Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008869.1 Hibiscus syriacus cultivar Beakdansim tig00112103_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: 118230
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:532 original size:14 final size:15
Alignment explanation
Indices: 490--545 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
480 CGTTTAAATA
*
490 AATCTCGAGTTTAAT
1 AATCTCGAGTTTAAC
505 AATCTCGAGTTTAAC
1 AATCTCGAGTTTAAC
520 AATCTCG-GTTTAAC
1 AATCTCGAGTTTAAC
534 AAATCTCGAGTT
1 -AATCTCGAGTT
546 AAAACTTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
14 7 0.18
15 28 0.74
16 3 0.08
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (15 bp):
AATCTCGAGTTTAAC
Found at i:2101 original size:15 final size:16
Alignment explanation
Indices: 2082--2120 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2072 CGAGATCACA
2082 ATCATCATCCA-AATC
1 ATCATCATCCATAATC
*
2097 GTCATCAT-CATAATC
1 ATCATCATCCATAATC
2112 ATCATCATC
1 ATCATCATC
2121 ACTCAAAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (16 bp):
ATCATCATCCATAATC
Found at i:17693 original size:33 final size:33
Alignment explanation
Indices: 17653--17751 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 33
17643 AGTTAAAATG
17653 ATTAAAGTTATTTAAAAGTTATTAATAAAATAA
1 ATTAAAGTTATTTAAAAGTTATTAATAAAATAA
* * *
17686 ATTAAAGTCATTT---A-TT-TTATTAAAAT-G
1 ATTAAAGTTATTTAAAAGTTATTAATAAAATAA
17713 ATTAAAGTTATTTAAAAGTTATTAATAAAATAA
1 ATTAAAGTTATTTAAAAGTTATTAATAAAATAA
17746 ATTAAA
1 ATTAAA
17752 ATGATTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
27 12 0.22
28 9 0.17
29 2 0.04
30 2 0.04
31 2 0.04
32 9 0.17
33 18 0.33
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (33 bp):
ATTAAAGTTATTTAAAAGTTATTAATAAAATAA
Found at i:17718 original size:27 final size:29
Alignment explanation
Indices: 17645--17726 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 29
17635 AGCTAAGTAG
17645 TTAAAATGATTAAAGTTATTTAAAAGTTATTA
1 TTAAAATGATTAAAGTTATTT---AGTTATTA
* * *
17677 ATAAAATAAATTAAAGTCATTTA-TT-TTA
1 TTAAAAT-GATTAAAGTTATTTAGTTATTA
17705 TTAAAATGATTAAAGTTATTTA
1 TTAAAATGATTAAAGTTATTTA
17727 AAAGTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 13 0.30
28 9 0.21
29 2 0.05
30 1 0.02
32 6 0.14
33 12 0.28
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (29 bp):
TTAAAATGATTAAAGTTATTTAGTTATTA
Found at i:18009 original size:18 final size:20
Alignment explanation
Indices: 17968--18010 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
17958 TTTAGGTATC
*
17968 AAAATGAGAGAAATAATGAG
1 AAAATGAGAGAAATAATAAG
*
17988 AAAATGA-A-AAATAATAAT
1 AAAATGAGAGAAATAATAAG
18006 AAAAT
1 AAAAT
18011 ATATCGCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 1 0.05
20 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (20 bp):
AAAATGAGAGAAATAATAAG
Found at i:21495 original size:20 final size:20
Alignment explanation
Indices: 21470--21562 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
21460 TTTTCCCAAT
21470 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
21490 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
21510 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
21531 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
21552 TCGCAATGCGA
1 TCGCAATGCGA
21563 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:21512 original size:41 final size:41
Alignment explanation
Indices: 21467--21562 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
21457 CGATTTTCCC
*
21467 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
21508 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
21549 AAATCGCAATGCGA
1 AATTCGCAATGCGA
21563 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:21575 original size:41 final size:41
Alignment explanation
Indices: 21489--21623 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
21479 GAATAAGTAA
* * * *
21489 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
21530 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
21571 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
21612 TTCGCAACGCGA
1 ATCGCAACGCGA
21624 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:21576 original size:20 final size:20
Alignment explanation
Indices: 21551--21645 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
21541 AATTGAGAAA
*
21551 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
21571 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
21592 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
21612 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
21632 TTCGCAACGCGATA
1 ATCGCAACGCGATA
21646 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:21861 original size:22 final size:22
Alignment explanation
Indices: 21833--21876 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21823 CACTCTCTCA
21833 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
21855 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
21877 TATCTAAATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:22149 original size:20 final size:20
Alignment explanation
Indices: 22120--22163 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
22110 GCGATTTTAG
22120 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
22140 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
22160 TTTC
1 TTTC
22164 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:23502 original size:18 final size:18
Alignment explanation
Indices: 23481--23525 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
23471 TCCACTTCGG
*
23481 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
23499 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
23517 GAGCCATCA
1 GAGCCATCA
23526 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:24051 original size:19 final size:20
Alignment explanation
Indices: 23997--24063 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
23987 TAGTTTACTT
* *
23997 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
24017 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
24037 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
24056 TCGCAACG
1 TCGCAACG
