Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008714.1 Hibiscus syriacus cultivar Beakdansim tig00111767_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: 59186
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4121 original size:12 final size:12
Alignment explanation
Indices: 4106--4154 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
4096 AGAAAATAAA
*
4106 AAGAATAAGAAT
1 AAGAATAAAAAT
*
4118 AAGAATAAGAAT
1 AAGAATAAAAAT
4130 AAGAATAAAAAT
1 AAGAATAAAAAT
4142 AA-AATAAAAAT
1 AAGAATAAAAAT
4153 AA
1 AA
4155 TTAATGTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
11 11 0.31
12 25 0.69
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.16
Consensus pattern (12 bp):
AAGAATAAAAAT
Found at i:4129 original size:18 final size:18
Alignment explanation
Indices: 4106--4154 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
4096 AGAAAATAAA
*
4106 AAGAATAAGAATAAGAAT
1 AAGAATAAGAATAAAAAT
4124 AAGAATAAGAATAAAAAT
1 AAGAATAAGAATAAAAAT
*
4142 AA-AATAAAAATAA
1 AAGAATAAGAATAA
4155 TTAATGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.16
Consensus pattern (18 bp):
AAGAATAAGAATAAAAAT
Found at i:4697 original size:19 final size:18
Alignment explanation
Indices: 4649--4707 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
4639 AAAGATAATA
* *
4649 AAAAATATTAATATAAAG
1 AAAAATAATAAAATAAAG
*
4667 AAAAAAAATAAAATAATAG
1 AAAAATAATAAAATAA-AG
* *
4686 ATAAATAATAAAATAAAT
1 AAAAATAATAAAATAAAG
4704 AAAA
1 AAAA
4708 TTGAGTAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 17 0.52
19 16 0.48
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAAATAATAAAATAAAG
Found at i:5144 original size:7 final size:7
Alignment explanation
Indices: 5132--5157 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5122 TCTCAGTCCC
5132 CTCATTT
1 CTCATTT
5139 CTCATTT
1 CTCATTT
5146 CTCATTT
1 CTCATTT
5153 CTCAT
1 CTCAT
5158 ATCCTCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (7 bp):
CTCATTT
Found at i:6190 original size:37 final size:36
Alignment explanation
Indices: 6133--6583 Score: 559
Period size: 37 Copynumber: 12.1 Consensus size: 36
6123 CAAAAACTAA
* * *
6133 AAAATATTTTAAAAATTATATATTATATGT-TTTTC
1 AAAATGTTTTAAAAACTATATATTATATATATTTTC
*
6168 AAAACCGATTTTAAAAACTATATATTATATATACTTTTC
1 AAAA-TG-TTTTAAAAACTATATATTATATATA-TTTTC
*
6207 AAAATGTTTTCAAAACTATATATTATATATATATATATATTC
1 AAAATGTTTTAAAAAC--TATA-TAT-TATATATAT-T-TTC
*
6249 AAAATGTTTTCAAAACTATATATTATATATA-TTTC
1 AAAATGTTTTAAAAACTATATATTATATATATTTTC
*
6284 AAAATGTTTTAAAAACTATATATTATATAAATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATATTTTC
*
6320 AAAATGTTTTAAAAACTATATATTATGTATTTATTTTC
1 AAAATGTTTTAAAAACTATATATTA--TATATATTTTC
6358 AAAATGTTTTAAAAAACTATATATTATATA-ATTTTTC
1 AAAATGTTTT-AAAAACTATATATTATATATA-TTTTC
*
6395 AAAATGTTTTAAAAACTATATATTATATATATATTTTT
1 AAAATGTTTTAAAAACTATATA-T-TATATATATTTTC
* *
6433 AAAATGTTTTAAAAAATATA-ATTATATATATATTTT
1 AAAATGTTTTAAAAACTATATATTATATATAT-TTTC
*
6469 AAAATGTTTTGAAAACTATATATTATATATATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATATTTTC
* *
6505 AAAAACGTTTTAAAAACTATATATATATATATATATTC
1 -AAAATGTTTTAAAAACTATATAT-TATATATATTTTC
* *
6543 AAAGTGTTTTAAAAACTATATATTATATATATATTTT
1 AAAATGTTTTAAAAACTATATATTATATATAT-TTTC
6580 AAAA
1 AAAA
6584 AATTTATTTA
Statistics
Matches: 369, Mismatches: 24, Indels: 44
0.84 0.05 0.10
Matches are distributed among these distances:
35 45 0.12
36 78 0.21
37 109 0.30
38 69 0.19
39 32 0.09
40 8 0.02
41 9 0.02
42 19 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATATTATATATATTTTC
Found at i:8681 original size:21 final size:21
Alignment explanation
Indices: 8655--8694 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8645 CCAGAATGGG
*
8655 GGGAATCGATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
8676 GGGAATCAATACCCCTTCA
1 GGGAATCAATACCCCTTCA
8695 AATATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (21 bp):
GGGAATCAATACCCCTTCATA
Found at i:8829 original size:19 final size:19
Alignment explanation
Indices: 8801--8867 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
8791 GAGCCTCGGG
* * *
8801 TTACTGTTCAAACAGTGAT
1 TTACTATTCAAATAGTAAT
8820 TTACTATTCAAATAGTAAT
1 TTACTATTCAAATAGTAAT
* *
8839 TTACTGTTCAAATAGTAAA
1 TTACTATTCAAATAGTAAT
8858 TTACTATTCA
1 TTACTATTCA
8868 TAAAAACATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (19 bp):
TTACTATTCAAATAGTAAT
Found at i:8964 original size:29 final size:31
Alignment explanation
Indices: 8932--8991 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
8922 AAATTTTGAA
*
8932 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
8961 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
8992 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:11513 original size:21 final size:21
Alignment explanation
