Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009622.1 Hibiscus syriacus cultivar Beakdansim tig00117011_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: 790348
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 4
Found at i:673251 original size:94 final size:94
Alignment explanation
Indices: 673105--673484 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
673095 ATGGATTGCA
* *
673105 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
673169 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
* *
673198 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATATACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
**
673263 TTAGCAGAATTGGTAGCAACCGAACAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
673292 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
673357 TTAGCAGAATTGACAGCAACCGAATAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
* *
673386 TTAC-TTCAACCAAAACACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
673450 TTTAGCAGTATTGACAGCAACCGAATAAAT
65 TTTAGCAGAATTGACAGCAACCGAACAAAT
673480 TTACT
1 TTACT
673485 AAGCAATCTA
Statistics
Matches: 271, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
93 22 0.08
94 249 0.92
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGACAGCAACCGAACAAAT
Found at i:675194 original size:20 final size:20
Alignment explanation
Indices: 675169--675231 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
675159 TTTTGGTTGA
675169 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
675189 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
675208 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
675229 AAT
1 AAT
675232 CGCAACGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:675253 original size:33 final size:33
Alignment explanation
Indices: 675167--675288 Score: 127
Period size: 33 Copynumber: 3.5 Consensus size: 33
675157 TCTTTTGGTT
*
675167 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAAC-A-AG-A-G--AATCGCAACG-A
** *
675207 GAAATGACTATCGCAACGAGAGAATCGCAACGA
1 GAAATGAAAATCGCAACAAGAGAATCGCAACGA
* *
675240 TAAATGAAAATCGCAACAAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACAAGAGAATCGCAACGA
675273 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
675289 TGCGATTTTG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
33 43 0.60
34 10 0.14
36 1 0.01
37 1 0.01
38 2 0.03
40 15 0.21
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACAAGAGAATCGCAACGA
Found at i:675339 original size:21 final size:21
Alignment explanation
Indices: 675313--675376 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
675303 CGCGTTGCGA
675313 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
** *
675334 TTCTCTCGTTGCGATAGTCCT
1 TTCTCTCGTTGCGATTTTCAT
675355 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
675375 TT
1 TT
675377 TCATGTTGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.09, C:0.22, G:0.17, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:675377 original size:20 final size:19
Alignment explanation
Indices: 675320--675391 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
675310 CGATTCTCTC
675320 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
** *
675340 CGTTGCGATAGTCCTTTTCGT
1 -GTTGCGATTTTCATTTTC-T
675361 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
*
675381 GTTGCAATTTT
1 GTTGCGATTTT
675392 AAGTTTAGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.51
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:675977 original size:20 final size:20
Alignment explanation
Indices: 675952--676103 Score: 171
Period size: 20 Copynumber: 7.5 Consensus size: 20
675942 CTTTAAAAAT
675952 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
675972 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
675992 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
** * *
676013 CGCACTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
676033 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
676053 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
676073 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
676093 CGTGTTGCGAT
1 CGCGTTGCGAT
676104 AGTCAGAATC
Statistics
Matches: 106, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
20 89 0.84
21 17 0.16
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:676038 original size:40 final size:40
Alignment explanation
Indices: 675954--676103 Score: 246
Period size: 40 Copynumber: 3.7 Consensus size: 40
675944 TTAAAAATCG
*
675954 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
**
675995 CGTTGCGATTTACGGATACGCACTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
676035 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
676075 CGTTGCGATTTACGGATACGTGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
676104 AGTCAGAATC
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 75 0.74
41 26 0.26
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:676082 original size:60 final size:61
Alignment explanation
Indices: 675951--676144 Score: 193
Period size: 60 Copynumber: 3.2 Consensus size: 61
675941 GCTTTAAAAA
* * *
