Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001544.1 Hibiscus syriacus cultivar Beakdansim tig00003033_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: 116281
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3796 original size:20 final size:20
Alignment explanation
Indices: 3767--3814 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3757 AATGATTTTC
* *
3767 TTTT-AAAAGCAAAATTAGA
1 TTTTGAAAAGCAAAATGAAA
3786 TTTTGAAAAGCAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
3806 TTTTGAAAA
1 TTTTGAAAA
3815 ATGATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:8135 original size:22 final size:22
Alignment explanation
Indices: 8101--8168 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
8091 CTCATTTCAG
* *
8101 TGCTAA-GTCACTTT-GTATTAG
1 TGCTAATG-CACTTTAGTATCAA
**
8122 TGCATAATGCACTTTCTTATCAA
1 TGC-TAATGCACTTTAGTATCAA
8145 TGCTAATGCACTTTAGTATCAA
1 TGCTAATGCACTTTAGTATCAA
8167 TG
1 TG
8169 GCAAGGCACT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
22 28 0.72
23 8 0.21
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (22 bp):
TGCTAATGCACTTTAGTATCAA
Found at i:8177 original size:22 final size:22
Alignment explanation
Indices: 8101--8179 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
8091 CTCATTTCAG
* * *
8101 TGCTAAGTCACTTT-GTATTAG
1 TGCTAAGGCACTTTAGTATCAA
* **
8122 TGCATAATGCACTTTCTTATCAA
1 TGC-TAAGGCACTTTAGTATCAA
*
8145 TGCTAATGCACTTTAGTATCAA
1 TGCTAAGGCACTTTAGTATCAA
8167 TGGC-AAGGCACTT
1 T-GCTAAGGCACTT
8180 CCGTTAATCG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 3 0.06
22 35 0.74
23 9 0.19
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (22 bp):
TGCTAAGGCACTTTAGTATCAA
Found at i:10785 original size:31 final size:31
Alignment explanation
Indices: 10747--10817 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
10737 CTTTTAAAAC
* *
10747 TTACAATATAATCCCCCAATATTTAGTCCGT
1 TTACAATATAATCCCCCAACATTTAGTCCAT
** * *
10778 TTACAATATGGTTCCCCAACATTTAGTCTAT
1 TTACAATATAATCCCCCAACATTTAGTCCAT
10809 TTACAATAT
1 TTACAATAT
10818 GGTCCCCGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (31 bp):
TTACAATATAATCCCCCAACATTTAGTCCAT
Found at i:10818 original size:31 final size:30
Alignment explanation
Indices: 10760--10824 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
10750 CAATATAATC
* *
10760 CCCCAATATTTAGTCCGTTTACAATATGGTT
1 CCCCAACATTTAGTCCATTTACAATATGG-T
*
10791 CCCCAACATTTAGTCTATTTACAATATGGT
1 CCCCAACATTTAGTCCATTTACAATATGGT
10821 CCCC
1 CCCC
10825 GACGTAACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (30 bp):
CCCCAACATTTAGTCCATTTACAATATGGT
Found at i:17999 original size:3 final size:3
Alignment explanation
Indices: 17993--18039 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
17983 TGTTGTCGTC
*
17993 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT CATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT -ATT ATT ATT
18040 GATTTTACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:23075 original size:34 final size:34
Alignment explanation
Indices: 23033--23098 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
23023 TCAGATTTAA
23033 TTTAAATTTATTTCGAGTCTGATAAATCGGATAG
1 TTTAAATTTATTTCGAGTCTGATAAATCGGATAG
*
23067 TTTAAATTTATTTCTAGTCTGATAAATCGGAT
1 TTTAAATTTATTTCGAGTCTGATAAATCGGAT
23099 CGAGTGAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (34 bp):
TTTAAATTTATTTCGAGTCTGATAAATCGGATAG
Found at i:23621 original size:21 final size:21
Alignment explanation
Indices: 23597--23649 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
23587 ACACTTAGGG
23597 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
23618 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
23639 TACCGATTCCC
1 AACCGATTCCC
23650 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:23866 original size:13 final size:13
Alignment explanation
Indices: 23845--23899 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
23835 AAGTTCGATA
*
23845 AATTCAAATACTT
1 AATTGAAATACTT
23858 AATTGAAATACTT
1 AATTGAAATACTT
* *
23871 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
23885 AATTGAAATACTT
1 AATTGAAATACTT
23898 AA
1 AA
23900 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:23981 original size:32 final size:33
Alignment explanation
Indices: 23885--23983 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
23875 AACTCAACAT
* * *
23885 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
23918 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
23951 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
23983 A
1 A
23984 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:24002 original size:21 final size:21
Alignment explanation
Indices: 23978--24017 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23968 ACTTCAAGTT
23978 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
23999 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
24018 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:26345 original size:11 final size:12
Alignment explanation
Indices: 26324--26369 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
26314 TCCGGATAAA
26324 AACCGGTTTTTT
1 AACCGGTTTTTT
26336 AACCGGTTTTTTT
1 AACCGG-TTTTTT
26349 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
26363 ATCCGGT
1 AACCGGT
26370 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:26354 original size:15 final size:14
Alignment explanation
Indices: 26323--26362 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
26313 TTCCGGATAA
26323 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
26336 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
26349 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
26363 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:31915 original size:39 final size:38
Alignment explanation
