Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001639.1 Hibiscus syriacus cultivar Beakdansim tig00003278_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: 76485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5822 original size:2 final size:2
Alignment explanation
Indices: 5815--5845 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5805 CTCCAAACAA
5815 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
5846 GTGAAACCAC
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:10831 original size:2 final size:2
Alignment explanation
Indices: 10824--10858 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10814 AAATAAAACC
10824 AT AT 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 AT AT A
10859 ATCATCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13042 original size:186 final size:185
Alignment explanation
Indices: 12696--13096 Score: 481
Period size: 186 Copynumber: 2.2 Consensus size: 185
12686 TTAAACAGAC
* * * * * * *
12696 AATAATATCTTTTAATTTGAAATATTCAAAATATAAAACTCCTTTTACCATTCAAACTTAAATAT
1 AATAATATCTTTTAATTTGCAATAGTCAAAAGATAAAACTCATTTCACCATTCAAACTTAAACAA
* * * *
12761 ATATTTTAATTTGAAATATACAAAGTATATAATTATCTTTAATATTCAAAGTTAAAAAGGTAACA
66 ATATTTTAATTTGAAATATACAAAGTAAATAATTATCTTTAACATTCAAAATTAAAAAGATAACA
* * * ** * *
12826 AATACATTTTAAATTGATATATTCAAAGAGTAGTTATCTTATTAATGTTCAAATTA
131 AATA-ATTTTAAATTAATATATTAAAAGAGTAATTATCCAACTAATATTCAAATTA
* * *
12882 AATAATAT-GTTTAATTTGCAATGGTCAAAAGAT-AAACTCATTTCACTATTCAAACTTAAACAA
1 AATAATATCTTTTAATTTGCAATAGTCAAAAGATAAAACTCATTTCACCATTCAAACTTAAACAA
*
12945 ATATTATTTAATTTGAAATATACAAAAG-AAATAATTATCTTGTAACATTTAAAATTAAAAAGAT
66 ATA-T-TTTAATTTGAAATATAC-AAAGTAAATAATTATCTT-TAACATTCAAAATTAAAAAGAT
*
13009 AACAAAT-ATTTCTAAATTAACT-TATTAAAAGAGTAATTGTCCAACTAATATTCAAATTA
127 AACAAATAATTT-TAAATTAA-TATATTAAAAGAGTAATTATCCAACTAATATTCAAATTA
*
13068 AA-ATTATCTTTTAATTTGCAATAGTCAAA
1 AATAATATCTTTTAATTTGCAATAGTCAAA
13097 TGGACAATGA
Statistics
Matches: 182, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
184 28 0.15
185 29 0.16
186 95 0.52
187 30 0.16
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (185 bp):
AATAATATCTTTTAATTTGCAATAGTCAAAAGATAAAACTCATTTCACCATTCAAACTTAAACAA
ATATTTTAATTTGAAATATACAAAGTAAATAATTATCTTTAACATTCAAAATTAAAAAGATAACA
AATAATTTTAAATTAATATATTAAAAGAGTAATTATCCAACTAATATTCAAATTA
Found at i:14566 original size:3 final size:3
Alignment explanation
Indices: 14558--14582 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14548 TATTTGTAAT
14558 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
14583 CATCATCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15445 original size:50 final size:49
Alignment explanation
Indices: 15362--15471 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 49
15352 GTAGCAGTAA
** * *
15362 AGCGCGCGCCCTGCATCGCGCTATACGCTGATTTGGTGCCACGTGGAGTAT
1 AGCGCGC-CCCTGCCCCGCGATATACGCTGATTTGGCGCCACGTGG-GTAT
* * *
15413 AGCGTGCCCCTGCCCCGCGATATACGGTGATTTGGCGCCATGTGGGTAT
1 AGCGCGCCCCTGCCCCGCGATATACGCTGATTTGGCGCCACGTGGGTAT
*
15462 ATCGCGCCCC
1 AGCGCGCCCC
15472 CTGATCCGCG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 12 0.24
50 32 0.64
51 6 0.12
ACGTcount: A:0.15, C:0.32, G:0.31, T:0.23
Consensus pattern (49 bp):
AGCGCGCCCCTGCCCCGCGATATACGCTGATTTGGCGCCACGTGGGTAT
Found at i:15719 original size:17 final size:18
Alignment explanation
Indices: 15682--15720 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
15672 ATATTATGTA
15682 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
15700 TTTACTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
15717 TTTA
1 TTTA
15721 GTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:15978 original size:111 final size:111
Alignment explanation
Indices: 15784--16005 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
15774 TGGAAATCAT
* * * *
15784 ATATCTCTACACTTTGCTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTTTTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
15849 TATTTGGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 CAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
15895 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
15960 CAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 CAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
16006 TTTTTGAAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
CAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:18105 original size:48 final size:45
Alignment explanation
Indices: 18025--18116 Score: 130
Period size: 48 Copynumber: 2.0 Consensus size: 45
18015 CAGGCATCGA
* *
18025 TAATTTTTTTTATTATATTTGTATTTACTTTATTTTGTTAAATTG
1 TAATTTTTTTTATTATATTTATACTTACTTTATTTTGTTAAATTG
*
18070 TAATTTTTTTTATTTCTCATTTAATACTTACTTTATTTTGTTAAATT
1 TAATTTTTTTTA-TTAT-ATTT-ATACTTACTTTATTTTGTTAAATT
18117 TGTTGGGCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
45 12 0.29
46 3 0.07
47 4 0.10
48 22 0.54
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.65
Consensus pattern (45 bp):
TAATTTTTTTTATTATATTTATACTTACTTTATTTTGTTAAATTG
Found at i:22426 original size:16 final size:17
Alignment explanation
