Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005683.1 Hibiscus syriacus cultivar Beakdansim tig00013289_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: 55127
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1424 original size:108 final size:107
Alignment explanation
Indices: 1257--1451 Score: 295
Period size: 107 Copynumber: 1.8 Consensus size: 107
1247 TTCTCAAAGA
** * *
1257 TGTCGAAATGATCTTTTACACGAAGGGGAAAGGGGTGGTCTCACTTCGAAAATGATTTAGTGTAA
1 TGTCGAAACAATCTTTTACACGAAGGGGAAAGGGGTGGTCCCACTTCAAAAATGATTTAGTGTAA
1322 TAAATTTGTGATAAACAA-GTGGTCCCTAGCAGAGTCACCAAGC
66 T-AATTTGTGATAAA-AACGTGGTCCCTAGCAGAGTCACCAAGC
* *
1365 TGTCGAAACAATCTTTTACCCGAAGGGGAAA-GGGTGGTCCCACTTCAAAAATGATTTTAGTGTG
1 TGTCGAAACAATCTTTTACACGAAGGGGAAAGGGGTGGTCCCACTTCAAAAATGA-TTTAGTGTA
1429 ATAATTTGTGATAAAAACGTGGT
65 ATAATTTGTGATAAAAACGTGGT
1452 TCACAGAGTC
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
106 2 0.03
107 39 0.49
108 38 0.48
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (107 bp):
TGTCGAAACAATCTTTTACACGAAGGGGAAAGGGGTGGTCCCACTTCAAAAATGATTTAGTGTAA
TAATTTGTGATAAAAACGTGGTCCCTAGCAGAGTCACCAAGC
Found at i:2420 original size:22 final size:23
Alignment explanation
Indices: 2381--2428 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2371 GATAAAACAT
*
2381 ATACATCATTTAAAATACAAACC
1 ATACATCATTTAAAATACAAAAC
* *
2404 ATACAT-ATTTTATATACAAAAC
1 ATACATCATTTAAAATACAAAAC
2426 ATA
1 ATA
2429 ACACATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (23 bp):
ATACATCATTTAAAATACAAAAC
Found at i:3898 original size:26 final size:26
Alignment explanation
Indices: 3863--3974 Score: 156
Period size: 26 Copynumber: 4.4 Consensus size: 26
3853 TGGCAGCAGT
*
3863 GGTGGCTGTTGAGTGGTCCAAGCGGC
1 GGTGGTTGTTGAGTGGTCCAAGCGGC
*
3889 GGTGGTTGTTGAGTGGTCCAAGCGGT
1 GGTGGTTGTTGAGTGGTCCAAGCGGC
3915 GGTGGTTGTTGAGTGGTCCAAGCGGC
1 GGTGGTTGTTGAGTGGTCCAAGCGGC
** * *
3941 GGTGG--CATGAGTGGTCCAAGTGGT
1 GGTGGTTGTTGAGTGGTCCAAGCGGC
3965 GGTGGTTGTT
1 GGTGGTTGTT
3975 CTGGAAACCC
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
24 20 0.27
26 55 0.73
ACGTcount: A:0.12, C:0.13, G:0.46, T:0.29
Consensus pattern (26 bp):
GGTGGTTGTTGAGTGGTCCAAGCGGC
Found at i:3925 original size:52 final size:50
Alignment explanation
Indices: 3861--3974 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 50
3851 GTTGGCAGCA
* **
3861 GTGGTGGCTGTTGAGTGGTCCAAGCGGCGGTGGTTGTTGAGTGGTCCAAGCG
1 GTGGTGGTTGTTGAGTGGTCCAAGCGGCGGTGG--CATGAGTGGTCCAAGCG
*
3913 GTGGTGGTTGTTGAGTGGTCCAAGCGGCGGTGGCATGAGTGGTCCAAGTG
1 GTGGTGGTTGTTGAGTGGTCCAAGCGGCGGTGGCATGAGTGGTCCAAGCG
3963 GTGGTGGTTGTT
1 GTGGTGGTTGTT
3975 CTGGAAACCC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 26 0.45
52 32 0.55
ACGTcount: A:0.11, C:0.13, G:0.46, T:0.29
Consensus pattern (50 bp):
GTGGTGGTTGTTGAGTGGTCCAAGCGGCGGTGGCATGAGTGGTCCAAGCG
Found at i:4181 original size:6 final size:6
Alignment explanation
Indices: 4167--4239 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
4157 TGTAAAATAA
* * * * * *
4167 AATTTT AATTAT AATTAT TATTTT AAATAT TATTAAT ACAATAT -A-TAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATT-AT A-ATTAT AATTAT
4215 AATTAT AATTAT AATTAT AA-TAT AA
1 AATTAT AATTAT AATTAT AATTAT AA
4240 ATAATAACGG
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
4 3 0.06
5 7 0.13
6 37 0.70
7 4 0.08
8 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTAT
Found at i:5412 original size:35 final size:34
Alignment explanation
Indices: 5319--5426 Score: 90
Period size: 37 Copynumber: 3.1 Consensus size: 34
5309 AGCAGACTGT
* * *
5319 TTGTCACATTTGAGATTGTTTCTCTTAAAACAAA
1 TTGTCTCACTTGAGATTGTTTTTCTTAAAACAAA
* * ** *
5353 GTTTTGTCTCATTTTAGACAGTTTTTCTTGAAACAAA
1 ---TTGTCTCACTTGAGATTGTTTTTCTTAAAACAAA
* *
5390 TTGATCTCACTTGAGATTGTTTTCCTAAAAACAAA
1 TTG-TCTCACTTGAGATTGTTTTTCTTAAAACAAA
5425 TT
1 TT
5427 TTATGTCGCT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
34 3 0.05
35 26 0.46
