Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004472.1 Hibiscus syriacus cultivar Beakdansim tig00009860_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: 60563
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1463 original size:13 final size:12
Alignment explanation
Indices: 1445--1484 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1435 ATTATGCTTG
*
1445 AAAAGAAAAGGAA
1 AAAAGAAAA-AAA
1458 AAAAGAAAAAAA
1 AAAAGAAAAAAA
1470 AGAAAGAAAAAAA
1 A-AAAGAAAAAAA
1483 AA
1 AA
1485 GGGGGGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:3045 original size:84 final size:83
Alignment explanation
Indices: 2626--3186 Score: 942
Period size: 83 Copynumber: 6.7 Consensus size: 83
2616 AACTGGAACG
2626 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAA
* *
2691 TCAATCATTGAATTTAAA
66 CCAATCATTGAATTTGAA
*
2709 AGATGAATGTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAA
* *
2774 TCAATCATTGAATTTAAA
66 CCAATCATTGAATTTGAA
* *
2792 AGATGAATGTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTAAAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAA
2857 CCAATCATTGAATTTGAA
66 CCAATCATTGAATTTGAA
* *
2875 AGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTCTGATCTGTTTTGGTAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA--TCTGATCTGGTTTGGTAA
2940 AACCAATCATTGAATTTGAA
64 AACCAATCATTGAATTTGAA
*
2960 AGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
3025 ACCAATCATTGAATTTGAA
65 ACCAATCATTGAATTTGAA
*
3044 AGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTAAA
1 AGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
* * *
3109 ACCAGTTATTGAATTTGTA
65 ACCAATCATTGAATTTGAA
* *
3128 AGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
3187 ATATGAAACC
Statistics
Matches: 456, Mismatches: 19, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
83 249 0.55
84 128 0.28
85 48 0.11
86 31 0.07
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (83 bp):
AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAA
CCAATCATTGAATTTGAA
Found at i:4324 original size:113 final size:113
Alignment explanation
Indices: 4054--4542 Score: 737
Period size: 113 Copynumber: 4.3 Consensus size: 113
4044 GTGTCAGTAA
*
4054 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
4119 AACCTTATGCTCAAATCCATCA-TTCGATGGATCAGCTTTTCCAGAGTTCG
66 AACCTTTTGCTCAAATCCATCACTT-GATGGATCAACTTTTCC--AGTTCG
*
4169 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * *
4234 AACCTTTTGCTCAAATCTATCACTTGATGAATTATCTTTTCCAGTTCG
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCG
*
4282 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
4347 AACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCG
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCG
*
4395 AGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
** * * * * * * * *
4460 AACCTTTTATTTAAATTCATCAATTGATGGATTAACATTGCCAGGTAG
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCG
4508 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG
4543 AATTTGTTCA
Statistics
Matches: 346, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
113 234 0.68
115 98 0.28
116 14 0.04
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCG
Found at i:4606 original size:92 final size:92
Alignment explanation
Indices: 4446--4620 Score: 226
Period size: 92 Copynumber: 1.9 Consensus size: 92
4436 GTTCATAATG
* * * * *
4446 AGAAGAATTTGTTCAACCTTTTATTTAAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGT
1 AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCAGGTAAAGT
4511 TCATAATGAGAAGAACTCGTCATCTGA
66 TCATAATGAGAAGAACTCGTCATCTGA
* * * * * * *
4538 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCTAGAG-AAAT
