Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006073.1 Hibiscus syriacus cultivar Beakdansim tig00014377_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: 63321
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10783 original size:20 final size:20
Alignment explanation
Indices: 10727--10914 Score: 168
Period size: 20 Copynumber: 9.3 Consensus size: 20
10717 AAATTCGCGT
*
10727 TGCGATTTACGAAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
* * * *
10748 CGTGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
*
10769 TGTGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
10789 TGTGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
10809 TGTGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* * *
10829 TACGATTACGT-ATTCGCAT
1 TGCGATTACGTAAATCGCAA
*
10848 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
*
10868 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
* *
10888 TGCGATTTACGT-AATCACAT
1 TGCGA-TTACGTAAATCGCAA
10908 TGCGATT
1 TGCGATT
10915 TTCCTAATTC
Statistics
Matches: 152, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
19 12 0.08
20 120 0.79
21 19 0.12
22 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:10813 original size:40 final size:40
Alignment explanation
Indices: 10727--10977 Score: 177
Period size: 40 Copynumber: 6.2 Consensus size: 40
10717 AAATTCGCGT
* * * * *
10727 TGCGATTTACGAAAATCGCAACGTGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCG-ATTACG-TAATCGCAA
* *
10769 TGTGA-TTACGTAAATCGCAATGTGATTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGATTACGT-AATCGCAA
* * * *
10809 TGTGA-TTACGTAAATCGCAATACGATTACGTATTCGCAT
1 TGCGATTTACGTAAATCGCAATGCGATTACGTAATCGCAA
* *
10848 TGCGATTTACGT-AATCGCATTGCGATTTACGTAATCGCAT
1 TGCGATTTACGTAAATCGCAATGCGA-TTACGTAATCGCAA
* * * * * **
10888 TGCGATTTACGT-AATCACATTGCGATTTTCCTAATTCACGT
1 TGCGATTTACGTAAATCGCAATGCGA-TTACGTAA-TCGCAA
* * **
10929 TGCGATTTTCGTAAATCGCAACGCGAATTTGGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCG-ATTACGT-AATCGCAA
*
10971 TGAGATT
1 TGCGATT
10978 CTGACTATCG
Statistics
Matches: 174, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
39 21 0.12
40 92 0.53
41 32 0.18
42 26 0.15
43 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (40 bp):
TGCGATTTACGTAAATCGCAATGCGATTACGTAATCGCAA
Found at i:10836 original size:60 final size:61
Alignment explanation
Indices: 10727--10915 Score: 190
Period size: 60 Copynumber: 3.1 Consensus size: 61
10717 AAATTCGCGT
* * * * *
10727 TGCGATTTACGAAAATCGCAACGTGAATTAGGAAAATCGCAATGTGATTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGTG-ATTACGTAAATCGCAATGCGATTACGTAAATCGCAA
* * * *
10789 TGTGA-TTACGTAAATCGCAATGTGATTACGTAAATCGCAATACGATTACGT-ATTCGCAT
1 TGCGATTTACGTAAATCGCAATGTGATTACGTAAATCGCAATGCGATTACGTAAATCGCAA
* * * * *
10848 TGCGATTTACGT-AATCGCATTGCGATTTACGT-AATCGCATTGCGATTTACGT-AATCACAT
1 TGCGATTTACGTAAATCGCAATGTGA-TTACGTAAATCGCAATGCGA-TTACGTAAATCGCAA
10908 TGCGATTT
1 TGCGATTT
10916 TCCTAATTCA
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
59 32 0.30
60 55 0.51
61 17 0.16
62 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (61 bp):
TGCGATTTACGTAAATCGCAATGTGATTACGTAAATCGCAATGCGATTACGTAAATCGCAA
Found at i:10915 original size:20 final size:20
Alignment explanation
Indices: 10761--10948 Score: 168
Period size: 20 Copynumber: 9.3 Consensus size: 20
10751 GAATTAGGAA
* *
10761 AATCGCAATGTGA-TTACGT
1 AATCGCATTGCGATTTACGT
* *
10780 AAATCGCAATGTGA-TTACGT
1 -AATCGCATTGCGATTTACGT
* *
10800 AAATCGCAATGTGA-TTACGT
1 -AATCGCATTGCGATTTACGT
* *
10820 AAATCGCAATACGA-TTACGT
1 -AATCGCATTGCGATTTACGT
*
10840 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
10860 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
10880 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* * *
10900 AATCACATTGCGATTTTCCT
1 AATCGCATTGCGATTTACGT
* * *
10920 AATTCACGTTGCGATTTTCGT
1 AA-TCGCATTGCGATTTACGT
10941 AAATCGCA
1 -AATCGCA
10949 ACGCGAATTT
Statistics
Matches: 152, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
19 10 0.07
20 121 0.80
21 19 0.12