Indices: 22376--22426 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
22366 AAAAAACATA
22376 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
22393 GA-TT-AAA-TTATGAGT
1 AATTTGAAAGTTA-GAGT
22408 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
22424 AAT
1 AAT
22427 GAATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.11
15 8 0.29
16 10 0.36
17 4 0.14
18 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:28530 original size:20 final size:20
Alignment explanation
Indices: 28426--28537 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 20
28416 AAATGACCAA
28426 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAACAT
* * **
28445 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGAACAT
* ** ***
28465 CAGAATCGCAAATC-AGTTTT
1 CAAAATCGCAACGCGA-ACAT
*
28485 CAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGAACAT
*
28505 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAACAT
28524 CATAAATCGCAACG
1 CA-AAATCGCAACG
28538 TGTATCCGTA
Statistics
Matches: 70, Mismatches: 19, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
19 17 0.24
20 52 0.74
21 1 0.01
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (20 bp):
CAAAATCGCAACGCGAACAT
Found at i:28552 original size:20 final size:20
Alignment explanation
Indices: 28487--28756 Score: 281
Period size: 20 Copynumber: 13.5 Consensus size: 20
28477 TCAGTTTTCA
** *
28487 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
28507 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
28527 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28547 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28567 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28587 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28607 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
28627 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28647 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
28667 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28687 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
28707 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28727 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
28747 AAATCACAAC
1 AAATCGCAAC
28757 ACTGAAATTT
Statistics
Matches: 220, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 219 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:29478 original size:24 final size:24
Alignment explanation
Indices: 29439--29485 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29429 AAATTTGGTC
29439 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
29463 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
29486 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:29677 original size:12 final size:12
Alignment explanation
Indices: 29660--29684 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29650 ATATAATCCT
29660 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29672 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29684 G
1 G
29685 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:32060 original size:19 final size:19
Alignment explanation
Indices: 32020--32117 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
32010 GATTCTCTCG
32020 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
32040 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
32059 TTGCGA--TTC---TCTAA
1 TTGCGATTTTCATTTCGCA
32073 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32092 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32111 TTGCGAT
1 TTGCGAT
32118 AGTTAATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.13
16 3 0.04
17 3 0.04
19 39 0.57
20 15 0.22
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:32068 original size:53 final size:52
Alignment explanation
Indices: 32001--32117 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 52
31991 GAAATGAAAA
**
32001 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTAATTGCGATTTTCATTT-CGCATTGCGATTTTCATT
32054 TCGCATTGCGATTCTCTAATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTAATTGCGATTTTCATTTCGCATTGCGATTTTCATT
32106 TCGCATTGCGAT
1 TCGCATTGCGAT
32118 AGTTAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTAATTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:32227 original size:33 final size:33
Alignment explanation
Indices: 32175--32323 Score: 142
Period size: 33 Copynumber: 4.3 Consensus size: 33
32165 CCATTACATT
32175 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
* *
32209 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* * * *
32241 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAGAA
32280 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
32313 TCGCAATGCGA
1 TCGCAATGCGA
32324 TTTTCATTTC
Statistics
Matches: 93, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
31 7 0.08
32 7 0.08
33 42 0.45
34 10 0.11
35 1 0.01
36 2 0.02
38 10 0.11
39 7 0.08
40 7 0.08
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:32231 original size:19 final size:19
Alignment explanation
Indices: 32175--32304 Score: 163
Period size: 19 Copynumber: 7.3 Consensus size: 19