1 AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCAG-GTAAAG
4602 TTCATAATGAGAAGAACTC
65 TTCATAATGAGAAGAACTC
4621 ATTTGAAGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
92 69 0.99
93 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (92 bp):
AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCAGGTAAAGT
TCATAATGAGAAGAACTCGTCATCTGA
Found at i:4632 original size:92 final size:92
Alignment explanation
Indices: 4438--4636 Score: 206
Period size: 92 Copynumber: 2.2 Consensus size: 92
4428 AAGAAGAAGT
* * * *
4438 TCATAATG-AGAAGAATTTGTTCAACCTTTTATTTAAATTCATCAATTGATGGATTAACATTGCC
1 TCATAA-GAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCC
* *
4502 AGGTAGAGTTCATAATGAGAAGAACTCG
65 AGGTAAAGTTCATAATGAGAAGAACTCA
** * * * * * *
4530 TCATCTGAAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCTA
1 TCATAAGAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCA
*
4595 GAG-AAATTTCATAATGAGAAGAACTCA
66 G-GTAAAGTTCATAATGAGAAGAACTCA
*
4622 T-TTGAAGAAGAAGAA
1 TCAT-AAGAAGAAGAA
4637 GTTCACAATG
Statistics
Matches: 86, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
91 2 0.02
92 83 0.97
93 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (92 bp):
TCATAAGAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCA
GGTAAAGTTCATAATGAGAAGAACTCA
Found at i:4906 original size:3 final size:3
Alignment explanation
Indices: 4898--4979 Score: 92
Period size: 3 Copynumber: 26.7 Consensus size: 3
4888 ATGTTATTTA
* * * *
4898 TAT TAT TAT TTT TAT AAT TAT TAT TAT TAT TAT TAT AAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
4946 TAT TAT TAT TAA TAT ATAT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TA
4980 CAAAATTCAG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 59 0.91
4 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:6555 original size:13 final size:13
Alignment explanation
Indices: 6534--6563 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6524 GGCCACCGAA
*
6534 GGCGGTGGCTGGC
1 GGCGATGGCTGGC
6547 GGCGATGGCTGGC
1 GGCGATGGCTGGC
6560 GGCG
1 GGCG
6564 GAAGAACACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.23, G:0.60, T:0.13
Consensus pattern (13 bp):
GGCGATGGCTGGC
Found at i:6999 original size:30 final size:33
Alignment explanation
Indices: 6927--7000 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 33
6917 GATTTAGTCC
6927 TATAATTTTAATAATTAATATTTTAATCTCGAGTT
1 TATAATTTT-ATAATT-ATATTTTAATCTCGAGTT
6962 TAT-ATTTT-TAATT-TATTTTAATCT-GA-TAT
1 TATAATTTTATAATTATATTTTAATCTCGAGT-T
6991 TATAATTTTA
1 TATAATTTTA
7001 GATAAGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
28 1 0.03
29 6 0.17
30 16 0.44
32 5 0.14
34 5 0.14
35 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (33 bp):
TATAATTTTATAATTATATTTTAATCTCGAGTT
Found at i:7940 original size:2 final size:2
Alignment explanation
Indices: 7933--7999 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
7923 ATTTGTCGGA
7933 AT AT AT AT AT AT 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 AT AT AT AT AT AT
7975 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8000 GTTTTGGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14745 original size:14 final size:14
Alignment explanation
Indices: 14718--14749 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
14708 TCTAGAACAC
14718 TCATCAAGGAAAAA
1 TCATCAAGGAAAAA
14732 TCATCCAAGGAAAAA
1 TCAT-CAAGGAAAAA
14747 TCA
1 TCA
14750 AATATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (14 bp):
TCATCAAGGAAAAA
Found at i:15962 original size:20 final size:20
Alignment explanation
Indices: 15913--15962 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
15903 CGATTTTCCA
15913 AATTCGCAACGCGAATATGT
1 AATTCGCAACGCGAATATGT
* * *
15933 AAATCACAACGCGAATTTGT
