Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005677.1 Hibiscus syriacus cultivar Beakdansim tig00013276_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: 135918
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6116 original size:50 final size:50
Alignment explanation
Indices: 6053--6154 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
6043 TTTATCCTAT
6053 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
6103 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
6153 TT
1 TT
6155 CAATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:17909 original size:11 final size:13
Alignment explanation
Indices: 17872--17904 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17862 ATAACTAATA
*
17872 ATATT-AATTAAT
1 ATATTAAATAAAT
17884 ATATTAAATAAAT
1 ATATTAAATAAAT
17897 ATATTAAA
1 ATATTAAA
17905 AATATTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:21354 original size:134 final size:128
Alignment explanation
Indices: 21004--21491 Score: 798
Period size: 128 Copynumber: 3.8 Consensus size: 128
20994 ACTATTCACA
* *
21004 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCTTA
1 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
21069 TTATGTCACTTATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
* * * *
21132 TGAAGGCGCGTTCTCGGGTGCGCGCCTTCCATTATTTTGCCAGATAATATATTATCATTGCCCTA
1 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
21197 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
*
21260 TGAAGGCGCGTTCTCGGGGGGGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT
1 TGAAGGCGCGTTCTC------GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT
21325 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGG
60 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGG
21390 GACT
125 GACT
* * *
21394 TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
21459 TTATGTCACTCATGTCCCTCGGGGACACTAGAT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT
21492 GGATTGTGAA
Statistics
Matches: 336, Mismatches: 17, Indels: 14
0.92 0.05 0.04
Matches are distributed among these distances:
128 214 0.64
129 1 0.00
134 121 0.36
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:21490 original size:262 final size:262
Alignment explanation
Indices: 21019--21491 Score: 849
Period size: 262 Copynumber: 1.8 Consensus size: 262
21009 GCGCGTTCCC
* *
21019 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCTTATTATGTCACTTATGT
1 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
* * *
21084 CCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCTCGG
66 CCCTCGGGGACACTAATCATATCAGTACCTATTATTTCTCAGGGGACTTGAAAGCGCGTTCCCGG
*
21149 GTGCGCGCCTTCCATTATTTTGCCAGATAATATATTATCATTGCCCTATTATGTCACTCATGTCC
131 GGGCGCGCCTTCCATTATTTTGCCAGATAATATATTATCATTGCCCTATTATGTCACTCATGTCC
21214 CTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCTCGGGG
196 CTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCTCGGGG
21279 GG
261 GG
*
21281 GGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
21346 CCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACTTGAAAGCGCGTTCCCG
66 CCCTCGGGGACACTA-ATCATATCAGTACCTATTATTTCTCAGGGGACTTGAAAGCGCGTTCCCG
* *
21410 GGGGCGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTCATGTC
130 GGGGCGCGCCTTCCATTATTTTGCCAGATAATATATTATCATTGCCCTATTATGTCACTCATGTC
21475 CCTCGGGGACACTAGAT
195 CCTCGGGGACACTAGAT
21492 GGATTGTGAA
Statistics
Matches: 201, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
262 200 1.00
263 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (262 bp):
GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
CCCTCGGGGACACTAATCATATCAGTACCTATTATTTCTCAGGGGACTTGAAAGCGCGTTCCCGG
GGGCGCGCCTTCCATTATTTTGCCAGATAATATATTATCATTGCCCTATTATGTCACTCATGTCC
CTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCTCGGGG
GG
Found at i:21892 original size:34 final size:34
Alignment explanation
Indices: 21853--21959 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
21843 TAAGTTGAAA
* *
21853 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
21887 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
21921 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
21955 TTTAA
1 TTTAA
21960 AATATTATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:22529 original size:21 final size:21
Alignment explanation
Indices: 22478--22571 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