Indices: 11487--11528 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11477 CCAGAATGGG
*
11487 GGGAATCGATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
11508 GGGAATCAATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
11529 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
GGGAATCAATACCCCTTCATA
Found at i:11658 original size:19 final size:19
Alignment explanation
Indices: 11634--11700 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
11624 GAGCCTCGGG
*
11634 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
11653 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
11672 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
11691 TTACTATTCA
1 TTACTGTTCA
11701 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:11797 original size:29 final size:31
Alignment explanation
Indices: 11765--11824 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
11755 AAATTTTGAA
*
11765 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
11794 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
11825 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:11939 original size:20 final size:21
Alignment explanation
Indices: 11909--11947 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11899 ATACCCTAGG
11909 TAAGAGAAGTATCAATACTCT
1 TAAGAGAAGTATCAATACTCT
*
11930 TAAG-GAAGTATCGATACT
1 TAAGAGAAGTATCAATACT
11948 ACCGACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (21 bp):
TAAGAGAAGTATCAATACTCT
Found at i:15655 original size:15 final size:15
Alignment explanation
Indices: 15631--15673 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
15621 TTATATCTCA
15631 TCTT-ATTTCTCTTC
1 TCTTCATTTCTCTTC
15645 TCTTCATTTCTTCTTC
1 TCTTCATTTC-TCTTC
15661 -CTTCATCTTCTCT
1 TCTTCAT-TTCTCT
15674 AAGTAGCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.15
15 14 0.54
16 8 0.31
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (15 bp):
TCTTCATTTCTCTTC
Found at i:18095 original size:22 final size:22
Alignment explanation
Indices: 18038--18096 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
18028 ACGCGATTCT
18038 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
18060 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
18081 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
18097 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:18110 original size:20 final size:20
Alignment explanation
Indices: 18085--18141 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
18075 TTTTCCGACT
18085 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
18105 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
18125 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
18142 ACTATTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:18151 original size:20 final size:20
Alignment explanation
Indices: 18128--18191 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
18118 TATGTAAATC
* *
18128 GCAATGCGATTATGACTATT
1 GCAATGCGATTCTGACTGTT
*
18148 GCAATGCGATTCTGACTGTC
1 GCAATGCGATTCTGACTGTT
*
18168 GCAACGCGATTCTGACTGTT
1 GCAATGCGATTCTGACTGTT
18188 GCAA
1 GCAA
18192 CACTGAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (20 bp):
GCAATGCGATTCTGACTGTT
Found at i:19063 original size:24 final size:24
Alignment explanation
Indices: 19012--19065 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
19002 GTATTCGAAA
*
19012 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
19036 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
19060 TTTGAT
1 TTTGAT
19066 GATGTTTCAG
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):
TTTGATCTTGGTCAATACCCAGAC
Found at i:19287 original size:14 final size:14
Alignment explanation
Indices: 19268--19294 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19258 GAATAAGAAA
19268 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
19282 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
19295 ATGCCACGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:20737 original size:18 final size:19
Alignment explanation
Indices: 20714--20800 Score: 113
Period size: 20 Copynumber: 4.5 Consensus size: 19
20704 GAAACTTAAA
*
20714 ATCGCAACACG-AATGACT
1 ATCGCAACGCGAAATGACT
20732 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
20752 ATCACAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
20772 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
20792 ATCGCAACG
1 ATCGCAACG
20801 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.16
19 2 0.03
20 50 0.81
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:20750 original size:20 final size:20
Alignment explanation
Indices: 20725--20800 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
20715 TCGCAACACG
20725 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
20745 AATGACTATCACAACGCGAA