Indices: 31869--31969 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 38
31859 TCAAAAAAAA
* *
31869 ATTAATTATCACTATTAGATTAATAAATTTACTTTCTAT
1 ATTAATTATAAC-ATTAGATTAATAAATTCACTTTCTAT
*
31908 ATTAATTATGAACATTAGATTAATAAATTCATTTTCTAT
1 ATTAATTAT-AACATTAGATTAATAAATTCACTTTCTAT
* *
31947 TTTAATTATGACCATTAGATTAA
1 ATTAATTAT-AACATTAGATTAA
31970 AAAAATTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 54 0.96
40 2 0.04
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (38 bp):
ATTAATTATAACATTAGATTAATAAATTCACTTTCTAT
Found at i:32382 original size:39 final size:39
Alignment explanation
Indices: 32333--32433 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
32323 TTTTTAAAAA
*
32333 ATTAATTATGAGTATTAGATTAATAAATTTACTTTCTAT
1 ATTAATTATGAATATTAGATTAATAAATTTACTTTCTAT
**
32372 ATTAATTATGAATATTAGATTAATAAATTTGTTTTCTAT
1 ATTAATTATGAATATTAGATTAATAAATTTACTTTCTAT
* * *
32411 TTTAATTCTGAACATTAGATTAA
1 ATTAATTATGAATATTAGATTAA
32434 AAAAATTGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.49
Consensus pattern (39 bp):
ATTAATTATGAATATTAGATTAATAAATTTACTTTCTAT
Found at i:32457 original size:464 final size:454
Alignment explanation
Indices: 31864--32775 Score: 1520
Period size: 464 Copynumber: 2.0 Consensus size: 454
31854 TTAATTCAAA
31864 AAAAAATTAATTATCACTATTAGATTAATAAATTTACTTTCTATATTAATTATGAACATTAGATT
1 AAAAAATTAATTATCACTATTAGATTAATAAATTTACTTTCTATATTAATTATGAACATTAGATT
*
31929 AATAAATTCATTTTCTATTTTAATTATGACCATTAGATTAAAAAAATTGATTATAACCATTAAAT
66 AATAAATTCATTTTCTATTTTAATTATGAACATTAGATTAAAAAAATTGATTATAACCATTAAAT
*
31994 TAATTTTATTAAATGATTTATTTATTTATTATTAGTTTTATTAGATTAAAAATTAGATTATATAA
131 TAATTTTATTAAATGATTTATTTATTTATTATTAATTTTATTAGATTAAAAATTAGATTATATAA
*
32059 AATGATTTTAAAAACTGTTAAGTTTAAATCATTATTATGATATAATAATTAATTAATAATTTAAC
196 AATGATTTTAAAAACTGTTAAGTTTAAATCACTATTATGATATAATAATTAATTAATAATTTAAC
*
32124 TTAGAATTTTAATATATATATATATATAACTTGTAAGTTATAAAACTTTTAATTGGCAACTGATA
261 TTAG-A----AAT-T-TA-ATATATATAACTCGTAAGTTAT-AAACTTTTAATTGGCAACTGATA
32189 TTATAATATGACAACTAACAAAATAATTATTCACCATTGAAAGCACATGATTAATTATGATAATT
317 TTATAATATGACAACTAACAAAATAATTATTCACCATTGAAAGCACATGATTAATTATGATAATT
32254 AGATTAATAAATTTATTTTTGA-TAAGTTGATATATAAATATATTCAAAAGTGTAATAAAATTTA
382 AGATTAATAAATTTATTTTTGATTAA-TTGATATATAAATATATTCAAAAGTGTAATAAAA-TTA
32318 ATAAATTTTT
445 ATAAATTTTT
* * *
32328 AAAAAATTAATTATGAGTATTAGATTAATAAATTTACTTTCTATATTAATTATGAATATTAGATT
1 AAAAAATTAATTATCACTATTAGATTAATAAATTTACTTTCTATATTAATTATGAACATTAGATT
** * *
32393 AATAAATTTGTTTTCTATTTTAATTCTGAACATTAGATTAAAAAAATTGATTATAACTATTAAAT
66 AATAAATTCATTTTCTATTTTAATTATGAACATTAGATTAAAAAAATTGATTATAACCATTAAAT
*
32458 TAATTTTATTAAATGATTTATTTATTTATTATTAATTTTATTAGATTAGAAATTAGATTATATAA
131 TAATTTTATTAAATGATTTATTTATTTATTATTAATTTTATTAGATTAAAAATTAGATTATATAA
* * *
32523 AATGATTTTAAAAACTTTTAAGTTTAAATCACTATTATGATATAATAATTGATTAATAATTTAAG
196 AATGATTTTAAAAACTGTTAAGTTTAAATCACTATTATGATATAATAATTAATTAATAATTTAAC
*
32588 TTAGAAATTTAATATATATAACTCGTAAGTTGTAAACTTTTAATTGGCAACTGATATTATAATAT
261 TTAGAAATTTAATATATATAACTCGTAAGTTATAAACTTTTAATTGGCAACTGATATTATAATAT
* * * ** *
32653 TACAACTAACAAAATAATTATTCGCCATTTAAAGTGCATGATTCATTATGATAATTAGATTAATA
326 GACAACTAACAAAATAATTATTCACCATTGAAAGCACATGATTAATTATGATAATTAGATTAATA
32718 AATTTATTTTTGATTAATTGATATATAAATATATTCAAAAGTGTAATAAAATTAATAA
391 AATTTATTTTTGATTAATTGATATATAAATATATTCAAAAGTGTAATAAAATTAATAA
32776 TTAATGGTTG
Statistics
Matches: 425, Mismatches: 22, Indels: 12
0.93 0.05 0.03
Matches are distributed among these distances:
454 7 0.02
455 138 0.32
456 23 0.05
457 2 0.00
458 1 0.00
459 3 0.01
463 1 0.00
464 250 0.59
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (454 bp):
AAAAAATTAATTATCACTATTAGATTAATAAATTTACTTTCTATATTAATTATGAACATTAGATT
AATAAATTCATTTTCTATTTTAATTATGAACATTAGATTAAAAAAATTGATTATAACCATTAAAT
TAATTTTATTAAATGATTTATTTATTTATTATTAATTTTATTAGATTAAAAATTAGATTATATAA
AATGATTTTAAAAACTGTTAAGTTTAAATCACTATTATGATATAATAATTAATTAATAATTTAAC
TTAGAAATTTAATATATATAACTCGTAAGTTATAAACTTTTAATTGGCAACTGATATTATAATAT
GACAACTAACAAAATAATTATTCACCATTGAAAGCACATGATTAATTATGATAATTAGATTAATA
AATTTATTTTTGATTAATTGATATATAAATATATTCAAAAGTGTAATAAAATTAATAAATTTTT
Found at i:36569 original size:2 final size:2
Alignment explanation
Indices: 36562--36604 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
36552 TTCAGTTATA
* *
36562 TG TG TG TG TG TG TG TG TG TG CG TG TA TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36604 T
1 T
36605 TGAACATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.02, G:0.47, T:0.49
Consensus pattern (2 bp):
TG
Found at i:42172 original size:3 final size:3
Alignment explanation
Indices: 42166--42194 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
42156 ATAATAATAA
42166 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42195 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42962 original size:8 final size:8
Alignment explanation
Indices: 42951--42987 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
42941 AGAGAGAAGT
42951 AAAATGAG
1 AAAATGAG
42959 AAAATGAG
1 AAAATGAG
42967 AAAATGAG
1 AAAATGAG
42975 AAAATGAG
1 AAAATGAG
42983 AAAAT
1 AAAAT
42988 TTTGGCCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.14
Consensus pattern (8 bp):
AAAATGAG
Found at i:43540 original size:17 final size:18
Alignment explanation
Indices: 43510--43551 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
43500 ACTCATAGGT
*
43510 ATAATTTGACAAAAT-TA
1 ATAATTTAACAAAATATA
*
43527 ATAATTTAATAAAATGATA
1 ATAATTTAACAAAAT-ATA
43546 ATAATT
1 ATAATT
43552 ATTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (18 bp):
ATAATTTAACAAAATATA
Found at i:46704 original size:40 final size:40
Alignment explanation
Indices: 46622--46704 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
46612 TAGCTGATGC
* *
46622 AATGAAAACAAATGACTAAGAACTTGTCAAGGAATGTGGA
1 AATGAAAACAAATGACTAAGAACTTGTCAAGGAATATCGA