24064 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:24071 original size:14 final size:14
Alignment explanation
Indices: 24052--24109 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
24042 ATGCGAAATG
24052 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
24066 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
24082 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
24098 AAAATCGCAACG
1 AAAATCGCAACG
24110 CGAAATGAAA
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:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:24094 original size:32 final size:33
Alignment explanation
Indices: 24036--24126 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
24026 GGAAATGGCT
*
24036 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
24069 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
24101 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
24127 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:24120 original size:19 final size:19
Alignment explanation
Indices: 23997--24131 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
23987 TAGTTTACTT
* **
23997 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
24017 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
24037 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
24056 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
24070 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
24088 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
24102 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
24121 TCGCAATGCGA
1 TCGCAACGCGA
24132 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:24162 original size:14 final size:14
Alignment explanation
Indices: 24143--24182 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
24133 TTGTGTTTCG
24143 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
24157 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
24171 CGTTGTGATTTT
1 CGTTGCGATTTT
24183 CATTTCGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:24217 original size:20 final size:19
Alignment explanation
Indices: 24183--24237 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
24173 TTGTGATTTT
*
24183 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
24202 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
24222 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
24238 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:26121 original size:14 final size:14
Alignment explanation
Indices: 26102--26137 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
26092 ATTGTTTAAT
26102 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
26116 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
26130 TGATTTGT
1 TGATTTGT
26138 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:26276 original size:19 final size:19
Alignment explanation
Indices: 26254--26321 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
26244 ATCGCAACGA
26254 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
26273 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
26292 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
26306 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
26322 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:26365 original size:20 final size:20
Alignment explanation
Indices: 26340--26396 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
26330 TCGCATTGCG
*
26340 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
26360 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
**
26380 ATTTTCGTATTGCGATA
1 ATTTTCGCGTTGCGATA
26397 GTCAAATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:26783 original size:14 final size:14
Alignment explanation
Indices: 26764--26799 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
26754 ATTGTTTAAT
26764 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
26778 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
26792 TGATTTGT
1 TGATTTGT
26800 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:27373 original size:14 final size:14
Alignment explanation
Indices: 27354--27389 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
27344 ATTGTTTAAT
27354 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
27368 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
27382 TGATTTGT
1 TGATTTGT
27390 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:27485 original size:590 final size:590
Alignment explanation
Indices: 26360--28186 Score: 3609
Period size: 590 Copynumber: 3.1 Consensus size: 590
26350 TGCGATAACC
* *
26360 ATTTTCGCGTTGCGATAACCATTTTCGTATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
26425 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
26490 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
26555 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
26620 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
26685 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
26750 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
26815 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
*
26880 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATACGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
26945 TTGCG
586 TTGCG
26950 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
27015 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
27080 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
27145 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGATGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
27210 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
27275 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
27340 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
27405 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
27470 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
27535 TTGCG
586 TTGCG
27540 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
27605 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
27670 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
27735 ATATTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