1 AATTCGCAACGCGAATATGT
15953 AATTCGCAAC
1 AATTCGCAAC
15963 ATAGAAGTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
AATTCGCAACGCGAATATGT
Found at i:16519 original size:20 final size:20
Alignment explanation
Indices: 16496--16545 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
16486 TTTGAAACTA
*
16496 AAATTCGCAACAAGAAAATT
1 AAATTCGCAACAAGAAAATG
* *
16516 AAATTCGCAATACGAAAATG
1 AAATTCGCAACAAGAAAATG
*
16536 AAAATCGCAA
1 AAATTCGCAA
16546 TTCGATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACAAGAAAATG
Found at i:16582 original size:20 final size:20
Alignment explanation
Indices: 16548--16609 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
16538 AATCGCAATT
*
16548 CGATTTT-AGTTTCGCGTTG
1 CGATTTTCATTTTCGCGTTG
*
16567 CGATTTTCATTTTCGCGCTG
1 CGATTTTCATTTTCGCGTTG
*
16587 CGATTTTCATTTTCGTGTTG
1 CGATTTTCATTTTCGCGTTG
16607 CGA
1 CGA
16610 ATTTAAGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (20 bp):
CGATTTTCATTTTCGCGTTG
Found at i:16620 original size:20 final size:20
Alignment explanation
Indices: 16550--16620 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
16540 TCGCAATTCG
*
16550 ATTTTAGTTTCGCGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
* * *
16570 TTTTCATTTTCGCGCTGCGA
1 ATTTCAGTTTCGCGTTGCGA
* * *
16590 TTTTCATTTTCGTGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
*
16610 ATTTAAGTTTC
1 ATTTCAGTTTC
16621 AAAAACTACT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.49
Consensus pattern (20 bp):
ATTTCAGTTTCGCGTTGCGA
Found at i:18868 original size:21 final size:21
Alignment explanation
Indices: 18736--18874 Score: 161
Period size: 21 Copynumber: 6.6 Consensus size: 21
18726 ATTCACCTGT
* *
18736 CATCATTCAAGAGGCTCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
18757 TATCATTCAAAAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
18778 CATCGTTCAAGAGACCCCTTC
1 CATCGTTCAAGAGGCCCCTCC
* *
18799 TATCGTTCAAGAAGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
18820 CATCATTCAAGAGGTCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
18841 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
18862 CACCGTTCAAGAG
1 CATCGTTCAAGAG
18875 CCTGATTCAC
Statistics
Matches: 97, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 97 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.23
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:20410 original size:20 final size:20
Alignment explanation
Indices: 20385--20422 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20375 TTTGCATTGC
*
20385 GATTTTTGCGCTGCGAAATT
1 GATTTTCGCGCTGCGAAATT
*
20405 GATTTTCGCGTTGCGAAA
1 GATTTTCGCGCTGCGAAA
20423 CTTTCGAGTT
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:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (20 bp):
GATTTTCGCGCTGCGAAATT
Found at i:23019 original size:24 final size:24
Alignment explanation
Indices: 22985--23038 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
22975 CTGAAACATC
22985 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
23009 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
23033 ATCAAA
1 ATCAAA
23039 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:23996 original size:20 final size:20
Alignment explanation
Indices: 23971--24160 Score: 81
Period size: 20 Copynumber: 9.4 Consensus size: 20
23961 AAATAAAAGC
23971 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
23991 TGTTGCG-AATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTCG
* ** *
24011 AGTTGCGAAAACAAAATTTG
1 TGTTGCGAAATTAAAATTCG
* * *
24031 TGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
* * *
24051 TGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
** *
24071 TGTTGCGAAAAGGAAACTT-G
