Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005972.1 Hibiscus syriacus cultivar Beakdansim tig00014041_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: 75705
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:190 original size:20 final size:20
Alignment explanation
Indices: 142--200 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
132 AATAGTTTCT
** *
142 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
162 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
182 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
201 AGAGAATCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:479 original size:20 final size:21
Alignment explanation
Indices: 454--519 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
444 TCTGAGAGAT
454 GGAGATAGG-CGGATTTCGCC
1 GGAGATAGGACGGATTTCGCC
* * *
474 GGAGATGGGACGGATTTTGTC
1 GGAGATAGGACGGATTTCGCC
* * *
495 GGAGATGGGGATGGATTTCGTC
1 GGAGAT-AGGACGGATTTCGCC
517 GGA
1 GGA
520 TATGGGTGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.21
21 15 0.38
22 16 0.41
ACGTcount: A:0.20, C:0.12, G:0.44, T:0.24
Consensus pattern (21 bp):
GGAGATAGGACGGATTTCGCC
Found at i:489 original size:21 final size:21
Alignment explanation
Indices: 454--525 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
444 TCTGAGAGAT
* *
454 GGAGATAGG-CGGATTTCGCC
1 GGAGATGGGACGGATTTCGTC
*
474 GGAGATGGGACGGATTTTGTC
1 GGAGATGGGACGGATTTCGTC
*
495 GGAGATGGGGATGGATTTCGTC
1 GGAGAT-GGGACGGATTTCGTC
*
517 GGATATGGG
1 GGAGATGGG
526 TGAGAGAGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 8 0.18
21 18 0.41
22 18 0.41
ACGTcount: A:0.19, C:0.11, G:0.44, T:0.25
Consensus pattern (21 bp):
GGAGATGGGACGGATTTCGTC
Found at i:510 original size:22 final size:22
Alignment explanation
Indices: 463--525 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
453 TGGAGATAGG
*
463 CGGATTTCGCCGGAGAT-GGGA
1 CGGATTTCGTCGGAGATGGGGA
*
484 CGGATTTTGTCGGAGATGGGGA
1 CGGATTTCGTCGGAGATGGGGA
* *
506 TGGATTTCGTCGGATATGGG
1 CGGATTTCGTCGGAGATGGG
526 TGAGAGAGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 15 0.42
22 21 0.58
ACGTcount: A:0.17, C:0.13, G:0.43, T:0.27
Consensus pattern (22 bp):
CGGATTTCGTCGGAGATGGGGA
Found at i:799 original size:20 final size:19
Alignment explanation
Indices: 693--827 Score: 108
Period size: 20 Copynumber: 6.7 Consensus size: 19
683 CGCTTTGAAA
*
693 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
714 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
734 ATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATAG-TAGT
* * * *
754 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
775 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
795 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
815 ATCGCATTGCGAT
1 ATCGCATTGCGAT
828 TTTCCCCCAA
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.05
20 64 0.67
21 25 0.26
22 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:799 original size:61 final size:61
Alignment explanation
Indices: 693--830 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
683 CGCTTTGAAA
* * * * *
693 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
754 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
815 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
831 CCCCCAATTC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:940 original size:21 final size:21
Alignment explanation
Indices: 900--940 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
890 ACTGTAGACC
