *
193055 TTTT-CTTTTTTCTTTAT
1 TTTTGCTTTTTTTTTTCT
** * *
193072 TTTTAATTTGTTTTTGCT
1 TTTTGCTTTTTTTTTTCT
193090 TTTTGCTTTTTTCTTTTTTCT
1 TTTTGC--TTTT-TTTTTTCT
193111 TTTTGCTTTTTTTTTTCT
1 TTTTGCTTTTTTTTTTCT
*
193129 TTTTGCTTTTTTTCTTCT
1 TTTTGCTTTTTTTTTTCT
193147 T
1 T
193148 CTCTTTTTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
17 4 0.06
18 38 0.61
19 4 0.06
20 3 0.05
21 13 0.21
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTGCTTTTTTTTTTCT
Found at i:193155 original size:17 final size:16
Alignment explanation
Indices: 193089--193162 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
193079 TTGTTTTTGC
* *
193089 TTTTTGCTTTTTTCTT
1 TTTTTTCTTTTCTCTT
* *
193105 TTTTCTT-TTTGCTTTT
1 TTTT-TTCTTTTCTCTT
193121 TTTTTTCTTTT-TGC-T
1 TTTTTTCTTTTCT-CTT
193136 TTTTTTCTTCTTCTCTT
1 TTTTTTCTT-TTCTCTT
*
193153 TTTGTTCTTT
1 TTTTTTCTTT
193163 ATTGGATCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
15 13 0.29
16 21 0.47
17 11 0.24
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTTTCTCTT
Found at i:193155 original size:32 final size:32
Alignment explanation
Indices: 193089--193162 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
193079 TTGTTTTTGC
* * * *
193089 TTTTTGCTTTTTTCTTTTTTCTTTTTGCTTTT
1 TTTTTTCTTTTTGCTTTTTTCTTCTTGCTCTT
193121 TTTTTTCTTTTTGCTTTTTTTCTTCTT-CTCTT
1 TTTTTTCTTTTTGC-TTTTTTCTTCTTGCTCTT
*
193153 TTTGTTCTTT
1 TTTTTTCTTT
193163 ATTGGATCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 25 0.69
33 11 0.31
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (32 bp):
TTTTTTCTTTTTGCTTTTTTCTTCTTGCTCTT
Found at i:196334 original size:6 final size:6
Alignment explanation
Indices: 196325--196384 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
196315 AAAAGAAAAC
* * *
196325 AATAAA AATAAA AATAAA AATGAA AATGAA AATAAA AATAAA AATGAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
196373 ACT-AA AATAAA A
1 AATAAA AATAAA A
196385 CAAGAATAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 4 0.08
6 44 0.92
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:196356 original size:18 final size:18
Alignment explanation
Indices: 196325--196384 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
196315 AAAAGAAAAC
*
196325 AATAAAAATAAAAATAAA
1 AATAAAAATGAAAATAAA
*
196343 AATGAAAATGAAAATAAA
1 AATAAAAATGAAAATAAA
*
196361 AATAAAAATGAAACT-AA
1 AATAAAAATGAAAATAAA
196378 AATAAAA
1 AATAAAA
196385 CAAGAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
17 9 0.24
18 29 0.76
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (18 bp):
AATAAAAATGAAAATAAA
Found at i:196361 original size:24 final size:23
Alignment explanation
Indices: 196329--196384 Score: 94
Period size: 24 Copynumber: 2.4 Consensus size: 23
196319 GAAAACAATA
196329 AAAATAAAAATAAAAATGAAAAT
1 AAAATAAAAATAAAAATGAAAAT
*
196352 GAAAATAAAAATAAAAATGAAACT
1 -AAAATAAAAATAAAAATGAAAAT
196376 AAAATAAAA
1 AAAATAAAA
196385 CAAGAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 9 0.29
24 22 0.71
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAATAAAAATAAAAATGAAAAT
Found at i:196621 original size:18 final size:18
Alignment explanation
Indices: 196582--196625 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
196572 ATAATGATAT
*
196582 TAATAAAAAATTAAAAGA
1 TAATAAAAAAGTAAAAGA
196600 -AATAAATAAAGTAAAA-A
1 TAATAAA-AAAGTAAAAGA
196617 TAATAAAAA
1 TAATAAAAA
196626 GGACCAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
TAATAAAAAAGTAAAAGA
Found at i:201456 original size:16 final size:17
Alignment explanation
Indices: 201429--201463 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
201419 TTCCCCATCA
*
201429 TCTTCTCCTTTTCTTCT