22 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:11883 original size:24 final size:24
Alignment explanation
Indices: 11826--11885 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
11816 TAGTCAGTAT
11826 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
11850 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
11874 TCGAATTTTGAT
1 TCGAAATTTGAT
11886 GATTTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:14436 original size:19 final size:20
Alignment explanation
Indices: 14355--14447 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 20
14345 GGCATTCATT
*
14355 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
14375 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
14396 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
14416 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
14435 TGAAAATCGCAAC
1 TGACTATCGCAAC
14448 AAGAGAATCA
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 15 0.27
20 27 0.48
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:14467 original size:33 final size:33
Alignment explanation
Indices: 14421--14547 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
14411 GGAAATGACT
*
14421 ATCGCAATGCGAAATGAAAATCGCAACAAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
14454 ATCACAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
14487 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
14520 ATCGCAAAGCGAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
14548 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:14510 original size:19 final size:19
Alignment explanation
Indices: 14401--14512 Score: 91
Period size: 19 Copynumber: 6.4 Consensus size: 19
14391 CTTAATGTCT
* **
14401 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
14421 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
14440 ATCGCAA--C--AA-GAGA
1 ATCGCAATGCGAAATGAAA
*
14454 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
14473 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
14487 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
14506 ATCGCAA
1 ATCGCAA
14513 CGAGGGAATC
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.26
15 3 0.04
16 3 0.04
17 3 0.04
18 3 0.04
19 33 0.45
20 9 0.12
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:14600 original size:19 final size:19
Alignment explanation
Indices: 14576--14622 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
14566 GTGATTTTGT
14576 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
14595 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTCATTTCG
*
14614 CATTGCGAT
1 CGTTGCGAT
14623 AGTCATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:14630 original size:19 final size:19
Alignment explanation
Indices: 14587--14630 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
14577 GTTGCGATTT
* **
14587 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
*
14606 TTATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
14625 TCATTT
1 TCATTT
14631 TTGCTTTCAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:16146 original size:21 final size:21
Alignment explanation
Indices: 16117--16197 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
16107 GAATGGTGGG
*
16117 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
16138 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
16159 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
16180 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
16198 AGGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:16179 original size:42 final size:41
Alignment explanation
Indices: 16102--16210 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
16092 GTGAATCGGG
* *
16102 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCAACGATGATAGGGGC
* *
16144 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCAACG-ATGATAGGGGC
* * * *
16186 CTCTTCAACGATAGGAGTGGACTCT
1 CTCTTGAACGGTGGGAGGGGACTCT
16211 TAAGGGATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
41 4 0.07
42 49 0.86
43 4 0.07
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCAACGATGATAGGGGC
Found at i:16682 original size:33 final size:33
