Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004337.1 Hibiscus syriacus cultivar Beakdansim tig00009506_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: 62975
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:4233 original size:3 final size:3
Alignment explanation
Indices: 4225--4305 Score: 135
Period size: 3 Copynumber: 27.0 Consensus size: 3
4215 CTATTGATAA
4225 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
4273 TAT TAT TAT TAT TGT TGT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4306 AAATGGATGT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4704 original size:47 final size:48
Alignment explanation
Indices: 4635--4731 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 48
4625 GGAATGGTGA
*
4635 TGATTCAAACTTTTGTGCA-CCCCTTAGTCTTGCCATAACAATCTTAT
1 TGATTCAAACTTTTGTGCACCCCCTTAGTCTGGCCATAACAATCTTAT
*
4682 TGATTCAAACTTTTGTGCACCCCCCTTAGTGTGGCCATAACAATCTTAT
1 TGATTCAAACTTTTGTGCA-CCCCCTTAGTCTGGCCATAACAATCTTAT
4731 T
1 T
4732 CTTAGTGACA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 19 0.41
49 27 0.59
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (48 bp):
TGATTCAAACTTTTGTGCACCCCCTTAGTCTGGCCATAACAATCTTAT
Found at i:5196 original size:35 final size:36
Alignment explanation
Indices: 5134--5214 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 36
5124 TTAAAACTTG
* *
5134 CAAAATAATCCTCAATTTTATTTTAAACCCCAAATTC
1 CAAAATAAT-CTCAATTATATTATAAACCCCAAATTC
5171 CAAAATAAT-TCAATTATATTATAAACCCCAAATTC
1 CAAAATAATCTCAATTATATTATAAACCCCAAATTC
5206 CAAAATAAT
1 CAAAATAAT
5215 ATTGAGTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 33 0.79
37 9 0.21
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (36 bp):
CAAAATAATCTCAATTATATTATAAACCCCAAATTC
Found at i:5763 original size:34 final size:35
Alignment explanation
Indices: 5697--5775 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 35
5687 TGGTTAACTC
* **
5697 AATGTTATTGAAGTATTTTAGAATTTTTGGTTTAG
1 AATGTAATTGAAGTATTTTAGAATTTGGGGTTTAG
* *
5732 AATGTAATTGAATTA-TTTGGAATTTGGGGTTTAG
1 AATGTAATTGAAGTATTTTAGAATTTGGGGTTTAG
*
5766 AATGAAATTG
1 AATGTAATTG
5776 GTTAACTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
34 25 0.66
35 13 0.34
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.46
Consensus pattern (35 bp):
AATGTAATTGAAGTATTTTAGAATTTGGGGTTTAG
Found at i:5831 original size:34 final size:34
Alignment explanation
Indices: 5793--5864 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
5783 CAATGTTATT
** *
5793 TTGAAGTATTTTAGAATTTTTGG-TTAGAATGTAA
1 TTGAAGTA-TTTAGAATTTGGGGTTTAGAATGAAA
* *
5827 TTGAATTATTTGGAATTTGGGGTTTAGAATGAAA
1 TTGAAGTATTTAGAATTTGGGGTTTAGAATGAAA
5861 TTGA
1 TTGA
5865 GGATTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (34 bp):
TTGAAGTATTTAGAATTTGGGGTTTAGAATGAAA
Found at i:5847 original size:88 final size:87
Alignment explanation
Indices: 5686--5863 Score: 331
Period size: 88 Copynumber: 2.0 Consensus size: 87
5676 ACATGAAATC
5686 TTGGTTAACTCAATGTTATTGAAGTATTTTAGAATTTTTGGTTTAGAATGTAATTGAATTATTTG
1 TTGGTTAACTCAATGTTATTGAAGTATTTTAGAATTTTTGGTTTAGAATGTAATTGAATTATTTG
5751 GAATTTGGGGTTTAGAATGAAA
66 GAATTTGGGGTTTAGAATGAAA
5773 TTGGTTAACTCAATGTTATTTTGAAGTATTTTAGAATTTTTGG-TTAGAATGTAATTGAATTATT
1 TTGGTTAACTCAATGTTA--TTGAAGTATTTTAGAATTTTTGGTTTAGAATGTAATTGAATTATT
5837 TGGAATTTGGGGTTTAGAATGAAA
64 TGGAATTTGGGGTTTAGAATGAAA
5861 TTG
1 TTG
5864 AGGATTATTT
Statistics
Matches: 89, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