37 28 0.49
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (34 bp):
TTGTCTCACTTGAGATTGTTTTTCTTAAAACAAA
Found at i:5526 original size:68 final size:66
Alignment explanation
Indices: 5327--5581 Score: 221
Period size: 68 Copynumber: 3.7 Consensus size: 66
5317 GTTTGTCACA
* * * * *
5327 TTTGAGATTGTTTCTCTTAAAACAAAGTTTTGTCTCA-TTTTAGACAGTTTTTCTTGAAACA-AA
1 TTTGAGATTGTTTCTCTCAAAACAAA-TTTTGTCT-AGCTTGAGACAGTTTATCTTTAAACATAA
5390 TTGATCTC
64 ---A-C-C
* * * * * *
5398 ACTTGAGATTGTTT-TCCTAAAAACAAATTTTATGTCGCTTGAGACAGTTTCTCTTTAAACATAA
1 -TTTGAGATTGTTTCT-CTCAAAACAAATTTTGTCTAGCTTGAGACAGTTTATCTTTAAACATAA
5462 ACC
64 ACC
* * * *
5465 TTTTATATTGTTTCTCTCCAAACAAAGTATTTGTCTAGCTTGAGAAAGTTTAT-TTTGAAACATA
1 TTTGAGATTGTTTCTCTCAAAACAAA-T-TTTGTCTAGCTTGAGACAGTTTATCTTT-AAACATA
*
5529 AGCC
63 AACC
*
5533 TTTGAGATTGTTTCTCTCAAAACAAATTTTGTCTCGCTTGAGACAGTTT
1 TTTGAGATTGTTTCTCTCAAAACAAATTTTGTCTAGCTTGAGACAGTTT
5582 TCTCTCGAAA
Statistics
Matches: 151, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
66 39 0.26
67 7 0.05
68 53 0.35
69 1 0.01
71 27 0.18
72 24 0.16
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (66 bp):
TTTGAGATTGTTTCTCTCAAAACAAATTTTGTCTAGCTTGAGACAGTTTATCTTTAAACATAAAC
C
Found at i:6530 original size:123 final size:121
Alignment explanation
Indices: 6266--6549 Score: 417
Period size: 123 Copynumber: 2.3 Consensus size: 121
6256 CAACGCCTTA
* * *
6266 TGAAAGCGGCTAGAACTCTTCAACATGGATGAATAGTGTCATCTTCAACACCATATTATTTTCGG
1 TGAAAGCGGCTA-AACTCTTCAACATGGATGAGTAGTGTCACCTTCAACACCATATTATTTGCGG
*
6331 ATTGACTCAATTTCCTCAACGAGAAAGAACAACGTCATCTTCAGTAAACAATTTATC
65 ATTGACTCAATTTCCTCAACGAGAAAGAACAACATCATCTTCAGTAAACAATTTATC
* * * *
6388 TGAAAGCGACCAAGACTCTTCAAACATGGATGAGTGGTGTCGCCTTCAACACCATATTATTTGCG
1 TGAAAGCGGCTAA-ACTCTTC-AACATGGATGAGTAGTGTCACCTTCAACACCATATTATTTGCG
* *
6453 GATTGACTCGATTTCCTCAACGAGAAAGAACAACATCATCTTCAGTAAATAATTTATC
64 GATTGACTCAATTTCCTCAACGAGAAAGAACAACATCATCTTCAGTAAACAATTTATC
* *
6511 TGAAAGCGGCTATATCTCTTC-ACATGGATGAGCAGTGTC
1 TGAAAGCGGCTA-AACTCTTCAACATGGATGAGTAGTGTC
6550 GTCTTTAACA
Statistics
Matches: 144, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
121 17 0.12
122 17 0.12
123 109 0.76
124 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (121 bp):
TGAAAGCGGCTAAACTCTTCAACATGGATGAGTAGTGTCACCTTCAACACCATATTATTTGCGGA
TTGACTCAATTTCCTCAACGAGAAAGAACAACATCATCTTCAGTAAACAATTTATC
Found at i:7195 original size:10 final size:10
Alignment explanation
Indices: 7163--7206 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
7153 TTTGGTGCTG
7163 AAACAAGATA
1 AAACAAGATA
*
7173 AAATAAGATTA
1 AAACAAGA-TA
7184 AAACAAGATA
1 AAACAAGATA
*
7194 AAGAAAAGATA
1 AA-ACAAGATA
7205 AA
1 AA
7207 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 11 0.38
11 18 0.62
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (10 bp):
AAACAAGATA
Found at i:7206 original size:21 final size:21
Alignment explanation
Indices: 7163--7203 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
7153 TTTGGTGCTG
*
7163 AAACAAGATAAAATAAGATTA
1 AAACAAGATAAAAAAAGATTA
7184 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAA-AAAAGAT
7204 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (21 bp):
AAACAAGATAAAAAAAGATTA
Found at i:11496 original size:1 final size:1
Alignment explanation
Indices: 11492--11556 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
11482 AAATTTTGGC
* * * * *** *
11492 TTTTTTGTTTTTTTTTTGTTTTTTGTTTCTTTTTTTTTTTGCCTTTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11557 GAAAAAAATA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:11527 original size:25 final size:24
Alignment explanation
Indices: 11493--11556 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 24
11483 AATTTTGGCT
11493 TTTTTGTTTTTTTTT--TGTTTTTTG
1 TTTTT-TTTTTTTTTCCT-TTTTTTG
11517 TTTCTTTTTTTTTTTGCCTTTTTTTG
1 TTT-TTTTTTTTTTT-CCTTTTTTTG
11543 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