46662 AATGAAAACAAATGACTAAGAACTTGTCAAGGAATATCGA
1 AATGAAAACAAATGACTAAGAACTTGTCAAGGAATATCGA
46702 AAT
1 AAT
46705 CCAATAAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.20
Consensus pattern (40 bp):
AATGAAAACAAATGACTAAGAACTTGTCAAGGAATATCGA
Found at i:49095 original size:92 final size:92
Alignment explanation
Indices: 48938--49191 Score: 454
Period size: 92 Copynumber: 2.8 Consensus size: 92
48928 AAATTACTAT
* *
48938 TATATACAATAAAGCTTGAGTTATCCCCCTAAAGAAATTGGTTAATCGCCCCAGTTTTATGGATA
1 TATATATAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATCGCCCCAGTTTTATGGATA
49003 ATATTCAACTAGCATGATATATTATTA
66 ATATTCAACTAGCATGATATATTATTA
49030 TATATATAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATCGCCCCAGTTTTATGGATA
1 TATATATAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATCGCCCCAGTTTTATGGATA
49095 ATATTCAACTAGCATGATATATTATTA
66 ATATTCAACTAGCATGATATATTATTA
* * **
49122 TATATATAATAAAGCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCCCAACTTTATGGATA
1 TATATATAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATCGCCCCAGTTTTATGGATA
49187 ATATT
66 ATATT
49192 TAGCGAACTT
Statistics
Matches: 156, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 156 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (92 bp):
TATATATAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATCGCCCCAGTTTTATGGATA
ATATTCAACTAGCATGATATATTATTA
Found at i:49213 original size:92 final size:90
Alignment explanation
Indices: 48932--49294 Score: 415
Period size: 92 Copynumber: 4.0 Consensus size: 90
48922 CATATTAAAT
* * **
48932 TACTATTATATACAATAAAGCTTGAGTTATCCCCCTAAAGAAATTGGTTAATCGCCCCAGTTTTA
1 TACTATTATATACAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATAGCCCCAACTTTA
48997 TGGATAATATTCAACTAGCATGATA
66 TGGATAATATTCAACTAGCATGATA
* * * **
49022 TATTATTATATATATAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATCGCCCCAGTTT
1 TACTA-T-TATATACAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATAGCCCCAACTT
49087 TATGGATAATATTCAACTAGCATGATA
64 TATGGATAATATTCAACTAGCATGATA
* * *
49114 TATTATTATATATATAATAAAGCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCCCAACTT
1 TACTA-T-TATATACAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATAGCCCCAACTT
* * * * *
49179 TATGGATAATATTTAGCGAACTTG-TA
64 TATGGATAATATTCAACTAGCATGATA
* * * * * * * * *
49205 TTACTATTATATGCAATAAAGATTGAGCTGTCCCTCTAGAGCAATTGGTTAACAGCTCCGACTTT
1 -TACTATTATATACAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATAGCCCCAACTTT
*
49270 ATGGATAAGT-TTCAACTAGCCTGAT
65 ATGGATAA-TATTCAACTAGCATGAT
49295 TGAGTTAAAT
Statistics
Matches: 241, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
90 69 0.29
91 6 0.02
92 166 0.69
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (90 bp):
TACTATTATATACAATAAAGCTTGAGTTGTCCCCCTAAAGAAATTGGTTAATAGCCCCAACTTTA
TGGATAATATTCAACTAGCATGATA
Found at i:52254 original size:123 final size:123
Alignment explanation
Indices: 52086--53114 Score: 1481
Period size: 123 Copynumber: 8.3 Consensus size: 123
52076 TAGGATGTTT
* * * *
52086 TCAACATTTCCA-AAAGAGTTGATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAAAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *** * *
52150 TGAGAAGAACTTGTGCAACCTTTTACTCAACTCTATTGTAGAAGGAGATAGGTCAGCA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
* * *
52208 TCAACATTTCCAGAAGGAGTTCATAATTAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* ** * *
52273 TGAGAAGAACTTGTTCAACCTTTTACTTGA-TGCTATCACAAAAGGAGATAGATCAATA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACT-CTATCACAGAAGGAGATAGATCAACA
* * * *
52331 TCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
52396 TGAGAAAAACTTGTTCAACCTTTTGCTCATCTTTATCACAGAAGGAGATAGATCAACA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
* * *
52454 TCAACAATTCTAGAAGAAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * * *
52519 TGAGAAGAACTTATTCAACTTTTTTCTCAACTCTATCACAGAAAGAGATAAATCAACA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
*
52577 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
** * * *
52642 TGAGAAGAACTTGTTCATTCTTTTGTTCAACTCTATCATAGAAGGAGATAGATCAGCA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
* *
52700 TCAACATTTCTAGAAGGAGTTTATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGAAGTTCA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGA-G--GAAGAAGAAGTTCA
*
52765 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGAA-TCTATCACAGAAAGAGATAGATCAACA
63 TAATGAGAAGAACTTGTTCAACCTTTTGCTC-AACTCTATCACAGAAGGAGATAGATCAACA
* * *
52826 TCAACATTTCCAGAAAGAGTTTATAATGAGAAGAACTCATCTAAAGAGAAAGAATAAGAAGTTCA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAG---GAAGAAGAAGTTCA
* *
52891 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGAA-TCTATCACATAAAGAGATAGATCAACA
63 TAATGAGAAGAACTTGTTCAACCTTTTGCTC-AACTCTATCACAGAAGGAGATAGATCAACA
*
52952 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAAAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
*
53017 TGAGAAGAACGTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
* *
53075 TCAACATTTCTAGAAGGAGTTTATAATGAGAATAACTCAT
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCAT
53115 ATGAGAAGTC
Statistics
Matches: 819, Mismatches: 79, Indels: 17
0.90 0.09 0.02
Matches are distributed among these distances:
122 15 0.02
123 567 0.69
124 2 0.00
125 1 0.00
126 232 0.28
127 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (123 bp):
TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
Found at i:53767 original size:28 final size:28
Alignment explanation
Indices: 53735--53794 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
53725 TTAATTATTC
53735 CAAAT-TTGATAAATTACATCATAAAT-TT
1 CAAATCTT-ATAAATTACATCAT-AATCTT
*
53763 CAAATCTTATAAATTATATCATAATCTT
1 CAAATCTTATAAATTACATCATAATCTT
53791 CAAA
1 CAAA