32165 CCATTACATT
32175 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
32195 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
32209 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
32228 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
32247 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
32261 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
32280 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
32299 TCGCAA
1 TCGCAA
32305 CGAGAGAATC
Statistics
Matches: 96, Mismatches: 4, Indels: 21
0.79 0.03 0.17
Matches are distributed among these distances:
14 20 0.21
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 58 0.60
20 6 0.06
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:32341 original size:19 final size:19
Alignment explanation
Indices: 32313--32448 Score: 166
Period size: 19 Copynumber: 7.6 Consensus size: 19
32303 AACGAGAGAA
*
32313 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32332 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
32346 TCCCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32365 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
32385 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
32401 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32418 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32437 TCGCATTGCGAT
1 TCGCATTGCGAT
32449 AGTCAATTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 22
0.79 0.04 0.17
Matches are distributed among these distances:
14 16 0.16
16 10 0.10
17 10 0.10
19 47 0.47
20 18 0.18
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:32342 original size:52 final size:52
Alignment explanation
Indices: 32175--32323 Score: 289
Period size: 52 Copynumber: 2.8 Consensus size: 52
32165 CCATTACATT
32175 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
32228 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
32280 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
32324 TTTTCATTTC
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 87 0.91
53 9 0.09
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:32356 original size:33 final size:33
Alignment explanation
Indices: 32313--32448 Score: 125
Period size: 33 Copynumber: 3.9 Consensus size: 33
32303 AACGAGAGAA
*
32313 TCGCAATGCGATTTTCATTTCGCATTGCGATTC
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTC
*
32346 TCCCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 TCGCATTGCGATTTTCATTT-CGCATTGCGA--TTC
* * *
32382 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-
1 ---TCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTC
32418 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
32449 AGTCAATTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
31 9 0.11
32 4 0.05
33 31 0.37
34 10 0.12
36 3 0.04
37 2 0.02
39 14 0.17
40 6 0.07
41 4 0.05
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTC
Found at i:32381 original size:53 final size:52
Alignment explanation
Indices: 32313--32448 Score: 236
Period size: 53 Copynumber: 2.6 Consensus size: 52
32303 AACGAGAGAA
*
32313 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
* *
32365 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
32418 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
32449 AGTCAATTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
52 31 0.39
53 49 0.61
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
Found at i:32574 original size:14 final size:14
Alignment explanation
Indices: 32555--32591 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
32545 CATCAATTAC
32555 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
32569 ACAAATCATCTTTT
1 ACAAATCAACTTTT
32583 ACAAATCAA
1 ACAAATCAA
32592 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:34588 original size:14 final size:14
Alignment explanation
Indices: 34569--34625 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
34559 GCGAAATGAA
*
34569 AATCGCAACGACAG
1 AATCGCAACGAAAG
34583 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
34600 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
34616 AATCGCAACG
1 AATCGCAACG
34626 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:34596 original size:33 final size:33
Alignment explanation
Indices: 34550--34642 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
34540 GCGAAACCAA
*
34550 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
34583 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
34616 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
34643 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:34607 original size:19 final size:19
Alignment explanation
Indices: 34513--34647 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
34503 TAGTTTACTT
* *
34513 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
34533 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
34552 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34571 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
34585 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
34604 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