1 TCTTCTCCTTTTATTCT
201446 TCTTC-CCTTTTATTCT
1 TCTTCTCCTTTTATTCT
201462 TC
1 TC
201464 ACTAAAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (17 bp):
TCTTCTCCTTTTATTCT
Found at i:208238 original size:21 final size:21
Alignment explanation
Indices: 208213--208266 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
208203 AATTTAAAAT
208213 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTGCTACA
*
208234 GTGTATCGATGCACTGCTATA
1 GTGTATCGATGCACTGCTACA
*
208255 GTGTACCGATGC
1 GTGTATCGATGC
208267 CTACAGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
GTGTATCGATGCACTGCTACA
Found at i:209025 original size:168 final size:171
Alignment explanation
Indices: 208824--209165 Score: 645
Period size: 168 Copynumber: 2.0 Consensus size: 171
208814 CATATCACCA
208824 AAAGCATATACATCACATATATTGTACTTGTTATTATCTCTTTATTAGCCCATGTACACATGTAA
1 AAAGCATATACATCACATATATTGTACTTGTTATTATCTCTTTATTAGCCCATGTACACATGTAA
208889 TTCAGTGTAAACAATAATAACAATATATCATATAATAATGCAAACAC-TTTG-A-TTTTATAGGC
66 TTCAGTGTAAACAATAATAACAATATATCATATAATAATGCAAACACTTTTGAACTTTTATAGGC
208951 CCATGTACATTACTGAGAACTTAAGGTATTCGAGTACATTG
131 CCATGTACATTACTGAGAACTTAAGGTATTCGAGTACATTG
208992 AAAGCATATACATCACATATATTGTACTTGTTATTATCTCTTTATTAGCCCATGTACACATGTAA
1 AAAGCATATACATCACATATATTGTACTTGTTATTATCTCTTTATTAGCCCATGTACACATGTAA
209057 TTCAGTGTAAACAATAATAACAATATATCATATAATAATGCAAACACTTTTGATATCTTTTATAG
66 TTCAGTGTAAACAATAATAACAATATATCATATAATAATGCAAACACTTTTGA-A-CTTTTATAG
209122 GCCCATGTACATTACTGAGAACTTAAGGTATTCGAGTACATTG
129 GCCCATGTACATTACTGAGAACTTAAGGTATTCGAGTACATTG
209165 A
1 A
209166 GGTTGTGCAC
Statistics
Matches: 169, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
168 112 0.66
169 4 0.02
171 1 0.01
173 52 0.31
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (171 bp):
AAAGCATATACATCACATATATTGTACTTGTTATTATCTCTTTATTAGCCCATGTACACATGTAA
TTCAGTGTAAACAATAATAACAATATATCATATAATAATGCAAACACTTTTGAACTTTTATAGGC
CCATGTACATTACTGAGAACTTAAGGTATTCGAGTACATTG
Found at i:209252 original size:22 final size:22
Alignment explanation
Indices: 209227--209280 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
209217 ATGTGAAATT
209227 TGTCTTGAATGACCTATGTATA
1 TGTCTTGAATGACCTATGTATA
* * *
209249 TGTCTCGAAGGACCTCTGTATA
1 TGTCTTGAATGACCTATGTATA
*
209271 TGTCCTGAAT
1 TGTCTTGAAT
209281 AACCACGTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (22 bp):
TGTCTTGAATGACCTATGTATA
Found at i:209582 original size:21 final size:20
Alignment explanation
Indices: 209551--209594 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
209541 ATATAACCAT
**
209551 ATATGTCATATATTGTTCAC
1 ATATGTCATATATTCATCAC
209571 ATATGTTCATATATTCATCAC
1 ATATG-TCATATATTCATCAC
209592 ATA
1 ATA
209595 GCATATAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (20 bp):
ATATGTCATATATTCATCAC
Found at i:211354 original size:30 final size:30
Alignment explanation
Indices: 211318--211395 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
211308 CTTTTTAAAA
* *
211318 TTATACTTTGGTCCCTAAACTTT-TCAAAGT
1 TTATACTTTGGTCACTAAACTTTACCAAA-T
211348 TTATACTTTGGTCAAC-AAACTTTACCAAAT
1 TTATACTTTGGTC-ACTAAACTTTACCAAAT
*
211378 TTATAATTTGGTCACTAA
1 TTATACTTTGGTCACTAA
211396 CTAAATCCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.05
30 35 0.83
31 5 0.12
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (30 bp):
TTATACTTTGGTCACTAAACTTTACCAAAT
Found at i:217762 original size:31 final size:32
Alignment explanation
Indices: 217722--217787 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
217712 TACGGGTTGC
*
217722 TTTTGGTTCAGGTTG-TTTCGGTTCGAGTTCT
1 TTTTAGTTCAGGTTGATTTCGGTTCGAGTTCT
217753 TTTTAGTTCAGGTTGATTTCGGTTCGAGTTCT