** *
900 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
921 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
941 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:10717 original size:29 final size:29
Alignment explanation
Indices: 10668--10737 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
10658 ATGATTTGAT
** * **
10668 AAATTT-ATGACTATTTTATGACTTGTAA
1 AAATTTAATGACTAAGTGATGACTTCAAA
*
10696 AAATTTAATGACTAAGTGATGATTTCAAA
1 AAATTTAATGACTAAGTGATGACTTCAAA
10725 ATAATTTAATGAC
1 A-AATTTAATGAC
10738 CTCTAATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 6 0.18
29 17 0.50
30 11 0.32
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (29 bp):
AAATTTAATGACTAAGTGATGACTTCAAA
Found at i:12802 original size:12 final size:12
Alignment explanation
Indices: 12778--12813 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
12768 GACCCGATCT
12778 GACCCGTTGACCC
1 GACCCG-TGACCC
12791 GACCCGTGACCC
1 GACCCGTGACCC
12803 GACCCGGTGAC
1 GACCC-GTGAC
12814 ATTCTGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.17, C:0.44, G:0.28, T:0.11
Consensus pattern (12 bp):
GACCCGTGACCC
Found at i:12875 original size:29 final size:29
Alignment explanation
Indices: 12842--12987 Score: 211
Period size: 29 Copynumber: 5.0 Consensus size: 29
12832 AAAAGGTAAT
*
12842 ATTCTGGGAAATATTTTGAAAAATGTGAC
1 ATTCTGGGAAATATTTTGAAAAAAGTGAC
*
12871 ATTCTGGGAAATATTTTGAAAAAGGTGAC
1 ATTCTGGGAAATATTTTGAAAAAAGTGAC
** *
12900 ATTCTAAGAAATATTTTTGAAAAATGTGAC
1 ATTCTGGGAAATA-TTTTGAAAAAAGTGAC
*
12930 ATTCTGGGAAATATTTTGAAAAAAATGAC
1 ATTCTGGGAAATATTTTGAAAAAAGTGAC
* *
12959 ATTCTAGGAATTATTTTGAAAAAAGTGAC
1 ATTCTGGGAAATATTTTGAAAAAAGTGAC
12988 TTTGGAAATT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
29 79 0.75
30 26 0.25
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (29 bp):
ATTCTGGGAAATATTTTGAAAAAAGTGAC
Found at i:12927 original size:59 final size:58
Alignment explanation
Indices: 12809--12987 Score: 236
Period size: 59 Copynumber: 3.1 Consensus size: 58
12799 ACCCGACCCG
* * * * *
12809 GTGACATTCTGAG-AAT-TTTTGTGAAAAGGTAATATTCTGGGAAATATTTTGAAAAAT
1 GTGACATTCTGGGAAATATTTTG-AAAAAGGTGACATTCTAGGAAATATTTTGAAAAAT
*
12866 GTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTAAGAAATATTTTTGAAAAAT
1 GTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTAGGAAATA-TTTTGAAAAAT
** * *
12925 GTGACATTCTGGGAAATATTTTGAAAAAAATGACATTCTAGGAATTATTTTGAAAAAA
1 GTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTAGGAAATATTTTGAAAAAT
12983 GTGAC
1 GTGAC
12988 TTTGGAAATT
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
57 12 0.11
58 37 0.34
59 59 0.55
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.34
Consensus pattern (58 bp):
GTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTAGGAAATATTTTGAAAAAT
Found at i:12959 original size:88 final size:86
Alignment explanation
Indices: 12808--12987 Score: 245
Period size: 88 Copynumber: 2.1 Consensus size: 86
12798 GACCCGACCC
* * **
12808 GGTGACATTCTGAGAATTTTTGTGAAAAGGTAATATTCTGGGAAATATTTTGAAAAATGTGACAT
1 GGTGACATTCTAAGAATTTTTGTGAAAAGGTAACATTCTGGGAAATATTTTGAAAAAAATGACAT
*
12873 TCTGGGAAATATTTTGAAAAA
66 TCTAGGAAATATTTTGAAAAA
* *
12894 GGTGACATTCTAAGAAATATTTT-TGAAAAATGTGACATTCTGGGAAATATTTTGAAAAAAATGA
1 GGTGACATTCTAAG-AAT-TTTTGTG-AAAAGGTAACATTCTGGGAAATATTTTGAAAAAAATGA
*
12958 CATTCTAGGAATTATTTTGAAAAA
63 CATTCTAGGAAATATTTTGAAAAA
*
12982 AGTGAC
1 GGTGAC
12988 TTTGGAAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
86 13 0.16
87 5 0.06
88 64 0.78
