Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000518.1 Hibiscus syriacus cultivar Beakdansim tig00000985_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: 57737
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:798 original size:29 final size:30
Alignment explanation
Indices: 761--819 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
751 CTTACCTTAA
761 AGGTTTAGGGTTTTAGAATGATTA-TAAAG
1 AGGTTTAGGGTTTTAGAATGATTATTAAAG
790 AGGTTTAGGGTTTTAGAATGATTATTAAAG
1 AGGTTTAGGGTTTTAGAATGATTATTAAAG
820 TTTAAGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (30 bp):
AGGTTTAGGGTTTTAGAATGATTATTAAAG
Found at i:4675 original size:21 final size:21
Alignment explanation
Indices: 4646--4702 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
4636 CTAATAGGAT
*
4646 TTGATAGTATCGATACCCCTAG
1 TTGA-AGTATCGATACCCATAG
*
4668 TTGAAGTATCAATACCCATAG
1 TTGAAGTATCGATACCCATAG
4689 TTGAAGTATCGATA
1 TTGAAGTATCGATA
4703 TTGTTAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (21 bp):
TTGAAGTATCGATACCCATAG
Found at i:4987 original size:41 final size:41
Alignment explanation
Indices: 4956--5283 Score: 354
Period size: 41 Copynumber: 7.9 Consensus size: 41
4946 ACATCGCAAA
* * *
4956 AGACTCTTTCTTTAGTGGCGTTTTTATACAAACGCTGCTAT
1 AGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAT
* * * * *
4997 AGACTCATACTATAGTGACGGTTTTACAAAAACGCCGCTAT
1 AGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAT
* * *
5038 AAACTCATACTTTAGTGGCGTTTTTATATAAACACCGCTAT
1 AGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAT
* * * *
5079 AGACTCGTACTTTTGTGGCATTTTAATACCAAACGCCGCTAT
1 AGACTCATACTTTAGTGGCGTTTTTATA-CAAACGCCGCTAT
* * *
5121 AGACGCGTACTTTAGTGGCATTTTTATACAAACGCCGCTAT
1 AGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAT
*
5162 AGACTCATACTTTAGTGGCGTTTTTATATAAACGCCGCTAT
1 AGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAT
** * *
5203 AGACTTGTACTTTTA-TGGCGTTTTAATACCAAACGCCGCTAC
1 AGACTCATAC-TTTAGTGGCGTTTTTATA-CAAACGCCGCTAT
* * * *
5245 AAACACGTACTTCAGTGGCG-TTTTAGTACCAAACGCCGC
1 AGACTCATACTTTAGTGGCGTTTTTA-TA-CAAACGCCGC
5284 AATTGTCATA
Statistics
Matches: 243, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
41 167 0.69
42 76 0.31
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (41 bp):
AGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTAT
Found at i:5145 original size:83 final size:82
Alignment explanation
Indices: 4956--5283 Score: 365
Period size: 83 Copynumber: 4.0 Consensus size: 82
4946 ACATCGCAAA
* * * * *
4956 AGACTCTTTCTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCATACTATAGTGACGGTTT
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGTGGC-GTTT
5021 TACA-A-AAACGCCGCTAT
65 TA-ATACAAACGCCGCTAT
* * * * * * *
5038 AAACTCATACTTTAGTGGCGTTTTTATATAAACACCGCTATAGACTCGTACTTTTGTGGCATTTT
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTT
5103 AATACCAAACGCCGCTAT
66 AATA-CAAACGCCGCTAT
* *
5121 AGACGCGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTT
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTT
* *
5186 TATATAAACGCCGCTAT
66 AATACAAACGCCGCTAT
* * * * * * *
5203 AGACTTGTACTTTTA-TGGCGTTTTAATACCAAACGCCGCTACAAACACGTACTTCAGTGGCGTT