1 TTTTAGTTCAGGTTGATTTCGGTTCGAGTTCT
217785 TTT
1 TTT
217788 CGATTCATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 14 0.42
32 19 0.58
ACGTcount: A:0.09, C:0.12, G:0.26, T:0.53
Consensus pattern (32 bp):
TTTTAGTTCAGGTTGATTTCGGTTCGAGTTCT
Found at i:217788 original size:16 final size:16
Alignment explanation
Indices: 217737--217789 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
217727 GTTCAGGTTG
217737 TTTCGGTTCGAGTTCT
1 TTTCGGTTCGAGTTCT
** **
217753 TTTTAGTTC-AGGTTGA
1 TTTCGGTTCGA-GTTCT
217769 TTTCGGTTCGAGTTCT
1 TTTCGGTTCGAGTTCT
217785 TTTCG
1 TTTCG
217790 ATTCATGTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (16 bp):
TTTCGGTTCGAGTTCT
Found at i:222175 original size:22 final size:23
Alignment explanation
Indices: 222130--222176 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
222120 AACCCTAAAC
222130 AAGCCCAAACATCATATCTGCTA
1 AAGCCCAAACATCATATCTGCTA
* * *
222153 AAGCCCAGA-ATCGTATCTTCTA
1 AAGCCCAAACATCATATCTGCTA
222175 AA
1 AA
222177 CTCGCGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (23 bp):
AAGCCCAAACATCATATCTGCTA
Found at i:244270 original size:14 final size:14
Alignment explanation
Indices: 244251--244278 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
244241 ATATTTTAAG
244251 TTCATCCTCAAATT
1 TTCATCCTCAAATT
244265 TTCATCCTCAAATT
1 TTCATCCTCAAATT
244279 ATGGCTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
TTCATCCTCAAATT
Found at i:244331 original size:59 final size:60
Alignment explanation
Indices: 244264--244384 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
244254 ATCCTCAAAT
* * * * *
244264 TTTCATCCTCAAATTATGGCTCTC-TTCTAAATTAATCCTTAAATTTTTGAACATTCTAA
1 TTTCATCCTCAAACTATGACTCTCTTTCTAAATTAATCCTCAAACTTTTGAACATTCCAA
* ** *
244323 TTTCATCCTTAAACTATGACTCTCTTTCTAAATTGGTCCTCAAACTTTTGAATATTCCAA
1 TTTCATCCTCAAACTATGACTCTCTTTCTAAATTAATCCTCAAACTTTTGAACATTCCAA
244383 TT
1 TT
244385 CTATCCCTAG
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 21 0.40
60 31 0.60
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (60 bp):
TTTCATCCTCAAACTATGACTCTCTTTCTAAATTAATCCTCAAACTTTTGAACATTCCAA
Found at i:244620 original size:60 final size:59
Alignment explanation
Indices: 244540--244683 Score: 180
Period size: 60 Copynumber: 2.4 Consensus size: 59
244530 TTTGGGGGAT
* * * * *
244540 CAATTTATAATGAAGATCATAGTTTAGGGATGACATTGAAATGTTCAAAAGTTTGAGAAC
1 CAATTTAAAATGAAG-TCATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGAAC
* * * *
244600 TAATTTAAAATGATAGTCATAATTTAGGGATGAAATTAAAATATTTAAAAGTTTAAGCAC
1 CAATTTAAAATGA-AGTCATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGAAC
244660 CAATTTAAAATGAGAGTCATAGTT
1 CAATTTAAAATGA-AGTCATAGTT
244684 GAAGACATTT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 69 0.97
61 2 0.03
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (59 bp):
CAATTTAAAATGAAGTCATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGAAC
Found at i:247110 original size:27 final size:27
Alignment explanation
Indices: 247080--247132 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
247070 GGACAATCAT
*
247080 CACCACCATGAACATCACCATCACCAG
1 CACCACCACGAACATCACCATCACCAG
247107 CACCACCACGAACATCACCATCACCA
1 CACCACCACGAACATCACCATCACCA
247133 TGACAGCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.47, G:0.06, T:0.09
Consensus pattern (27 bp):
CACCACCACGAACATCACCATCACCAG
Found at i:247125 original size:15 final size:15
Alignment explanation
Indices: 247077--247126 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
247067 GGGGGACAAT
*
247077 CATCACCACCATGAA
1 CATCACCACCACGAA
*
247092 CATCACCATCAC---
1 CATCACCACCACGAA
*