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (86 bp):
GGTGACATTCTAAGAATTTTTGTGAAAAGGTAACATTCTGGGAAATATTTTGAAAAAAATGACAT
TCTAGGAAATATTTTGAAAAA
Found at i:16027 original size:5 final size:5
Alignment explanation
Indices: 16017--16050 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
16007 ATTTTGATCA
16017 GGTCG GGTCG GGTCG GGTCG GGTCG GGTTCG GGT
1 GGTCG GGTCG GGTCG GGTCG GGTCG GG-TCG GGT
16051 TTAGGGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.00, C:0.18, G:0.59, T:0.24
Consensus pattern (5 bp):
GGTCG
Found at i:16483 original size:37 final size:38
Alignment explanation
Indices: 16431--16504 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
16421 TTTTGTTCGG
*
16431 GTCGGGTCGG-GTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGATTTTTTTAAGTGTGATATTCGGGTCGA
16468 GTCGGGTCGGATTTTTTTAAGTGTGATATTCGGGTCG
1 GTCGGGTCGGATTTTTTTAAGTGTGATATTCGGGTCG
16505 GATCGAGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 10 0.29
38 25 0.71
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.39
Consensus pattern (38 bp):
GTCGGGTCGGATTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:16728 original size:255 final size:244
Alignment explanation
Indices: 16226--16810 Score: 833
Period size: 255 Copynumber: 2.4 Consensus size: 244
16216 TTCTGGTCGG
* *
16226 GTCGGGTCGGGTTTTTTAAGTGTGATATTGGGGTC-AGGTTCGGGTTTAGGGT-AAAAAAACGGA
1 GTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGAGGTTCGGGTTTAGGGTGAAAAAAACGGA
* *
16289 CTGACCCGAAAAATATATATAATTCGGGTCGGGCCGGATTAAGTCACTGTTTTTATTAAATAAAA
66 CCGACCCGAAAAATATATATAATTCGGGTCGGGCCGGATTAAGTCAATGTTTTTATTAAATAAAA
* * *
16354 ATAATTTTTTATTATTTCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
131 ATAATTTTTTATCATGTCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGATAAAACTT
*
16419 TATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
196 TATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAA
16468 GTCGGGTCGGATTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTGAAAAAA
1 GTCGGGTCGG-TTTTTTTAAGTGTGATATTCGGGTC-GA--G-GTTCGGGTTTAGGGTGAAAAAA
* *
16533 ACCGGACCGACTCG-AAAATATATATAATTCGGGTCGGGTCGGATTAAGTCAATGTTTTTATTAA
61 A-CGGACCGACCCGAAAAATATATATAATTCGGGTCGGGCCGGATTAAGTCAATGTTTTTATTAA
* * *
16597 ATAAAAATTATTATTATT-TCAGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCGGGTCGGG
125 ATAAAAATAATT-TT-TTATCA--T---GTCGGGTCGAATTTCTAATTCATATATTCGGGTCGGG
16661 TCGGATAAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAA
183 TCGGATAAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAA
* *
16723 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCG-GGTTCTGGTTTAGGGTG-AAAAAACAT
1 GTCGGGTC-GGTTTTTTTAAGTGTGATATTCGGGTCGAGGTTCGGGTTTAGGGTGAAAAAAAC-G
**
16786 GTTCGACCCGAAAAA-ATATATAATT
64 GACCGACCCGAAAAATATATATAATT
16811 TTACCTTATA
Statistics
Matches: 307, Mismatches: 18, Indels: 29
0.87 0.05 0.08
Matches are distributed among these distances:
242 10 0.03
243 23 0.07
245 1 0.00
247 1 0.00
248 16 0.05
249 89 0.29
250 33 0.11
251 3 0.01
252 1 0.00
254 1 0.00
255 127 0.41
256 2 0.01
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.36
Consensus pattern (244 bp):
GTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGAGGTTCGGGTTTAGGGTGAAAAAAACGGA
CCGACCCGAAAAATATATATAATTCGGGTCGGGCCGGATTAAGTCAATGTTTTTATTAAATAAAA
ATAATTTTTTATCATGTCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGATAAAACTT
TATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAA
Found at i:16733 original size:37 final size:38
Alignment explanation
