Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007165.1 Hibiscus syriacus cultivar Beakdansim tig00018776_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: 79645
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3041 original size:31 final size:31
Alignment explanation
Indices: 3006--3064 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2996 TTTAATCACA
*
3006 TTATCGTTTTATTAGGTTTTGGCCACTTATG
1 TTATCGTTTTATTAAGTTTTGGCCACTTATG
*
3037 TTATCGTTTTATTAAGTTTTGGTCACTT
1 TTATCGTTTTATTAAGTTTTGGCCACTT
3065 GGACGTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (31 bp):
TTATCGTTTTATTAAGTTTTGGCCACTTATG
Found at i:4496 original size:31 final size:31
Alignment explanation
Indices: 4429--4497 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4419 ATTCAATGTC
** * *
4429 CAAGTGACCAAAACTTAATACAACGATAACA
1 CAAGTGACCAAAACACAATAAAACAATAACA
* *
4460 TAAGTGACCAAAACACAATAAAACAATAACG
1 CAAGTGACCAAAACACAATAAAACAATAACA
4491 CAAGTGA
1 CAAGTGA
4498 TTAAAAGTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.54, C:0.20, G:0.12, T:0.14
Consensus pattern (31 bp):
CAAGTGACCAAAACACAATAAAACAATAACA
Found at i:20551 original size:81 final size:81
Alignment explanation
Indices: 20454--20614 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 81
20444 TGGCAAGGAT
*
20454 AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATGTGGCAGCTATAATCAAATATGCA
1 AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATATGGCAGCTATAATCAAATATGCA
20519 TGTGGCAGTGGAAGAC
66 TGTGGCAGTGGAAGAC
20535 AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATATGGCAGCTATAATCAAATATGCA
1 AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATATGGCAGCTATAATCAAATATGCA
*
20600 TGTGGTAGTGGAAGA
66 TGTGGCAGTGGAAGA
20615 TATAATGGTG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.25
Consensus pattern (81 bp):
AATTGAGTAGAAACTACATGAATTAACATGTGCATGAAAATATGGCAGCTATAATCAAATATGCA
TGTGGCAGTGGAAGAC
Found at i:25796 original size:18 final size:18
Alignment explanation
Indices: 25769--25805 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25759 GTGGGGATTT
* *
25769 ATAGATTAAGAGAAATAA
1 ATAGAATAAGAAAAATAA
25787 ATAGAATAAGAAAAATAA
1 ATAGAATAAGAAAAATAA
25805 A
1 A
25806 AAGATTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (18 bp):
ATAGAATAAGAAAAATAA
Found at i:26491 original size:23 final size:21
Alignment explanation
Indices: 26457--26504 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
26447 CTAAAAATCT
26457 TAAAAACAAAGAAAAGATAATTCC
1 TAAAAACAAAG---AGATAATTCC
26481 TAAAAAC-AAGAGATAATTCC
1 TAAAAACAAAGAGATAATTCC
26501 TAAA
1 TAAA
26505 GATAATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.58
23 3 0.12
24 7 0.29
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.19
Consensus pattern (21 bp):
TAAAAACAAAGAGATAATTCC
Found at i:33451 original size:23 final size:23
Alignment explanation
Indices: 33381--33454 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
33371 ACATATAGGT
*
33381 CAATGAAAGCAGAACCATCTGAA-
1 CAATGAAAGCAGAACCATC-AAAC
* **
33404 CAACGAAATTA-AACCACATACAAAC
1 CAATGAAAGCAGAA-C-CAT-CAAAC
33429 CAATGAAAGCAGAACCATCAAAC
1 CAATGAAAGCAGAACCATCAAAC
33452 CAA
1 CAA
33455 CAAGCACTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
22 2 0.05
23 17 0.44
24 8 0.21
25 10 0.26
26 2 0.05
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.11
Consensus pattern (23 bp):
CAATGAAAGCAGAACCATCAAAC
Found at i:39749 original size:20 final size:20
Alignment explanation
Indices: 39724--39773 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
39714 TTAGTTTCCA
39724 AAATCGCAACGCGAATCTGT
1 AAATCGCAACGCGAATCTGT
39744 AAATCGCAACGCGAATCTGT
1 AAATCGCAACGCGAATCTGT
39764 AAATCGCAAC
1 AAATCGCAAC
39774 ACATAAGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGAATCTGT
Found at i:39790 original size:20 final size:21
Alignment explanation
Indices: 39767--39813 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
39757 AATCTGTAAA
* *
39767 TCGCAACACATAAGTC-AAAT
1 TCGCAACAAAGAAGTCAAAAT
39787 TCGCAACAAAGAAGTCAAAAT
1 TCGCAACAAAGAAGTCAAAAT
39808 TCGCAA
1 TCGCAA
39814 AGCGCGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.47, C:0.23, G:0.13, T:0.17
Consensus pattern (21 bp):