34618 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34637 TCGCAATGCGA
1 TCGCAACGCGA
34648 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:34665 original size:19 final size:19
Alignment explanation
Indices: 34643--34771 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
34633 AAAATCGCAA
34643 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
34662 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
34676 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
34695 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
34709 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
34728 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
34747 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
34767 TGCGA
1 TGCGA
34772 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:34685 original size:33 final size:33
Alignment explanation
Indices: 34643--34734 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
34633 AAAATCGCAA
34643 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
34676 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
34709 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
34735 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:34974 original size:93 final size:93
Alignment explanation
Indices: 34815--35195 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
34805 TTGAATGGAT
34815 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34880 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
34908 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34973 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
35001 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
35066 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
35094 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
35159 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
35187 AAATTTACT
1 AAATTTACT
35196 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 285 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:36938 original size:19 final size:18
Alignment explanation
Indices: 36899--37009 Score: 102
Period size: 14 Copynumber: 6.8 Consensus size: 18
36889 GTTGAAATGA
36899 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
36914 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
36931 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
36947 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
36964 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
36979 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
36996 AAATCGCAATGCGA
1 AAATCGCAACGCGA
37010 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 23
0.75 0.04 0.22
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 18 0.23
17 8 0.10
18 20 0.25
19 8 0.10
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:36974 original size:32 final size:32
Alignment explanation
Indices: 36892--37004 Score: 199
Period size: 32 Copynumber: 3.5 Consensus size: 32
36882 TCTTTTGGTT
36892 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
*
36925 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGA-AATCGCAACGAGAGAATCGCAACGC
36958 GAAATGAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAATCGCAACGAGAGAATCGCAACGC
36990 GAAATGAAATCGCAA
1 GAAATGAAATCGCAA
37005 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
32 41 0.53
33 36 0.47
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (32 bp):
GAAATGAAATCGCAACGAGAGAATCGCAACGC
Found at i:37040 original size:14 final size:14
Alignment explanation
Indices: 37021--37077 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
37011 TTTGGTTTCG
37021 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
37035 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
37054 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
37068 CGTTGCGATT
1 CGTTGCGATT
37078 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:37053 original size:33 final size:33
Alignment explanation
Indices: 37005--37085 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
36995 GAAATCGCAA
**
37005 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
37038 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
37071 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
37086 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:37088 original size:21 final size:21
Alignment explanation
Indices: 37062--37137 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
37052 CGCGTTGCGA
37062 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
37083 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
37103 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
37124 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
37138 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:37118 original size:41 final size:41
Alignment explanation
Indices: 37061--37138 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
37051 TCGCGTTGCG
*
37061 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
37102 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