Alignment explanation
Indices: 16645--16719 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
16635 AAAAATGACT
16645 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
* **
16678 ATCGCAACAAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
*
16711 ATTGCAACG
1 ATCGCAACG
16720 CGATTATAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACACGAAATGAAA
Found at i:16765 original size:20 final size:20
Alignment explanation
Indices: 16728--16765 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16718 CGCGATTATA
*
16728 GTTTCGCGTTGTGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
*
16748 GTTTCGCGTTGCGGTTTT
1 GTTTCGCGTTGCGATTTT
16766 CATTCTCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.32, T:0.53
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:16991 original size:94 final size:93
Alignment explanation
Indices: 16882--17161 Score: 435
Period size: 94 Copynumber: 3.1 Consensus size: 93
16872 ATGGATTGTA
* *
16882 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
16947 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
16975 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
17040 TTAGCAGAATTGGCATCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
17069 TTACTTCAACCAAAAGACAACA-AAAGACAAATATTAACTTCACAGTGTT----AATAAACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
* *
17129 TAGCAGTATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
17157 TTACT
1 TTACT
17162 AAGCAATCTA
Statistics
Matches: 176, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
88 40 0.23
92 26 0.15
93 21 0.12
94 89 0.51
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:18880 original size:20 final size:20
Alignment explanation
Indices: 18855--18917 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
18845 TTTTGGTTGA
18855 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
18875 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
18894 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
18915 AAT
1 AAT
18918 CGCAACGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:18944 original size:33 final size:33
Alignment explanation
Indices: 18853--18974 Score: 136
Period size: 33 Copynumber: 3.5 Consensus size: 33
18843 TCTTTTGGTT
18853 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
**
18892 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
18926 TAAATTAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
18959 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
18975 TGCGATTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
33 42 0.58
34 11 0.15
36 1 0.01
37 1 0.01
38 3 0.04
40 15 0.21
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:19019 original size:40 final size:39
Alignment explanation
Indices: 18975--19069 Score: 102
Period size: 41 Copynumber: 2.4 Consensus size: 39
18965 AAAATCGCAA
*
18975 TGCGATTTTGGTTTCGCGTTGCGATTTTCATTTCTC-TCGT
1 TGCGATTTTAGTTTCGCGTTGCGATTTTCATTT-TCAT-GT
* * * *
19015 TGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCATGT
1 TGCGAT-TTTAGTTTCGCGTTGCGATTTTCATTTTCATGT
19055 TGCGATTTTAAGTTT
1 TGCGATTTT-AGTTT
19070 AGAAACTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
39 1 0.02
40 20 0.45
41 23 0.52
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.51
Consensus pattern (39 bp):
TGCGATTTTAGTTTCGCGTTGCGATTTTCATTTTCATGT
Found at i:19038 original size:20 final size:20
Alignment explanation
Indices: 18986--19063 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
18976 GCGATTTTGG
*
18986 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
**
19006 TTCTC-TCGTTGCGATAGTCAT
1 TT-TCGT-GTTGCGATTTTCAT
19027 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
19047 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
19064 AAGTTTAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 32 0.65
21 17 0.35
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:19643 original size:21 final size:21
Alignment explanation
Indices: 19599--19735 Score: 136
Period size: 21 Copynumber: 6.7 Consensus size: 21
19589 GCTATGTAAA