27800 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
27865 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
27930 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
27995 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
28060 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
28125 TTGCG
586 TTGCG
28130 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAA
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAA
28187 ACATTTTTAT
Statistics
Matches: 1231, Mismatches: 6, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
590 1231 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (590 bp):
ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
TTGCG
Found at i:27963 original size:14 final size:14
Alignment explanation
Indices: 27944--27979 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
27934 ATTGTTTAAT
27944 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
27958 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
27972 TGATTTGT
1 TGATTTGT
27980 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:30750 original size:20 final size:19
Alignment explanation
Indices: 30705--30845 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
30695 TCTTTTGGTT
30705 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
30724 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
30745 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
30764 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
30778 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
30797 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
30811 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
30830 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
30846 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 39 0.42
20 26 0.28
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:30787 original size:33 final size:33
Alignment explanation
Indices: 30730--30828 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
30720 ACGAGATAAT
* *
30730 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
30764 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
30797 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
30829 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:30822 original size:19 final size:19
Alignment explanation
Indices: 30800--30850 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
30790 GCGACGAGAG
30800 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
30819 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
30838 AATCGCAATGCGA
1 AATCGCAACGCGA
30851 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:30879 original size:19 final size:19
Alignment explanation
Indices: 30846--30912 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
30836 AAAATCGCAA
**
30846 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
30865 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
30884 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
30904 TGCGATTTT
1 TGCGATTTT
30913 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:31504 original size:21 final size:21
Alignment explanation
Indices: 31471--31550 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
31461 TGCGAAAGTA
* * *
31471 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
31492 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
31512 AGTATCGCATTGCGATTTTCTC
1 AGTATCGCATTGCGATTTT-TC
* *
31534 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
31551 ACTTATTCGC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 16 0.35
21 26 0.57
22 4 0.09
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:31527 original size:20 final size:20
Alignment explanation
Indices: 31434--31527 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
31424 CGCTAAGTAA
*
31434 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
31454 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
31474 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
31495 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
31515 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
31528 TTTCTCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:31546 original size:41 final size:41
Alignment explanation
Indices: 31455--31589 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
31445 AAAGTCAGTA
* * * * *
31455 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* *
31495 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* ** * *
31537 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
*
31578 TCCCGTTGCGAT
1 TCGCGTTGCGAT
31590 TTACTTATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 71 0.92
42 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:31560 original size:20 final size:20
Alignment explanation
Indices: 31516--31608 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
31506 ATAGTCAGTA
*
31516 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
31537 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
31557 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* * *
31578 TCCCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
31598 TCGCATTGCGA
1 TCGCATTGCGA
31609 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 27 0.47
21 30 0.53
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:31590 original size:41 final size:41
Alignment explanation
Indices: 31516--31611 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
31506 ATAGTCAGTA
* * *
31516 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCCCGTTGCGATTTACTTAT
31557 TCGCATTGCGAATTTCCCAATTCCCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCCCGTTGCGATTTACTTAT
31598 TCGCATTGCGAATT
1 TCGCATTGCGAATT
31612 GGGAAAATCG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCCCGTTGCGATTTACTTAT
Found at i:34879 original size:21 final size:21
Alignment explanation
Indices: 34854--34900 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
34844 TCAAAAATAT
34854 TAAAAA-AATTAATATTTTAAA
1 TAAAAATAA-TAATATTTTAAA
34875 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
34896 TAAAA
1 TAAAA