87 18 0.20
88 48 0.54
89 23 0.26
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (87 bp):
TTGGTTAACTCAATGTTATTGAAGTATTTTAGAATTTTTGGTTTAGAATGTAATTGAATTATTTG
GAATTTGGGGTTTAGAATGAAA
Found at i:9802 original size:21 final size:21
Alignment explanation
Indices: 9773--9915 Score: 130
Period size: 21 Copynumber: 6.7 Consensus size: 21
9763 AAAGTATCAT
* *
9773 AGTATACAAATTACTACTACA
1 AGTACACAAAATACTACTACA
*
9794 AGTACACAAAGTACTACTACA
1 AGTACACAAAATACTACTACA
* *
9815 AGTACACAAAACACT-CTTGCCA
1 AGTACACAAAATACTAC-T-ACA
* *
9837 TAGTACACAAAGTACTACTCCA
1 -AGTACACAAAATACTACTACA
*
9859 AGTACACAAAATACT-CTTACC
1 AGTACACAAAATACTAC-TACA
*
9880 A-TAACACAAAATACTACTTCA
1 AGT-ACACAAAATACTACTACA
*
9901 AGTACACAAAGTACT
1 AGTACACAAAATACT
9916 CTTACGAATA
Statistics
Matches: 101, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.03
21 76 0.75
22 7 0.07
23 14 0.14
24 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.22
Consensus pattern (21 bp):
AGTACACAAAATACTACTACA
Found at i:9819 original size:12 final size:12
Alignment explanation
Indices: 9784--9819 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
9774 GTATACAAAT
9784 TACTACTACAAG
1 TACTACTACAAG
9796 TAC-AC-A-AAG
1 TACTACTACAAG
9805 TACTACTACAAG
1 TACTACTACAAG
9817 TAC
1 TAC
9820 ACAAAACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.29
10 3 0.14
11 3 0.14
12 9 0.43
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.22
Consensus pattern (12 bp):
TACTACTACAAG
Found at i:9887 original size:65 final size:64
Alignment explanation
Indices: 9769--9915 Score: 176
Period size: 65 Copynumber: 2.3 Consensus size: 64
9759 ACACAAAGTA
* * *
9769 TCATAGTATACAAATTACTACTACAAGTACACAAAGTACTACTACAAGTACACAAAACACT-CT
1 TCATAGTACACAAAGTACTACTACAAGTACACAAAATACTACTACAAGTACACAAAACACTACT
* * *
9832 TGCCATAGTACACAAAGTACTACTCCAAGTACACAAAATACT-CTTACCA-TAACACAAAATACT
1 T--CATAGTACACAAAGTACTACTACAAGTACACAAAATACTAC-TACAAGT-ACACAAAACACT
9895 ACT
62 ACT
9898 TCA-AGTACACAAAGTACT
1 TCATAGTACACAAAGTACT
9916 CTTACGAATA
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
63 16 0.22
64 4 0.05
65 50 0.68
66 3 0.04
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23
Consensus pattern (64 bp):
TCATAGTACACAAAGTACTACTACAAGTACACAAAATACTACTACAAGTACACAAAACACTACT
Found at i:9903 original size:42 final size:43
Alignment explanation
Indices: 9797--9920 Score: 178
Period size: 44 Copynumber: 2.9 Consensus size: 43
9787 TACTACAAGT
* *
9797 ACACAAAGTACTACTACAAGTACACAAAACACTCTTGCCATAG
1 ACACAAAGTACTACTACAAGTACACAAAATACTCTTACCATAG
*
9840 TACACAAAGTACTACTCCAAGTACACAAAATACTCTTACCATA-
1 -ACACAAAGTACTACTACAAGTACACAAAATACTCTTACCATAG
* * *
9883 ACACAAAATACTACTTCAAGTACACAAAGTACTCTTAC
1 ACACAAAGTACTACTACAAGTACACAAAATACTCTTAC
9921 GAATATGCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
42 35 0.47
44 39 0.53
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.22
Consensus pattern (43 bp):
ACACAAAGTACTACTACAAGTACACAAAATACTCTTACCATAG
Found at i:16732 original size:20 final size:20
Alignment explanation
Indices: 16707--16758 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
16697 GTTAGAAAAT
16707 TGGAGAATAATTGAATAAAC
1 TGGAGAATAATTGAATAAAC
16727 TGGAGAATAATTGAATAAAC
1 TGGAGAATAATTGAATAAAC
*
16747 TGAAGAATAATT
1 TGGAGAATAATT
16759 CCATAAACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.04, G:0.19, T:0.27
Consensus pattern (20 bp):
TGGAGAATAATTGAATAAAC