22468 TATGGTATAA
*
22478 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
* *
22499 AA-ACTGGTGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* * *
22520 AACCCTGTGGGCTCGGAATAT
1 AACCCTGCGGGCTAGGAATGT
*
22541 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
22562 AACCCTGCGG
1 AACCCTGCGG
22572 AGATGGCATA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.20
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:24654 original size:20 final size:21
Alignment explanation
Indices: 24629--24680 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
24619 TTTTCCCAAT
*
24629 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24649 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
24670 TCGCAATGCGA
1 TCGCAATGCGA
24681 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:24694 original size:20 final size:20
Alignment explanation
Indices: 24669--24769 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
24659 AATTGGGAAA
*
24669 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
24689 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
24710 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
24730 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
24750 TTCACAATGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
24770 TTCGTAATGA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.72
21 15 0.22
22 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:24778 original size:20 final size:20
Alignment explanation
Indices: 24670--24783 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
24660 ATTGGGAAAA
*
24670 TCGCAATGCGATACTGACTA
1 TCGCAATGCGATACTGACTT
* * **
24690 TCGCAACGCGATAAT-ACAAAA
1 TCGCAATGCGATACTGAC--TT
*
24711 TCGCAACGCGATACTGACTT
1 TCGCAATGCGATACTGACTT
*
24731 TCGCAACGCGATACTGACTT
1 TCGCAATGCGATACTGACTT
* *
24751 TCACAATGCGATTCTGACTT
1 TCGCAATGCGATACTGACTT
* *
24771 TCGTAATGAGATA
1 TCGCAATGCGATA
24784 ATACAGAATC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGATACTGACTT
Found at i:24804 original size:41 final size:40
Alignment explanation
Indices: 24667--24803 Score: 150
Period size: 41 Copynumber: 3.4 Consensus size: 40
24657 CGAATTGGGA
*
24667 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
* *
24707 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 -AAATCGCAATGCGATACTGACTTTCGCAACGCGATAAT-AC
** * * * * *
24749 -TTTCACAATGCGATTCTGACTTTCGTAATGAGATAATAC
1 AAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
24788 AGAATCGCAATGCGAT
1 A-AATCGCAATGCGAT
24804 TTTCAAAGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 28 0.36
41 46 0.59
42 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (40 bp):
AAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:24970 original size:12 final size:12
Alignment explanation
Indices: 24937--24982 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
24927 CTCTCTGTCG
24937 ACATCCGTTCCT
1 ACATCCGTTCCT
* *
24949 ATATCTGTTCCT
1 ACATCCGTTCCT
*
24961 ACGTCCGTTCCT
1 ACATCCGTTCCT
24973 ACATCC-TTCC
1 ACATCCGTTCC
24983 CCATCCGGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.15, C:0.39, G:0.09, T:0.37
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:25170 original size:14 final size:14
Alignment explanation
Indices: 25153--25206 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
25143 GAAAATCGCA
25153 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
25167 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
25184 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
25200 TTGCGAT
1 TTGCGAT
25207 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:27293 original size:19 final size:20
Alignment explanation
Indices: 27238--27305 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
27228 GAAACTTAAA
*
27238 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
27258 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* * **
27278 ATCTCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
27297 ATCGCAACG
1 ATCGCAACG
27306 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:27313 original size:14 final size:14
Alignment explanation
Indices: 27294--27351 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
27284 ATGCGAAATG
27294 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
27308 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