53795 CTCTATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 24 0.83
29 2 0.07
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (28 bp):
CAAATCTTATAAATTACATCATAATCTT
Found at i:53923 original size:4 final size:4
Alignment explanation
Indices: 53914--53955 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
53904 TACGCATGAT
** *
53914 ATAC ATAC ATAC ATAC ATAC ATGT ATAC ATAC ATAT ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
53956 GTAAAACATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:53987 original size:12 final size:12
Alignment explanation
Indices: 53908--53987 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 12
53898 TGTTTGTACG
53908 CATGATATACATA
1 CATGA-ATACATA
53921 CAT-ACATACATA
1 CATGA-ATACATA
*
53933 CATGTATACATA
1 CATGAATACATA
53945 CAT--AT--ATA
1 CATGAATACATA
* *
53953 CATGTAAAACATG
1 CATG-AATACATA
*
53966 CAT-CATACATA
1 CATGAATACATA
53977 CATGAATACAT
1 CATGAATACAT
53988 TATATATACA
Statistics
Matches: 52, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
8 6 0.12
10 2 0.04
11 9 0.17
12 27 0.52
13 8 0.15
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (12 bp):
CATGAATACATA
Found at i:54006 original size:12 final size:12
Alignment explanation
Indices: 53912--53955 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
53902 TGTACGCATG
53912 ATATACATACAT
1 ATATACATACAT
*
53924 ACATACATACAT
1 ATATACATACAT
*
53936 GTATACATACAT
1 ATATACATACAT
53948 ATATACAT
1 ATATACAT
53956 GTAAAACATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (12 bp):
ATATACATACAT
Found at i:55128 original size:43 final size:43
Alignment explanation
Indices: 55081--55447 Score: 459
Period size: 43 Copynumber: 8.5 Consensus size: 43
55071 GAGCATGCAT
* * * * *
55081 AAACGGTAAGGTCTTACCCTTTCACACAACAAAAGAGCCT-GAG
1 AAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGG
* * * *
55124 AAAC-GATAAGGTCTTACCCTTGCACATAGCAAAGGAGCATGGGG
1 AAACTG-TAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGG
*
55168 AAACTGTAAGGCTTATCCTTGCACACAACAAAGGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
* * * *
55211 AAATTGTAAGGCTTACCCTTGCACACAATAAAGGAACTTGGAG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
** *
55254 AAACTGTAAGGCTTACCCTTATACACAACAAAGAAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
* * * *
55297 AAACTATAAGGTTTACCCTTGCACACAACAATGAAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
* *
55340 AAACTGTAAGGCTTACCCTTTCACACAGCAAAGGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
*
55383 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGAG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
*
55426 AATCTGTAAGGTCTTACCCTTG
1 AAACTGTAAGG-CTTACCCTTG
55448 TACATAGCAG
Statistics
Matches: 282, Mismatches: 38, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
42 1 0.00
43 259 0.92
44 21 0.07
45 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (43 bp):
AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
Found at i:64224 original size:18 final size:18
Alignment explanation
Indices: 64197--64231 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64187 GCTAAAACTC
*
64197 AAATTCAATATGCAACCT
1 AAATTCAATATACAACCT
*
64215 AAATTTAATATACAACC
1 AAATTCAATATACAACC
64232 CATATCCAAT
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:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATTCAATATACAACCT
Found at i:66860 original size:39 final size:39
Alignment explanation
Indices: 66817--66895 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
66807 CACTTGGATA
*
66817 TGGATTGTGATGATTATATGTTAATAATCTCAAATGTAT
1 TGGATTGTGATGATTATATGTTAATAAACTCAAATGTAT
*
66856 TGGATTGTGATGATTATATGTTAATAAACTCAAGTGTAT
1 TGGATTGTGATGATTATATGTTAATAAACTCAAATGTAT
66895 T
1 T
66896 ATGTAAGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (39 bp):
TGGATTGTGATGATTATATGTTAATAAACTCAAATGTAT
Found at i:68261 original size:18 final size:18
Alignment explanation
Indices: 68238--68282 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
68228 ATCTAGCTAA
*
68238 AACCCAAATTCAATATGC
1 AACCCAAATTCAATATAC
*
68256 AACCCAAATTTAATATAC
1 AACCCAAATTCAATATAC
*
68274 AACCTAAAT
1 AACCCAAAT
68283 CTAATACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (18 bp):
AACCCAAATTCAATATAC
Found at i:68287 original size:18 final size:18
Alignment explanation
Indices: 68238--68288 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
68228 ATCTAGCTAA
*
68238 AACCCAAAT-TCAATATGC
1 AACCCAAATCT-AATATAC
*
68256 AACCCAAATTTAATATAC
1 AACCCAAATCTAATATAC
*
68274 AACCTAAATCTAATA
1 AACCCAAATCTAATA
68289 CCCTTAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.25
Consensus pattern (18 bp):
AACCCAAATCTAATATAC
Found at i:70818 original size:25 final size:25
Alignment explanation
Indices: 70784--70835 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
70774 GTATTGGTCC
* *
70784 CTCGTCCCCGTCCCCATTTAAAAAA
1 CTCGTACCCGTCCCCACTTAAAAAA
*
70809 CTCGTACCCGTCCCCGCTTAAAAAA
1 CTCGTACCCGTCCCCACTTAAAAAA
70834 CT
1 CT
70836 GCGGGGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.40, G:0.10, T:0.23
Consensus pattern (25 bp):
CTCGTACCCGTCCCCACTTAAAAAA
Found at i:70939 original size:12 final size:12
Alignment explanation
Indices: 70924--70948 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70914 ATTATTTAAA
70924 CGGGTATCGGGC
1 CGGGTATCGGGC
70936 CGGGTATCGGGC
1 CGGGTATCGGGC
70948 C
1 C
70949 AGTTATATAT
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:0.08, C:0.28, G:0.48, T:0.16
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:70995 original size:34 final size:36
Alignment explanation
Indices: 70952--71036 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 36
70942 TCGGGCCAGT
70952 TATATATATTTAAATTAAATATATAAATATTATATA
1 TATATATATTTAAATTAAATATATAAATATTATATA
* *
70988 TATATATTTTAATTTAAATTAAATTTATTAATATTATATA