Found at i:24376 original size:21 final size:23
Alignment explanation
Indices: 24328--24377 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 23
24318 TGAATTAATG
24328 ATTATAATCAATTTAATATATGAA
1 ATTATAA-CAATTTAATATATGAA
24352 ATTATAA-AATTTAA-ATAAT-AA
1 ATTATAACAATTTAATAT-ATGAA
24373 ATTAT
1 ATTAT
24378 TTTTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.36
22 9 0.36
24 7 0.28
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTATAACAATTTAATATATGAA
Found at i:24387 original size:18 final size:19
Alignment explanation
Indices: 24361--24396 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24351 AATTATAAAA
24361 TTTAAATAATA-AATTATT
1 TTTAAATAATAGAATTATT
*
24379 TTTATATAATAGAATTAT
1 TTTAAATAATAGAATTAT
24397 ATAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTAAATAATAGAATTATT
Found at i:25676 original size:30 final size:30
Alignment explanation
Indices: 25642--25708 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
25632 TACTTAGCCT
25642 ATTTCATGATTATGCATC-TTATTCTAGCTC
1 ATTTCATGATTATG-ATCTTTATTCTAGCTC
** *
25672 ATTTCATTCTTATGATCTTTATTTTAGCTC
1 ATTTCATGATTATGATCTTTATTCTAGCTC
*
25702 ATGTCAT
1 ATTTCAT
25709 TCATACACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (30 bp):
ATTTCATGATTATGATCTTTATTCTAGCTC
Found at i:25709 original size:30 final size:30
Alignment explanation
Indices: 25651--25710 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
25641 TATTTCATGA
*
25651 TTATGCATCTTATTCTAGCTCATTTCATTC
1 TTATGCATCTTATTCTAGCTCATGTCATTC
*
25681 TTATG-ATCTTTATTTTAGCTCATGTCATTC
1 TTATGCATC-TTATTCTAGCTCATGTCATTC
25711 ATACACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (30 bp):
TTATGCATCTTATTCTAGCTCATGTCATTC
Found at i:26130 original size:20 final size:20
Alignment explanation
Indices: 26087--26130 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
26077 GCTAGCTTGT
26087 TTCA-CTAGCCACCAATGTC
1 TTCATCTAGCCACCAATGTC
*
26106 ATCATCTAGCCACCATATG-C
1 TTCATCTAGCCACCA-ATGTC
26126 TTCAT
1 TTCAT
26131 GTGCAAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.71
21 3 0.14
ACGTcount: A:0.27, C:0.34, G:0.09, T:0.30
Consensus pattern (20 bp):
TTCATCTAGCCACCAATGTC
Found at i:28894 original size:95 final size:96
Alignment explanation
Indices: 28673--28896 Score: 321
Period size: 96 Copynumber: 2.3 Consensus size: 96
28663 ATACCGAAAG
*
28673 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGTCTACATCGAATCTAAAATGGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGTCAACATCGAATCTAAAATGGGTATCGAT
**
28738 ACTGGAAGGGGTATCGATACCATAATATATA
66 ACCAGAAGGGGTATCGATACCATAATATATA
*
28769 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAG-CAACATCGAAT-TAAAAATTGGTATCG
1 GTAGTATCGATACCATGGTAAGGGTATCGATACC-AGTCAACATCGAATCT-AAAATGGGTATCG
**
28832 ATACCAGAAGGGGGTATCTTTACCAT-AT-TATA
64 ATACCAGAA-GGGGTATCGATACCATAATATATA
* *
28864 GTAGTATCGATACCATGATAGGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCGATAC
28897 TATAGGGCCA
Statistics
Matches: 117, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
95 36 0.31
96 65 0.56
97 16 0.14
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (96 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACCAGTCAACATCGAATCTAAAATGGGTATCGAT
ACCAGAAGGGGTATCGATACCATAATATATA
Found at i:29328 original size:57 final size:57
Alignment explanation
Indices: 29236--29718 Score: 625
Period size: 57 Copynumber: 8.5 Consensus size: 57
29226 TTTGAAAATA
* *