27324 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
27340 AAAATCGCAACG
1 AAAATCGCAACG
27352 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:27336 original size:32 final size:33
Alignment explanation
Indices: 27282--27356 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 33
27272 ATGGCTATCT
27282 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
27315 CAATGCGAAATG-AAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
27347 CAACGCGAAA
1 CAATGCGAAA
27357 CACAAATCGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 29 0.71
33 12 0.29
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCG
Found at i:27385 original size:19 final size:19
Alignment explanation
Indices: 27363--27478 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
27353 GAAACACAAA
27363 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
27382 TCGCGTTGAGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
27398 T--CATTGAGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27415 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
27431 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27448 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27467 TCGCATTGCGAT
1 TCGCATTGCGAT
27479 AGCCATTTCC
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 13 0.17
15 6 0.08
16 6 0.08
17 6 0.08
18 6 0.08
19 41 0.53
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:27409 original size:33 final size:33
Alignment explanation
Indices: 27366--27462 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
27356 ACACAAATCG
*
27366 CATTGCGATTTTCATTTCGCGTTGAGATTTTGT
1 CATTGCGATTTTCATTTCGCGTTGCGATTTTGT
* *
27399 CATTGAGATTTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCGTTGCGATTTTGT
*
27432 CGTTGCGATTTTCATTTCGCGTTGCGATTTT
1 CATTGCGATTTTCATTTCGCGTTGCGATTTT
27463 CATTTCGCAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.48
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTTTGT
Found at i:27497 original size:20 final size:19
Alignment explanation
Indices: 27432--27517 Score: 91
Period size: 19 Copynumber: 4.4 Consensus size: 19
27422 GCGATTTTGT
**
27432 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
**
27451 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
27470 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
27490 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
27510 TGTTGCGA
1 CGTTGCGA
27518 AAGTAAACTA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
19 32 0.55
20 23 0.40
21 3 0.05
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:28027 original size:18 final size:18
Alignment explanation
Indices: 28006--28044 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
27996 CAGATGATGA
*
28006 CTCTGGGTGAGGTGATAG
1 CTCTGGGCGAGGTGATAG
*
28024 CTCTGGGCGAGGTGATGG
1 CTCTGGGCGAGGTGATAG
28042 CTC
1 CTC
28045 CCGAAGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.18, G:0.44, T:0.26
Consensus pattern (18 bp):
CTCTGGGCGAGGTGATAG
Found at i:29496 original size:19 final size:19
Alignment explanation
Indices: 29472--29548 Score: 110
Period size: 19 Copynumber: 4.3 Consensus size: 19
29462 AGGAGCCGTT
*
29472 TGAGCCGAGCCGCTTGAGC
1 TGAGCCGAGCCGTTTGAGC
29491 TGAGCCGAGCCGTTT-A--
1 TGAGCCGAGCCGTTTGAGC
29507 --AGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
29524 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
29543 TGAGCC
1 TGAGCC
29549 AAGCGAGCCG
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
14 13 0.25
15 1 0.02
18 1 0.02
19 37 0.71
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (19 bp):
TGAGCCGAGCCGTTTGAGC
Found at i:29501 original size:33 final size:33
Alignment explanation
Indices: 29464--29548 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
29454 GAAGCCTGAG
29464 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
* *
29497 GAGCCGTTTAAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
*
29530 GAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCC
29549 AAGCGAGCCG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.20
Consensus pattern (33 bp):
GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
Found at i:29548 original size:14 final size:14
Alignment explanation
Indices: 29464--29530 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
29454 GAAGCCTGAG
29464 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