TCGCAACAAAGAAGTCAAAAT
Found at i:39996 original size:22 final size:22
Alignment explanation
Indices: 39968--40018 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
39958 CTACGGCGAC
**
39968 ATCCGTCCCCATCTCCGGTGAA
1 ATCCGTCCCCATCTCCGACGAA
39990 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
40012 ATCCGTC
1 ATCCGTC
40019 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:40408 original size:19 final size:20
Alignment explanation
Indices: 40384--40437 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
40374 AAATGGCAAC
40384 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
* *
40403 GCGATTTTCATTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
40423 GCGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
40438 AGAAACTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:42193 original size:21 final size:21
Alignment explanation
Indices: 42169--42218 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
42159 TGGTGCATGG
42169 CGTGATGAGGTACA-GTCTTTA
1 CGTGATGAGGTACAGGT-TTTA
* *
42190 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTACAGGTTTTA
*
42211 CGCGATGA
1 CGTGATGA
42219 CAATGGTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTACAGGTTTTA
Found at i:42583 original size:21 final size:21
Alignment explanation
Indices: 42530--42593 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
42520 CTGATTCACC
42530 TGTCATCGTTCAAGAGGCCTCT
1 TGTCATCGTTCAAGAGGCC-CT
** *
42552 CAT-ATCCTTCAAGAGGCCCT
1 TGTCATCGTTCAAGAGGCCCT
42572 TGTCATCGTTCAAGAGGTCCCT
1 TGTCATCGTTCAAGAGG-CCCT
42594 CCCACCGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 3 0.09
21 26 0.76
22 5 0.15
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TGTCATCGTTCAAGAGGCCCT
Found at i:43992 original size:64 final size:64
Alignment explanation
Indices: 43915--44063 Score: 217
Period size: 64 Copynumber: 2.3 Consensus size: 64
43905 AAATTGATGT
43915 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
* * * *** * *
43979 ATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTTCTTGTTTAATTT
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
*
44043 ATCTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
44064 GTTTTAAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 75 1.00
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
Found at i:44187 original size:20 final size:20
Alignment explanation
Indices: 44164--44218 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
44154 TTTTCGCGTT
* *
44164 GCGATAGTCAAATTCGCAAG
1 GCGAAAGTCAAATTCGCAAC
*
44184 GCGAAAGTTAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
44204 GCGAAAGTCAAATTC
1 GCGAAAGTCAAATTC
44219 ACGTTGCGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:44235 original size:14 final size:14
Alignment explanation
Indices: 44216--44245 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
44206 GAAAGTCAAA
44216 TTCACGTTGCGATT
1 TTCACGTTGCGATT
44230 TTCACGTTGCGATT
1 TTCACGTTGCGATT
44244 TT
1 TT
44246 GCGTTTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (14 bp):
TTCACGTTGCGATT
Found at i:44496 original size:6 final size:6
Alignment explanation
Indices: 44487--44521 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
44477 TTGTGATTGG
**
44487 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
44522 CATTTGCTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:44503 original size:18 final size:18
Alignment explanation
Indices: 44480--44520 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
44470 AAGCCGGTTG
*
44480 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
44498 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
44516 TGATT
1 TGATT
44521 TCATTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:44750 original size:16 final size:16
Alignment explanation
Indices: 44728--44767 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
44718 GAAATCATTG
*
44728 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
44744 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
44760 AAAAATTA
1 AAAAATTA
44768 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:45051 original size:20 final size:20
Alignment explanation
Indices: 44945--45077 Score: 83