37139 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:37264 original size:33 final size:33
Alignment explanation
Indices: 37217--37287 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
37207 AATACTAACT
* *
37217 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
37250 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
37283 TGAAA
1 TGAAA
37288 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:37521 original size:22 final size:22
Alignment explanation
Indices: 37469--37523 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
37459 TGGTTGTGAG
**
37469 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
37491 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
37513 GGATTTCTTCG
1 GGATTTCTTCG
37524 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:37695 original size:20 final size:20
Alignment explanation
Indices: 37670--37863 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
37660 CTTTAAATAT
37670 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37690 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
37712 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37731 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
37751 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
37771 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37791 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37811 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
37831 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
37851 CGCGTTGCGATTT
1 CGCGTTGCGATTT
37864 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:37857 original size:60 final size:60
Alignment explanation
Indices: 37670--37863 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
37660 CTTTAAATAT
**
37670 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
37731 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
37791 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
37851 CGCGTTGCGATTT
1 CGCGTTGCGATTT
37864 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:37880 original size:21 final size:21
Alignment explanation
Indices: 37850--37932 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
37840 ATTTTCATAT
*
37850 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
37871 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
37892 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
37913 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
37933 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:37923 original size:42 final size:43
Alignment explanation
Indices: 37830--37928 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
37820 ATTTATGTGT
* *
37830 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
37871 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
37913 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
37929 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:46140 original size:93 final size:91
Alignment explanation
Indices: 45943--46150 Score: 247
Period size: 93 Copynumber: 2.3 Consensus size: 91
45933 TTTGGTTTGT
* *
45943 TTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACTTAACGTATAATTATTGTCTCCTTTTAG
1 TTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACATAACGTATAATTATTGTCTCATTTTAG
*
46008 TATCTCACCGTTAAAAACTTAATATG
66 TATCTCACCGTTAAAAACTTAACATG
* ** * * * * * *
46034 TTTAATATTTAAACTTTCAATTTTGTTCAAAATCATACATAATGTTTAGTTTTTTGTTTTATTTT
1 TTTAGTACCTAAACTTTCAATTTT-TTCAAAATCATACATAACGTATA-ATTATTGTCTCATTTT
*
46099 AGTATC-CAACCGTTAAAAACTTAACGTG
64 AGTATCTC-ACCGTTAAAAACTTAACATG
* *
46127 TTTAGTACCTAAACTATCGATTTT
1 TTTAGTACCTAAACTTTCAATTTT
46151 AGTCCGTTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
91 21 0.22
92 21 0.22
93 54 0.56
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (91 bp):
TTTAGTACCTAAACTTTCAATTTTTTCAAAATCATACATAACGTATAATTATTGTCTCATTTTAG
TATCTCACCGTTAAAAACTTAACATG
Found at i:47071 original size:21 final size:22
Alignment explanation
Indices: 47047--47097 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
47037 TGGTGTGAGG
47047 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
* *
47068 ATGTTTTTGGTATTTTTATTTA
1 ATGTTTTTAGTATTTTTATTAA
47090 AT-TTTTTA
1 ATGTTTTTA
47098 AATAATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:52376 original size:38 final size:40
Alignment explanation
Indices: 52254--52394 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 40
52244 TTCAGGACTG
* *
52254 AAATGTATTAGG-AGAGATATATTGAAAAAAACTGTAATT
1 AAATGTATTAGGAAGAGATACATTGAAAAAAACTATAATT
* *
52293 AAATGTATTA-GAAGAGATAGATTGAAAAAAAAAACTATAACT
1 AAATGTATTAGGAAGAGATACATTG---AAAAAAACTATAATT
52335 AAATGTATTAGGAA-AGATACATTG-AAAAAACTATAATT
1 AAATGTATTAGGAAGAGATACATTGAAAAAAACTATAATT
*
52373 AAATGCATTAGGAGAGAGATAC
1 AAATGTATTAGGA-AGAGATAC
52395 TGAAATGTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
38 26 0.29
39 22 0.25
40 6 0.07
42 32 0.36
43 3 0.03
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (40 bp):
AAATGTATTAGGAAGAGATACATTGAAAAAAACTATAATT
Found at i:52399 original size:38 final size:38
Alignment explanation
Indices: 52254--52399 Score: 134