1 TATATA---T-ATTTAAATTAAATATATAAATATTATATA
71028 TATATATAT
1 TATATATAT
71037 ATATAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
36 8 0.19
37 1 0.02
39 1 0.02
40 33 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TATATATATTTAAATTAAATATATAAATATTATATA
Found at i:71006 original size:40 final size:40
Alignment explanation
Indices: 70959--71034 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
70949 AGTTATATAT
70959 ATTTAAATTAAATATATAAATATTATATATATATATTTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATTTTA
* *
70999 ATTTAAATTAAATTTATTAATATTATATATATATAT
1 ATTTAAATTAAATATATAAATATTATATATATATAT
71035 ATATATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
ATTTAAATTAAATATATAAATATTATATATATATATTTTA
Found at i:71048 original size:40 final size:39
Alignment explanation
Indices: 70952--71059 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 39
70942 TCGGGCCAGT
* * *
70952 TATATATATTTA-AATTAAATATATAAATATTATATATA
1 TATATATATTAATAATTAAATTTATTAATATTATATATA
70990 TATAT-T-TTAATTTAAATTAAATTTATTAATATTATATATA
1 TATATATATTAA--T-AATTAAATTTATTAATATTATATATA
71030 TATATATATATAATAATT--ATTT-TTAATATT
1 TATATATAT-TAATAATTAAATTTATTAATATT
71060 TATCGGGTCG
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
36 3 0.05
37 9 0.15
38 9 0.15
40 33 0.55
41 2 0.03
42 1 0.02
43 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (39 bp):
TATATATATTAATAATTAAATTTATTAATATTATATATA
Found at i:72009 original size:2 final size:2
Alignment explanation
Indices: 72002--72107 Score: 212
Period size: 2 Copynumber: 53.0 Consensus size: 2
71992 AAACAAAATA
72002 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
72044 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
72086 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
72108 TAATACCAAA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72520 original size:21 final size:21
Alignment explanation
Indices: 72496--72538 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
72486 TATTTGAATT
*
72496 AATTAATATATA-ACAAACATA
1 AATTAATAAATATAC-AACATA
*
72517 AATTTATAAATATACAACATA
1 AATTAATAAATATACAACATA
72538 A
1 A
72539 TATCAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAATAAATATACAACATA
Found at i:72560 original size:4 final size:4
Alignment explanation
Indices: 72553--72900 Score: 268
Period size: 4 Copynumber: 86.8 Consensus size: 4
72543 AAAATTATAT
72553 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
72601 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * *
72649 ATAG ATAG ATAT ACAAC ATA- ATATC A-AA ATTAT ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG A-TAG ATAG ATA-G ATAG A-TAG ATAG ATAG ATAG ATAG
* * * * * *
72698 ATAG ACAG ACAG ACAG ACAT ATAG ATAG ACAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * * * * * *
72746 ACAT ATAG ATAT ACAG AGAG ACAG ATAG AGAG ACAG ACAG ACAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * * * * * * *
72794 ATAA ACAA ATAG ATAG ACAG AGAG ACAG ATAG AGAG ACAG ACAG ACAA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * * * * *
72842 ATAG ATAG ATAG ACAG ACAG AGAG ACAG ACAG ACAG ACAG ACAG ACAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
72890 ATAT ATAG ATA
1 ATAG ATAG ATA
72901 CTAAATCAAA
Statistics
Matches: 294, Mismatches: 45, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
3 4 0.01
4 285 0.97
5 5 0.02
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.18
Consensus pattern (4 bp):
ATAG
Found at i:73075 original size:21 final size:21
Alignment explanation
Indices: 73051--73099 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
73041 AATTTGAATT
*
73051 AATTAATATATATCAAACATA
1 AATTAATAAATATCAAACATA
* *
73072 AATTTATAAATATCCAACATA
1 AATTAATAAATATCAAACATA
73093 ATATTAA
1 A-ATTAA
73100 AATAATACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTAATAAATATCAAACATA
Found at i:76356 original size:14 final size:16
Alignment explanation
Indices: 76323--76360 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
76313 TAAAATATTT
76323 AAATATAAAACAAGTA
1 AAATATAAAACAAGTA
76339 AAAT-TAAAACAA-TA
1 AAATATAAAACAAGTA
76353 AAATATAA
1 AAATATAA
76361 TTAGAACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 11 0.52
16 4 0.19
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATATAAAACAAGTA
Found at i:77792 original size:3 final size:3
Alignment explanation
Indices: 77784--77855 Score: 78
Period size: 3 Copynumber: 24.3 Consensus size: 3
77774 TAAAATTATT
*
77784 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TATT TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA
**
77828 TAA TAA TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
77856 TTAAGTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 6 0.10
3 47 0.81
4 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:77817 original size:25 final size:25
Alignment explanation
Indices: 77784--77855 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 25
77774 TAAAATTATT
77784 TAATAATAAT-ATAATATAT-ATAA
1 TAATAATAATAATAATATATAATAA
77807 T-ATAATAATAAT-AT-T-TAATAA
1 TAATAATAATAATAATATATAATAA
*
77828 TAATAATAATAATAAT-TTTAATAA
1 TAATAATAATAATAATATATAATAA
77852 TAAT
1 TAAT
77856 TTAAGTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.02
21 6 0.14
22 21 0.48
23 6 0.14
24 10 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATAATAATAATAATATATAATAA
Found at i:79023 original size:75 final size:75
Alignment explanation
Indices: 78028--78997 Score: 1787
Period size: 75 Copynumber: 12.9 Consensus size: 75
78018 TGCACTGAAG
* * *
78028 GGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAACCATCATGCACTGTAGGACTTACA
1 GGCTTT-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACA
78093 GATGACCCTAA
65 GATGACCCTAA
* * *
78104 GGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACA
1 GGCTTT-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACA
78169 GATGACCCTAA
65 GATGACCCTAA
*
78180 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78245 ATGACCCTAA
66 ATGACCCTAA
* *
78255 GGCTTTAAAACATCAAAAAGCTCCCGAAGGGTTTTTGGAAGCATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78320 ATGACCCTAA
66 ATGACCCTAA
78330 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78395 ATGACCCTAA
66 ATGACCCTAA
*
78405 GGCTTTAAAACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78470 ATGACCCTAA
66 ATGACCCTAA
78480 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78545 ATGACCCTAA
66 ATGACCCTAA
*
78555 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78620 ATGACCCTAA
66 ATGACCCTAA
*
78630 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATACACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78695 ATGACCCTAA
66 ATGACCCTAA
78705 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
*
78770 ATAACCCTAA
66 ATGACCCTAA
78780 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78845 ATGACCCTAA
66 ATGACCCTAA
*
78855 GGCTTTGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78920 ATGACCCTAA
66 ATGACCCTAA
*
78930 GGCTTTAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
1 GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
78995 ATG
66 ATG
78998 TGGGAAATAG
Statistics
Matches: 870, Mismatches: 24, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
75 792 0.91
76 78 0.09
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (75 bp):
GGCTTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
ATGACCCTAA
Found at i:79478 original size:22 final size:22
Alignment explanation
Indices: 79444--79495 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
79434 CGTAAAGCTT
* *
79444 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
79466 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
79488 TCATCTTT
1 TCATCTTT
79496 GAATAGTGTA
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:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:82198 original size:92 final size:92
Alignment explanation
Indices: 82075--82352 Score: 484
Period size: 92 Copynumber: 3.0 Consensus size: 92
82065 TTCATCTTTT
* *
82075 AATTCCAATGATTGGTTCTGTGGTTCCTACCAAACCAGATCAGATAATTCAAAGAACACTTCCAG
1 AATT-CAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
* *
82140 AAGATGCTATTAGCACATTCCTCTTCCA
65 AAGATGCTATGAGCACATTCATCTTCCA
* * *
82168 AATTCAATAATTGGTTATGTGGTTCATACCAAACCAGATCATATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
82233 AGATGCTATGAGCACATTCATCTTCCA
66 AGATGCTATGAGCACATTCATCTTCCA
82260 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
82325 AGATGCTATGAGCACATTCATCTTCCA
66 AGATGCTATGAGCACATTCATCTTCCA
82352 A
1 A
82353 TTTCTACTAT
Statistics
Matches: 175, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 171 0.98
93 4 0.02
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (92 bp):
AATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
AGATGCTATGAGCACATTCATCTTCCA
Found at i:90757 original size:3 final size:3
Alignment explanation
Indices: 90749--90819 Score: 65
Period size: 3 Copynumber: 23.3 Consensus size: 3
90739 TAAAATTATT
* *
90749 TAA TAA TAA T-A TAA TATA TATA TAA T-A TTA TAA TAA TATT TAA TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TA-A TAA TAA
**
90795 TAA TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
90820 TTAAGTAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
2 4 0.07
3 44 0.77
4 9 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:90784 original size:22 final size:22
Alignment explanation
Indices: 90749--90819 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
90739 TAAAATTATT
90749 TAATAATAAT-ATAATATATATA
1 TAATAATAATAATAATATATA-A
* *
90771 TAAT-ATTATAATAATATTTAA
1 TAATAATAATAATAATATATAA
*
90792 TAATAATAATAATAAT-TTTAA
1 TAATAATAATAATAATATATAA
90813 TAATAAT
1 TAATAAT
90820 TTAAGTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
21 21 0.48
22 23 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAATAATAATAATATATAA
Found at i:94268 original size:21 final size:21
Alignment explanation
Indices: 94244--94286 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
94234 TATTCTAATT
94244 AATTCATAAATACCAAAAATA
1 AATTCATAAATACCAAAAATA
* *
94265 AATTTATAAATACCAAACATA
1 AATTCATAAATACCAAAAATA
94286 A
1 A
94287 TATCAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
AATTCATAAATACCAAAAATA
Found at i:94516 original size:21 final size:21
Alignment explanation
Indices: 94492--94534 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
94482 TATTCTAATT
94492 AATTCATAAATACCAAAAATA
1 AATTCATAAATACCAAAAATA
* *
94513 AATTTATAAATACCAAACATA
1 AATTCATAAATACCAAAAATA
94534 A
1 A
94535 TATCAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
AATTCATAAATACCAAAAATA
Found at i:94558 original size:248 final size:250
Alignment explanation
Indices: 94111--94623 Score: 994
Period size: 248 Copynumber: 2.1 Consensus size: 250
94101 GACTAAATCA
*
94111 AAATAATATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTAGAATCTAA
1 AAATAAAATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTAGAATCTAA
94176 AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
66 AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
94241 ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
131 ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
94306 CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
196 CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
*
94361 AAATAAAATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTGGAATCT-A
1 AAATAAAATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTAGAATCTAA
94425 AAATACT-AATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
66 AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
94489 ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
