Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004987.1 Hibiscus syriacus cultivar Beakdansim tig00011188_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: 61443
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5943 original size:183 final size:182
Alignment explanation
Indices: 5518--6508 Score: 1409
Period size: 183 Copynumber: 5.5 Consensus size: 182
5508 TCATTCAAAT
* * *
5518 ATGTATCGATACATAACAATATAACAGGT-AAA-ATG--ATAATCAGG-TTCAATATGAC-AAAC
1 ATGTATCGATACGTAACAATATAACAGGTAAAATATGACAAAATC-GGTTTCATTATGACAAAAC
*
5577 CGATAAAGCGCTACCAGATATG-TGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTA-TG
65 CGGTAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATTG
* * * *
5640 AAATTTAAA-AAAAACAATAATAGTGCCTATAAAGTATCGATATTTTAT-AA-
130 AATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
* * *
5690 ATGTATCGATACGTAACAATATAAAATGTAAAATATGACAAAACCGGTTTCATTATGACAAAACC
1 ATGTATCGATACGTAACAATATAACAGGTAAAATATGACAAAATCGGTTTCATTATGACAAAACC
*
5755 GGTAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTTAAATAAGTATC-AGTACTTATTG
66 GGTAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGA-TACTTATTG
**
5819 AATTTTAAAGAAAAGTGATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
130 AATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
* *
5872 ATGTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATCGATTTCATTATGACAAAAT
1 ATGTATCGATACGTAACAATATAACAGGT-AAAATATGACAAAATCGGTTTCATTATGACAAAAC
* * *
5937 CGGTAAAGCGCTACC-GAATATGTTGAAGGTGTCGATTTCATTCAAATAAGTATCGATACTTATG
65 CGGTAAAGCGCTACCAG-ATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATT
* *
6001 GAATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATATTTTACAAAC
129 GAATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
* **
6055 ATGTATCGGTACGTAACAATAT-ACAGGTAAAATATGAC-AAGCCGGTTTCATTATGAC-AAACC
1 ATGTATCGATACGTAACAATATAACAGGTAAAATATGACAAAATCGGTTTCATTATGACAAAACC
* *
6117 GGTAAAGCGCTACCGGATATGTTGAAGGTATCGATTCCATTCAAAT-A--ATCGATACTTATGGA
66 GGTAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATTGA
* * *
6179 ATTTTAAAGAAAAACAATAATAGCTCCTATAAAGTATCGATACTTTAAAAAC
131 ATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
* *
6231 ATGTATCGATACATAACAATATAACATGTAAAATATGA-AAAATCGGTTTCATTATGACAAAACC
1 ATGTATCGATACGTAACAATATAACAGGTAAAATATGACAAAATCGGTTTCATTATGACAAAACC
* * * *
6295 GGTAAATCGTTACCAGATATGTTGAAGGTATCAATTTCATTCAAATAAGTATCGATACTT-TTGG
66 GGTAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATT-G
*
6359 AATTTAAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
130 AATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
*
6412 ATGTATCGATACGTAACAATATAACAGGTAAAATATGACAAAAT-GG-TTCATTATGACGAAACC
1 ATGTATCGATACGTAACAATATAACAGGTAAAATATGACAAAATCGGTTTCATTATGACAAAACC
* * *
6475 GAT-AAGCGCTATCGGATATGTTGAAGGTATCGAT
66 GGTAAAGCGCTACCAGATATGTTGAAGGTATCGAT
6509 ACTTTAATAA
Statistics
Matches: 733, Mismatches: 62, Indels: 41
0.88 0.07 0.05
Matches are distributed among these distances:
172 26 0.04
173 3 0.00
174 3 0.00
175 2 0.00
176 97 0.13
177 57 0.08
178 83 0.11
179 83 0.11
180 70 0.10
181 110 0.15
182 39 0.05
183 159 0.22
184 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (182 bp):
ATGTATCGATACGTAACAATATAACAGGTAAAATATGACAAAATCGGTTTCATTATGACAAAACC
GGTAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATTGA
ATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
Found at i:6371 original size:357 final size:360
Alignment explanation
Indices: 5518--6508 Score: 1467
Period size: 357 Copynumber: 2.8 Consensus size: 360
5508 TCATTCAAAT
* *
5518 ATGTATCGATACATAACAATATAACAGGT-AAA-ATG-ATAATCAGG-TTCAATATGAC-AAACC
1 ATGTATCGATACATAACAATATAACAGGTAAAATATGAAAAATC-GGTTTCATTATGACAAAACC
* * *
5578 GATAAAGCGCTACCAGATATG-TGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATGAA
65 GGTAAAGCGCTACCAGATATGTTGAAGGTATCGATTTCATTCAAATAAGTATCGATACTTATGGA
* *
5642 ATTTAAAA-AAAA-CAATAATAGTGCCTATAAAGTATCGATATTTTATAA-ATGTATCGATACGT
130 ATTTAAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATATTTTAAAACATGTATCGATACGT
* *
5704 AACAATATAAAATGTAAAATATGACAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTACC
195 AACAATATAACAGGTAAAATATGAC-AAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTACC
* * * *
5769 AGATATGTTGAAGGTATCGATTCCATTTAAATAAGTATCAGTACTTATTGAATTTTAAAGAAAAG
259 GGATATGTTGAAGGTATCGATTCCATTCAAATAAG-ATCAGTACTTATGGAATTTTAAAGAAAAA
** *
5834 TGATAATAGCGCCTATAAAGTATCGATACTTTATAAAC
323 CAATAATAGCGCCTATAAAGTATCGATACTTTAAAAAC
* * *
5872 ATGTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATCGATTTCATTATGACAAAAT
1 ATGTATCGATACATAACAATATAACAGGT-AAAATATGA-AAAATCGGTTTCATTATGACAAAAC
*
5937 CGGTAAAGCGCTACC-GAATATGTTGAAGGTGTCGATTTCATTCAAATAAGTATCGATACTTATG
64 CGGTAAAGCGCTACCAG-ATATGTTGAAGGTATCGATTTCATTCAAATAAGTATCGATACTTATG
* *
6001 GAATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATATTTTACAAACATGTATCGGTA
128 GAATTTAAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATATTTTA-AAACATGTATCGATA
*
6066 CGTAACAATAT-ACAGGTAAAATATGACAAGCCGGTTTCATTATGAC-AAACCGGTAAAGCGCTA
192 CGTAACAATATAACAGGTAAAATATGACAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTA
6129 CCGGATATGTTGAAGGTATCGATTCCATTCAAAT-A-ATC-GATACTTATGGAATTTTAAAGAAA
257 CCGGATATGTTGAAGGTATCGATTCCATTCAAATAAGATCAG-TACTTATGGAATTTTAAAGAAA
*
6191 AACAATAATAGCTCCTATAAAGTATCGATACTTTAAAAAC
321 AACAATAATAGCGCCTATAAAGTATCGATACTTTAAAAAC
*
6231 ATGTATCGATACATAACAATATAACATGTAAAATATGAAAAATCGGTTTCATTATGACAAAACCG
1 ATGTATCGATACATAACAATATAACAGGTAAAATATGAAAAATCGGTTTCATTATGACAAAACCG
* * * *
6296 GTAAATCGTTACCAGATATGTTGAAGGTATCAATTTCATTCAAATAAGTATCGATACTTTTGGAA
66 GTAAAGCGCTACCAGATATGTTGAAGGTATCGATTTCATTCAAATAAGTATCGATACTTATGGAA
*
6361 TTTAAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACGT
131 TTTAAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATATTTTA-AAACATGTATCGATACGT
** * * *
6426 AACAATATAACAGGTAAAATATGACAAAATGG-TTCATTATGACGAAACCGAT-AAGCGCTATCG
195 AACAATATAACAGGTAAAATATGACAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTACCG
6489 GATATGTTGAAGGTATCGAT
260 GATATGTTGAAGGTATCGAT
6509 ACTTTAATAA
Statistics
Matches: 578, Mismatches: 42, Indels: 31
0.89 0.06 0.05
Matches are distributed among these distances:
354 28 0.05
356 3 0.01
357 196 0.34
358 39 0.07
359 102 0.18
360 22 0.04
361 48 0.08
362 53 0.09
363 50 0.09
364 16 0.03
365 21 0.04
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (360 bp):
ATGTATCGATACATAACAATATAACAGGTAAAATATGAAAAATCGGTTTCATTATGACAAAACCG
GTAAAGCGCTACCAGATATGTTGAAGGTATCGATTTCATTCAAATAAGTATCGATACTTATGGAA
TTTAAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATATTTTAAAACATGTATCGATACGTA
ACAATATAACAGGTAAAATATGACAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTACCGG
ATATGTTGAAGGTATCGATTCCATTCAAATAAGATCAGTACTTATGGAATTTTAAAGAAAAACAA
TAATAGCGCCTATAAAGTATCGATACTTTAAAAAC
Found at i:6421 original size:540 final size:532
Alignment explanation
Indices: 5513--6508 Score: 1529
Period size: 540 Copynumber: 1.9 Consensus size: 532
5503 CAATATCATT
* * *
5513 CAAATATGTATCGATACATAACAATATAACAGGTAAAATGATAATCAGGTTCAATATGACAAACC
1 CAAACATGTATCGATACATAACAATATAACAGGTAAAATGACAAGCAGGTTCAATATGACAAACC
5578 GATAAAGCGCTACCAGATATGTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATGAAA
66 GATAAAGCGCTACCAGATATGTGAAGGTATCGATTCCATTCAAATAAG-ATCGATACTTATGAAA
* * *
5643 TTTAAAAAAAACAATAATAGTGCCTATAAAGTATCGATATTTTATAAATGTATCGATACGTAACA
130 TTTAAAAAAAACAATAATAGTGCCTATAAAGTATCGATATTTAAAAAATGTATCGATACATAACA
5708 ATATAAAATGTAAAATATGACAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTACCAGAT
195 ATATAAAATGTAAAATATGACAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTACCAGAT
* * * **
5773 ATGTTGAAGGTATCGATTCCATTTAAATAAGTATCAGTACTTATTGAATTTTAAAGAAAAGTGAT
260 ATGTTGAAGGTATCAATTCCATTCAAATAAGTATCAGTACTTATTGAATTTAAAAGAAAAGCAAT
5838 AATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACGTAACAATATAACAGGTAA
325 AATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACGTAACAATATAACAGGT-A
* * * *
5903 AAATATGACAAAATCGATTTCATTATGACAAAATCGGTAAAGCGCTACCGAATATGTTGAAGGTG
389 AAATATGACAAAAT-G-GTTCATTATGACAAAACCGAT-AAGCGCTACCGAATATGTTGAAGGTA
5968 TCGATTTCATTCAAATAAGTATCGATACTTATGGAATTTTAAAGAAAAGCAATAATAGCGCCTAT
451 TCGATTTCATTCAAATAAGTATCGATACTTATGGAATTTTAAAGAAAAGCAATAATAGCGCCTAT
6033 AAAGTATCGATATTTTA
516 AAAGTATCGATATTTTA
* * * *
6050 CAAACATGTATCGGTACGTAACAATAT-ACAGGTAAAATATGACAAGCCGGTTTCATTATGACAA
1 CAAACATGTATCGATACATAACAATATAACAGGT-AAA-ATGACAAGCAGG-TTCAATATGACAA
* *
6114 ACCGGTAAAGCGCTACCGGATATGTTGAAGGTATCGATTCCATTCAAAT-A-ATCGATACTTATG
63 ACCGATAAAGCGCTACCAGATATG-TGAAGGTATCGATTCCATTCAAATAAGATCGATACTTAT-
*
6177 GAATTTTAAAGAAAAACAATAATAGCT-CCTATAAAGTATCGATACTTTAAAAACATGTATCGAT
126 GAAATTTAAA-AAAAACAATAATAG-TGCCTATAAAGTATCGATA-TTTAAAAA-ATGTATCGAT
* * * *
6241 ACATAACAATATAACATGTAAAATATGA-AAAATCGGTTTCATTATGACAAAACCGGTAAATCGT
187 ACATAACAATATAAAATGTAAAATATGACAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGC
*
6305 TACCAGATATGTTGAAGGTATCAATTTCATTCAAATAAGTATC-GATACTT-TTGGAATTTAAAA
252 TACCAGATATGTTGAAGGTATCAATTCCATTCAAATAAGTATCAG-TACTTATT-GAATTTAAAA
6368 GAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACGTAACAATA
315 GAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACGTAACAATA
* * *
6433 TAACAGGTAAAATATGACAAAATGGTTCATTATGACGAAACCGATAAGCGCTATCGGATATGTTG
380 TAACAGGTAAAATATGACAAAATGGTTCATTATGACAAAACCGATAAGCGCTACCGAATATGTTG
6498 AAGGTATCGAT
445 AAGGTATCGAT
6509 ACTTTAATAA
Statistics
Matches: 418, Mismatches: 30, Indels: 23
0.89 0.06 0.05
Matches are distributed among these distances:
536 34 0.08
537 56 0.13
538 19 0.05
539 84 0.20
540 189 0.45
541 36 0.09
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (532 bp):
CAAACATGTATCGATACATAACAATATAACAGGTAAAATGACAAGCAGGTTCAATATGACAAACC
GATAAAGCGCTACCAGATATGTGAAGGTATCGATTCCATTCAAATAAGATCGATACTTATGAAAT
TTAAAAAAAACAATAATAGTGCCTATAAAGTATCGATATTTAAAAAATGTATCGATACATAACAA
TATAAAATGTAAAATATGACAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTACCAGATA
TGTTGAAGGTATCAATTCCATTCAAATAAGTATCAGTACTTATTGAATTTAAAAGAAAAGCAATA
ATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACGTAACAATATAACAGGTAAA
ATATGACAAAATGGTTCATTATGACAAAACCGATAAGCGCTACCGAATATGTTGAAGGTATCGAT
TTCATTCAAATAAGTATCGATACTTATGGAATTTTAAAGAAAAGCAATAATAGCGCCTATAAAGT
ATCGATATTTTA
Found at i:8618 original size:116 final size:115
Alignment explanation
Indices: 8434--8688 Score: 329
Period size: 116 Copynumber: 2.2 Consensus size: 115
8424 ACAAATTCGG
** * *
8434 TAATTAACCTATT-TGTTATCGTCGGATTTCCAAAAGCTCTATCGCTTAAAAAGGACTACCTATA
1 TAATTAACCGGTTATGTTATCGTCAGATTTCCAAAAGCTCCATCGCTTAAAAAGGACTACCTATA
* * *
8498 TACGTTATATAAGTGCTATCTAATATGTTATTAGT-TTGATAATGTTTCCAG
66 TACGTTATATAAATGCTACCTAATAT-TTATT-GTCTTGATAATGTTTCCAA
* * *
8549 TAATTAACTGGTTATGTTATCGTCAGATTTCC-AAAGCTCCATCAGCTTTAACAAGGGCTACCTA
1 TAATTAACCGGTTATGTTATCGTCAGATTTCCAAAAGCTCCATC-GC-TTAAAAAGGACTACCTA
* *
8613 T-TACGTTATATAAATGTTACCTAATATTTATTGTGCTTGATAATGTTTCGAA
64 TATACGTTATATAAATGCTACCTAATATTTATTGT-CTTGATAATGTTTCCAA
8665 TAATTAACCGGTTATGTTATCGTC
1 TAATTAACCGGTTATGTTATCGTC
8689 TATATATTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
114 2 0.02
115 25 0.20
116 79 0.65
117 16 0.13
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (115 bp):
TAATTAACCGGTTATGTTATCGTCAGATTTCCAAAAGCTCCATCGCTTAAAAAGGACTACCTATA
TACGTTATATAAATGCTACCTAATATTTATTGTCTTGATAATGTTTCCAA
Found at i:18654 original size:3 final size:3
Alignment explanation
Indices: 18646--18676 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
18636 CGGGCAACGG
18646 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
18677 AATAACTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20801 original size:20 final size:22
Alignment explanation
Indices: 20753--20801 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
20743 GTCCATCCAT
* *
20753 TACCGATATTGTTCTTTGTAAG
1 TACCGATATTGTTCTATGAAAG
*
20775 TATCGATATTGTTC-AT-AAAG