11557 GAAAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 12 0.33
25 13 0.36
26 10 0.28
27 1 0.03
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.88
Consensus pattern (24 bp):
TTTTTTTTTTTTTTCCTTTTTTTG
Found at i:11539 original size:26 final size:22
Alignment explanation
Indices: 11494--11557 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 22
11484 ATTTTGGCTT
11494 TTTTGTTTTTTTTTTGTTTTTTG
1 TTTT-TTTTTTTTTTGTTTTTTG
11517 TTTCTTTTTTTTTTTGCCTTTTTTTG
1 TTT-TTTTTTTTTTTG---TTTTTTG
11543 TTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTG
11558 AAAAAAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
23 14 0.38
24 1 0.03
25 12 0.32
26 10 0.27
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (22 bp):
TTTTTTTTTTTTTTGTTTTTTG
Found at i:17121 original size:11 final size:10
Alignment explanation
Indices: 17104--17144 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
17094 TCTATATTCC
17104 TTTTTATTAT
1 TTTTTATTAT
17114 TCTTTTATTCAT
1 T-TTTTATT-AT
17126 TTTTTATATAT
1 TTTTTAT-TAT
17137 TTTTTATT
1 TTTTTATT
17145 CTATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.07
11 22 0.79
12 4 0.14
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:17122 original size:21 final size:22
Alignment explanation
Indices: 17089--17145 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
17079 CTTTTTTTTC
17089 TATTTTCTATATTC-CTTTTTAT-
1 TATTTT-T-TATTCACTTTTTATA
*
17111 TATTCTTTTATTCATTTTTTATA
1 TATT-TTTTATTCACTTTTTATA
17134 TATTTTTTATTC
1 TATTTTTTATTC
17146 TATTATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 5 0.16
22 20 0.65
23 6 0.19
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTTTATTCACTTTTTATA
Found at i:17141 original size:22 final size:24
Alignment explanation
Indices: 17104--17159 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 24
17094 TCTATATTCC
17104 TTTTTAT-TATTCTTTTATTC-AT
1 TTTTTATATATTCTTTTATTCTAT
17126 TTTTTATATATT-TTTTATTCTAT
1 TTTTTATATATTCTTTTATTCTAT
17149 TATTATTATAT
1 T-TT-TTATAT
17160 TCCACACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 15 0.50
23 7 0.23
24 2 0.07
25 6 0.20
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTATATATTCTTTTATTCTAT
Found at i:27679 original size:43 final size:43
Alignment explanation
Indices: 27626--27708 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
27616 AATACTACGC
*
27626 TTAGGATGAAAACCCGAAAGGGCGTCCTA-AGTAAAAAAAACAT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTATA-TAAAAAAAACAT
*
27669 TTAGGGTGAAAACCCGAAAGGGCGCCCTATATAAAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTATATAAAAAAAA
27709 AGAGCAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.16
Consensus pattern (43 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTATATAAAAAAAACAT
Found at i:28672 original size:105 final size:105
Alignment explanation
Indices: 28518--29690 Score: 1997
Period size: 105 Copynumber: 11.2 Consensus size: 105
28508 ATGTCGCGCC
* *
28518 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
28583 ATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
28623 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
28688 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
28728 ACTCCAGACAACACAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
28793 ATTTTAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
28833 ACTCCAGACAACGTAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTAAACAACAATTTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
28898 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
28938 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAATAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
29003 ATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
29043 ACTCCAGACAACACAAGTTCAACTTCACGACGGAGGGACCGCTGGTTGTCAACAAACAAATTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCC
*
29108 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