131 ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
94554 CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
196 CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
94609 AAATAAAATATATAT
1 AAATAAAATATATAT
94624 CTCATATATT
Statistics
Matches: 261, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
248 192 0.74
249 8 0.03
250 61 0.23
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (250 bp):
AAATAAAATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTAGAATCTAA
AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
Found at i:98818 original size:29 final size:29
Alignment explanation
Indices: 98786--98862 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
98776 ACATGGGGAT
98786 AAATTAAAATAAATTAAAATTACATGGAC
1 AAATTAAAATAAATTAAAATTACATGGAC
*
98815 AAATTAAAATAAATTAAAATTACATGGCC
1 AAATTAAAATAAATTAAAATTACATGGAC
* *
98844 GAATTAAAATAAATAAAAA
1 AAATTAAAATAAATTAAAA
98863 AACATATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (29 bp):
AAATTAAAATAAATTAAAATTACATGGAC
Found at i:99893 original size:42 final size:42
Alignment explanation
Indices: 99838--99924 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
99828 CTCGAAGGGT
* *
99838 TTAATCATCATGCTCAAAAGACTTACAGATAACCCAAAGGAC
1 TTAAACATCATGCTCAAAAGACTTACAGATAACCCAAACGAC
* ** * *
99880 TTAAACATTATGCTTGAAAGACTTACTGATTACCCAAACGAC
1 TTAAACATCATGCTCAAAAGACTTACAGATAACCCAAACGAC
99922 TTA
1 TTA
99925 CCAACTTTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.26
Consensus pattern (42 bp):
TTAAACATCATGCTCAAAAGACTTACAGATAACCCAAACGAC
Found at i:100131 original size:42 final size:41
Alignment explanation
Indices: 100062--100157 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 41
100052 TTGCGGATTG
* * *
100062 CCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGA
1 CCCGAAGGACTTAGCATCATGCTCGAAAGACTAACAAATGA
* ** *
100103 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTAACTGATGG
1 CCCGAAGGACTT-AGCATCATGCTCGAAAGACTAACAAATGA
100145 CCCGAAGGACTTA
1 CCCGAAGGACTTA
100158 TAAATTTTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 12 0.26
42 34 0.74
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (41 bp):
CCCGAAGGACTTAGCATCATGCTCGAAAGACTAACAAATGA
Found at i:100263 original size:233 final size:233
Alignment explanation
Indices: 99841--101872 Score: 2760
Period size: 233 Copynumber: 8.7 Consensus size: 233
99831 GAAGGGTTTA
* * * * * * * *
99841 ATCATCATGCTCAAAAGACTTACAGATAACCCAAAGGACTTAAACATTATGCTTGAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
** * * ** * * *
99906 TGATTACCCAAACGACTTACCAACTTTGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * * *
99971 CAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTCCTCATTTTTCGAGAGACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* * **
100036 ATC-CGACCTGAAGGTCTTGCGGATTGCCCGAAGGACTT
196 ATCATG-CCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* *
100074 ATCATCTTGCTCGAAAGACTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTAAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* ** *
100139 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAATTTACTAGGTAAGAAAGTTTTCTTTCTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* *
100204 CAAAAATTTCAATTTTCAAATTTAAATGATAAACCTTTCTCATATTTCGATAAACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* * * *
100269 ATCCTGTCCGAAGATCTTATGGATGGCCCGAAGGACTT
196 ATCATGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* * * *
100307 ATCATCTTGCTCGAAAGAATTACAAATGACACGAAGGATTTAAGCATCATGCTCGAAACACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* *
100372 TGATGGCGATGGCCCGAATGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCAT
66 ---T---GATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTT
* * * * *
100437 AATTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAATCATTTCTCATATTTTGATAGACATGT
125 ACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGT
*
100502 GAAAACATCATGCCCGAAGGTCTTATCGA-TGCCCCGAAGGACTT
190 GAAAACATCATGCCCGAAGGTCTTATGGATTG-CCCGAAGGACTT
* * * * *
100546 ATCATCTTGCTCAAAAGACTTATATATAACCCGAAGGATTTAAGCATCATGCTCGAGAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * * *
100611 TAATGGCCCGAAGAACTTATAAACTTTGAAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
100676 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* * * *
100741 ATCATGTCCGAAGGTCTTATGGA-TGGCTGAAGAACTT
196 ATCATGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* * * * * *
100778 AGCATCTTTCTCAAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTTGAAAGACTTAT
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * *
100843 TGATGGCCCAAAGGACTTAAAAATTTTAGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
** * *
100908 CAAAAATTTCAAATTTT-TGATTTAAATAAGAAACATTTCTCATATTTCGATAGACATGTGAAAA
131 CAAAAATTTC-AATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAA
* *
100972 CATCTTGCCCGAAGGTCTTATGGA-TGACCCGAAGGACAT
195 CATCATGCCCGAAGGTCTTATGGATTG-CCCGAAGGACTT
* * *
101011 ATCATCTTGCTCGATAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAGAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
*
101076 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGATAAGAAACCTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * * *
101141 CAAAAAATTCAATTTTCAAATTTAAATTAGAAACATTTCTCATATTTCAATAGACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* * * * *
101206 ATCTTGCCCGAAGGTCTTTTGGATAGACCGAAAGACTT
196 ATCATGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* * *
101244 ATCATCTTACTCGAAAGACTTACAGATGACTCGAAAGATTTAAGCATCATGCTCGAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * *
101309 TGATGGCTCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTATGAAACCTTTCTTATTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * * *
101374 CAAAAATTTCAAATTTCATATTTAAATGAGAAACCTTTCTTATAATTCGATAGACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