29478 GAGCCGCTTGAGCTGAGCC
1 GAGCCG-TT----TGAGCC
*
29497 GAGCCGTTTAAGCC
1 GAGCCGTTTGAGCC
*
29511 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
29525 GAGCCG
1 GAGCCG
29531 AGCCGTTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.19
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:30723 original size:18 final size:18
Alignment explanation
Indices: 30697--30731 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30687 TCGAAAGGAC
*
30697 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
30715 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
30732 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:33799 original size:20 final size:20
Alignment explanation
Indices: 33751--33809 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
33741 AATAGTTTCT
** *
33751 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
33771 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
** *
33791 GAATTTGACTATCACAACG
1 GAAAATGACTATCGCAACG
33810 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:34099 original size:22 final size:22
Alignment explanation
Indices: 34072--34115 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34062 GATGGAGATA
34072 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
34094 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
34116 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:34336 original size:20 final size:20
Alignment explanation
Indices: 34308--34375 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
34298 TGTATTATCA
34308 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
34328 CGTTTCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
* *
34348 CGTTGCGAAAGTCAGTATCT
1 CGTTGCGAAAGTCAGAATCG
34368 CGTTGCGA
1 CGTTGCGA
34376 TTTTGTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:34389 original size:61 final size:61
Alignment explanation
Indices: 34324--34440 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
34314 GAAAGTCAGA
* * * * * *
34324 ATCGCGTTTCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* *
34385 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
34441 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:34409 original size:20 final size:20
Alignment explanation
Indices: 34384--34437 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
34374 GATTTTGTAT
34384 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
34404 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
34424 TATCGCATTGCGAT
1 TATCGCATTGCGAT
34438 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:34456 original size:61 final size:61
Alignment explanation
Indices: 34324--34458 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
34314 GAAAGTCAGA
* * * * * * ** *
34324 ATCGCGTTTCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* *
34385 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
34447 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
34459 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:38912 original size:14 final size:14
Alignment explanation
Indices: 38893--38928 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
38883 TCATCACCGT
38893 CCGCCGTCCGTCGA
1 CCGCCGTCCGTCGA
38907 CCGCCGTCCGTCGA
1 CCGCCGTCCGTCGA
38921 CCGCCGTC
1 CCGCCGTC
38929 TGCCGCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.06, C:0.53, G:0.28, T:0.14
Consensus pattern (14 bp):
CCGCCGTCCGTCGA
Found at i:52401 original size:59 final size:60
Alignment explanation
Indices: 52297--52462 Score: 187
Period size: 60 Copynumber: 2.8 Consensus size: 60
52287 GTATGACCAT
* * * * * *
52297 CATTTTAAATTGGTCCTTAAATTTTTAAATATTCTAATTTCATCCCTAAACCACGAATA-A
1 CATTTTAAATTAGTCCTCAAACTTTTGAACATTCTAATTTCATCCCTAAACCA-GAACATA
* * * *
52357 CATTTTAAATTAATCCTCAAACTTTTGAACATTC-AATTTCATCCC-AAACTATAACATT
1 CATTTTAAATTAGTCCTCAAACTTTTGAACATTCTAATTTCATCCCTAAACCAGAACATA
*
52415 CATTCTAAATTAGTCCTCAAACTTTTTGAACATTCTAATTTCA-CCCTA
1 CATTTTAAATTAGTCCTCAAAC-TTTTGAACATTCTAATTTCATCCCTA
52463 CGTTATATTT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 3 0.03
58 25 0.28
59 26 0.29
60 36 0.40
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.39
Consensus pattern (60 bp):
CATTTTAAATTAGTCCTCAAACTTTTGAACATTCTAATTTCATCCCTAAACCAGAACATA
Found at i:52915 original size:17 final size:17
Alignment explanation