1 AGACTCGTAC-TTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACTCATACTTTAGTGGCGTT
*
5267 TTAGTACCAAACGCCGC
64 TTAATA-CAAACGCCGC
5284 AATTGTCATA
Statistics
Matches: 206, Mismatches: 34, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
80 1 0.00
81 6 0.03
82 81 0.39
83 109 0.53
84 9 0.04
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (82 bp):
AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTT
AATACAAACGCCGCTAT
Found at i:5154 original size:124 final size:123
Alignment explanation
Indices: 4956--5283 Score: 424
Period size: 124 Copynumber: 2.6 Consensus size: 123
4946 ACATCGCAAA
* * * * * * * * *
4956 AGACTCTTTCTTTAGTGGCGTTTTTATA-CAAACGCTGCTATAGACTCATACTATAGTGACGGTT
1 AGACTCGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTAGTGGC-GTT
* *
5020 TTACAAAAACGCCGCTATAAACTCATACTTTAGTGGCGTTTTTATATAAACACCGCTAT
65 TTATACAAACGCCGCTATAAACTCATACTTTAGTGGCGTTTTTATATAAACACCGCTAT
* * *
5079 AGACTCGTACTTTTGTGGCATTTTAATACCAAACGCCGCTATAGACGCGTACTTTAGTGGCATTT
1 AGACTCGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTAGTGGC-GTT
* *
5144 TTATACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTATATAAACGCCGCTAT
65 TTATACAAACGCCGCTATAAACTCATACTTTAGTGGCGTTTTTATATAAACACCGCTAT
* * * * *
5203 AGACTTGTACTTTTATGGCGTTTTAATACCAAACGCCGCTACAAACACGTACTTCAGTGGCGTTT
1 AGACTCGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTAGTGGCGTTT
5268 TAGTACCAAACGCCGC
66 TA-TA-CAAACGCCGC
5284 AATTGTCATA
Statistics
Matches: 178, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
123 28 0.16
124 140 0.79
125 10 0.06
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (123 bp):
AGACTCGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTAGTGGCGTTT
TATACAAACGCCGCTATAAACTCATACTTTAGTGGCGTTTTTATATAAACACCGCTAT
Found at i:9032 original size:43 final size:43
Alignment explanation
Indices: 8915--9367 Score: 418
Period size: 43 Copynumber: 10.6 Consensus size: 43
8905 GGTAATTAGT
* * * *
8915 GGCGTTTGTATCCAAAAACGCCGTTATAGTTATGACGTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
* * * *
8958 GGTGTTTGT-TCTAAAAACGCTGCTACAGATCTGACCTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
* * *
9000 GGCGTTTGTATCCAAAATCGCTGCTATAGATCTGACATTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
* * **
9043 GGCGTTT-TTTCCAAAAACGTCGCTATAGATCCAACCTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
* * * * *
9085 GGCGTTTAT-TCCAAAAATGCCTCTATAGATCTCGATCTTTTAC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGC
* * * *
9128 GGCGTTTGTA-GCAAAAACGCCGCTACATATCTGACCTTTTAC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
* * *
9170 GGCGTTTGTATACAAAAACGCCGCTATAAATCTGACCTTTTGT
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
* * ** * * **
9213 AGTGTTTGT-TCCAAAAATACCACTATAGATCTCGATCTTTTAT
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGC
* *
9256 GGCGTTTGTAT--AAAAACGCCGCTATATATCTCGACCTTTGGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGC
* * *
9298 GGTGTTTGTTTCC-AAAACGCCGCTATAGATCTTGACTTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATC-TGACCTTTTGC
* * *
9341 GGCGTTTTTATTTCACAAACGCCGCTA
1 GGCGTTTGTA-TCCAAAAACGCCGCTA
9368 ACATTAGCGG
Statistics