** *
19599 TCGCATTGCGATAGT-CAGAT
1 TCGCATTGCGATTTTCCAAAT
*
19619 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
19640 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
* **
19661 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCAAAT
* * *
19681 TCGCATTGTGA-TTTACATAT
1 TCGCATTGCGATTTTCCAAAT
*
19701 TCGCATTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
19722 TCGCATTGCGATTT
1 TCGCATTGCGATTT
19736 ACGTATTCGC
Statistics
Matches: 94, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
19 3 0.03
20 32 0.34
21 59 0.63
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:19686 original size:20 final size:21
Alignment explanation
Indices: 19617--19748 Score: 146
Period size: 21 Copynumber: 6.4 Consensus size: 21
19607 CGATAGTCAG
* **
19617 ATTCGCATTGCGATTTCCCAA
1 ATTCGCATTGCGATTTACGTA
* * *
19638 ATTCGCGTTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTA
19659 ATTCGCATTGCGATTTACGTA
1 ATTCGCATTGCGATTTACGTA
* *
19680 A-TCGCATTGTGATTTACAT-
1 ATTCGCATTGCGATTTACGTA
*
19699 ATTCGCATTGCGATTTTCCG-A
1 ATTCGCATTGCGA-TTTACGTA
19720 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
19740 ATTCGCATT
1 ATTCGCATT
19749 ACGAATTTGG
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.01
20 40 0.42
21 54 0.57
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.39
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACGTA
Found at i:19725 original size:61 final size:62
Alignment explanation
Indices: 19619--19748 Score: 199
Period size: 61 Copynumber: 2.1 Consensus size: 62
19609 ATAGTCAGAT
* * *
19619 TCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTCACAAATTCGCATTGCGATTTTCCGAATTCGCATTGCGATTTACGTAA
* * *
19681 TCGCATTGTGATTT-ACATATTCGCATTGCGATTTTCCGAATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTCACAAATTCGCATTGCGATTTTCCGAATTCGCATTGCGATTTACGTAA
19742 TCGCATT
1 TCGCATT
19749 ACGAATTTGG
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 49 0.79
62 13 0.21
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (62 bp):
TCGCATTGCGATTTCACAAATTCGCATTGCGATTTTCCGAATTCGCATTGCGATTTACGTAA
Found at i:19767 original size:41 final size:41
Alignment explanation
Indices: 19596--19774 Score: 148
Period size: 41 Copynumber: 4.4 Consensus size: 41
19586 GGCGCTATGT
* * * *
19596 AAATCGCATTGCGATAGT-CAGATTCGCATTGCG-ATTTCCC
1 AAATCGCATTGCGAT-TTACATATTCGCATTACGAATTTCCG
* * * * *
19636 AAATTCGCGTTGCGATTTTCCTAATTCGCATTGCG-ATTTACG
1 AAA-TCGCATTGCGATTTACAT-ATTCGCATTACGAATTTCCG
* * * *
19678 TAATCGCATTGTGATTTACATATTCGCATTGCGATTTTCCG
1 AAATCGCATTGCGATTTACATATTCGCATTACGAATTTCCG
* * **
19719 AATTCGCATTGCGATTTACGTATTCGCATTACGAATTTGGG
1 AAATCGCATTGCGATTTACATATTCGCATTACGAATTTCCG
*
19760 AAATCGCAATGCGAT
1 AAATCGCATTGCGAT
19775 AGTCAGAATC
Statistics
Matches: 112, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
40 16 0.14
41 77 0.69
42 19 0.17
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (41 bp):
AAATCGCATTGCGATTTACATATTCGCATTACGAATTTCCG
Found at i:19792 original size:82 final size:82
Alignment explanation
Indices: 19596--19793 Score: 229
Period size: 82 Copynumber: 2.4 Consensus size: 82
19586 GGCGCTATGT
* *
19596 AAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAAT
1 AAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTCCCAAATTCGCATTGCGATTTACCTAAT
*
19661 TCGCATTGCGATTTACG
66 TCGCATTACGATTTACG
* * * * * * *
19678 TAATCGCATTGTGAT-TTACATATTCGCATTGCGATTTTCCGAATTCGCATTGCGATTTACGT-A
1 AAATCGCATTGCGATAGT-CAGATTCGCATTGCGATTTCCCAAATTCGCATTGCGATTTACCTAA
**
19741 TTCGCATTACGAATTTGGG
65 TTCGCATTACG-ATTTACG
* * *
19760 AAATCGCAATGCGATAGTCAGAATCGCGTTGCGA
1 AAATCGCATTGCGATAGTCAGATTCGCATTGCGA
19794 ATCTAGAAAC
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
81 12 0.13
82 81 0.86
83 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (82 bp):
AAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTCCCAAATTCGCATTGCGATTTACCTAAT
TCGCATTACGATTTACG
Found at i:20314 original size:41 final size:41
Alignment explanation
Indices: 20257--20338 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
20247 CCTTCGTGAA