Indices: 52893--52925 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52883 GTTAAAAAAT
52893 TATTTAAAAATTTATTG
1 TATTTAAAAATTTATTG
52910 TATTTAAAAATTTATT
1 TATTTAAAAATTTATT
52926 AATAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTTAAAAATTTATTG
Found at i:60595 original size:46 final size:46
Alignment explanation
Indices: 60507--60599 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
60497 TATTATATCT
* * * * **
60507 CAGTCAATAGGTTAACATCAAGCTTAGATTGTTATCGGTTTTTTAA
1 CAGTCAATAAGTTAACATCAAGCTTAGACTATCATCAATTTTTTAA
*
60553 CAGTCAATAAGTTAACATCAATCTTAGACTATCATCAATTTTTTAA
1 CAGTCAATAAGTTAACATCAAGCTTAGACTATCATCAATTTTTTAA
60599 C
1 C
60600 GACAAATACG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (46 bp):
CAGTCAATAAGTTAACATCAAGCTTAGACTATCATCAATTTTTTAA
Found at i:60793 original size:12 final size:13
Alignment explanation
Indices: 60776--60831 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 13
60766 ATACCCTAAA
60776 ATTAAT-TATATT
1 ATTAATATATATT
60788 ATTAATATATATAT
1 ATTAATATATAT-T
60802 ATATATATATATATAT
1 AT-TA-ATATATAT-T
60818 ATATATATATATAT
1 AT-TA-ATATATAT
60832 ATCCAGAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.15
13 5 0.12
14 3 0.08
15 2 0.05
16 24 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTAATATATATT
Found at i:60799 original size:2 final size:2
Alignment explanation
Indices: 60792--60833 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
60782 TATATTATTA
60792 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60834 CCAGAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61314 original size:60 final size:60
Alignment explanation
Indices: 61194--61343 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 60
61184 TATTTGGATG
* * * * * * * * *
61194 AATTTGGGGATGAAATTGGAAGATTTAAAATTTTAAGGAATGATTTATAATAAGGGTCAT
1 AATTTGAGGATGAAATTGAAATATTTAAAAGTTTAAGGAATAATTTAGAACAAAGATCAT
* * *
61254 AGTTTGAGGATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTTAGAACAAATATCAT
1 AATTTGAGGATGAAATTGAAATATTTAAAAGTTTAAGGAATAATTTAGAACAAAGATCAT
* *
61314 AATTTAAGGATTAAATT-ACAATATTTAAAA
1 AATTTGAGGATGAAATTGA-AATATTTAAAA
61344 ATTGAAATAC
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
59 1 0.01
60 73 0.99
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (60 bp):
AATTTGAGGATGAAATTGAAATATTTAAAAGTTTAAGGAATAATTTAGAACAAAGATCAT
Found at i:70828 original size:4 final size:4
Alignment explanation
Indices: 70812--70842 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
70802 GATCCTGCTA
*
70812 TATG TATG GATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
70843 AAGCATACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:74528 original size:87 final size:87
Alignment explanation
Indices: 74303--74542 Score: 248
Period size: 87 Copynumber: 2.8 Consensus size: 87
74293 AGATTCAGTG
* * * * * * * *
74303 AATTCATCAAGTATGTCTCATAAAGATCACCCAAATCATGGGCAACGAACTCCTTAAAAGTGTAA
1 AATTCATCAAGTATGTCTCATTAGGATCACCCAAATCATGGACTACGAATTCATTGAGAGTGTAA
*
74368 AACACAACATCTCAAATAAGTA
66 AACACAACATCTCAAATAAATA
*** * * * * * * *
74390 AATTCATCAAGTCCCTCTCACTAGGATCACTCAAATCCTGGAATATGAATTCATCGAGAGTCTAA
1 AATTCATCAAGTATGTCTCATTAGGATCACCCAAATCATGGACTACGAATTCATTGAGAGTGTAA
* *
74455 AACCCAACCTCTCAAATAAATA
66 AACACAACATCTCAAATAAATA
* * *
74477 AATTCATCAAGTATGTCTCATTAGGACCACCCAAATCTTGGTCTA-GAAATTCATTGAGAGTGTA
1 AATTCATCAAGTATGTCTCATTAGGATCACCCAAATCATGGACTACG-AATTCATTGAGAGTGTA
74541 AA
65 AA
74543 GCTTATCCTT
Statistics
Matches: 120, Mismatches: 32, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
86 1 0.01
87 119 0.99
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (87 bp):
AATTCATCAAGTATGTCTCATTAGGATCACCCAAATCATGGACTACGAATTCATTGAGAGTGTAA
AACACAACATCTCAAATAAATA
Found at i:74886 original size:22 final size:22
Alignment explanation
Indices: 74836--74889 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
74826 TAAAATAAGT
74836 ATATAAAT-TATATTTTTAATA
1 ATATAAATATATATTTTTAATA
* * *
74857 ATTTTAAATATATATTTTTATTG
1 A-TATAAATATATATTTTTAATA
74880 ATATAAATAT
1 ATATAAATAT
74890 TTAGCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
ATATAAATATATATTTTTAATA
Found at i:79740 original size:331 final size:327
Alignment explanation
Indices: 79260--79926 Score: 894
Period size: 337 Copynumber: 2.0 Consensus size: 327
79250 ACTCGAAATA
* * * *
79260 AAAAAGAATCTTAAATTTAACTCGAATCTGAACTTTAAATATATGAAAATGTTATATTGTTTTTT