1 TGTTGCG-AAATTAAAATTCG
*
24091 TGTTGCGAAA-AAGAAATTCG
1 TGTTGCGAAATTA-AAATTCG
*
24111 CGTTGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATT-A-AAATTCG
* *
24131 AGTTGCGAATTTAAAATTTCG
1 TGTTGCGAAATTAAAA-TTCG
*
24152 TGTAGCGAA
1 TGTTGCGAA
24161 TTTGGAAAAT
Statistics
Matches: 131, Mismatches: 25, Indels: 27
0.72 0.14 0.15
Matches are distributed among these distances:
18 1 0.01
19 22 0.17
20 79 0.60
21 27 0.21
22 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:24017 original size:40 final size:40
Alignment explanation
Indices: 23972--24180 Score: 154
Period size: 40 Copynumber: 5.2 Consensus size: 40
23962 AATAAAAGCT
23972 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
** * * * **
24012 GTTGCGAAAACAAAATTTGTGTTGCGATTTAGAAAATCTT
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
* * * *** * * *
24052 GTTGCG-ATTTAGAAAATCTTGTTGCGAAAAGGAAACTTGT
1 GTTGCGAAATTA-AAATTCGTGTTGCGAATTCGAAAATCGA
* *
24092 GTTGCGAAA-AAGAAATTCGCGTTGCGAATTC-AGAAATCGA
1 GTTGCGAAATTA-AAATTCGTGTTGCGAATTCGA-AAATCGA
* * * *
24132 GTTGCGAATTTAAAATTTCGTGTAGCGAATTTGGAAAATCGC
1 GTTGCGAAATTAAAA-TTCGTGTTGCGAA-TTCGAAAATCGA
24174 GTTGCGA
1 GTTGCGA
24181 TTGCAGAAAC
Statistics
Matches: 125, Mismatches: 37, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
39 3 0.02
40 93 0.74
41 13 0.10
42 15 0.12
43 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
Found at i:24055 original size:60 final size:60
Alignment explanation
Indices: 23983--24201 Score: 183
Period size: 60 Copynumber: 3.6 Consensus size: 60
23973 TTGCGAAATT
*
23983 AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTTGTGTTGCGATTTAG
1 AAAA-TCGCGTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTTGTGTTGCGATTTAG
** * * ** ** * ***
24044 AAAATCTTGTTGCGATTTAGAAAATCTTGTTGCGAAAAGGAAACTTGTGTTGCGAAAAAG
1 AAAATCGCGTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTTGTGTTGCGATTTAG
* *** * *
24104 AAATTCGCGTTGCGAATTC-AGAAATCGAGTTGCGAATTTAAAATTTCGTGTAGCGAATTTGG
1 AAAATCGCGTTGCGAATTCGA-AAATCGAGTTGCGAAAACAAAATTT-GTGTTGCG-ATTTAG
*
24166 AAAATCGCGTTGCG-ATTGCAGAAACT-GAGTTGCGAA
1 AAAATCGCGTTGCGAATT-C-GAAAATCGAGTTGCGAA
24202 TTTGGAAACT
Statistics
Matches: 122, Mismatches: 30, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
59 1 0.01
60 77 0.63
61 14 0.11
62 26 0.21
63 3 0.02
64 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (60 bp):
AAAATCGCGTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTTGTGTTGCGATTTAG
Found at i:24128 original size:21 final size:21
Alignment explanation
Indices: 24102--24203 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 21
24092 GTTGCGAAAA
*
24102 AGAAATTCGCGTTGCGAATTC
1 AGAAATTCGAGTTGCGAATTC
*
24123 AGAAA-TCGAGTTGCGAATTT
1 AGAAATTCGAGTTGCGAATTC
* * *
24143 A-AAATTTCGTGTAGCGAATTT
1 AGAAA-TTCGAGTTGCGAATTC
* * *
24164 GGAAAATCGCGTTGCG-ATTGC
1 AGAAATTCGAGTTGCGAATT-C
*
24185 AGAAACT-GAGTTGCGAATT
1 AGAAATTCGAGTTGCGAATT
24204 TGGAAACTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 3 0.05
20 24 0.38
21 34 0.53
22 3 0.05
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (21 bp):
AGAAATTCGAGTTGCGAATTC
Found at i:24209 original size:20 final size:20
Alignment explanation
Indices: 24156--24221 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
24146 ATTTCGTGTA
* *
24156 GCGAATTTGGAAAATCGCGTT
1 GCGAATTTGGAAACT-GAGTT
24177 GCG-A-TTGCAGAAACTGAGTT
1 GCGAATTTG--GAAACTGAGTT
*
24197 GCGAATTTGGAAACTGTGTT
1 GCGAATTTGGAAACTGAGTT
24217 GCGAA
1 GCGAA
24222 ATTAGAGTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 3 0.08
20 23 0.61
21 9 0.24
22 3 0.08
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (20 bp):
GCGAATTTGGAAACTGAGTT
Found at i:27160 original size:44 final size:44