Period size: 20 Copynumber: 6.6 Consensus size: 20
44935 AAAATTCGTA
* *
44945 TTGCGAATTCGAAAAT-AGAG
1 TTGCGAATTTGAAAATCA-CG
*
44965 TTGCGAA-TTCAGAAATCGA-G
1 TTGCGAATTTGA-AAATC-ACG
* *
44985 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAAATCA-CG
* * * *
45006 TTGTGAATTTGTAAATCGCA
1 TTGCGAATTTGAAAATCACG
**
45026 ACGCGAATTTGAAAATCACG
1 TTGCGAATTTGAAAATCACG
* *
45046 TTGCGAATTTGGAAATCGCG
1 TTGCGAATTTGAAAATCACG
*
45066 TTGTGAATTTGA
1 TTGCGAATTTGA
45078 CTTCTGTGTT
Statistics
Matches: 85, Mismatches: 22, Indels: 12
0.71 0.18 0.10
Matches are distributed among these distances:
19 3 0.04
20 63 0.74
21 18 0.21
22 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCACG
Found at i:45064 original size:40 final size:41
Alignment explanation
Indices: 44947--45064 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 41
44937 AATTCGTATT
* * ** **
44947 GCGAATTCGAAAAT-AGAGTTGCGAATTCAGAAATCG-AGTT
1 GCGAATTTGAAAATCAGCGTTGCGAATTTGGAAATCGCA-AC
* * * *
44987 GCGAATTTGAAATTCAGTGTTGTGAATTTGTAAATCGCAAC
1 GCGAATTTGAAAATCAGCGTTGCGAATTTGGAAATCGCAAC
45028 GCGAATTTGAAAATCA-CGTTGCGAATTTGGAAATCGC
1 GCGAATTTGAAAATCAGCGTTGCGAATTTGGAAATCGC
45065 GTTGTGAATT
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
40 30 0.48
41 32 0.51
42 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (41 bp):
GCGAATTTGAAAATCAGCGTTGCGAATTTGGAAATCGCAAC
Found at i:46109 original size:22 final size:22
Alignment explanation
Indices: 46068--46135 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
46058 CTCGTATAAA
46068 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
46091 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
46113 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
46135 T
1 T
46136 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:46380 original size:30 final size:30
Alignment explanation
Indices: 46345--46407 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
46335 TCATATCGCG
*
46345 TAGACATAGT-ATTTCCATACCTTTAACACA
1 TAGACATA-TCATTTACATACCTTTAACACA
*
46375 TAGACATATCATTTACATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTAACACA
46405 TAG
1 TAG
46408 TTCATATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (30 bp):
TAGACATATCATTTACATACCTTTAACACA
Found at i:46462 original size:29 final size:29
Alignment explanation
Indices: 46429--46500 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
46419 TTTTCTGCAT
* **
46429 ATTCAAGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
46458 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
46487 ATTCATGTCATGTA
1 ATTCATGTCATGTA
46501 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:46922 original size:68 final size:67
Alignment explanation
Indices: 46803--46955 Score: 209
Period size: 68 Copynumber: 2.3 Consensus size: 67
46793 TTTTTCTCAT
* * *
46803 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT-CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TAC-
46868 A-TGA
63 ATTGA
* * * *
46872 GGGGGTATCGGTTCCTCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCATT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACATT
46937 GA
66 GA
46939 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
46956 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 1 0.01
67 21 0.28
68 41 0.55
69 12 0.16
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACATT
GA
Found at i:53061 original size:22 final size:22
Alignment explanation
Indices: 53020--53087 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
53010 CTCGTATAAA
53020 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
53043 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
53065 TGCACCGAAGTGCCCATAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
53087 T
1 T
53088 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 32 0.73
23 12 0.27
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:53332 original size:30 final size:30
Alignment explanation
Indices: 53297--53359 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
53287 TCATATCGCG
*
53297 TAGACATAGT-ATTTCCATACCTTTAACACA
1 TAGACATA-TCATTTACATACCTTTAACACA
*
53327 TAGACATATCATTTACATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTAACACA
53357 TAG
1 TAG