1 AAAAAGAATCTTAAATTTAACTCGAATCTAAACCTTAAATACATGAAAATGTTATATTATTTTTT
* * *
79325 TTAAATCAACACATAAATATTATTATTAATAATTTTTTAAAAATAATAAAATCTTAATGTATTAT
66 TTAAATCAACACATAAATAATATTATTAATAATTTTTTAAAAATAATAAAATCTCAATATATTAT
*
79390 ATTTTCGAGTTACTCGTGAGCTTTTCGAGTCGAGTATTAAATAGCTCG-T-TTCGACTCGTTAAG
131 ATTTTCGAGTTACTCGTGAGCTTTTCGAGTCGAGTATCAAATAGCTCGTTGTTCGACTCGTTAAG
* * * * *
79453 CACTCGAGTCAAGCTCGAGCTT-GAGTCGAGTATTTATCGAACTTTGACTGAGTTGATCTCGAGT
196 AACTCGAGTCAAGCTCGAGCTTAG-GTCAAGTATTTATCGAACTTTGACTAAATCGATCTCGAGT
* *
79517 AGCTCACAATCGATCTAATCTCATTTACAGCCATAGACATAACCATGCACTATAAACCCCACGAT
260 AGCTCACAATCGATCTAATCTCATTTACAACCATAGACATAACCATGCACTATAAACCCCACAAT
79582 TGT
325 TGT
* * * *
79585 AAAAAGAATCTTAAATTTAACTCGAATTTAAACCTTAAATACAT-TAAAT-TTTTTTTATATATT
1 AAAAAGAATCTTAAATTTAACTCGAATCTAAACCTTAAATACATGAAAATGTTATATTAT-T-TT
79648 TTTTAAATCAACACATAAATGTTAATATTATTAATAATTTATTTTTAAAAATAATAAAATCTCAA
64 TTTTAAATCAACACATAAA---TAATATTATTAATAA--T-TTTTTAAAAATAATAAAATCTCAA
* * *
79713 TATATTATATTTTTGAGTTACTCGTGAGCTTTTCGATTCGAGTATCAAGTAGCTCGTTTCGAGTT
123 TATATTATATTTTCGAGTTACTCGTGAGCTTTTCGAGTCGAGTATCAAATAGCTCG-TT---GTT
* *
79778 CGACTCGTTAAGAACTCGAGTCGAGCTCGATCTTAGGTCAAGTATTTATCGAACTTTGACTAAAT
184 CGACTCGTTAAGAACTCGAGTCAAGCTCGAGCTTAGGTCAAGTATTTATCGAACTTTGACTAAAT
* * ** ** **
79843 CGATCTCGAGTATCTCACGATTTATCTCGTCTCATTTACAACTTTAGACATAACCATGCACTATA
249 CGATCTCGAGTAGCTCACAATCGATCTAATCTCATTTACAACCATAGACATAACCATGCACTATA
79908 AACCCCACAATTGT
314 AACCCCACAATTGT
79922 AAAAA
1 AAAAA
79927 AAAAAAAAGG
Statistics
Matches: 295, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
323 6 0.02
324 5 0.02
325 61 0.21
328 14 0.05
330 1 0.00
331 74 0.25
333 1 0.00
337 132 0.45
338 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (327 bp):
AAAAAGAATCTTAAATTTAACTCGAATCTAAACCTTAAATACATGAAAATGTTATATTATTTTTT
TTAAATCAACACATAAATAATATTATTAATAATTTTTTAAAAATAATAAAATCTCAATATATTAT
ATTTTCGAGTTACTCGTGAGCTTTTCGAGTCGAGTATCAAATAGCTCGTTGTTCGACTCGTTAAG
AACTCGAGTCAAGCTCGAGCTTAGGTCAAGTATTTATCGAACTTTGACTAAATCGATCTCGAGTA
GCTCACAATCGATCTAATCTCATTTACAACCATAGACATAACCATGCACTATAAACCCCACAATT
GT
Found at i:80320 original size:2 final size:2
Alignment explanation
Indices: 80313--80339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80303 TCCAAATGGT
80313 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
80340 GCAAGTGCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:84636 original size:21 final size:21
Alignment explanation
Indices: 84610--84660 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
84600 TACTTGAAAC
*
84610 ATTATTATTTCTACCGATTTT
1 ATTATTATTTCTACCAATTTT
* *
84631 ATTATTTTTTCTATCAATTTT
1 ATTATTATTTCTACCAATTTT
84652 ATTATTATT
1 ATTATTATT
84661 AACGTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTATTATTTCTACCAATTTT
Found at i:85153 original size:2 final size:2
Alignment explanation
Indices: 85146--85176 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
85136 AAGGGCAACA
85146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85177 CAAATAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85736 original size:6 final size:6
Alignment explanation
Indices: 85727--85757 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
85717 CATTACCATT
85727 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
85758 GACGAGACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:86266 original size:5 final size:5
Alignment explanation
Indices: 86237--86284 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
86227 CGTCGCCGTC
* *
86237 TCGTC TCGTC TCGTG TCGTG TCGTG TCGTGG TCGTGG TCGTG CTCGTG
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGT-G TCGT-G TCGTG -TCGTG
86285 GTAATACGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
5 24 0.60
6 16 0.40
ACGTcount: A:0.00, C:0.25, G:0.38, T:0.38
Consensus pattern (5 bp):
TCGTG
Found at i:86272 original size:6 final size:6
Alignment explanation
Indices: 86247--86286 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
86237 TCGTCTCGTC
*
86247 TCGT-G TCGT-G TCGT-G TCGTGG TCGTGG TCGTGC TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
86287 AATACGTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 14 0.44
6 18 0.56
ACGTcount: A:0.00, C:0.20, G:0.42, T:0.38
Consensus pattern (6 bp):
TCGTGG
Found at i:86286 original size:12 final size:11