Alignment explanation
Indices: 27097--27185 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
27087 GTTGTCATCC
* * *
27097 TGGTGTTTTCTGCTTTTCTCAGATTGTTCTTTCGGTTCATGCAA
1 TGGTGTTTTCAGCTTTTCTCAGATTGATCTTTCGGTTCAGGCAA
*
27141 TGGTGTTTTCAGCTTTTCTCATATTGATCTTTCGGTTCAGGCAA
1 TGGTGTTTTCAGCTTTTCTCAGATTGATCTTTCGGTTCAGGCAA
27185 T
1 T
27186 TGTCACGCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.48
Consensus pattern (44 bp):
TGGTGTTTTCAGCTTTTCTCAGATTGATCTTTCGGTTCAGGCAA
Found at i:31081 original size:40 final size:40
Alignment explanation
Indices: 30993--31119 Score: 155
Period size: 40 Copynumber: 3.1 Consensus size: 40
30983 TATAGTGAAT
* * ** * *
30993 CTCGAAGACGTATTGCAGTCCATGCGACTTTCCATGCTCCC
1 CTCGAAGACGTATTGGAGTCTATATGCCTTACC-TGCTCCC
* *
31034 TTTGAAGACGTATTGGAGTCTATATGCCTTACCTGCTCCC
1 CTCGAAGACGTATTGGAGTCTATATGCCTTACCTGCTCCC
* *
31074 CTCGAAGACGTATTGGAGTATATATGCCTTACTTGCTCCC
1 CTCGAAGACGTATTGGAGTCTATATGCCTTACCTGCTCCC
31114 CTCGAA
1 CTCGAA
31120 TACGCATGCA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 49 0.66
41 25 0.34
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (40 bp):
CTCGAAGACGTATTGGAGTCTATATGCCTTACCTGCTCCC
Found at i:31987 original size:17 final size:18
Alignment explanation
Indices: 31965--32006 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
31955 TTAGTAGATT
31965 ATTTTTAGATTAAAT-TA
1 ATTTTTAGATTAAATGTA
*
31982 ATTTTTATATTAAATGTA
1 ATTTTTAGATTAAATGTA
*
32000 ATATTTA
1 ATTTTTA
32007 AATTGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTTTAGATTAAATGTA
Found at i:32322 original size:21 final size:20
Alignment explanation
Indices: 32289--32332 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
32279 AGCGATGGTG
*
32289 TTATTATTATTTAATAAAATA
1 TTATAATTATTT-ATAAAATA
* *
32310 TTATAATTGTTTATTAAATA
1 TTATAATTATTTATAAAATA
32330 TTA
1 TTA
32333 AAAATATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATAATTATTTATAAAATA
Found at i:33281 original size:5 final size:5
Alignment explanation
Indices: 33265--34126 Score: 1251
Period size: 5 Copynumber: 174.6 Consensus size: 5
33255 TAAAAAAATG
33265 TATAA TTATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA -TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33316 TATAA TAT-A -ATAA TATAA TATAA TATAA TAATATA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA T-ATA-A TATAA TATAA TATAA
33366 TAT-A TATAATA TATAA TATAA TAT-A TATAA TATAA TATAA TATAA TATAA
1 TATAA TAT-A-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33416 TAT-A -ATAA TATAA TATAA TATAA TATAA TATAA TATATA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATAA TATAA
33465 TATAA TATAA TATAA TATAA TATAA TATAATA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TAT-A-A TATAA TATAA TATAA TATAA
33517 TATAA TATAA TATAA TATAA TA-AA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* *
33566 TATAA TATAA TAT-A TATAA TATAATA TATAA TATAA TCTAA TCT-A -ATAA
1 TATAA TATAA TATAA TATAA TAT-A-A TATAA TATAA TATAA TATAA TATAA
* * * * * * *
33615 TCTAA TCTAA TCTAA TATAA TCTAA TCTAA TATAA TCTAA TCTAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * *
33665 TCTAA TCTAA TAT-A -ATAA TCTAA TATAA TAT-A TA-ATA TAATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA-A T-ATAA TATAA
33713 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33762 TAT-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33811 TAT-A TATAA TATAA TATAA TAT-A -ATAA TATATA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATAA TATAA TATAA
33859 TATAA TATAA TATAA TAT-A -ATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33907 TATAA TATAATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A