Indices: 16686--16758 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
16676 TTTTGTTCGG
16686 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
16723 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
16759 GGGTTCTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 11 0.31
38 24 0.69
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.40
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
Found at i:17218 original size:12 final size:11
Alignment explanation
Indices: 17194--17223 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17184 TGTAAGTTGT
*
17194 AAAATAAACAA
1 AAAAAAAACAA
17205 AAAAAAAACAA
1 AAAAAAAACAA
17216 AAAAAAAA
1 AAAAAAAA
17224 TAAGAAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:21420 original size:19 final size:19
Alignment explanation
Indices: 21404--21444 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
21394 ATCACTATAT
21404 GCTTACCTGAACACTATTA
1 GCTTACCTGAACACTATTA
21423 GCTTACCTGAACACTATTA
1 GCTTACCTGAACACTATTA
21442 GCT
1 GCT
21445 AGCCATTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (19 bp):
GCTTACCTGAACACTATTA
Found at i:29612 original size:155 final size:155
Alignment explanation
Indices: 29326--29623 Score: 386
Period size: 155 Copynumber: 1.9 Consensus size: 155
29316 TATATATAAC
* * * * *
29326 ATTTTAGGCGCGACCGATTTTATTACAAAGAAAATTAACACTCCAGATCGCAATCTAATTTCTAA
1 ATTTTAGGCGCAACCAAATTTATTACAAAGAAAATTAACACTCCAGATCACAACCTAATTTCTAA
* * * *
29391 GTGAATCATAATATTCTTGAGCTAACTAGATTTCTTATAGATATTCGTAACAATTCTAGTTGTTA
66 GTGAACCATAATATTATTGAGCTAACCAGATTTCTTATAGATATTCATAACAATTCTAGTTGTTA
29456 ACTTATTTTGTTAAACTCTAGTAAT
131 ACTTATTTTGTTAAACTCTAGTAAT
* * * * *
29481 ATTTTAGGTGCAACCAAATTTATTACAAA-AAAATTAACATTTCAGATTACAACCTAATTTCTTA
1 ATTTTAGGCGCAACCAAATTTATTACAAAGAAAATTAACACTCCAGATCACAACCTAATTTCTAA
* * * *
29545 GTGAACCATAATATTATTG-GGTACAACCAGATTTCTTATAGATTTTCATAATATATTC-AGTTT
66 GTGAACCATAATATTATTGAGCT--AACCAGATTTCTTATAGATATTCATAACA-ATTCTAGTTG
29608 TTAACTTATTTTGTTA
128 TTAACTTATTTTGTTA
29624 TTGTGAAAAT
Statistics
Matches: 122, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
153 2 0.02
154 46 0.38
155 70 0.57
156 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (155 bp):
ATTTTAGGCGCAACCAAATTTATTACAAAGAAAATTAACACTCCAGATCACAACCTAATTTCTAA
GTGAACCATAATATTATTGAGCTAACCAGATTTCTTATAGATATTCATAACAATTCTAGTTGTTA
ACTTATTTTGTTAAACTCTAGTAAT
Found at i:38541 original size:2 final size:2
Alignment explanation
Indices: 38534--38565 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
38524 TTATTATTCA
38534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38566 AAGCTAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39482 original size:61 final size:60
Alignment explanation
Indices: 39406--39538 Score: 230
Period size: 61 Copynumber: 2.2 Consensus size: 60
39396 AAGTTTGAGG
*
39406 ACTAATTTAAAATGAGAGTCATTGTTTATGGATGAAATTGAAATATTAAAAAATCTAAAAA
1 ACTAATTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATTAAAAAATCT-AAAA
* *
39467 ACTAGTTTAAAATGAGAGTCGTTGTTTATGGAAGAAATTGAAATATTAAAAAATCTAAAA
1 ACTAATTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATTAAAAAATCTAAAA
39527 ACTAATTTAAAA
1 ACTAATTTAAAA
39539 GTAAAATTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
60 15 0.22
61 53 0.78
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (60 bp):
ACTAATTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATTAAAAAATCTAAAA
Found at i:41283 original size:14 final size:14
Alignment explanation