Alignment explanation
Indices: 86236--86284 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
86226 CCGTCGCCGT
*
86236 CTCGTCTCGT-
1 CTCGTGTCGTG
86246 CTCGTGTCGTG
1 CTCGTGTCGTG
86257 -TCGTGTCGTG
1 CTCGTGTCGTG
*
86267 GTCGTGGTCGTG
1 CTCGT-GTCGTG
86279 CTCGTG
1 CTCGTG
86285 GTAATACGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 19 0.56
11 5 0.15
12 10 0.29
ACGTcount: A:0.00, C:0.27, G:0.37, T:0.37
Consensus pattern (11 bp):
CTCGTGTCGTG
Found at i:86400 original size:41 final size:41
Alignment explanation
Indices: 86343--86441 Score: 171
Period size: 41 Copynumber: 2.4 Consensus size: 41
86333 AAATTCTTAA
*
86343 GAAAAGCACAACGCGATTTTCAACTATCGCAATGCGAAATG
1 GAAAAGCACAACGCGATTTTCAACTATCGCAACGCGAAATG
86384 GAAAAGCACAACGCGATTTTCAACTATCGCAACGCGAAATG
1 GAAAAGCACAACGCGATTTTCAACTATCGCAACGCGAAATG
* *
86425 GAAAAGCGCAACACGAT
1 GAAAAGCACAACGCGAT
86442 CGCATTGCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.16
Consensus pattern (41 bp):
GAAAAGCACAACGCGATTTTCAACTATCGCAACGCGAAATG
Found at i:86416 original size:21 final size:21
Alignment explanation
Indices: 86351--86420 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
86341 AAGAAAAGCA
86351 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
* ** ** * * *
86372 CAATGCGAAATGGAA-AAGCA
1 CAACGCGATTTTCAACTATCG
86392 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
86413 CAACGCGA
1 CAACGCGA
86421 AATGGAAAAG
Statistics
Matches: 32, Mismatches: 16, Indels: 2
0.64 0.32 0.04
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
CAACGCGATTTTCAACTATCG
Found at i:86436 original size:20 final size:20
Alignment explanation
Indices: 86370--86436 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
86360 TTTCAACTAT
*
86370 CGCAATGCGAAATGGAAAAG
1 CGCAACGCGAAATGGAAAAG
* ** ** * *
86390 CACAACGCGATTTTCAACTAT
1 CGCAACGCGAAATGGAA-AAG
86411 CGCAACGCGAAATGGAAAAG
1 CGCAACGCGAAATGGAAAAG
86431 CGCAAC
1 CGCAAC
86437 ACGATCGCAT
Statistics
Matches: 31, Mismatches: 15, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.13
Consensus pattern (20 bp):
CGCAACGCGAAATGGAAAAG
Found at i:87393 original size:60 final size:60
Alignment explanation
Indices: 87277--87394 Score: 132
Period size: 60 Copynumber: 2.0 Consensus size: 60
87267 ATAGTCGAGT
* * * * * *
87277 GATCATTTTGTAATTTTTCATAGTCGATGGACTCAACAAAGCAACTTCTTACAGTTGATG
1 GATCATTTTATAACTTTTAATAGTCAATGGACTCAACAAAACAACTTCATACAGTTGATG
* *
87337 GATCATTTTATAACTTTTAATAGTCAAAT-GACTCAATAAAAC-ACTATCATATAGTTGA
1 GATCATTTTATAACTTTTAATAGTC-AATGGACTCAACAAAACAACT-TCATACAGTTGA
87395 CGAACCATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
59 3 0.06
60 43 0.90
61 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTCAATGGACTCAACAAAACAACTTCATACAGTTGATG
Found at i:88996 original size:29 final size:29
Alignment explanation
Indices: 88953--89008 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
88943 ATCCCCTTAT
* *
88953 AATTTTATAAGTTCAAATTTATTCTCTGA
1 AATTTTATAAATTCAAATTTATCCTCTGA
88982 AATTTTATAAATTCAAATTTATCCTCT
1 AATTTTATAAATTCAAATTTATCCTCT
89009 AACACAAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (29 bp):
AATTTTATAAATTCAAATTTATCCTCTGA
Found at i:91692 original size:17 final size:17
Alignment explanation
Indices: 91672--91705 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
91662 GGTTAATTGT
*
91672 CGTTAACAGTTAACATA
1 CGTTAACAATTAACATA
91689 CGTTAACAATTAACATA
1 CGTTAACAATTAACATA
91706 TTAAGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (17 bp):
CGTTAACAATTAACATA
Found at i:100967 original size:2 final size:2
Alignment explanation
Indices: 100960--100984 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
100950 CTCTAGTATG
100960 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
100985 GTGTGTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105633 original size:21 final size:21
Alignment explanation
Indices: 105586--105626 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
105576 AATTAAAAAT
*
105586 CTTTTTCTTAAACTTAGTAAA
1 CTTTTTCTTAAAATTAGTAAA
*
105607 CTTTTTTTTAAAATTAGTAA
1 CTTTTTCTTAAAATTAGTAA
105627 CATTTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (21 bp):
CTTTTTCTTAAAATTAGTAAA
Found at i:106503 original size:22 final size:22
Alignment explanation
Indices: 106475--106526 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
106465 ATGCCTAGAT
*