** * * *
101439 ATCATGCCCGAAGAACTTATGGATAGTCCGAATGACTT
196 ATCATGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* * *
101477 ATCATCTTGCTCGAAAGACTTACAGATTAGCCGAAGGATTTAAGCATCATGCTCGAAAGAATTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * * *
101542 TAATGGTCCGAAGGTCTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTGT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * * * * *
101607 AAAAAATTTTAATTTTCAGATTTAAATGAGAAACGTTTCTCATATTTCGTTAGACATGTGAAAAT
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* * * *
101672 ATCCTGCCTGAAGGTCTTATGGATTTCCTGAAGGACTT
196 ATCATGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* *
101710 ATCATCTTGCTCGAAAAACTTACAGATGACCCGAAGGATTTAAGCATCTTGCTCGAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * * *
101775 TGATGACCCAAAGGACTTATAAATATTGGAAATAGTTTACTATGTAAGAAACCTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * *
101840 CAGAAATTTCAAATTTCAGATTTAAATGAGAAA
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAA
101873 TATTTTGTAA
Statistics
Matches: 1592, Mismatches: 195, Indels: 24
0.88 0.11 0.01
Matches are distributed among these distances:
232 208 0.13
233 1175 0.74
234 2 0.00
236 2 0.00
238 1 0.00
239 204 0.13
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (233 bp):
ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
ATCATGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
Found at i:100825 original size:42 final size:42
Alignment explanation
Indices: 100774--100862 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
100764 TGGCTGAAGA
* * *
100774 ACTT-AGCATCTTTCTCAAAAGACTTATAGATGACCCGAAGG
1 ACTTAAGCATCATGCTCAAAAGACTTATAGATGACCCAAAGG
* ** * *
100815 ATTTAAGCATCATGCTTGAAAGACTTATTGATGGCCCAAAGG
1 ACTTAAGCATCATGCTCAAAAGACTTATAGATGACCCAAAGG
100857 ACTTAA
1 ACTTAA
100863 AAATTTTAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (42 bp):
ACTTAAGCATCATGCTCAAAAGACTTATAGATGACCCAAAGG
Found at i:101033 original size:41 final size:41
Alignment explanation
Indices: 100988--101091 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 41
100978 GCCCGAAGGT
* * *
100988 CTTATGGATGACCCGAAGGACAT-ATCATCTTGCTCGATAGA
1 CTTAT-GATGACCCGAAGGACATAAGCATCATGCTCGAGAGA
**
101029 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAGAGA
1 CTTAT-GATGACCCGAAGGACATAAGCATCATGCTCGAGAGA
*
101071 CTTACTGATGGCCCGAAGGAC
1 CTTA-TGATGACCCGAAGGAC
101092 TTATAAATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (41 bp):
CTTATGATGACCCGAAGGACATAAGCATCATGCTCGAGAGA
Found at i:101277 original size:20 final size:20
Alignment explanation
Indices: 101252--101327 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
101242 TTATCATCTT
101252 ACTCGAAAGACTTACAGATG
1 ACTCGAAAGACTTACAGATG
* *
101272 ACTCGAAAGATTTA-AGCATC
1 ACTCGAAAGACTTACAG-ATG
*
101292 ATGCTCGAAAGACTTACTGATG
1 A--CTCGAAAGACTTACAGATG
* *
101314 GCTCGAAGGACTTA
1 ACTCGAAAGACTTA
101328 TAAATTTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.04
20 28 0.62
22 14 0.31
23 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (20 bp):
ACTCGAAAGACTTACAGATG
Found at i:103508 original size:2 final size:2
Alignment explanation
Indices: 103501--103542 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
103491 CATGCACATG
103501 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
103543 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:103510 original size:12 final size:11
Alignment explanation
Indices: 103495--103540 Score: 62
Period size: 10 Copynumber: 4.4 Consensus size: 11
103485 CATGCACATG
103495 CACATGCACACA
1 CACAT-CACACA
103507 CACA-CACACA
1 CACATCACACA
103517 CACA-CACACA
1 CACATCACACA
103527 CACA-CACACA
1 CACATCACACA
103537 CACA
1 CACA
103541 CATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 30 0.88
12 4 0.12
ACGTcount: A:0.48, C:0.48, G:0.02, T:0.02
Consensus pattern (11 bp):
CACATCACACA
Found at i:103547 original size:2 final size:2
Alignment explanation
Indices: 103542--103602 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
103532 ACACACACAC
103542 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
*
103584 GT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
103603 ATCCCTTATC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112088 original size:3 final size:3
Alignment explanation
Indices: 112080--112109 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
112070 ACATAATAGA
112080 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
112110 AAGGCACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:112100 original size:16 final size:16
Alignment explanation
Indices: 112079--112109 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
112069 AACATAATAG
112079 AAATAATAATAATAAT
1 AAATAATAATAATAAT
112095 AAATAATAATAATAA
1 AAATAATAATAATAA
112110 AAGGCACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:112101 original size:13 final size:13
Alignment explanation
Indices: 112083--112110 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
112073 TAATAGAAAT
112083 AATAATAATAATA
1 AATAATAATAATA
112096 AATAATAATAATA
1 AATAATAATAATA
112109 AA
1 AA
112111 AGGCACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:112187 original size:24 final size:23
Alignment explanation
Indices: 112130--112224 Score: 86
Period size: 23 Copynumber: 4.1 Consensus size: 23
112120 ACGGGTGACA
* *
112130 TCACGAACATGTTCGTTTAATGT
1 TCACGAACGTGTTCATTTAATGT
112153 TCACGAACGTGTTCATTTATATGT
1 TCACGAACGTGTTCATTTA-ATGT
* **
112177 TCA-TAAGCGTGTTCATTTAGCGT
1 TCACGAA-CGTGTTCATTTAATGT
* * *
112200 TCACG-ACATGCTCATTTAGTGT
1 TCACGAACGTGTTCATTTAATGT
112222 TCA
1 TCA
112225 TTATCATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
22 16 0.27
23 25 0.42
24 19 0.32
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (23 bp):
TCACGAACGTGTTCATTTAATGT
Done.