Matches: 330, Mismatches: 68, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
42 157 0.48
43 158 0.48
44 4 0.01
45 11 0.03
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (43 bp):
GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
Found at i:9059 original size:85 final size:85
Alignment explanation
Indices: 8915--9367 Score: 446
Period size: 85 Copynumber: 5.3 Consensus size: 85
8905 GGTAATTAGT
* * * * * *
8915 GGCGTTTGTATCCAAAAACGCCGTTATAGTTATGACGTTTTGCGGTGTTTGTTCTAAAAACGCTG
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGTGTTTGTTCCAAAAACGCCG
*
8980 CTACAGATCTGACCTTTTGC
66 CTATAGATCTGACCTTTTGC
* * * * * *
9000 GGCGTTTGTATCCAAAATCGCTGCTATAGATCTGACATTTTGCGGCGTTTTTTCCAAAAACGTCG
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGTGTTTGTTCCAAAAACGCCG
**
9065 CTATAGATCCAACCTTTTGC
66 CTATAGATCTGACCTTTTGC
* * * * * * **
9085 GGCGTTTAT-TCCAAAAATGCCTCTATAGATCTCGATCTTTTACGGCGTTTGTAGCAAAAACGCC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGTGTTTGTTCCAAAAACGCC
* * *
9149 GCTACATATCTGACCTTTTAC
65 GCTATAGATCTGACCTTTTGC
* * ** ** *
9170 GGCGTTTGTATACAAAAACGCCGCTATAAATCTGACCTTTTGTAGTGTTTGTTCCAAAAATACCA
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGTGTTTGTTCCAAAAACGCCG
* **
9235 CTATAGATCTCGATCTTTTAT
66 CTATAGATCT-GACCTTTTGC
* *
9256 GGCGTTTGTAT--AAAAACGCCGCTATATATCTCGACCTTTGGCGGTGTTTGTTTCC-AAAACGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGTGTTTG-TTCCAAAAACGC
*
9318 CGCTATAGATCTTGACTTTTTGC
64 CGCTATAGATC-TGACCTTTTGC
* * *
9341 GGCGTTTTTATTTCACAAACGCCGCTA
1 GGCGTTTGTA-TCCAAAAACGCCGCTA
9368 ACATTAGCGG
Statistics
Matches: 296, Mismatches: 63, Indels: 15
0.79 0.17 0.04
Matches are distributed among these distances:
84 38 0.13
85 202 0.68
86 44 0.15
88 12 0.04
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (85 bp):
GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGTGTTTGTTCCAAAAACGCCG
CTATAGATCTGACCTTTTGC
Found at i:14091 original size:3 final size:3
Alignment explanation
Indices: 14080--14141 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
14070 ATTAAAAAAA
*
14080 TAT TA- TAT TAT TA- TAT TA- TAT TAT TA- TATT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
14122 TAA TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
14142 ATAATTTTGG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 8 0.16
3 40 0.80
4 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:14144 original size:18 final size:17
Alignment explanation
Indices: 14080--14141 Score: 78
Period size: 18 Copynumber: 3.8 Consensus size: 17
14070 ATTAAAAAAA
14080 TATTA-TATTATTATAT
1 TATTATTATTATTATAT
14096 TA-TATTATTA-TAT-T
1 TATTATTATTATTATAT
*
14110 TATTATTAATATTAATAT
1 TATTATTATTATT-ATAT
14128 TATTATTATTATTA
1 TATTATTATTATTA
14142 ATAATTTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.08
15 12 0.31
16 8 0.21
17 3 0.08
18 13 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTATTATTATTATAT
Found at i:16046 original size:30 final size:27
Alignment explanation
Indices: 15963--16046 Score: 69
Period size: 30 Copynumber: 2.9 Consensus size: 27
15953 TTCTACGATT
* *
15963 TTTTTAATCATTTAAATGTATGTTTTTG
1 TTTTTAATCCTTTAAAT-TATGTTTTTC
* * *
15991 TTATTTAATCCCTTATATTTTTGTTTATTC