247104 CAGCACCACCACGAA
1 CATCACCACCACGAA
247119 CATCACCA
1 CATCACCA
247127 TCACCATGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
12 10 0.37
15 17 0.63
ACGTcount: A:0.38, C:0.46, G:0.06, T:0.10
Consensus pattern (15 bp):
CATCACCACCACGAA
Found at i:252027 original size:5 final size:5
Alignment explanation
Indices: 252017--252183 Score: 334
Period size: 5 Copynumber: 33.4 Consensus size: 5
252007 CGTAGGGTGC
252017 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
252067 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
252117 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
252167 ATATT ATATT ATATT AT
1 ATATT ATATT ATATT AT
252184 TAGTTATGTG
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 162 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:255301 original size:16 final size:16
Alignment explanation
Indices: 255248--255301 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
255238 TAAGAAGAAG
*
255248 AAAAAATTAAGAATATAA
1 AAAAAATTTA-AA-ATAA
** *
255266 AAAAAATTTAACTTAT
1 AAAAAATTTAAAATAA
255282 AAAAAATTTAAAATAA
1 AAAAAATTTAAAATAA
255298 AAAA
1 AAAA
255302 TTATAGCAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 19 0.66
17 1 0.03
18 9 0.31
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAAAATTTAAAATAA
Found at i:269192 original size:35 final size:35
Alignment explanation
Indices: 269146--269216 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
269136 CCAACAAAGA
* *
269146 AGAGTTGGATTAGGACTTAAATACTAGTCTAGAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
269181 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
269216 A
1 A
269217 AGGTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:269708 original size:2 final size:2
Alignment explanation
Indices: 269703--269747 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
269693 ATTTTTTATT
269703 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
269745 TA T
1 TA T
269748 TACTTTGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:281803 original size:109 final size:109
Alignment explanation
Indices: 281612--282058 Score: 779
Period size: 109 Copynumber: 4.1 Consensus size: 109
281602 GGGTCATCCA
* *
281612 CGATTTCAACCCCATGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
1 CGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
* *
281677 AAGGGACGGCTAGTTGTCGACAAACAACTTCCCAATTTCAGAGC
66 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
281721 CGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAGCTTCACAACG
1 CGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
281786 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
66 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
281830 CGATTTTAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
1 CGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
* *
281895 AAGGGACGACTGGTTGTCAACAAATAACTTCCCAATTTCAGAGC
66 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
281939 CGATTTCAACCCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
1 CGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
* *
282004 AAGGGACGGTTGGTTGTCAACAAACAACTTCCCAA-TTCTAGAGT
66 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTC-AGAGC
282048 CGATTTCAACT
1 CGATTTCAACT
282059 TGTATTGGAT
Statistics
Matches: 321, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
108 3 0.01
109 318 0.99
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (109 bp):
CGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
Found at i:282557 original size:35 final size:35
Alignment explanation
Indices: 282511--282582 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
282501 CCAACAAAGA