53360 TTCATATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (30 bp):
TAGACATATCATTTACATACCTTTAACACA
Found at i:53414 original size:29 final size:29
Alignment explanation
Indices: 53381--53452 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
53371 TTTTCTGCAT
* **
53381 ATTCAAGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
53410 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
53439 ATTCATGTCATGTA
1 ATTCATGTCATGTA
53453 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:53872 original size:68 final size:67
Alignment explanation
Indices: 53755--53905 Score: 214
Period size: 68 Copynumber: 2.2 Consensus size: 67
53745 TTTTTCTCAT
* * *
53755 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA-
1 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TAC-AT
53819 TGAG
64 TGAG
* * * *
53823 GGGGTATCGGTTCCTCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCATTG
1 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACATTG
53888 AG
66 AG
53890 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
53906 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
66 1 0.01
67 21 0.28
68 52 0.70
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACATTG
AG
Found at i:56214 original size:17 final size:18
Alignment explanation
Indices: 56175--56221 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
56165 TGTTTCTGAG
*
56175 GGAATTAGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
56193 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
56210 GGAATTGGAATC
1 GGAATTGGAATC
56222 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:57653 original size:49 final size:48
Alignment explanation
Indices: 57576--57671 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 48
57566 TTTTATGTTA
57576 CCAATAGAATGATACATGTGTACGAATCTTAACTTCAATCAATCAATT
1 CCAATAGAATGATACATGTGTACGAATCTTAACTTCAATCAATCAATT
*
57624 CCAATAGAATGATATTATGTGTACGAATCTTAACTTCAATCAATCAAT
1 CCAATAGAATGATA-CATGTGTACGAATCTTAACTTCAATCAATCAAT
57672 CACACATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 14 0.30
49 32 0.70
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (48 bp):
CCAATAGAATGATACATGTGTACGAATCTTAACTTCAATCAATCAATT
Found at i:59179 original size:47 final size:48
Alignment explanation
Indices: 59093--59184 Score: 111
Period size: 47 Copynumber: 1.9 Consensus size: 48
59083 AGAATAAAAT
*
59093 AATAAAATAATAAATATAAATAGTTTAAAATAAAAGATAATGATATAA
1 AATAAAATAATAAATATAAATAGTTTAAAATAAAAGATAAAGATATAA
*
59141 AATAAAATAA-ATAAT-TAAATA-TTTATAAGAT-AAGGATAAAGATA
1 AATAAAATAATA-AATATAAATAGTTTA-AA-ATAAAAGATAAAGATA
59185 AAACGGGAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
46 4 0.10
47 20 0.51
48 15 0.38
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (48 bp):
AATAAAATAATAAATATAAATAGTTTAAAATAAAAGATAAAGATATAA
Found at i:62313 original size:54 final size:53
Alignment explanation
Indices: 62227--62679 Score: 627
Period size: 54 Copynumber: 8.4 Consensus size: 53
62217 TGCATTTTTA
* *
62227 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCG
1 TATCGGCACTATGTGTGCAACCCAC-AAATTCATAATGAGTTTGTGAATTACCG
*
62281 TATCGGCACTATGTGTGCAACCCACAACATTCATAACGAGTTTGTGAATTACCG
1 TATCGGCACTATGTGTGCAACCCACAA-ATTCATAATGAGTTTGTGAATTACCG
* * *
62335 TATCGACACTATGTGTGCAACCCATGAAATTTATAATGAGTTTGTGAATTACCG
1 TATCGGCACTATGTGTGCAACCCA-CAAATTCATAATGAGTTTGTGAATTACCG
* * *
62389 TATCGGCACTATATGTGCAACCCACAAAATTCGTAATGAGTTTGTGAATTATCG
1 TATCGGCACTATGTGTGCAACCCAC-AAATTCATAATGAGTTTGTGAATTACCG
** * *
62443 TATCAACACTATATGTGCAACCCACATAATTCATAATGAGTTTTTGAATTACCG
1 TATCGGCACTATGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCG
*
62497 TATCGGCACTATGTCTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCG
1 TATCGGCACTATGTGTGCAACCCAC-AAATTCATAATGAGTTTGTGAATTACCG
* * *
62551 TATCGACACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCG
1 TATCGGCACTATGTGTGCAACCCAC-AAATTCATAATGAGTTTGTGAATTACCG
* * * * *
62605 TATCAGTACTATGCGTGCAACGCACAGAATTCATAATGAGTTTGTAAATTACCG
1 TATCGGCACTATGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCG
*
62659 TATCGACACTATGTGTGCAAC
1 TATCGGCACTATGTGTGCAAC
62680 TCTCATAATA
Statistics
Matches: 354, Mismatches: 39, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