1 TT-TTTAATCCTTTA-AATTATGTTT-TTC
16021 TATTTTAATCCTTTAAATTCATGTTT
1 T-TTTTAATCCTTTAAATT-ATGTTT
16047 GTGCTAGATA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
28 2 0.05
29 19 0.44
30 21 0.49
31 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.61
Consensus pattern (27 bp):
TTTTTAATCCTTTAAATTATGTTTTTC
Found at i:16122 original size:19 final size:20
Alignment explanation
Indices: 16087--16137 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
16077 CTCTTTTAAC
* *
16087 AATT-AATTTGAAGTAAATT
1 AATTAAATTTTAAGTAAATG
16106 AATTAAATTTTAA-TAAATG
1 AATTAAATTTTAAGTAAATG
* *
16125 AATCATATTTTAA
1 AATTAAATTTTAA
16138 CATTATATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (20 bp):
AATTAAATTTTAAGTAAATG
Found at i:17446 original size:16 final size:16
Alignment explanation
Indices: 17425--17456 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17415 GCTTAATCAT
17425 CATAAATAAAAGAAAG
1 CATAAATAAAAGAAAG
17441 CATAAATAAAAGAAAG
1 CATAAATAAAAGAAAG
17457 GTATTGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.12, T:0.12
Consensus pattern (16 bp):
CATAAATAAAAGAAAG
Found at i:22368 original size:92 final size:92
Alignment explanation
Indices: 22211--22403 Score: 325
Period size: 92 Copynumber: 2.1 Consensus size: 92
22201 AGTCTATATT
* *
22211 ATCCATGTGAGTATCTTGAAGGCTCACATCAGCATGAAATGACAGAAATGATCCATATGGGGCAT
1 ATCCATGTGAGTATCCTGAAGGCTCACATCAGCATGAAATAACAGAAATGATCCATATGGGGCAT
22276 TTTGAAGGCCCATTTCAGACAAAAATG
66 TTTGAAGGCCCATTTCAGACAAAAATG
* *
22303 ATCCAT-TGAAGTATCCTGAAGGCTCACATCAGCATGAAATAATAGAGATGATCCATATGGGGCA
1 ATCCATGTG-AGTATCCTGAAGGCTCACATCAGCATGAAATAACAGAAATGATCCATATGGGGCA
22367 TTTTGAAGGCCCATTTCAGACAAAAATG
65 TTTTGAAGGCCCATTTCAGACAAAAATG
*
22395 ATTCATGTG
1 ATCCATGTG
22404 GGGAAATTAA
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
91 2 0.02
92 90 0.96
93 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (92 bp):
ATCCATGTGAGTATCCTGAAGGCTCACATCAGCATGAAATAACAGAAATGATCCATATGGGGCAT
TTTGAAGGCCCATTTCAGACAAAAATG
Found at i:22417 original size:92 final size:91
Alignment explanation
Indices: 22229--22437 Score: 294
Period size: 92 Copynumber: 2.3 Consensus size: 91
22219 GAGTATCTTG
* *
22229 AAGGCTCACATCAGCATGAAATGACAGAAATGATCCATATGGGGCATTTTGAAGGCCCATTTCAG
1 AAGGCTCACATCAGCATGAAATAATAGAAATGATCCATATGGGGCATTTTGAAGGCCCATTTCAG
* *
22294 ACAAAAATGATCCATTGAAGTATCCTG
66 ACAAAAATGATCCATTGAAGAAT-CTA
*
22321 AAGGCTCACATCAGCATGAAATAATAGAGATGATCCATATGGGGCATTTTGAAGGCCCATTTCAG
1 AAGGCTCACATCAGCATGAAATAATAGAAATGATCCATATGGGGCATTTTGAAGGCCCATTTCAG
* **
22386 ACAAAAATGATTCATGTGGGGAAAT-TA
66 ACAAAAATGATCCAT-TGAAG-AATCTA
* *
22413 AAGGCTCACATCAGCAAGAAGTAAT
1 AAGGCTCACATCAGCATGAAATAAT
22438 GTTGAACGCA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
92 100 0.95
93 3 0.03
94 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (91 bp):
AAGGCTCACATCAGCATGAAATAATAGAAATGATCCATATGGGGCATTTTGAAGGCCCATTTCAG
ACAAAAATGATCCATTGAAGAATCTA
Found at i:23825 original size:76 final size:76
Alignment explanation
Indices: 23568--23816 Score: 235
Period size: 76 Copynumber: 3.3 Consensus size: 76
23558 CAACATTTTC
* * * * * * **
23568 AAACAA-ATTTTGTCTCGCTTGAGACA-ATATCATTTAATACGAAG-GATTT-ATCTCACTGGAG