Indices: 41264--41308 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
41254 TGAGTCTGAA
41264 AAACATAAACGAAC
1 AAACATAAACGAAC
*
41278 AAACATAAATGAAC
1 AAACATAAACGAAC
* *
41292 AAACACAAACAAAC
1 AAACATAAACGAAC
41306 AAA
1 AAA
41309 TTATTGAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (14 bp):
AAACATAAACGAAC
Found at i:41808 original size:22 final size:22
Alignment explanation
Indices: 41759--41809 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
41749 GGAGTTAATA
* *
41759 AATTAATAACTTGAATACATAT
1 AATTAATAAATCGAATACATAT
** *
41781 GGTTAATAAATCGAATACATGT
1 AATTAATAAATCGAATACATAT
41803 AATTAAT
1 AATTAAT
41810 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (22 bp):
AATTAATAAATCGAATACATAT
Found at i:42382 original size:18 final size:19
Alignment explanation
Indices: 42341--42384 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
42331 TTATAACACT
*
42341 TAAAATAATGCATTTTTAA
1 TAAAATAATGCATCTTTAA
* *
42360 CAAAATAATTCA-CTTTAA
1 TAAAATAATGCATCTTTAA
42378 TAAAATA
1 TAAAATA
42385 TTGACGTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAATAATGCATCTTTAA
Found at i:43272 original size:139 final size:139
Alignment explanation
Indices: 42889--43275 Score: 356
Period size: 139 Copynumber: 2.8 Consensus size: 139
42879 CTAAAGGACT
* ** * * * *
42889 AAACCTAAAAT-GTAGAATCTAATTATTAATCCTAATGAATTTTAA-CTAAATA-TGGATCGAAA
1 AAACCTAAAATAG-AGACTCTAATTATTAATCCTAACCAATTTTAATC-AATTATTGAATTGAAT
* ** ** * * ** * * * *
42951 AATTAAAATAGAACCTCAGGCATGAA-GCAAGGACCAAATTAAAAACTCTCC-TAGTTTAAGGAC
64 AATTAAAATGGAACC-CAAACAAAAATGCAAGGACCAAATAAAAAATTAACCAAAATTAAATGAC
43014 TAAAGTGAAATC
128 TAAAGTGAAATC
* *
43026 AAACCTAAAATAGAGGCTCTAATTATTAATCCTAACCAATTTTATTCAATTATTGAATTGAATAA
1 AAACCTAAAATAGAGACTCTAATTATTAATCCTAACCAATTTTAATCAATTATTGAATTGAATAA
*
43091 TTAAAATGGAACCCAGACAAAAATGCAAGGACCAAATAAAAAATTAACCAAAATTAAATGACTAA
66 TTAAAATGGAACCCAAACAAAAATGCAAGGACCAAATAAAAAATTAACCAAAATTAAATGACTAA
43156 AGTGAAAGT-
131 AGTGAAA-TC
** * *
43165 AAACCTAAGGTGGAGACTCTAATTATTAATCCTAACCAATTTTAATCAATTATCT-ATTTGAATA
1 AAACCTAAAATAGAGACTCTAATTATTAATCCTAACCAATTTTAATCAATTAT-TGAATTGAATA
** * * ** * *
43229 ATTAATTTGGAACATCAAATATCAATGCGAGGACTAAATAAAAAATT
65 ATTAAAATGGAAC-CCAAACAAAAATGCAAGGACCAAATAAAAAATT
43276 TGCCTAAATT
Statistics
Matches: 206, Mismatches: 36, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
137 49 0.24
138 44 0.21
139 85 0.41
140 28 0.14
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (139 bp):
AAACCTAAAATAGAGACTCTAATTATTAATCCTAACCAATTTTAATCAATTATTGAATTGAATAA
TTAAAATGGAACCCAAACAAAAATGCAAGGACCAAATAAAAAATTAACCAAAATTAAATGACTAA
AGTGAAATC
Found at i:50013 original size:32 final size:32
Alignment explanation
Indices: 49946--50039 Score: 91
Period size: 32 Copynumber: 3.0 Consensus size: 32
49936 CAACCTAAGA
* * ** *
49946 GAGTACCTTGAGACTTTAGAGGTTATCCAATG
1 GAGTACCTTGAGACCTTAAAGCCTATCCAAGG
*
49978 GAGTACCTTGAGACCTTAAAGCCTATTCAAGG
1 GAGTACCTTGAGACCTTAAAGCCTATCCAAGG
* * * *
50010 GAGTACTTTGAG-CCTAAAAGCATACCCAAG
1 GAGTACCTTGAGACCTTAAAGCCTATCCAAG
50040 AGTCACCATA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 14 0.27
32 37 0.73
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (32 bp):
GAGTACCTTGAGACCTTAAAGCCTATCCAAGG
Found at i:50388 original size:53 final size:53
Alignment explanation
Indices: 50308--50416 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
50298 AAAGATCGGT
*
50308 CTAGGAGGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
1 CTAGGAAGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