20257 TCTTCAAGGTAAGGGAATGGAATGAGATTGCCACTAGGCTT
1 TCTTCAAGGTAAGGGAATGGAATGAGATTGCCACTAGGCTT
20298 TCTTCAAGGTAAGGGAATGGAATGAGATTGCCACTAGGCTT
1 TCTTCAAGGTAAGGGAATGGAATGAGATTGCCACTAGGCTT
20339 ACGATGTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (41 bp):
TCTTCAAGGTAAGGGAATGGAATGAGATTGCCACTAGGCTT
Found at i:27052 original size:15 final size:15
Alignment explanation
Indices: 27028--27109 Score: 137
Period size: 15 Copynumber: 5.5 Consensus size: 15
27018 TGAGACATTA
27028 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
27043 CCCACCCCGCATCCG
1 CCCGCCCCGCATCCG
*
27058 CCCGCCCCGCATCCT
1 CCCGCCCCGCATCCG
27073 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
27088 CCCGTCCCGCATCCG
1 CCCGCCCCGCATCCG
27103 CCCGCCC
1 CCCGCCC
27110 AGCTAAATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.07, C:0.67, G:0.17, T:0.09
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:28829 original size:21 final size:21
Alignment explanation
Indices: 28805--28854 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
28795 GATTACATAA
* *
28805 AATTTAATGATTATTTTGTAT
1 AATTTAATGATCATTTTATAT
28826 AATTCT-ATGATCATTTTATAT
1 AATT-TAATGATCATTTTATAT
28847 ATATTTAA
1 A-ATTTAA
28855 AAAAAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (21 bp):
AATTTAATGATCATTTTATAT
Found at i:32780 original size:21 final size:21
Alignment explanation
Indices: 32738--32780 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
32728 TTTATGGGCT
* * *
32738 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
32759 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
32780 A
1 A
32781 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:34133 original size:30 final size:29
Alignment explanation
Indices: 34094--34152 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
34084 GAGAATTTAC
* *
34094 ATGAACTACGTGATTACATGTATATGTGA
1 ATGAACTACGAGATTACATGAATATGTGA
* *
34123 ATGAAGCTACGAGCTTATATGAATATGTGA
1 ATGAA-CTACGAGATTACATGAATATGTGA
34153 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (29 bp):
ATGAACTACGAGATTACATGAATATGTGA
Found at i:34444 original size:23 final size:23
Alignment explanation
Indices: 34381--34449 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
34371 CATTATTATA
*
34381 TGGCACTACGGTGCAATTCTACG
1 TGGCACTATGGTGCAATTCTACG
* * * *
34404 CGGCACTCTGATGTAATTCTACG
1 TGGCACTATGGTGCAATTCTACG
* *
34427 TGGCACTTTGGTGCAATTATACG
1 TGGCACTATGGTGCAATTCTACG
34450 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTATGGTGCAATTCTACG
Found at i:42747 original size:25 final size:26
Alignment explanation
Indices: 42700--42751 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
42690 GAAGAATGAG
*
42700 AAAGGTTGTTCATTTTTTTGATTTTA
1 AAAGGTTGTTCATTTTTTCGATTTTA
42726 AAAGGTTGTTCA-TTTTTCGATTTTA
1 AAAGGTTGTTCATTTTTTCGATTTTA
42751 A
1 A
42752 TTGAATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (26 bp):
AAAGGTTGTTCATTTTTTCGATTTTA
Found at i:43960 original size:79 final size:79
Alignment explanation
Indices: 43826--43983 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
43816 ATCATTTCCA
*
43826 ACTTTTAAAATGAAAAAGGCCAAATCACATGTAAAATGGCCAACAAGTTGTTTTCAAAGAAATTA
1 ACTTTTAAAATGAAAAAGGCCAAATCACATGTAAAATGGCCAACAAGTTGCTTTCAAAGAAATTA
43891 CTTTTCATATTATC
66 CTTTTCATATTATC
43905 ACTTTTAAAATGAAAAAGGCCAAATCACATGTAAAATGGCCAACAAGTTGCTTTCAAAGAAATTA
1 ACTTTTAAAATGAAAAAGGCCAAATCACATGTAAAATGGCCAACAAGTTGCTTTCAAAGAAATTA
43970 CTTTTCATATTATC
66 CTTTTCATATTATC
43984 GTAGTAGTTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (79 bp):
ACTTTTAAAATGAAAAAGGCCAAATCACATGTAAAATGGCCAACAAGTTGCTTTCAAAGAAATTA
CTTTTCATATTATC
Found at i:45126 original size:15 final size:14
Alignment explanation
Indices: 45089--45130 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
45079 TATGCCCTAA
45089 TCTTAAATTGATAAC
1 TCTTAAATT-ATAAC
*
45104 -CCTAAATTATAATC
1 TCTTAAATTATAA-C
45118 TCTTAAATTATAA
1 TCTTAAATTATAA
45131 ACCCTAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 11 0.48
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (14 bp):
TCTTAAATTATAAC
Found at i:46216 original size:23 final size:23