Period size: 38 Copynumber: 3.7 Consensus size: 38
52244 TTCAGGACTG
* * *
52254 AAATGTATTAGGAGAGATATATTGAAAAAAACTGTAATT
1 AAATGTATTAGGAGAGAGATACTG-AAAAAACTATAATT
* *** *
52293 AAATGTATTAGAAGAGATAGATTGAAAAAAAAAACTATAACT
1 AAATGTATTAG--GAGAGAGA-T-ACTGAAAAAACTATAATT
52335 AAATGTATTAGGA-A-AGATACATTGAAAAAACTATAATT
1 AAATGTATTAGGAGAGAGATAC--TGAAAAAACTATAATT
*
52373 AAATGCATTAGGAGAGAGATACTGAAA
1 AAATGTATTAGGAGAGAGATACTGAAA
52400 TGTTTTGAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 33 0.38
39 13 0.15
40 8 0.09
41 6 0.07
42 24 0.28
43 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (38 bp):
AAATGTATTAGGAGAGAGATACTGAAAAAACTATAATT
Found at i:53601 original size:23 final size:23
Alignment explanation
Indices: 53564--53621 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
53554 TATATTTTAT
* *
53564 AATTAATAAACTTTAAAATGAAA
1 AATTATTAAATTTTAAAATGAAA
*
53587 ATTTATTAAATTTTAAAATGAAA
1 AATTATTAAATTTTAAAATGAAA
53610 AATTATTAAATT
1 AATTATTAAATT
53622 AAAAGTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (23 bp):
AATTATTAAATTTTAAAATGAAA
Found at i:55714 original size:3 final size:3
Alignment explanation
Indices: 55708--55738 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
55698 CTACTACTAC
55708 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
55739 GGAAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:61196 original size:29 final size:29
Alignment explanation
Indices: 61140--61198 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
61130 CCCGAACCGA
*
61140 TCGGGTCGCTTTTTTTATTTGGGTTCGGG
1 TCGGGTCGCGTTTTTTATTTGGGTTCGGG
61169 TCGGGTCG-GTTTTTTATGTTCGGG-TCGGG
1 TCGGGTCGCGTTTTTTAT-TT-GGGTTCGGG
61198 T
1 T
61199 TGGATTCGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 16 0.59
30 3 0.11
ACGTcount: A:0.03, C:0.14, G:0.37, T:0.46
Consensus pattern (29 bp):
TCGGGTCGCGTTTTTTATTTGGGTTCGGG
Found at i:67037 original size:32 final size:32
Alignment explanation
Indices: 66979--67043 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
66969 ATCACTTTGC
* *
66979 ATCAATTCGATAAAATTTGATGATCATTTTAT
1 ATCAATTCAATAAAATTTAATGATCATTTTAT
* *
67011 ATCAGTTCAATAAAATTTAATTATCATTTTAT
1 ATCAATTCAATAAAATTTAATGATCATTTTAT
67043 A
1 A
67044 GTTTTTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (32 bp):
ATCAATTCAATAAAATTTAATGATCATTTTAT
Found at i:72454 original size:35 final size:35
Alignment explanation
Indices: 72415--72540 Score: 173
Period size: 35 Copynumber: 3.6 Consensus size: 35
72405 AAAACAGTCA
*
72415 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
*
72450 TCAATTTCATTCT-AACCCTAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
* * *
72484 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
** *
72519 TCAATTAAATTTTAAACCCCAA
1 TCAATTTCATTCTAAACCCCAA
72541 ATTCTAAAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
34 33 0.40
35 49 0.60
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
Found at i:72456 original size:17 final size:17
Alignment explanation
Indices: 72434--72491 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
72424 TTTTAAACCC
72434 CAATTTCCAAAGTAATT
1 CAATTTCCAAAGTAATT
*** **
72451 CAATTT-CATTCTAACC
1 CAATTTCCAAAGTAATT
72467 CTAATTTCCAAAGTAATT
1 C-AATTTCCAAAGTAATT
72485 CAATTTC
1 CAATTTC
72492 ATTCTAAACC
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.38
Consensus pattern (17 bp):
CAATTTCCAAAGTAATT
Found at i:72473 original size:34 final size:35
Alignment explanation
Indices: 72415--72524 Score: 177
Period size: 35 Copynumber: 3.2 Consensus size: 35
72405 AAAACAGTCA
* *
72415 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCTAATTTCCAAAGTAAT
72450 TCAATTTCATTCT-AACCCTAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCTAATTTCCAAAGTAAT
* *
72484 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAATTTCCAAAGTAAT
72519 TCAATT
1 TCAATT
72525 AAATTTTAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
34 33 0.47
35 37 0.53
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAATTTCCAAAGTAAT
Found at i:72543 original size:35 final size:35
Alignment explanation
Indices: 72415--72560 Score: 168
Period size: 35 Copynumber: 4.2 Consensus size: 35
72405 AAAACAGTCA
* * *
72415 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * *
72450 TCAATTTCATTCT-AACCCTAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
72484 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * * *
72519 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
72554 TTAATTT
1 TCAATTT
72561 AAGGTTTAGA
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
34 33 0.34
35 65 0.66
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:72623 original size:34 final size:35
Alignment explanation
Indices: 72556--72629 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
72546 AAAATACTTT
* * *
72556 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
*
72591 AATTT-AGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
72625 AATTT
1 AATTT
72630 TGAACATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 2 0.06
34 27 0.79
35 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Done.