106475 GTTAAATGTAGTTAAAAACCTC
1 GTTAAATGTAATTAAAAACCTC
*
106497 GTTAAATGTAATTAAAAATCTC
1 GTTAAATGTAATTAAAAACCTC
106519 GTTAAATG
1 GTTAAATG
106527 ACATGTGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
GTTAAATGTAATTAAAAACCTC
Found at i:114184 original size:60 final size:60
Alignment explanation
Indices: 114087--114237 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 60
114077 TAAGTTCATC
* *
114087 GACTATTAAAAGTTATAAAATTATCTTAT--GACCATAGAGTGTTGATTTGTTGAGTCTCTA
1 GACTATTAAAAGTTACAAAATGA--TTATCCGACCATAGAGTGTTGATTTGTTGAGTCTCTA
* * * * *
114147 GACTATTAAAAGTTACAAAATGATTATCCGACTATAGAGTGTTGCTTTGTTGAGTGTTTC
1 GACTATTAAAAGTTACAAAATGATTATCCGACCATAGAGTGTTGATTTGTTGAGTCTCTA
* * *
114207 TACTATTAAAAGTTACAAAATGGTTACCCGA
1 GACTATTAAAAGTTACAAAATGATTATCCGA
114238 TTATTCGTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 4 0.05
60 75 0.95
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (60 bp):
GACTATTAAAAGTTACAAAATGATTATCCGACCATAGAGTGTTGATTTGTTGAGTCTCTA
Found at i:115867 original size:22 final size:22
Alignment explanation
Indices: 115839--115889 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
115829 GAATCTTTTA
* * * *
115839 ATCGTCGGAAGGTTGAGGACGT
1 ATCGTCGGAAGATTAACGACGG
115861 ATCGTCGGAAGATTAACGACGG
1 ATCGTCGGAAGATTAACGACGG
115883 ATCGTCG
1 ATCGTCG
115890 TCAACATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (22 bp):
ATCGTCGGAAGATTAACGACGG
Found at i:116135 original size:6 final size:6
Alignment explanation
Indices: 116127--116282 Score: 267
Period size: 6 Copynumber: 26.0 Consensus size: 6
116117 ATCATGGTAA
*
116127 GTATAA GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
116175 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
* *
116223 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT ATATAT ATATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
* *
116271 ATATAT ATATAT
1 GTATAT GTATAT
116283 TGATTGTATT
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 148 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (6 bp):
GTATAT
Found at i:121119 original size:23 final size:22
Alignment explanation
Indices: 121095--121136 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
121085 TATTTTAGTA
*
121095 AAACTTATTTTTTAAAATAATT
1 AAACTTAATTTTTAAAATAATT
*
121117 AAATTTAATTTTTAAAATAA
1 AAACTTAATTTTTAAAATAA
121137 AATTATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AAACTTAATTTTTAAAATAATT
Found at i:125370 original size:18 final size:18
Alignment explanation
Indices: 125340--125391 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
125330 ACAAACACCC
125340 TAATAAATT-TAAG-AACTA
1 TAAT-AATTATAAGTAAC-A
125358 TAATAATTATAAGTAACA
1 TAATAATTATAAGTAACA
* *
125376 TCATATTTATAAGTAA
1 TAATAATTATAAGTAA
125392 TTTATTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 4 0.13
18 23 0.77
19 3 0.10
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
TAATAATTATAAGTAACA
Found at i:125657 original size:4 final size:4
Alignment explanation
Indices: 125648--125678 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
125638 TATACACGAT
*
125648 TTAA TTAA TTAA TTAA CTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
125679 TATTTTGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (4 bp):
TTAA
Found at i:130090 original size:59 final size:59
Alignment explanation
Indices: 129988--130116 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
129978 AGCTAGGTAT
* * *
129988 CCATTTTGTAACTTTTGATAGTCGGGGACTCAACAAAGCAACATCTTATAATCAAGGGA
1 CCATTTTGTAACTTTTGATAGTCGGGGACTCAACAAAACAACATATTATAATCAAAGGA
* * * * *
130047 TCATTTTGTAACTTTTGATAGTCGGGGACTTAATAAAATAACATATTATAGTCAAAGGA
1 CCATTTTGTAACTTTTGATAGTCGGGGACTCAACAAAACAACATATTATAATCAAAGGA
130106 CCATTTGTGTA
1 CCATTT-TGTA
130117 GTTTACCCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 56 0.93
60 4 0.07
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (59 bp):
CCATTTTGTAACTTTTGATAGTCGGGGACTCAACAAAACAACATATTATAATCAAAGGA
Found at i:130853 original size:16 final size:16
Alignment explanation
Indices: 130832--130864 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
130822 AATTAAGGAT
130832 TAGGGATGATAACGGG
1 TAGGGATGATAACGGG
130848 TAGGGATGATAACGGG
1 TAGGGATGATAACGGG
130864 T
1 T
130865 CAAGTTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.42, T:0.21
Consensus pattern (16 bp):
TAGGGATGATAACGGG
Done.