*
282511 AGAGTTGGATTAGGACTCAAATACTAGTCTATAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
282546 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
282581 AG
1 AG
282583 GGTTTTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:283208 original size:2 final size:2
Alignment explanation
Indices: 283201--283227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
283191 TTATAAGTTG
283201 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 T
283228 TCATATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:286177 original size:35 final size:35
Alignment explanation
Indices: 286126--286193 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
286116 AACATAGTCC
* *
286126 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
* *
286161 TCAATTACATTTTAAACCCCAAATTCTAAAATA
1 TCAATTACATTCTAAACCCCAAATTCCAAAATA
286194 CTATAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
Found at i:286236 original size:34 final size:35
Alignment explanation
Indices: 286198--286271 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
286188 AAAATACTAT
286198 AATTTAGGG-TTAAAAAGTAATTAAAGTATTTTGA
1 AATTTAGGGTTTAAAAAGTAATTAAAGTATTTTGA
* * * * * *
286232 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAAAAAGTAATTAAAGTATTTTGA
286267 AATTT
1 AATTT
286272 TGAACATGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 8 0.24
35 25 0.76
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (35 bp):
AATTTAGGGTTTAAAAAGTAATTAAAGTATTTTGA
Found at i:288387 original size:30 final size:30
Alignment explanation
Indices: 288351--288411 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
288341 AGAGTTGAGG
*
288351 GTTACCTATGTCCTTCG-GGACATATGGATA
1 GTTACCTATGTCCTTCGAAG-CATATGGATA
*
288381 GTTACCTATGTTCTTCGAAGCATATGGATA
1 GTTACCTATGTCCTTCGAAGCATATGGATA
288411 G
1 G
288412 GTCCTTCGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGAAGCATATGGATA
Found at i:292071 original size:6 final size:6
Alignment explanation
Indices: 292060--292085 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
292050 TACATGTTTC
292060 AAGATA AAGATA AAGATA AAGATA AA
1 AAGATA AAGATA AAGATA AAGATA AA
292086 CAGGACAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAGATA
Found at i:297754 original size:12 final size:12
Alignment explanation
Indices: 297737--297762 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
297727 GGAATATAAT
297737 ATCATTTAAAAA
1 ATCATTTAAAAA
297749 ATCATTTAAAAA
1 ATCATTTAAAAA
297761 AT
1 AT
297763 AAAATATAAT
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:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCATTTAAAAA
Found at i:297834 original size:19 final size:19
Alignment explanation
Indices: 297788--297834 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
297778 TATTATTTTG
*
297788 TAAA-ATATAATAAAATAT
1 TAAATATATAATAAAACAT
* * *
297806 TATATTTATAATTAAACAT
1 TAAATATATAATAAAACAT
297825 TAAATATATA
1 TAAATATATA
297835 TTTGAAAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATATATAATAAAACAT
Found at i:298188 original size:32 final size:32
Alignment explanation
Indices: 298148--298229 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
298138 TGTTGACCTG
*
298148 AACT-AAAAACTGATCGATTTGATATTGAATC-
1 AACTCAAAAACTGATCAATTTGATATTG-ATCT
* *
298179 GACTCAAAAATTGATCAATTTGATATTGATCT
1 AACTCAAAAACTGATCAATTTGATATTGATCT
298211 AACTCAAAAA-TCGATCAAT
1 AACTCAAAAACT-GATCAAT
298230 CTAATAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
31 7 0.16
32 37 0.84
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (32 bp):
AACTCAAAAACTGATCAATTTGATATTGATCT
Found at i:298258 original size:16 final size:15