Alignment explanation
Indices: 46156--46236 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
46146 TATAAATTTA
* **
46156 CACCGTAGTGCCACGTAGAGTTTG
1 CACCGAAGTGCCACGTAGA-AATG
46180 TC-CCGAAG-GACCACGTAGAAATG
1 -CACCGAAGTG-CCACGTAGAAATG
* *
46203 CATCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAAATG
*
46226 CACCGTAGTGC
1 CACCGAAGTGC
46237 TGTCGGAACC
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
22 1 0.02
23 29 0.63
24 15 0.33
25 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAAATG
Found at i:50088 original size:20 final size:20
Alignment explanation
Indices: 50058--50233 Score: 113
Period size: 20 Copynumber: 8.7 Consensus size: 20
50048 GTTTCCATAT
*
50058 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
50078 TCGCATTGCGATT-TCCCAAA
1 TCGCAATGCGATTCTGAC-TA
* * *
50098 TTCGTATTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
50121 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
50141 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
50161 GCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
50181 TCGCAACGAGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
* *
50201 TCGCAACGCGATTCTGACCA
1 TCGCAATGCGATTCTGACTA
50221 TCGCAATGCGATT
1 TCGCAATGCGATT
50234 TTCAAAGCGC
Statistics
Matches: 120, Mismatches: 29, Indels: 14
0.74 0.18 0.09
Matches are distributed among these distances:
19 3 0.03
20 93 0.77
21 11 0.09
22 9 0.08
23 3 0.03
24 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:50130 original size:22 final size:22
Alignment explanation
Indices: 50073--50131 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
50063 ACGCGATTCT
50073 GACTATCGCATTGCGATTTCCC
1 GACTATCGCATTGCGATTTCCC
* * * *
50095 AAAT-TCGTATTGCGATTTTCC
1 GACTATCGCATTGCGATTTCCC
*
50116 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
50132 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTCCC
Found at i:50567 original size:17 final size:18
Alignment explanation
Indices: 50533--50577 Score: 83
Period size: 17 Copynumber: 2.6 Consensus size: 18
50523 TTTACTCATA
50533 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
50551 ATTTCACTTAG-TTAACC
1 ATTTCACTTAGATTAACC
50568 ATTTCACTTA
1 ATTTCACTTA
50578 TATTGCTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:52642 original size:24 final size:24
Alignment explanation
Indices: 52608--52661 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
52598 CTGAAACATC
52608 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
52632 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
52656 ATCAAA
1 ATCAAA
52662 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:53535 original size:20 final size:20
Alignment explanation
Indices: 53476--53538 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
53466 AAATTCAGTG
*
53476 TTGCGACAGTCAGAATCGCG
1 TTGCGACAGTCAGAATCGCA
53496 TTGCGACAGTCAGAATCGCA
1 TTGCGACAGTCAGAATCGCA
*
53516 TTGCGATAGTCAGAATCGCA
1 TTGCGACAGTCAGAATCGCA
53536 TTG
1 TTG
53539 TGATTTACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (20 bp):
TTGCGACAGTCAGAATCGCA
Found at i:53554 original size:20 final size:20
Alignment explanation
Indices: 53531--53631 Score: 166
Period size: 20 Copynumber: 5.0 Consensus size: 20
53521 ATAGTCAGAA
*
53531 TCGCATTGTGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
53551 TCGCATTGCAATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
53571 TCGTATTGCGATTTACATAC
1 TCGCATTGCGATTTACATAT
53591 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
53611 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
53631 T
1 T
53632 TGAATAACAA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:55650 original size:20 final size:21
Alignment explanation
Indices: 55625--55669 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
55615 ACATTCACAT
55625 AAATAAATATTAT-AATA-ATA
1 AAATAAA-ATTATAAATATATA
*
55645 AAATAAAATTTTAAATATATA
1 AAATAAAATTATAAATATATA
55666 AAAT
1 AAAT
55670 TTACGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 11 0.50
21 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAAATTATAAATATATA
Done.