1 AATGACTATCGCAACGCGAA
20765 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
20785 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
20801 AGAGAATCGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:21041 original size:18 final size:18
Alignment explanation
Indices: 21018--21067 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
21008 TTTACTAAGC
21018 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
21036 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
21054 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
21068 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:22737 original size:20 final size:20
Alignment explanation
Indices: 22714--22820 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
22704 TCTGAAACTT
22714 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
22734 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
22754 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
22774 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
22793 AAAATCGCAACACGAAACT-
1 AAAATCGCAACACGAAAATG
22812 AAAATCGCA
1 AAAATCGCA
22821 TTGCGATTCT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
19 23 0.32
20 50 0.68
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:23233 original size:22 final size:22
Alignment explanation
Indices: 23206--23248 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23196 GAGATAGACG
23206 GATTTCGACGGAGATGGGGACT
1 GATTTCGACGGAGATGGGGACT
** *
23228 GATTTCGTTGGAGGTGGGGAC
1 GATTTCGACGGAGATGGGGAC
23249 AGATGTCGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.12, G:0.44, T:0.26
Consensus pattern (22 bp):
GATTTCGACGGAGATGGGGACT
Found at i:23449 original size:20 final size:20
Alignment explanation
Indices: 23423--23578 Score: 109
Period size: 20 Copynumber: 7.7 Consensus size: 20
23413 GTGCTTTGAA
23423 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
23443 CATCGCATTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
23463 AATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
23483 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
23503 ATTCGCATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTC--AG
** * * *
23525 AATCGCAACGCGA-ATTTGGAA
1 AATCGCATTGCGATA-GT-CAG
*
23546 AATCGCAATGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
23566 AATCGCGTTGCGA
1 AATCGCATTGCGA
23579 ATCTGGAAAC
Statistics
Matches: 106, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
19 1 0.01
20 75 0.71
21 17 0.16
22 13 0.12
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:23843 original size:80 final size:81
Alignment explanation
Indices: 23749--23899 Score: 223
Period size: 80 Copynumber: 1.9 Consensus size: 81
23739 TTTTTATTAT
* * * *
23749 TTTTTTTAATATTTTTGGTAAAAAATTACCTAAAATATTA-TTATTTCTACTGATTTTGTTATTA
1 TTTTGTTAACATTTTCGGTAAAAAACTACCTAAAATATTATTTATTTCTACTGATTTTGTTATTA
23813 TTGGGCGTTTTATCGG
66 TTGGGCGTTTTATCGG
*** *
23829 TTTTGTTAACATTTTCGGTAAAGTGCTACCTAAAATATTATTTTTTTCTACTGATTTTGTTATTA
1 TTTTGTTAACATTTTCGGTAAAAAACTACCTAAAATATTATTTATTTCTACTGATTTTGTTATTA
23894 TTGGGC
66 TTGGGC
23900 ACTTTACAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
80 33 0.53
81 29 0.47
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (81 bp):
TTTTGTTAACATTTTCGGTAAAAAACTACCTAAAATATTATTTATTTCTACTGATTTTGTTATTA
TTGGGCGTTTTATCGG
Found at i:24212 original size:59 final size:58
Alignment explanation
Indices: 24149--24260 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
24139 AATTATAGGA
* ** *
24149 ATTGTATTGTTAAGTCTCCTGACTATTATAAGTTACAAAATGATC-TCCAATTATATAAT
1 ATTGTATTGTTAACTC-CCCAACTATTA-AACTTACAAAATGATCGTCCAATTATATAAT
* * *
24208 ATTGTTTTGTTAACTCCCCAACTATTAAACTTAGAAAATGATCGTCTAATTAT
1 ATTGTATTGTTAACTCCCCAACTATTAAACTTACAAAATGATCGTCCAATTAT
24261 TCATATGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
57 14 0.31
58 17 0.38
59 14 0.31
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (58 bp):
ATTGTATTGTTAACTCCCCAACTATTAAACTTACAAAATGATCGTCCAATTATATAAT
Found at i:25775 original size:2 final size:2
Alignment explanation
Indices: 25768--25797 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25758 TTCTTTAATC
25768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25798 TCATATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27932 original size:34 final size:34
Alignment explanation
Indices: 27863--27967 Score: 126
Period size: 34 Copynumber: 3.1 Consensus size: 34
27853 AAAGTAAATC
* *
27863 TAAA-TAA-TAAT-TATTTATTATTAATAAAATAA
1 TAAATTAACTAATCTATTTATTTTTTA-AAAATAA
*
27895 TAAATTAACTAATCTATTTATTTTTTAAAAATGA
1 TAAATTAACTAATCTATTTATTTTTTAAAAATAA
**
27929 TAAATTAACTAATCTATCAATTTTTTAATAAATAA
1 TAAATTAACTAATCTATTTATTTTTTAA-AAATAA
27964 TAAA
1 TAAA
27968 ATATTATTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