1 TACCGATATTGTTCTATGAAAG
20795 TACCGAT
1 TACCGAT
20802 TTTATTCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.39
21 1 0.04
22 13 0.57
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (22 bp):
TACCGATATTGTTCTATGAAAG
Found at i:23742 original size:20 final size:20
Alignment explanation
Indices: 23703--23812 Score: 150
Period size: 20 Copynumber: 5.5 Consensus size: 20
23693 CAAATTTTTT
**
23703 TATGAATAGTATTG-TACTG
1 TATGAATAGTACCGATACTG
23722 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
*
23742 TATGAATAGTACCGATATTG
1 TATGAATAGTACCGATACTG
*
23762 TATGAATAGTACCAATACTG
1 TATGAATAGTACCGATACTG
*
23782 TATGAATAGTATCGATACTG
1 TATGAATAGTACCGATACTG
* *
23802 TGTGAACAGTA
1 TATGAATAGTA
23813 ATGAACAATG
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 12 0.15
20 69 0.85
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGAATAGTACCGATACTG
Found at i:24258 original size:33 final size:33
Alignment explanation
Indices: 24216--24281 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
24206 TAAAGGGGTT
* * *
24216 TTGGTTCTAGCTGAGCCTGTTAAAAGCTAGGGA
1 TTGGTTCTAGCTGAGCCCGTGAAAAACTAGGGA
* *
24249 TTGGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 TTGGTTCTAGCTGAGCCCGTGAAAAACTAGGGA
24282 GTTGTAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (33 bp):
TTGGTTCTAGCTGAGCCCGTGAAAAACTAGGGA
Found at i:27203 original size:20 final size:20
Alignment explanation
Indices: 27164--27221 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
27154 AAATTTTTTT
* *
27164 TATGAATAATACTG-TACTG
1 TATGAATAGTACCGATACTG
27183 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
* * *
27203 TGTGAACAGTATCGATACT
1 TATGAATAGTACCGATACT
27222 AAAAAATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
TATGAATAGTACCGATACTG
Found at i:27682 original size:33 final size:32
Alignment explanation
Indices: 27643--27707 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
27633 CAAAGGGATT
* *
27643 TTGGTTCTAGCTGAGCCTGTTAAAAGCTAGGGA
1 TTGGTTCTAGCTGAGCCCGTGAAAA-CTAGGGA
* *
27676 TTGGTTCTAGTTTAGCCCGTGAAAACTAGGGA
1 TTGGTTCTAGCTGAGCCCGTGAAAACTAGGGA
27708 GTTATAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (32 bp):
TTGGTTCTAGCTGAGCCCGTGAAAACTAGGGA
Found at i:29595 original size:5 final size:6
Alignment explanation
Indices: 29578--29602 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29568 GTGATTGATC
29578 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
29603 AGAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:32108 original size:17 final size:17
Alignment explanation
Indices: 32082--32114 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
32072 TTTTGTTTTT
32082 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
32100 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
32115 CATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:40182 original size:24 final size:23
Alignment explanation
Indices: 40120--40220 Score: 94
Period size: 24 Copynumber: 4.3 Consensus size: 23