29149 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
29214 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
29254 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
29319 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
29359 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAATAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
29424 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
29464 ACTCCAGACGACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT-AACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
29528 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * **
29568 ACTCCAAACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAACGAACATTTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCC
* *
29633 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
29674 ACTCCAGACAACACAAG
1 ACTCCAGACAACGCAAG
29691 ACGAAGGATA
Statistics
Matches: 1005, Mismatches: 60, Indels: 5
0.94 0.06 0.00
Matches are distributed among these distances:
104 99 0.10
105 747 0.74
106 159 0.16
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:31130 original size:22 final size:22
Alignment explanation
Indices: 31105--31160 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 22
31095 TCTATATTCC
*
31105 TTTTTAT-TATTCTTTTATTCAT
1 TTTTTATATATT-TATTATTCAT
31127 TTTTTATATATTTATTATTCTAT
1 TTTTTATATATTTATTATTC-AT
31150 TATTATTATAT
1 T-TT-TTATAT
31161 TCCACACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 14 0.48
23 7 0.24
24 2 0.07
25 6 0.21
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTATATATTTATTATTCAT
Found at i:31350 original size:14 final size:15
Alignment explanation
Indices: 31319--31358 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
31309 TTTTATTCTC
*
31319 TTATTTTAT-T-TAT
1 TTATTTTATCTATCT
31332 TTATTTTA-CTATCT
1 TTATTTTATCTATCT
31346 TTATTTTATCTAT
1 TTATTTTATCTAT
31359 ATCTTTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 10 0.43
15 4 0.17
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTATCTATCT
Found at i:31894 original size:16 final size:16
Alignment explanation
Indices: 31861--31894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31851 TTTACCGGAT
**
31861 AAAAAACCGGTTTGAA
1 AAAAAACCGGTTAAAA
31877 AAAAAACCGGTTAAAA
1 AAAAAACCGGTTAAAA
31893 AA
1 AA
31895 CCGGTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (16 bp):
AAAAAACCGGTTAAAA
Found at i:34214 original size:21 final size:21
Alignment explanation
Indices: 34190--34229 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
34180 TTTATTTTAT
34190 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
34211 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
34230 AACTTGAAGT
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:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:34277 original size:33 final size:33
Alignment explanation
Indices: 34224--34322 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
34214 TTTGTTTCAA
34224 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
34256 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
34289 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
34322 T
1 T
34323 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:34351 original size:13 final size:13
Alignment explanation
Indices: 34308--34362 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
34298 TTGGAAGTAT
34308 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
34321 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
34335 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
34348 TTAAGTATTTGAA
1 TTAAGTATTTCAA
34361 TT
1 TT
34363 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:34585 original size:21 final size:21
Alignment explanation
Indices: 34559--34615 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
34549 AGAGCGTGGG
*
34559 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
34580 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