32 4 0.06
33 3 0.05
34 36 0.57
35 20 0.32
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (34 bp):
TAAATTAACTAATCTATTTATTTTTTAAAAATAA
Found at i:28709 original size:20 final size:21
Alignment explanation
Indices: 28684--28776 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
28674 TTTTCCCAAT
*
28684 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28704 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
28725 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28745 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
28766 TCGCAATGCGA
1 TCGCAATGCGA
28777 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:28729 original size:41 final size:41
Alignment explanation
Indices: 28684--28776 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
28674 TTTTCCCAAT
28684 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
28725 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
28766 TCGCAATGCGA
1 TCGCAATGCGA
28777 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:28789 original size:41 final size:41
Alignment explanation
Indices: 28703--28837 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
28693 GAATAAGTAA
** *
28703 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
28744 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
28785 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
28826 TTCGCAACGCGA
1 ATCGCAACGCGA
28838 TTCTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:28855 original size:20 final size:20
Alignment explanation
Indices: 28807--28859 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
28797 TAATACAAAA
* *
28807 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
28827 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
28847 TCGCAACGCGATT
1 TCGCAACGCGATT
28860 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:29479 original size:20 final size:19
Alignment explanation
Indices: 29433--29598 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
29423 GAAACCAAAA
*
29433 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
29452 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
29471 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
29491 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
29507 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
29524 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
29538 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
29557 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
29577 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
29597 TC
1 TC
29599 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:29514 original size:39 final size:39
Alignment explanation
Indices: 29438--29514 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
29428 CAAAATCGCA
* **
29438 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
29477 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
29515 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:29523 original size:33 final size:33
Alignment explanation
Indices: 29486--29573 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
29476 GTTGCGATTT
* *
29486 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
29519 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
29552 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
29574 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:31653 original size:42 final size:42
Alignment explanation
Indices: 31593--31715 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
31583 GCCCGACTCG
* * *
31593 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* ** *
31635 CCTATCATTCCTTGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
31677 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
31716 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:31673 original size:21 final size:21
Alignment explanation
Indices: 31649--31715 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
31639 TCATTCCTTG
31649 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
31670 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
31691 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
31712 AGAG
1 AGAG
31716 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:33094 original size:14 final size:14
Alignment explanation
Indices: 33075--33110 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33065 ATTGTTTAAT
33075 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
33089 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
33103 TGATTTGT
1 TGATTTGT
33111 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:33311 original size:19 final size:19
Alignment explanation
Indices: 33289--33439 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
33279 CGAAATTAAA