53 2 0.01
54 349 0.99
55 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (53 bp):
TATCGGCACTATGTGTGCAACCCACAAATTCATAATGAGTTTGTGAATTACCG
Found at i:62430 original size:108 final size:108
Alignment explanation
Indices: 62227--62679 Score: 692
Period size: 108 Copynumber: 4.2 Consensus size: 108
62217 TGCATTTTTA
* * *
62227 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
1 TATCGACACTATGTGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
* *
62292 TGTGTGCAACCCACAACATTCATAACGAGTTTGTGAATTACCG
66 TGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCG
* *
62335 TATCGACACTATGTGTGCAACCCATGAAATTTATAATGAGTTTGTGAATTACCGTATCGGCACTA
1 TATCGACACTATGTGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
* * *
62400 TATGTGCAACCCACAAAATTCGTAATGAGTTTGTGAATTATCG
66 TGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCG
* * *
62443 TATCAACACTATATGTGCAACCCAC-ATAATTCATAATGAGTTTTTGAATTACCGTATCGGCACT
1 TATCGACACTATGTGTGCAACCCACGA-AATTCATAATGAGTTTGTGAATTACCGTATCGGCACT
*
62507 ATGTCTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCG
65 ATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCG
* * * *
62551 TATCGACACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGTACTA
1 TATCGACACTATGTGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
* * * *
62616 TGCGTGCAACGCACAGAATTCATAATGAGTTTGTAAATTACCG
66 TGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCG
62659 TATCGACACTATGTGTGCAAC
1 TATCGACACTATGTGTGCAAC
62680 TCTCATAATA
Statistics
Matches: 312, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
107 1 0.00
108 311 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (108 bp):
TATCGACACTATGTGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
TGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCG
Found at i:62494 original size:162 final size:161
Alignment explanation
Indices: 62227--62748 Score: 691
Period size: 162 Copynumber: 3.3 Consensus size: 161
62217 TGCATTTTTA
*
62227 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTA
1 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTA
*
62292 TGTGTGCAACCCACAACATTCATAACGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACC
66 TGTGTGCAACCCACAA-ATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACC
** *
62357 CATGAAATTTATAATGAGTTTGTGAATTACCG
130 CACAAAATTCATAATGAGTTTGTGAATTACCG
* * ** * * *
62389 TATCGGCACTATATGTGCAACCCACAAAATTCGTAATGAGTTTGTGAATTATCGTATCAACACTA
1 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTA
* * * *
62454 TATGTGCAACCCACATAATTCATAATGAGTTTTTGAATTACCGTATCGGCACTATGTCTGCAACC
66 TGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACC
62519 CACAAAATTCATAATGAGTTTGTGAATTACCG
130 CACAAAATTCATAATGAGTTTGTGAATTACCG
* *
62551 TATCGACACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGTACTA
1 TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTA
* * *
62616 TGCGTGCAACGCACAGAATTCATAATGAGTTTGTAAATTACCGTATCGACACTATGTGTGCAA--
66 TGTGTGCAACCCACA-AATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACC
* * * *
62679 CTC-----TCATAATAAGTTTGTGAATAACTG
130 CACAAAATTCATAATGAGTTTGTGAATTACCG
* * * *
62706 TATCGACACTATGTGTACAA-TCCATGGAATTCATAATAAGTTT
1 TATCGGCACTATGTGTGCAACT-CACGGAATTCATAATGAGTTT
62749 ATGATTTTCC
Statistics
Matches: 318, Mismatches: 40, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
154 1 0.00
155 59 0.19
160 2 0.01
162 255 0.80
163 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (161 bp):
TATCGGCACTATGTGTGCAACTCACGGAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTA
TGTGTGCAACCCACAAATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCC
ACAAAATTCATAATGAGTTTGTGAATTACCG
Found at i:68033 original size:6 final size:6
Alignment explanation
Indices: 68019--68092 Score: 100
Period size: 6 Copynumber: 12.5 Consensus size: 6
68009 AATAAAAATT
*
68019 AAAATG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG
68067 AAAACTTG AAAA-G AAAA-G AAAA-G AAA
1 AAAAC--G AAAACG AAAACG AAAACG AAA
68093 GTAAACAATT
Statistics
Matches: 65, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
5 14 0.22
6 46 0.71
8 5 0.08
ACGTcount: A:0.69, C:0.11, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAACG
Done.