34601 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
34616 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:34806 original size:15 final size:15
Alignment explanation
Indices: 34781--34836 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
34771 ATCTGGAATA
*
34781 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
34796 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
34811 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
34828 TTAAAACCG
1 TTAAAACCG
34837 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:34845 original size:21 final size:18
Alignment explanation
Indices: 34800--34833 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34790 GTTTTTTTAT
34800 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
34817 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
34834 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:34954 original size:16 final size:18
Alignment explanation
Indices: 34926--34959 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
34916 TTTCTATGGG
34926 AAAAAACCGGAT-CGGAT
1 AAAAAACCGGATCCGGAT
34943 AAAAAACC-GATCCGGAT
1 AAAAAACCGGATCCGGAT
34960 CGGATTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (18 bp):
AAAAAACCGGATCCGGAT
Found at i:40233 original size:91 final size:91
Alignment explanation
Indices: 40104--40284 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 91
40094 TAATTAAAAA
* *
40104 TAATCTTTGTTTTTTTATATGGAGTATTCTGATATCTAATGTTTTATTTTAGAGCAAAAAGGCTC
1 TAATCTTTATTTTTTTATATGGAGTATTCTGATATCTAATGCTTTATTTTAGAGCAAAAAGGCTC
* *
40169 TTCTGTGAAATCTGTGGAGGGAATCG
66 TTCTGTGAAATCTATGGAGAGAATCG
* * * *
40195 TAATCTTTATTTTTTT-TCTGGGAGTATTTTGGTCTCTAATGCTTTATTTTAGAGCAAAAAGGCT
1 TAATCTTTATTTTTTTATAT-GGAGTATTCTGATATCTAATGCTTTATTTTAGAGCAAAAAGGCT
*
40259 CTTTTGTGAAATCTATGGAGAGAATC
65 CTTCTGTGAAATCTATGGAGAGAATC
40285 ATTAATCAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 2 0.03
91 78 0.98
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (91 bp):
TAATCTTTATTTTTTTATATGGAGTATTCTGATATCTAATGCTTTATTTTAGAGCAAAAAGGCTC
TTCTGTGAAATCTATGGAGAGAATCG
Found at i:46060 original size:145 final size:145
Alignment explanation
Indices: 45797--46084 Score: 540
Period size: 145 Copynumber: 2.0 Consensus size: 145
45787 CCTAGTATTC
*
45797 TTAGTGCTTGAACTTGGGAACTCAAGAAATAACAACAATTCTTTTATCACTGAGGTTGTTAGATT
1 TTAGTGCTTGAACTTGAGAACTCAAGAAATAACAACAATTCTTTTATCACTGAGGTTGTTAGATT
*
45862 CTATAATGTCCCAAATCTTGGGTTAGTAGTTTCAGGCTAATCCGAGTGGGTTTGAATAAAACCAC
66 CTATAATGTCCCAAATCTTGGGTTAATAGTTTCAGGCTAATCCGAGTGGGTTTGAATAAAACCAC
*
45927 TAACACCACTTTGGG
131 TAACACCAATTTGGG
*
45942 TTAGTGCTTGAACTTGAGACCTCAAGAAATAACAACAATTCTTTTATCACTGAGGTTGTTAGATT
1 TTAGTGCTTGAACTTGAGAACTCAAGAAATAACAACAATTCTTTTATCACTGAGGTTGTTAGATT
46007 CTATAATGTCCCAAATCTTGGGTTAATAGTTTCAGGCTAATCCGAGTGGGTTTGAATAAAACCAC
66 CTATAATGTCCCAAATCTTGGGTTAATAGTTTCAGGCTAATCCGAGTGGGTTTGAATAAAACCAC
46072 TAACACCAATTTG
131 TAACACCAATTTG
46085 AGTTGGTTTG
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 139 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (145 bp):
TTAGTGCTTGAACTTGAGAACTCAAGAAATAACAACAATTCTTTTATCACTGAGGTTGTTAGATT
CTATAATGTCCCAAATCTTGGGTTAATAGTTTCAGGCTAATCCGAGTGGGTTTGAATAAAACCAC
TAACACCAATTTGGG
Found at i:46125 original size:2 final size:2
Alignment explanation
Indices: 46118--46147 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46108 CCAAATTATT
46118 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46148 AAATTTAGGG
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):
TA
Found at i:48376 original size:23 final size:24
Alignment explanation
Indices: 48333--48378 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
48323 AATTAAAAAT
*
48333 ATTTATTTTTAAAATATAATTAAC
1 ATTTATTTTTAAAATAGAATTAAC
*
48357 ATTTATTTTTTAAA-AGAATTAA
1 ATTTATTTTTAAAATAGAATTAA
48379 ATAATTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTATTTTTAAAATAGAATTAAC
Done.