33289 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
33308 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
33323 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
33341 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
* *
33355 TTAGCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
33374 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
33389 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
33407 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
33426 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
33440 GGACATTAAG
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:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:33335 original size:33 final size:32
Alignment explanation
Indices: 33293--33419 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
33283 ATTAAATTCG
33293 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
33326 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
33359 CGTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
33392 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
33420 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:33382 original size:66 final size:66
Alignment explanation
Indices: 33286--33418 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
33276 ACGCGAAATT
* *
33286 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
33351 G
66 G
*
33352 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
33417 G
66 G
33418 A
1 A
33419 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:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:33656 original size:12 final size:12
Alignment explanation
Indices: 33641--33665 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33631 ATTTTAAAGA
33641 TGATTGCCTTTT
1 TGATTGCCTTTT
33653 TGATTGCCTTTT
1 TGATTGCCTTTT
33665 T
1 T
33666 CTTGACACCA
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:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (12 bp):
TGATTGCCTTTT
Found at i:36786 original size:33 final size:33
Alignment explanation
Indices: 36744--36806 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
36734 TCATTTGACC
* *
36744 ATCGCAATGCGAAATGCAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAAACGCAACGATAGA
*
36777 ATCGCAATGCGAAATGAAAAAGGCAACGAT
1 ATCGCAATGCGAAATGAAAAACGCAACGAT
36807 GATTAACATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAAACGCAACGATAGA
Found at i:37079 original size:20 final size:20
Alignment explanation
Indices: 37022--37070 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
37012 ATTCATTTGA
37022 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
37042 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
37062 TTATCGCAA
1 CTATCGCAA
37071 TGAGAAAATC
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:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:37139 original size:19 final size:19
Alignment explanation
Indices: 37117--37184 Score: 127
Period size: 19 Copynumber: 3.6 Consensus size: 19
37107 GATTTTCTCG
37117 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
37136 TTGCGCTTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37155 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37174 TTGCGATTTTC
1 TTGCGATTTTC
37185 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:39221 original size:20 final size:19
Alignment explanation
Indices: 39186--39252 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
39176 GAAACTTAAA
*
39186 ATCGCAACACGAAATGACT
1 ATCGCAACGCGAAATGACT
*
39205 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
39225 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
39244 ATCGCAACG
1 ATCGCAACG
39253 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:39260 original size:14 final size:14
Alignment explanation
Indices: 39241--39298 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
39231 ATGCGAAATG
*
39241 AAAATCGCAACGAC
1 AAAATCGCAACGAA
39255 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
39271 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
*
39287 AAAATTGCAACG
1 AAAATCGCAACG
39299 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.53
16 9 0.24
18 9 0.24
ACGTcount: A:0.50, C:0.21, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:39283 original size:32 final size:33
Alignment explanation
Indices: 39225--39315 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
39215 GGAAATGGCT
*
39225 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
39258 ATCGCAATGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
* *
39290 ATTGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
39316 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:39351 original size:14 final size:14
Alignment explanation
Indices: 39332--39389 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