34901 TTTTATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:35229 original size:109 final size:111
Alignment explanation
Indices: 35016--35250 Score: 352
Period size: 109 Copynumber: 2.1 Consensus size: 111
35006 TGTTATAATT
* *
35016 TTTTA-ATGTTTAATAAGTAAATAACTATTATACCGTACCTATTTATTGAAATTTTAATTTTAAT
1 TTTTAGATGTTTAATAAGTAAATAACTATTAGACCGTAACTATTTATTG-AA--TTAATTTTAAT
35080 TTTAAAATTATACTAAATTAATTTATACTTAAATTACAAGTGAAAGATA
63 TTTAAAATTATACTAAATTAATTTATACTTAAATTACAAGTGAAAGATA
* * *
35129 TTTTAGATGTTTAATAAGTAAATAACTATTAGGA-CTTAACTATTTATTG-A-TATTTTTATTTT
1 TTTTAGATGTTTAATAAGTAAATAACTATTA-GACCGTAACTATTTATTGAATTAATTTTAATTT
*
35191 TAAAATTATACTAAATTAATTTATACTTAATTTACAAGTGAAAGATA
65 TAAAATTATACTAAATTAATTTATACTTAAATTACAAGTGAAAGATA
35238 TTTTAGATGTTTA
1 TTTTAGATGTTTA
35251 GTATTTTTGT
Statistics
Matches: 114, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
109 69 0.61
112 1 0.01
113 5 0.04
114 38 0.33
115 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (111 bp):
TTTTAGATGTTTAATAAGTAAATAACTATTAGACCGTAACTATTTATTGAATTAATTTTAATTTT
AAAATTATACTAAATTAATTTATACTTAAATTACAAGTGAAAGATA
Found at i:36458 original size:16 final size:18
Alignment explanation
Indices: 36432--36465 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
36422 ACTCGACCAA
36432 TTTATTGTTAA-TAATTT
1 TTTATTGTTAATTAATTT
36449 TTTA-TGTTAATTAATTT
1 TTTATTGTTAATTAATTT
36466 CACTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TTTATTGTTAATTAATTT
Found at i:39382 original size:2 final size:2
Alignment explanation
Indices: 39375--39401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39365 TTATAATTAA
39375 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 A
39402 AGAAGATTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42307 original size:18 final size:18
Alignment explanation
Indices: 42284--42318 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42274 TTCCATCCGG
*
42284 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
42302 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
42319 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:43495 original size:19 final size:19
Alignment explanation
Indices: 43473--43555 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
43463 CTAGGCGGCT
*
43473 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
43492 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
43511 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
43525 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
43544 CGGCTCGGCTCA
1 CGGCTCGGCTCA
43556 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:43502 original size:14 final size:14
Alignment explanation
Indices: 43497--43563 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 14
43487 TCAAACGGCT
*
43497 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
43511 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
43525 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
43543 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
43558 CGGCTC
1 CGGCTC
43564 CTCAGGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 31 0.66
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:43522 original size:33 final size:33
Alignment explanation
Indices: 43479--43563 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
43469 GGCTCGGCTT
*
43479 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
43512 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
43545 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
43564 CTCAGGCTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:47333 original size:18 final size:18
Alignment explanation
Indices: 47310--47344 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47300 TTCCATCCGG
*
47310 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
47328 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
47345 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:48520 original size:19 final size:19
Alignment explanation
Indices: 48498--48580 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
48488 CTAGGCGGCT
*
48498 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
48517 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
48536 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
48550 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
48569 CGGCTCGGCTCA
1 CGGCTCGGCTCA
48581 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:48527 original size:14 final size:14
Alignment explanation
Indices: 48522--48588 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 14
48512 TCAAACGGCT
*
48522 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
48536 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
48550 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
48568 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
48583 CGGCTC
1 CGGCTC
48589 CTCAGGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 31 0.66
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:48547 original size:33 final size:33
Alignment explanation
Indices: 48504--48588 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
48494 GGCTCGGCTT
*
48504 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
48537 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
48570 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
48589 CTCAGGCTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:52502 original size:19 final size:19
Alignment explanation
Indices: 52478--52520 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
52468 ACGTGGAGAT
52478 TTTTCTGTTCCACTGAACA
1 TTTTCTGTTCCACTGAACA
52497 TTTTCTGTTCCACTGAACA
1 TTTTCTGTTCCACTGAACA
52516 TTTTC
1 TTTTC
52521 AGTACCCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (19 bp):
TTTTCTGTTCCACTGAACA
Found at i:53906 original size:16 final size:16
Alignment explanation
Indices: 53887--53932 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
53877 AAGATTACTT
* *
53887 TCTTAGTAGATAAGAA
1 TCTTTGTAGATAAAAA
53903 TCTTTGTAGATAAAAA
1 TCTTTGTAGATAAAAA
*
53919 TATTTGTAGATAAA
1 TCTTTGTAGATAAA
53933 GTTTTTAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.37