1 AAACAACA-TTTGTCTCGCTTGAGACAGATTTTATTCAAAAC-AAGACATTTCATTTCACTAAAG
23629 ATTGTTTTTCTTA
64 ATTGTTTTTCTTA
* * * * * * *
23642 AAATAGAC-TTCGTCTCACTTGAGACTG-TTTTACTT-GAAAGAAGACATTTCATTTGACTAAAG
1 AAACA-ACATTTGTCTCGCTTGAGACAGATTTTA-TTCAAAACAAGACATTTCATTTCACTAAAG
23704 ATTGTTTTTCTTA
64 ATTGTTTTTCTTA
* *
23717 AAACAAGATTTGTCTCGCTTGAGACAGATTTTATTCAAAACAAGACATTTCATTTCACTACATG-
1 AAACAACATTTGTCTCGCTTGAGACAGATTTTATTCAAAACAAGACATTTCATTTCACTA-AAGA
23781 TTGTTTTTCTTA
65 TTGTTTTTCTTA
*
23793 AAACAACATTTGTGTCGCTTGAGA
1 AAACAACATTTGTCTCGCTTGAGA
23817 TATTTTTTAC
Statistics
Matches: 140, Mismatches: 25, Indels: 18
0.77 0.14 0.10
Matches are distributed among these distances:
73 3 0.02
74 29 0.21
75 46 0.33
76 60 0.43
77 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (76 bp):
AAACAACATTTGTCTCGCTTGAGACAGATTTTATTCAAAACAAGACATTTCATTTCACTAAAGAT
TGTTTTTCTTA
Found at i:23906 original size:40 final size:40
Alignment explanation
Indices: 23835--24290 Score: 743
Period size: 40 Copynumber: 11.4 Consensus size: 40
23825 ACTCGAGATA
23835 AGAAGATTTTATCTCAATTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTC-ATTCAAGATTGTTTTTCCTTGAAAC
*
23876 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAT
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
23916 AGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
23956 AAAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
23996 AGAATATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
* * *
24036 ATAAGATTTTTTCTCACTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
24076 AGAAGATTTTATCTCATTCAAGATTATTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
* * *
24116 ATAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAT
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
24156 AGAAGATTTTATCTTC-TTCAATATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATC-TCATTCAAGATTGTTTTTCCTTGAAAC
* * *
24196 AAAAGATTTTATCTCACTCAAGATTGTTTTTCTTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
24236 AGAAGATTTTATCTCATTCAAGATTATTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
24276 AGAAGATTTTATCTC
1 AGAAGATTTTATCTC
24291 CCTTGAGATA
Statistics
Matches: 382, Mismatches: 31, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
39 2 0.01
40 363 0.95
41 17 0.04
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (40 bp):
AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
Found at i:24041 original size:23 final size:23
Alignment explanation
Indices: 24015--24083 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
24005 TATCTCATTC
24015 AAGATTGTTTTTCCTTGAAACAT
1 AAGATTGTTTTTCCTTGAAACAT
*
24038 AAGA-T-TTTTT-C-T--CAC-T
1 AAGATTGTTTTTCCTTGAAACAT
*
24054 CAAGATTGTTTTTCCTTGAAACAG
1 -AAGATTGTTTTTCCTTGAAACAT
24078 AAGATT
1 AAGATT
24084 TTATCTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 16
0.65 0.06 0.30
Matches are distributed among these distances:
16 1 0.03
17 6 0.17
18 1 0.03
19 6 0.17
20 2 0.06
21 6 0.17
22 1 0.03
23 12 0.34
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAT
Found at i:24422 original size:43 final size:42
Alignment explanation
Indices: 24346--24610 Score: 291