39322 TTGTGTTTCG
39332 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
39346 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
39362 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
39378 CGTTGCGATTTT
1 CGTTGCGATTTT
39390 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:39366 original size:32 final size:33
Alignment explanation
Indices: 39327--39405 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
39317 GCGATTTGTG
39327 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
39359 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
39392 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
39406 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:39404 original size:19 final size:17
Alignment explanation
Indices: 39327--39405 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
39317 GCGATTTGTG
39327 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
39343 TGTCG-TTGCGATTTCA
1 TTTCGCTTGCGATTTCA
39359 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
39375 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
39392 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
39406 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.30
15 3 0.06
16 12 0.24
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:39412 original size:19 final size:20
Alignment explanation
Indices: 39390--39433 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39380 TTGCGATTTT
*
39390 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTACGATAGC
* *
39409 CATTTCCGCGTTACGATAGT
1 CATTTCCGCATTACGATAGC
39429 CATTT
1 CATTT
39434 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTACGATAGC
Found at i:41616 original size:22 final size:22
Alignment explanation
Indices: 41591--41634 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41581 GATTTAGATA
41591 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
41613 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
41635 TGAGAGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:41847 original size:20 final size:20
Alignment explanation
Indices: 41822--41874 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
41812 GATTATGTAT
41822 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
41842 TATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
41862 TATCTCGTTGCGA
1 TATCGCGTTGCGA
41875 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:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:41887 original size:41 final size:41
Alignment explanation
Indices: 41842--41919 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
41832 CGAAAGTCAG
* * * *
41842 TATCGCGTTGCAAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTTGTAT
* *
41883 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTT
41920 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:41908 original size:20 final size:19
Alignment explanation
Indices: 41802--41916 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
41792 CGCTTTGAAA
*
41802 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* *
41823 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * *
41843 ATCGCGTTGCAAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
41863 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
41884 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
41904 ATCGCATTGCGAT
1 ATCGCATTGCGAT
41917 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.06
20 47 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:41934 original size:21 final size:21
Alignment explanation
Indices: 41905--41997 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
41895 ATAGTAAGTA
41905 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
41926 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
41946 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
41967 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
41987 TCGCATTGCGA
1 TCGCATTGCGA
41998 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:41935 original size:41 final size:41
Alignment explanation
Indices: 41885--41997 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 41
41875 TTTTGTATTA
*
41885 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGAT-GTAAGTATTCGCATTGCGATTTTCCCAAT
* **
41926 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
* **
41967 TCGCGTTGCGATTTACTTATTCGCATTGCGA
1 TCGCGTTGCGATGTAAGTATTCGCATTGCGA
41998 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 4 0.06
41 63 0.94
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
Found at i:44265 original size:43 final size:43
Alignment explanation
Indices: 44196--44287 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
44186 TTAAGAATAC
* *
44196 TTTTAATATGTTAGTTTGTTGTATTTGCGGATTGTTAC-TCTAG