Alignment explanation
Indices: 298211--298262 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
298201 ATATTGATCT
*
298211 AACTCAAAAATCGATC
1 AACT-AAAAATCAATC
* *
298227 AATCTAATAATAAATC
1 AA-CTAAAAATCAATC
298243 GAACTAAAAATCAATC
1 -AACTAAAAATCAATC
298259 AACT
1 AACT
298263 TGATATTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.54, C:0.19, G:0.04, T:0.23
Consensus pattern (15 bp):
AACTAAAAATCAATC
Found at i:300329 original size:16 final size:17
Alignment explanation
Indices: 300308--300350 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
300298 CATGTAAAAG
300308 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
300324 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
300341 AAATATTTAA
1 AAATATTTAA
300351 TCAAGTAGGA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:300500 original size:23 final size:24
Alignment explanation
Indices: 300457--300501 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
300447 AGTTTAAATA
*
300457 TTTAATAAATTATTATATATTTTT
1 TTTAATAAATAATTATATATTTTT
300481 TTTAA-AAATAATCTAT-TATTT
1 TTTAATAAATAAT-TATATATTT
300502 CAGCCTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTAATAAATAATTATATATTTTT
Found at i:305526 original size:10 final size:10
Alignment explanation
Indices: 305489--305565 Score: 62
Period size: 10 Copynumber: 8.4 Consensus size: 10
305479 AATTTAAATG
305489 TATAT-ATAA
1 TATATAATAA
305498 TAT-TAATAA
1 TATATAATAA
*
305507 TA-ATTA-AA
1 TATATAATAA
305515 TATATAATAA
1 TATATAATAA
* *
305525 TATATTATTA
1 TATATAATAA
305535 -ATA-AAT-A
1 TATATAATAA
305542 TATAT-ATATA
1 TATATAATA-A
305552 TATATAATAA
1 TATATAATAA
305562 TATA
1 TATA
305566 ATATTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
7 1 0.02
8 12 0.22
9 17 0.31
10 21 0.39
11 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATAATAA
Found at i:305527 original size:8 final size:8
Alignment explanation
Indices: 305492--305568 Score: 52
Period size: 8 Copynumber: 9.0 Consensus size: 8
305482 TTAAATGTAT
305492 ATATAATA
1 ATATAATA
*
305500 TTAATAATA
1 AT-ATAATA
305509 AT-TAA-A
1 ATATAATA
305515 TATATAATA
1 -ATATAATA
305524 ATATATTATTA
1 ATATA--A-TA
305535 ATA-AATA
1 ATATAATA
305542 TATATATATA
1 -ATATA-ATA
305552 TATATAATA
1 -ATATAATA
305561 ATATAATA
1 ATATAATA
305569 TTATTTTATA
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
6 1 0.02
7 7 0.12
8 21 0.37
9 12 0.21
10 11 0.19
11 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAATA
Found at i:305530 original size:29 final size:27
Alignment explanation
Indices: 305483--305568 Score: 93
Period size: 29 Copynumber: 3.1 Consensus size: 27
305473 CACGCAAATT
* *
305483 TAAATGTATATATAATATTAATAATAAT
1 TAAATATATATAT-ATATTAATAATAAA
*
305511 TAAATATATAATAATATATTATTAATAAA
1 TAAATATAT-AT-ATATATTAATAATAAA
*
305540 TATATATATATATATA-TAATAATATAA
1 TAAATATATATATATATTAATAATA-AA
305567 TA
1 TA
305569 TTATTTTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
26 7 0.14
27 9 0.18
28 10 0.20
29 22 0.44
30 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
TAAATATATATATATATTAATAATAAA
Found at i:305564 original size:37 final size:32
Alignment explanation
Indices: 305492--305571 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 32
305482 TTAAATGTAT
305492 ATATAATATTAATAATAATTAAATATATAATA
1 ATATAATATTAATAATAATTAAATATATAATA
*
305524 ATATATTATTAATAAATATATATATATATATATAATA
1 ATATAATATTAAT-AATA-AT-TA-A-ATATATAATA
305561 ATATAATATTA
1 ATATAATATTA
305572 TTTTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
32 12 0.29
33 4 0.10
34 2 0.05
35 2 0.05
36 1 0.02
37 20 0.49
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATTAATAATAATTAAATATATAATA
Done.