Period size: 43 Copynumber: 6.2 Consensus size: 42
24336 CCTGATTTTC
* * **
24346 AGGGGTTTCTTGAAGAAAACCTTGAGAGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGTTTGAG-GACCATCGTGATATGT
* * * *
24389 AGGGGTTTCTTGATGATAAGTTTTAAGGGCCATCATGATATGT
1 AGGGGTTTCTTGATGACAAG-TTTGAGGACCATCGTGATATGT
* * *
24432 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCATGATATGT
1 AGGGGTTTCTTGATGACAAGTTTG-AGGACCATCGTGATATGT
* *
24475 AGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGACAAGTTTGAG-GACCATCGTGATATGT
* * *
24518 AGGGGTTTATTGATGAAAAGCTTGAGAGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGTTTGAG-GACCATCGTGATATGT
*
24561 AGGGGTTTTTTGATGA-AAGGTTTGAGGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAA-GTTTGA-GGACCATCGTGATATGT
24604 AGGGGTT
1 AGGGGTT
24611 CTTTGGTGAC
Statistics
Matches: 195, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
42 8 0.04
43 180 0.92
44 7 0.04
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.31
Consensus pattern (42 bp):
AGGGGTTTCTTGATGACAAGTTTGAGGACCATCGTGATATGT
Found at i:24508 original size:86 final size:84
Alignment explanation
Indices: 24346--24611 Score: 329
Period size: 86 Copynumber: 3.1 Consensus size: 84
24336 CCTGATTTTC
* * *
24346 AGGGGTTTCTTGAAGAAAACCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGATGATAAGTT
1 AGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTT-TTGATGA-AAGTT
* * *
24411 TTA-AGGGCCATCATGATATGT
64 TGAGA-GACCATCGTGATATGT
* * *
24432 AGGGGTTCCTTGATGACAAGCTTGA-AGGACCATCATGATATGTAGGGGTTCTTTGATGACAAGC
1 AGGGGTTCCTTGATGAAAAGCTTGAGA-GACCATCGTGATATGTAGGGGTT-TTTGATGA-AAGT
*
24496 TTGAGAAACCATCGTGATATGT
63 TTGAGAGACCATCGTGATATGT
**
24518 AGGGGTTTATTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTTTTGATGAAAGGTT
1 AGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGG-TTTTTGATGAAA-GTT
*
24583 TGAGGGACCATCGTGATATGT
64 TGAGAGACCATCGTGATATGT
24604 AGGGGTTC
1 AGGGGTTC
24612 TTTGGTGACA
Statistics
Matches: 155, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
85 3 0.02
86 147 0.95
87 5 0.03
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (84 bp):
AGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTTTGATGAAAGTTTG
AGAGACCATCGTGATATGT
Found at i:24576 original size:129 final size:129
Alignment explanation
Indices: 24366--24622 Score: 365
Period size: 129 Copynumber: 2.0 Consensus size: 129
24356 TGAAGAAAAC
* * * * * *
24366 CTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGATGATAAGTTTTAAGGGCCATCATGATATG
1 CTTGAGAAACCATCGTGATATGTAGGGGTTTATTGATGAAAAGCTTGAAGGACCATCATGATATG
24431 TAGGGGTTCCTTGATGACAA-GCTTGAAGGACCATCATGATATGTAGGGGTTCTTTGATGACAAG
66 TAGGGGTTCCTTGATGA-AAGGCTTGAAGGACCATCATGATATGTAGGGGTTCTTTGATGACAAG
*
24495 CTTGAGAAACCATCGTGATATGTAGGGGTTTATTGATGAAAAGCTTG-AGAGACCATCGTGATAT
1 CTTGAGAAACCATCGTGATATGTAGGGGTTTATTGATGAAAAGCTTGAAG-GACCATCATGATAT
** * * * *
24559 GTAGGGGTTTTTTGATGAAAGGTTTGAGGGACCATCGTGATATGTAGGGGTTCTTTGGTGACAA
65 GTAGGGGTTCCTTGATGAAAGGCTTGAAGGACCATCATGATATGTAGGGGTTCTTTGATGACAA
24623 TTAAGAAACT
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
128 4 0.04
129 109 0.96
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (129 bp):