1 TTTTAATATGTTAGTTTGGTGAATTTGCGGATTGTTACAT-TAG
* * *
44239 TTTTAATTTGTTGGTTTGGTGAATTTGTGGATTGTTACATTAG
1 TTTTAATATGTTAGTTTGGTGAATTTGCGGATTGTTACATTAG
44282 TTTTAA
1 TTTTAA
44288 GGGTAAAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.54
Consensus pattern (43 bp):
TTTTAATATGTTAGTTTGGTGAATTTGCGGATTGTTACATTAG
Found at i:44489 original size:31 final size:31
Alignment explanation
Indices: 44416--44493 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
44406 CAGTTACGTT
44416 GGGGATCATATTGCAAACAGACTAAATGTTA
1 GGGGATCATATTGCAAACAGACTAAATGTTA
* * * *
44447 GGGTACCATATTGCAAACGGACTAAATGTTG
1 GGGGATCATATTGCAAACAGACTAAATGTTA
*
44478 GGGGATTATATTGCAA
1 GGGGATCATATTGCAA
44494 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGGATCATATTGCAAACAGACTAAATGTTA
Found at i:45127 original size:56 final size:56
Alignment explanation
Indices: 45057--45171 Score: 167
Period size: 56 Copynumber: 2.1 Consensus size: 56
45047 ATTTTACCTA
* ** * * *
45057 ACATGCCAGGATCCGACTGAATTCTGACTGATTACCTGATTTTATAGCTTTAACTG
1 ACATGCCAGAATCCGACTGAAACCTGACCGATTACCTGATTTGACAGCTTTAACTG
*
45113 ACATGTCAGAATCCGACTGAAACCTGACCGATTACCTGATTTGACAGCTTTAACTG
1 ACATGCCAGAATCCGACTGAAACCTGACCGATTACCTGATTTGACAGCTTTAACTG
45169 ACA
1 ACA
45172 CCTTCTTGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (56 bp):
ACATGCCAGAATCCGACTGAAACCTGACCGATTACCTGATTTGACAGCTTTAACTG
Found at i:45609 original size:31 final size:31
Alignment explanation
Indices: 45574--45637 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
45564 AATACATTCC
45574 CCCAACATTTAGT-TCGTTTACAATATGGTCT
1 CCCAACATTTAGTCT-GTTTACAATATGGTCT
*
45605 CCCAACATTTAGTCTGTTTGCAATATGGTCT
1 CCCAACATTTAGTCTGTTTACAATATGGTCT
45636 CC
1 CC
45638 AATGTAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (31 bp):
CCCAACATTTAGTCTGTTTACAATATGGTCT
Found at i:48708 original size:32 final size:32
Alignment explanation
Indices: 48651--48714 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
48641 GATACTCAGC
*
48651 ATTCCTACTTCATTTTTGACTTCATATAATGT
1 ATTCCTACTTCATTTTTGACTTCATACAATGT
* *
48683 ATTCCTACTTGATTTTTTA-TGTCATACAATGT
1 ATTCCTACTTCATTTTTGACT-TCATACAATGT
48715 TCTGTAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (32 bp):
ATTCCTACTTCATTTTTGACTTCATACAATGT
Found at i:51066 original size:3 final size:3
Alignment explanation
Indices: 51058--51089 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
51048 TTGCCCCCCT
51058 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
51090 ATTGCCACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:54208 original size:103 final size:105
Alignment explanation
Indices: 54030--54230 Score: 316
Period size: 104 Copynumber: 1.9 Consensus size: 105
54020 TTGATACAAT
* * *
54030 TATCAATATAAATTGTGATGAATTTGTTTGACACTAAAAATATATTTTGTGACCACCAATATTAT
1 TATCAATAAAAATTATGATAAATTTGTTTGACACTAAAAATATATTTTGTGACCACCAATATTAT
*
54095 CACACTAAGTA-ATATTTAGTGACCAACTGTTCGATACTA
66 CACACTAAGTATATATTTAGTGACCAAATGTTCGATACTA
* *
54134 TATCAATAAAAATTATGATAAATTTGTTTGACACTAAAAA-ATATTTTGTGATCACCAATGTTAT
1 TATCAATAAAAATTATGATAAATTTGTTTGACACTAAAAATATATTTTGTGACCACCAATATTAT
* *
54198 CACACTAAGTATTTTTTTAGTGACCAAATGTTC
66 CACACTAAGTATATATTTAGTGACCAAATGTTC
54231 ACACTATTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 33 0.38
104 55 0.62
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (105 bp):
TATCAATAAAAATTATGATAAATTTGTTTGACACTAAAAATATATTTTGTGACCACCAATATTAT
CACACTAAGTATATATTTAGTGACCAAATGTTCGATACTA
Found at i:54974 original size:21 final size:21
Alignment explanation
Indices: 54948--54993 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
54938 AATTTTTGGG
*
54948 CAAGGGGAATCAATACCCATT
1 CAAGGGGAACCAATACCCATT
* *
54969 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCAATACCCATT
54990 CAAG
1 CAAG
54994 CGAACAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCAATACCCATT
Found at i:55069 original size:22 final size:23
Alignment explanation
Indices: 55025--55069 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
55015 AATGTCATGG
*
55025 GGGAACCGGATACCCCCATAGGA
1 GGGAACCGGATACCCCCAAAGGA
* *
55048 GGGAACC-GATTCCCCTAAAGGA
1 GGGAACCGGATACCCCCAAAGGA
55070 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.31, C:0.29, G:0.29, T:0.11
Consensus pattern (23 bp):
GGGAACCGGATACCCCCAAAGGA
Found at i:56682 original size:23 final size:23
Alignment explanation
Indices: 56641--56698 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
56631 ATTATTATAT
56641 GGCACTACGGT--AATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
56662 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
56685 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
56699 TTTATATGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 11 0.33
23 22 0.67
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Done.