40110 GAGTCGAGGG
*
40120 TTCTACGCGGTCTTTCAGGACAA
1 TTCTACGCGGTCCTTCAGGACAA
* * *
40143 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCAGGAC-AA
* *
40167 TTCTACGCGGTTCTTCAAGACAA
1 TTCTACGCGGTCCTTCAGGACAA
** * *
40190 TTTCTACATGGTCCTTCGGGACAT
1 -TTCTACGCGGTCCTTCAGGACAA
40214 TTCTACG
1 TTCTACG
40221 TGTCACTTTG
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
23 25 0.42
24 35 0.58
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCAGGACAA
Found at i:40189 original size:47 final size:47
Alignment explanation
Indices: 40120--40220 Score: 134
Period size: 47 Copynumber: 2.1 Consensus size: 47
40110 GAGTCGAGGG
* **
40120 TTCTACGCGGTCTTTCAGGACAA-TTCTATGTGGTCCTTCGGGACAAA
1 TTCTACGCGGTCTTTCAAGACAATTTCTACATGGTCCTTCGGGAC-AA
*
40167 TTCTACGCGGT-TCTTCAAGACAATTTCTACATGGTCCTTCGGGACAT
1 TTCTACGCGGTCT-TTCAAGACAATTTCTACATGGTCCTTCGGGACAA
40214 TTCTACG
1 TTCTACG
40221 TGTCACTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 1 0.02
47 28 0.58
48 19 0.40
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (47 bp):
TTCTACGCGGTCTTTCAAGACAATTTCTACATGGTCCTTCGGGACAA
Found at i:51755 original size:23 final size:20
Alignment explanation
Indices: 51704--51763 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
51694 TTTTGGTGCA
*
51704 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
51723 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
51744 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
51764 CCATAGGGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:56685 original size:24 final size:24
Alignment explanation
Indices: 56599--56710 Score: 99
Period size: 23 Copynumber: 4.8 Consensus size: 24
56589 GAGTCGAGGG
* * *
56599 TTCTACGCGGTCTTTCAGGATAA-
1 TTCTACGTGGTCCTTCGGGATAAT
* *
56622 TTCTATGTGGTCCTTCGGGATAAA
1 TTCTACGTGGTCCTTCGGGATAAT
*
56646 TTCTACACT-GTCCTTCGGGATAAT
1 TTCTAC-GTGGTCCTTCGGGATAAT
*
56670 TTCTACGTGGTTCTTCGGGACT--T
1 TTCTACGTGGTCCTTCGGGA-TAAT
56693 TTCTACGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
56711 TGCATATTCT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
23 37 0.50
24 35 0.47
25 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGATAAT
Found at i:57602 original size:23 final size:23
Alignment explanation
Indices: 57576--57626 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
57566 AGTATGGGTT
* *
57576 AAAAAAAATTCAATTTCTCAATG
1 AAAAAAAATTAAATTTATCAATG
57599 AAAAAAAATTAAATTTATCAATG
1 AAAAAAAATTAAATTTATCAATG
57622 AAAAA
1 AAAAA
57627 GGGGGAGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAAAAAATTAAATTTATCAATG
Found at i:60268 original size:19 final size:19
Alignment explanation
Indices: 60231--60269 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
60221 TCAGGTGAGG
60231 TCAATGATCAATGATGGTT
1 TCAATGATCAATGATGGTT
*
60250 TCAAGTGATCGATGA-GGTT
1 TCAA-TGATCAATGATGGTT
60269 T
1 T
60270 TGAGAGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (19 bp):
TCAATGATCAATGATGGTT
Done.