CTTGAGAAACCATCGTGATATGTAGGGGTTTATTGATGAAAAGCTTGAAGGACCATCATGATATG
TAGGGGTTCCTTGATGAAAGGCTTGAAGGACCATCATGATATGTAGGGGTTCTTTGATGACAAG
Found at i:24777 original size:89 final size:89
Alignment explanation
Indices: 24624--24866 Score: 366
Period size: 89 Copynumber: 2.7 Consensus size: 89
24614 TGGTGACAAT
* * *
24624 TAAGAAACTGAGACTTCAGGGGTTTCTTGATTTTTTAAGTCCGTCGGGCCATCCATAAGACCTTC
1 TAAGAAACTAAGCCTTC-GGGGTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
24689 AGTGCAGGATGTTTTCAAATGAGATC
64 AGTGCAGGATGTTTTCAAATGAGATC
* *
24715 TAAGAAACTAAGCCTTCGGGAGTTTCTTGA-TTTTAAGTCCTTTGGGACATCCATAAGACCTTCA
1 TAAGAAACTAAGCCTTCGGG-GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
24779 GTGCAGGATGTTTTCAAATGAGATC
65 GTGCAGGATGTTTTCAAATGAGATC
*
24804 TAAGAAACTGAA-CCTTCGGGGGTTTCTTGATTTTTAAGTCATTCGGGCCA-CCATAAGACCTTC
1 TAAGAAACT-AAGCCTTC-GGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
24867 GGGAAAGATG
Statistics
Matches: 140, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
89 92 0.66
90 24 0.17
91 24 0.17
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (89 bp):
TAAGAAACTAAGCCTTCGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAG
TGCAGGATGTTTTCAAATGAGATC
Found at i:25123 original size:12 final size:12
Alignment explanation
Indices: 25106--25161 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
25096 AAAAATAATA
25106 TATTATTATATT
1 TATTATTATATT
25118 TATTATTATATT
1 TATTATTATATT
* *
25130 TATAATTA-ATAA
1 TATTATTATAT-T
25142 TATTATTAGTA-T
1 TATTATTA-TATT
25154 TATTATTA
1 TATTATTA
25162 ATAATAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 2 0.05
12 34 0.92
14 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TATTATTATATT
Found at i:25156 original size:24 final size:24
Alignment explanation
Indices: 25118--25167 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
25108 TTATTATATT
25118 TATTATTATATTTATAATTAATAA
1 TATTATTATATTTATAATTAATAA
*
25142 TATTATTAGTA-TTATTATTAATAA
1 TATTATTA-TATTTATAATTAATAA
25166 TA
1 TA
25168 ATTTTGGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TATTATTATATTTATAATTAATAA
Found at i:48931 original size:35 final size:36
Alignment explanation
Indices: 48851--48933 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
48841 AGATACTATC
* *
48851 TATTCATCACCACCTTCCATCACCATTTTCACGCCTA
1 TATT-ATCACCACATTCCATCACCATTATCACGCCTA
** * *
48888 TAACATCACCATATTCCATTACCA-TATCACGCCTA
1 TATTATCACCACATTCCATCACCATTATCACGCCTA
48923 TATTATCACCA
1 TATTATCACCA
48934 ACTTATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 19 0.50
36 17 0.45
37 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TATTATCACCACATTCCATCACCATTATCACGCCTA
Found at i:55220 original size:26 final size:29
Alignment explanation
Indices: 55191--55244 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 29
55181 TTAGTCACTG
*
55191 CCTTGCATGGTT-TATTT-A-TTATTTTT
1 CCTTCCATGGTTCTATTTGAGTTATTTTT
*
55217 CCTTCCATGTTTCTATTTGAGTTATTTT
1 CCTTCCATGGTTCTATTTGAGTTATTTT
55245 AGTCATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
27 5 0.22
28 1 0.04
29 7 0.30
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.59
Consensus pattern (29 bp):
CCTTCCATGGTTCTATTTGAGTTATTTTT
Done.