50361 CTAGGAAGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
1 CTAGGAAGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
50414 CTA
1 CTA
50417 AACCATAATG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.19
Consensus pattern (53 bp):
CTAGGAAGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
Found at i:50399 original size:26 final size:26
Alignment explanation
Indices: 50316--50399 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
50306 GTCTAGGAGG
50316 TCTACTGAGCATCAGCCTCGCTACGC
1 TCTACTGAGCATCAGCCTCGCTACGC
* * * * * *
50342 TCTACAGCACCACTCGAACCTAG-GAAG-
1 TCTACTG-AGCA-TC-AGCCTCGCTACGC
50369 TCTACTGAGCATCAGCCTCGCTACGC
1 TCTACTGAGCATCAGCCTCGCTACGC
50395 TCTAC
1 TCTAC
50400 AGCACCACTC
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 5 0.12
25 4 0.10
26 14 0.34
27 9 0.22
28 4 0.10
29 5 0.12
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (26 bp):
TCTACTGAGCATCAGCCTCGCTACGC
Found at i:50875 original size:20 final size:20
Alignment explanation
Indices: 50818--50875 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
50808 TGATTGATTC
* *
50818 GAGTTGACTCAATCTTG-TTT
1 GAGTTGACTCAATC-CGATCT
* * *
50838 GAATTGACTCGATTCGATCT
1 GAGTTGACTCAATCCGATCT
50858 GAGTTGACTCAATCCGAT
1 GAGTTGACTCAATCCGAT
50876 TTTAGAATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
GAGTTGACTCAATCCGATCT
Found at i:58822 original size:21 final size:21
Alignment explanation
Indices: 58785--58867 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
58775 TTTTGGTGCA
*
58785 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
58805 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
* *
58826 GAAGGGGAACCGATTTCCCCCAC
1 G-A-GGGAACCGATTCCCCCCAT
* * *
58849 AAGGGAATCGATACCCCCC
1 GAGGGAACCGATTCCCCCC
58868 TGGGGTACTG
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 10 0.20
21 22 0.45
22 2 0.04
23 15 0.31
ACGTcount: A:0.25, C:0.35, G:0.24, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:61864 original size:17 final size:17
Alignment explanation
Indices: 61842--61904 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
61832 TATAAATAAA
61842 TATTAAAATATTATATT
1 TATTAAAATATTATATT
** **
61859 TATTAAAATAAAATAAA
1 TATTAAAATATTATATT
61876 TA-TAAATATATTAATTATT
1 TATTAAA-ATATT-A-TATT
61895 TATTAAAATA
1 TATTAAAATA
61905 AGAATAATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
16 4 0.12
17 18 0.53
18 1 0.03
19 7 0.21
20 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTAAAATATTATATT
Found at i:61902 original size:36 final size:38
Alignment explanation
Indices: 61836--61996 Score: 138
Period size: 39 Copynumber: 4.3 Consensus size: 38
61826 TAATTTTATA
61836 AATAAATATTAAA-ATATT-A-TATTTATTAAAATAA-
1 AATAAATATTAAATATATTAATTATTTATTAAAATAAG
61870 AATAAATA-TAAATATATTAATTATTTATTAAAATAAG
1 AATAAATATTAAATATATTAATTATTTATTAAAATAAG
** * * *
61907 AATAATATATTAGGTATATTAATCATGTATT-AAATAAT
1 AATAA-ATATTAAATATATTAATTATTTATTAAAATAAG
* ** * *
61945 AAT-ATTATTAAAGTAATAAAAATTATAATATTAAAATAAA
1 AATAAATATTAAA-T-ATATTAATTAT-TTATTAAAATAAG
61985 AATATAATATTA
1 AATA-AATATTA
61997 TATTTTAAGG
Statistics
Matches: 101, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
33 4 0.04
34 13 0.13
35 1 0.01
36 20 0.20
37 7 0.07
38 20 0.20
39 21 0.21
40 9 0.09
42 6 0.06
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (38 bp):
AATAAATATTAAATATATTAATTATTTATTAAAATAAG
Found at i:61990 original size:19 final size:20
Alignment explanation