29236 TAAGAAATCATACTAAGTGTATGAATTACAGATAGGGTGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
29293 TAAAAAATCATACTAAGTGTATGAATTTCATATAGGGCGTTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
29350 TAAGAAATCATACTAAGTGTATGAATTTTAGATAGGGTGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
** * * *
29407 TAAGAAATCACGCTAAGTGTATGATTTTCAGATAGGGCTTTTCGTACTCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
29464 TAAGAAATCATACTAAGTGTATGAATTTTAGATAGGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
29521 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
** * * *
29578 TAAGAAATCATACTAAGTGTATGAATTTTTGATAGGGCG--T--TACACTAAATTGA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * * ** * *
29631 TAAGGAAATCATATTAAGCGTATTAATTTCCAGATAGGGCACTTT-GTGTGCTAACATGA
1 TAA-GAAATCATACTAAGTGTATGAATTT-CAGATAGGGC-GTTTCGTACGCTAAAATGT
* *
29690 TAATAAATTCATAGTAAGTGTATGAATTT
1 TAAGAAA-TCATACTAAGTGTATGAATTT
29719 TTGTATTGGA
Statistics
Matches: 374, Mismatches: 45, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
53 13 0.03
54 22 0.06
55 9 0.02
57 297 0.79
58 4 0.01
59 29 0.08
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:31648 original size:96 final size:94
Alignment explanation
Indices: 31538--31757 Score: 255
Period size: 96 Copynumber: 2.3 Consensus size: 94
31528 TACCGACAAT
* * *
31538 GTAGTATCAATACCATGGTAAGGGTATCGAGACC-AGTCTACATCGAATCTAAAA-TGGGTATTG
1 GTAGTATCAATACCATGGTAAGGGTATCAAGACCAAG-CAACATCGAATCAAAAATTGGG-ATTG
* *
31601 ATATCGGAAGGGGTATCAATACCATAATATATA
64 ATACCAGAAGGGGTATCAATACCAT-A-ATATA
* * * *
31634 GTAGTATCAATACCATGGTATGTGTATCAATACCAAGCAACATTGAATCAAAAATTGGGATTGAT
1 GTAGTATCAATACCATGGTAAGGGTATCAAGACCAAGCAACATCGAATCAAAAATTGGGATTGAT
** *
31699 ACCAGAAGGGGTATCGGTACCATAGTATA
66 ACCAGAAGGGGTATCAATACCATAATATA
* * *
31728 GTAGTATCGATACCATGATAGGGGTATCAA
1 GTAGTATCAATACCATGGTAAGGGTATCAA
31758 TACTATAGAG
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
94 30 0.28
95 1 0.01
96 69 0.65
97 6 0.06
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (94 bp):
GTAGTATCAATACCATGGTAAGGGTATCAAGACCAAGCAACATCGAATCAAAAATTGGGATTGAT
ACCAGAAGGGGTATCAATACCATAATATA
Found at i:31754 original size:20 final size:20
Alignment explanation
Indices: 31696--31760 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
31686 AATTGGGATT
31696 GATACCA-GA-AGGGGTATC
1 GATACCATGATAGGGGTATC
* **
31714 GGTACCATAGTATAGTAGTATC
1 GATACCAT-G-ATAGGGGTATC
31736 GATACCATGATAGGGGTATC
1 GATACCATGATAGGGGTATC
*
31756 AATAC
1 GATAC
31761 TATAGAGGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 6 0.17
20 14 0.39
21 2 0.06
22 14 0.39
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (20 bp):
GATACCATGATAGGGGTATC
Found at i:32345 original size:58 final size:57
Alignment explanation
Indices: 32102--32476 Score: 536
Period size: 57 Copynumber: 6.5 Consensus size: 57
32092 GTGCAAAATA
* *
32102 TAAGAAATCATACTAAGTGTACGAATTTCAGATAGGGCATTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
**
32159 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTTC-TACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGG-CATTTCGTACGCTAAAATGT
** *
32216 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
*
32273 TAAGAAATCATACTAAGGGTATGAATTTCAGATAAGGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGAT-AGGGCATTTCGTACGCTAAAATGT
* * *
32331 TAAGAAATCATACTAAGAGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
* *** * *
32388 TAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCACTTCGGGTGCTAACATGA
1 TAA-GAAATCATACTAAGTGTATGAATTTC-AGATAGGGCATTTCGTACGCTAAAATGT
*
32447 TAAGAAATTCATACTAAGTGTATGCATTTC
1 TAAGAAA-TCATACTAAGTGTATGAATTTC
32477 TATATTGGAC
Statistics
Matches: 291, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
56 4 0.01
57 155 0.53
58 86 0.30
59 46 0.16
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
Found at i:43403 original size:31 final size:31
Alignment explanation
Indices: 43217--43388 Score: 308
Period size: 31 Copynumber: 5.5 Consensus size: 31
43207 AGGGTCGAGG
*
43217 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
43248 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
43279 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
43310 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
43341 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
43372 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
43389 AGAATCTATG
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 136 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:47110 original size:62 final size:62
Alignment explanation
Indices: 46990--47114 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
46980 AGGGTCGAGG
* * **
46990 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAACATATGGACT
47052 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAA-CATATGGACT
47114 G
1 G
47115 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 57 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAACATATGGACT
Found at i:47114 original size:31 final size:31
Alignment explanation
Indices: 46990--47100 Score: 204
Period size: 31 Copynumber: 3.6 Consensus size: 31
46980 AGGGTCGAGG
46990 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
47021 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
47052 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
47083 GATTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
47101 AAATCTATGG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:50716 original size:31 final size:31
Alignment explanation
Indices: 50678--50818 Score: 255
Period size: 31 Copynumber: 4.5 Consensus size: 31
50668 AAGGGTCGAG
50678 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
50709 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
50740 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
50771 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
50802 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
50819 AGAATCTATG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 107 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:52998 original size:22 final size:25
Alignment explanation
Indices: 52977--53027 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
52967 TTTTCTTATT
52977 ATATAATATTGATGTGCATATTAGTTA
1 ATAT-ATATTGATGTGCATATTAG-TA
*
53004 ATATATTTTGATGTGCATA-TAGTA
1 ATATATATTGATGTGCATATTAGTA
53028 TCCATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 3 0.13
26 14 0.61
27 4 0.17
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (25 bp):
ATATATATTGATGTGCATATTAGTA
Found at i:56016 original size:15 final size:15
Alignment explanation
Indices: 55996--56034 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
55986 CACGATTAGA
55996 ATAAATAAACAAAAG
1 ATAAATAAACAAAAG
**
56011 ATAAATAAATGAAAG
1 ATAAATAAACAAAAG
56026 ATGAAATAA
1 AT-AAATAA
56035 GATAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (15 bp):
ATAAATAAACAAAAG
Done.