1 TATAA TAT-A-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33958 -ATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
34007 TATAA TATAA TAT-A -ATAA TATAA TATAA TATAA TATAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
34054 -ATAA TATAA TAT-A TAT-A TATATA TATAA TATAA TATAA TATAA TATAATA
1 TATAA TATAA TATAA TATAA TATA-A TATAA TATAA TATAA TATAA TAT-A-A
34104 TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TAT
34127 TTAAATTAAA
Statistics
Matches: 800, Mismatches: 12, Indels: 89
0.89 0.01 0.10
Matches are distributed among these distances:
3 17 0.02
4 57 0.07
5 665 0.83
6 38 0.05
7 23 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:34148 original size:19 final size:18
Alignment explanation
Indices: 34124--34189 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
34114 TATAATATAA
34124 TATTTAAATTAAATTAATT
1 TATTTAAATTAAATT-ATT
* *
34143 TATTTAACTTTAATTATT
1 TATTTAAATTAAATTATT
* * * *
34161 TATTTATATTTATTTCTT
1 TATTTAAATTAAATTATT
34179 TATTTATAATT
1 TATTTA-AATT
34190 TTATAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 23 0.59
19 16 0.41
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTAAATTAAATTATT
Found at i:34185 original size:18 final size:19
Alignment explanation
Indices: 34135--34186 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
34125 ATTTAAATTA
34135 AATTAATTTATTTA-ACTTT
1 AATT-ATTTATTTATACTTT
34154 AATTATTTATTTATA-TTT
1 AATTATTTATTTATACTTT
* *
34172 ATTTCTTTATTTATA
1 AATTATTTATTTATA
34187 ATTTTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTATTTATTTATACTTT
Found at i:36300 original size:2 final size:2
Alignment explanation
Indices: 36293--36354 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
36283 TTATTTCATA
36293 AT AT AT AT AT AT 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 AT AT AT AT AT AT
36335 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
36355 TGTGTTAAAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39088 original size:19 final size:19
Alignment explanation
Indices: 39066--39102 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39056 CAGTGGGCGG
*
39066 TGGGGTTGGTGGTGGACGA
1 TGGGGCTGGTGGTGGACGA
39085 TGGGGCTGGTGGTGGACG
1 TGGGGCTGGTGGTGGACG
39103 TTGCATGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.59, T:0.24
Consensus pattern (19 bp):
TGGGGCTGGTGGTGGACGA
Found at i:40417 original size:2 final size:2
Alignment explanation
Indices: 40410--40437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40400 ATATTTTTAA
40410 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
40438 GCACGTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40852 original size:19 final size:19
Alignment explanation
Indices: 40828--40867 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
40818 GAACGTTATC
40828 GAGTGAATGATTGTTCGGT
1 GAGTGAATGATTGTTCGGT
40847 GAGTGAATGATTGTTCGGT
1 GAGTGAATGATTGTTCGGT
40866 GA
1 GA
40868 TGGAGATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.38, T:0.35
Consensus pattern (19 bp):
GAGTGAATGATTGTTCGGT
Found at i:47501 original size:20 final size:20
Alignment explanation
Indices: 47472--47510 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47462 AGAGCTCATA
*
47472 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
47492 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
47511 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:58024 original size:14 final size:11
Alignment explanation
Indices: 57994--58019 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57984 ATTGCCTTAG
57994 GTTCTTTTGTT
1 GTTCTTTTGTT
58005 GTTCTTTTGTT
1 GTTCTTTTGTT
58016 GTTC
1 GTTC
58020 CTCTTCCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.19, T:0.69
Consensus pattern (11 bp):
GTTCTTTTGTT
Done.