Consensus pattern (16 bp):
TCTTTGTAGATAAAAA
Found at i:76249 original size:20 final size:20
Alignment explanation
Indices: 76224--76263 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
76214 TGGTTCACGG
76224 AATGTAAGATTATCAGTGAA
1 AATGTAAGATTATCAGTGAA
76244 AATGTAAGATTATCAGTGAA
1 AATGTAAGATTATCAGTGAA
76264 TAGGATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (20 bp):
AATGTAAGATTATCAGTGAA
Found at i:76490 original size:37 final size:37
Alignment explanation
Indices: 76417--76491 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
76407 GTTGAAAAAT
* *
76417 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
76454 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
76491 A
1 A
76492 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:92191 original size:48 final size:48
Alignment explanation
Indices: 92128--92259 Score: 205
Period size: 46 Copynumber: 2.8 Consensus size: 48
92118 TCAACTTCTC
* * **
92128 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTTTA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
*
92176 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
92222 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
92260 GCTGATTCAA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 43 0.57
48 33 0.43
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
Found at i:92193 original size:112 final size:112
Alignment explanation
Indices: 91995--92217 Score: 358
Period size: 112 Copynumber: 2.0 Consensus size: 112
91985 TTTGATCCCA
* * *
91995 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTTAGAGTAATTGGAACATGTCTCTCTTC
1 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
*
92060 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTCG
66 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT-CTTCG
* *
92108 ATTCAATGGATCAACT-TCTCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
1 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
**
92172 TTTAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTC
66 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTC
92218 TCCAAGATTT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
111 4 0.04
112 82 0.80
113 16 0.16
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (112 bp):
ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCG
Found at i:92423 original size:113 final size:113
Alignment explanation
Indices: 92176--92608 Score: 644
Period size: 113 Copynumber: 3.9 Consensus size: 113
92166 CTCTTCTTTA
* * *
92176 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* * *
92239 CAGAGTAAGTGGAACAAGTCT--GCTGATTCAATGGATAAACTTCCCC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
* * *
92285 AGATCTGATATTCCCTTCAAAGTAAGCAGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* * *
92350 TAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAGCTTTCCC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
*
92398 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTTTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
92463 CAGAGTAAGTGGAACAAGTCTACCCTGATTCAATGGATCAAC-TCCCTC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCC-C
*
92511 AGATCTGATATTCCCTTCAGATTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCC-T
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* * * *
92575 GAGTGACAGTGGAACAAGTCTACCCCGATTCAAT
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAAT
92609 CTTCCCTGAA
Statistics
Matches: 293, Mismatches: 26, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
109 31 0.11
111 46 0.16
112 33 0.11
113 183 0.62
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (113 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
Found at i:100788 original size:183 final size:181
Alignment explanation
Indices: 100482--100847 Score: 594
Period size: 183 Copynumber: 2.0 Consensus size: 181
100472 AAATTAAATG
*
100482 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATAATTATAAATAAAAATTTCAGATA
1 TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATAATTATAAATAAAAATTTCAGATA
100547 AATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTGAG
66 AATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTGAG
* *
100612 TTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATTTAATAT
131 TTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
100663 TTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT-
1 TTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAAT-A-ATATAATTAT-AAAT-AAAAATTTC
* * *
100726 ATAT-ATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
61 AGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAA
* *
100790 TTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
126 TTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
100846 TT
1 TT
100848 AAAATTTAAT
Statistics
Matches: 172, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
180 6 0.03
181 28 0.16
182 1 0.01
183 122 0.71
184 7 0.04
185 8 0.05
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (181 bp):
TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATAATTATAAATAAAAATTTCAGATA
AATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTGAG
TTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
Found at i:114087 original size:86 final size:86
Alignment explanation
Indices: 113924--114096 Score: 294
Period size: 86 Copynumber: 2.0 Consensus size: 86
113914 ACGCAAGTTT
*
113924 CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAACAGGGATCCGGGG
1 CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAACAGGCATCCGGGG
*
113989 GATACTGATCGTAAACAACTC
66 GAGACTGATCGTAAACAACTC
*
114010 CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAAACAGGCATCCGTG
1 CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTC-AAACAGGCATCCGGG
*
114075 GGAGA-TGCTCGTAAACAACTC
65 GGAGACTGATCGTAAACAACTC
114096 C
1 C
114097 GGTTCAAGAA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 65 0.79
87 17 0.21
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (86 bp):
CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAACAGGCATCCGGGG
GAGACTGATCGTAAACAACTC
Done.