Indices: 61959--61996 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
61949 TTATTAAAGT
61959 AATAAAAATTATAATATTAA
1 AATAAAAATTATAATATTAA
61979 AATAAAAA-TATAATATTA
1 AATAAAAATTATAATATTA
61997 TATTTTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAAAAATTATAATATTAA
Found at i:62138 original size:14 final size:13
Alignment explanation
Indices: 62074--62144 Score: 60
Period size: 13 Copynumber: 5.6 Consensus size: 13
62064 ATTAATTTTT
*
62074 TAATAATTTATTA
1 TAATAATATATTA
62087 T-AT-AT-TATTA
1 TAATAATATATTA
* *
62097 AAATAA-AAATATA
1 TAATAATATAT-TA
*
62110 TTATAATATATTA
1 TAATAATATATTA
62123 TAATAATATAATTA
1 TAATAATAT-ATTA
62137 TAATAATA
1 TAATAATA
62145 AAAATAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
10 5 0.11
11 4 0.09
12 5 0.11
13 17 0.37
14 15 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATAATATATTA
Found at i:66002 original size:33 final size:33
Alignment explanation
Indices: 65965--66048 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
65955 CGAGGGTGCA
*
65965 CCGAGGCCGCACACACCAAGGGTGCACCTAAGG
1 CCGAGGCCGCACACACCAAGGGAGCACCTAAGG
*
65998 CCGAGGCCGCGCACACCAAGGGAGCACCTAAGG
1 CCGAGGCCGCACACACCAAGGGAGCACCTAAGG
*
66031 CCGAGACCCGCACACACC
1 CCGAG-GCCGCACACACC
66049 GATAATGCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 36 0.78
34 10 0.22
ACGTcount: A:0.27, C:0.40, G:0.29, T:0.04
Consensus pattern (33 bp):
CCGAGGCCGCACACACCAAGGGAGCACCTAAGG
Found at i:68239 original size:23 final size:23
Alignment explanation
Indices: 68165--68232 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
68155 AAATGCATCG
* *
68165 AAGTGCCACGTACAATTGCACCA
1 AAGTGCCGCGTAAAATTGCACCA
68188 AAGTGCCGCGTAAAATTGCACCA
1 AAGTGCCGCGTAAAATTGCACCA
*
68211 AAGTGCCGCGTAGAATTGCACC
1 AAGTGCCGCGTAAAATTGCACC
68233 GTAGTGCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (23 bp):
AAGTGCCGCGTAAAATTGCACCA
Found at i:68496 original size:30 final size:31
Alignment explanation
Indices: 68462--68521 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
68452 TATCGTGTAG
*
68462 ACATATCA-TTTCCATACCTTTATCACATAA
1 ACATATAATTTTCCATACCTTTATCACATAA
68492 ACATATAATTTTCCATACCTTTATCACATA
1 ACATATAATTTTCCATACCTTTATCACATA
68522 GCTTATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.38
Consensus pattern (31 bp):
ACATATAATTTTCCATACCTTTATCACATAA
Found at i:68592 original size:25 final size:25
Alignment explanation
Indices: 68564--68626 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
68554 CTTAATACAT
68564 ATAATATGAATTCATG-TCATGTATC
1 ATAATATGAATT-ATGATCATGTATC
* *
68589 ATAATATGAAATGTGATCATGTATC
1 ATAATATGAATTATGATCATGTATC
*
68614 AAAATATTGAATT
1 ATAATA-TGAATT
68627 TAGACTTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 2 0.06
25 25 0.78
26 5 0.16
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (25 bp):
ATAATATGAATTATGATCATGTATC
Found at i:72047 original size:23 final size:22
Alignment explanation
Indices: 72021--72087 Score: 52
Period size: 23 Copynumber: 3.1 Consensus size: 22
72011 AAAATATACA
72021 AAAGTAAACAAATAAAAATTGCT
1 AAAGTAAA-AAATAAAAATTGCT
* *
72044 AAAG-CAAAAAT--TAATTGC-
1 AAAGTAAAAAATAAAAATTGCT
*
72062 AAGAGTAAGTAAATAAAAATTGCT
1 AA-AGTAA-AAAATAAAAATTGCT
72086 AA
1 AA
72088 GACGAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 11
0.67 0.10 0.22
Matches are distributed among these distances:
18 2 0.06
19 8 0.24
20 1 0.03
21 8 0.24
22 2 0.06
23 10 0.30
24 2 0.06
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.22
Consensus pattern (22 bp):
AAAGTAAAAAATAAAAATTGCT
Done.