675951 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTAC-G-TATTGTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACTCGTTGCGA-TTTACAGATATCG-CGTTGCGATTTACGTAT
* ** * *
676012 ACGCACTGCGATTTACGTATTCTCGTTGCGATTTACAGATA-CGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATATCGCGTTGCGATTTACGTAT
* * ** *
676072 TCTCGTTGCGATTTACGGATACGT-GTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTACGGATAC-TCGTTGCGAT-TTACAGATATCGCGTTGCGATTTACGTAT
676132 TCGCGTTGCGATT
1 TCGCGTTGCGATT
676145 CTGGAAAATT
Statistics
Matches: 109, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
59 1 0.01
60 77 0.71
61 29 0.27
62 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (61 bp):
TCGCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATATCGCGTTGCGATTTACGTAT
Found at i:676119 original size:40 final size:40
Alignment explanation
Indices: 675949--676126 Score: 209
Period size: 40 Copynumber: 4.4 Consensus size: 40
675939 GCGCTTTAAA
675949 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGT
* **
675990 -ATTGTCGTTGCGATTTACGGATACGCACTGCGATTTACGT
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTACGT
* * *
676030 ATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGT
* * * *
676070 ATTCTCGTTGCGATTTACGGATACGTGTTGCGATAGT-CAG-
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGAT-TTAC-GT
676110 AATCGCGTTGCGATTTA
1 AATCGCGTTGCGATTTA
676127 TATGTTCGCG
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
40 90 0.76
41 29 0.24
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (40 bp):
AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGT
Found at i:676529 original size:61 final size:60
Alignment explanation
Indices: 676460--676597 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
676450 AACTCAGTTC
* * *
676460 CAATTTCGCAACGCGAATATGTAAATCGCATTGC-GATTTTCCAAATTCGCAACGCGAAAGT
1 CAATTTCGCAACGCGAATATGTAAATCGCAATACAGA-ATT-CAAATTCGCAACGCGAAAGT
* * *
676521 CAATTTCGCAACGCGAATTTGTAAATCGCAATACAGAATTCAAATTCGCAATGCGATAGT
1 CAATTTCGCAACGCGAATATGTAAATCGCAATACAGAATTCAAATTCGCAACGCGAAAGT
* *
676581 TAAATTCGCAACGCGAA
1 CAATTTCGCAACGCGAA
676598 AGTTAAATGT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
60 33 0.49
61 33 0.49
62 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (60 bp):
CAATTTCGCAACGCGAATATGTAAATCGCAATACAGAATTCAAATTCGCAACGCGAAAGT
Found at i:676549 original size:20 final size:20
Alignment explanation
Indices: 676465--676551 Score: 61
Period size: 20 Copynumber: 4.3 Consensus size: 20
676455 AGTTCCAATT
*
676465 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
** * **
676485 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
* *
676505 TTCGCAACGCGAA--AGTCAATT
1 -TCGCAACGCGAATTTGT-AA-A
676526 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
676546 TCGCAA
1 TCGCAA
676552 TACAGAATTC
Statistics
Matches: 47, Mismatches: 15, Indels: 10
0.65 0.21 0.14
Matches are distributed among these distances:
20 34 0.72
21 11 0.23
22 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:676585 original size:20 final size:20
Alignment explanation
Indices: 676562--676605 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
676552 TACAGAATTC
* *
676562 AAATTCGCAATGCGATAGTT
1 AAATTCGCAACGCGAAAGTT
676582 AAATTCGCAACGCGAAAGTT
1 AAATTCGCAACGCGAAAGTT
676602 AAAT
1 AAAT
676606 GTTTTTATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTT
Found at i:676772 original size:22 final size:22
Alignment explanation
Indices: 676727--676774 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
676717 CTACGGCGAC
*
676727 ATCCATCCCCATCTCCGATAAA
1 ATCCATCCCCATCTCCGACAAA
* *
676749 ATCCATCCCCATTTCCGACGAA
1 ATCCATCCCCATCTCCGACAAA
676771 ATCC
1 ATCC
676775 GTCTATCTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.42, G:0.06, T:0.23
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACAAA
Found at i:677752 original size:17 final size:18
Alignment explanation
Indices: 677725--677763 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
677715 ATATAAACCT
677725 TAATAATAAATATTAAC-A
1 TAATAATAAAT-TTAACAA
677743 TAAT-ATAAATTTAACAA
1 TAATAATAAATTTAACAA
677760 TAAT
1 TAAT
677764 TTATAAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 11 0.55
18 4 0.20
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAATAAATTTAACAA
Found at i:679609 original size:6 final size:6
Alignment explanation
Indices: 679600--679639 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
679590 ATGGCGATGA
* * *
679600 TGAGAG TGAGAG TGGGAG TGGGAG TGAGAG TAAGAG TGAG
1 TGAGAG TGAGAG TGAGAG TGAGAG TGAGAG TGAGAG TGAG
679640 GAGGAAGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.53, T:0.17
Consensus pattern (6 bp):
TGAGAG
Found at i:684289 original size:2 final size:2
Alignment explanation
Indices: 684277--684311 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
684267 TGTGAAATGA
684277 AT AT GAT 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
684312 GATTAGAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:684548 original size:15 final size:14
Alignment explanation
Indices: 684524--684553 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
684514 TCGATTTAAA
684524 TTTTTTTTAATTTT
1 TTTTTTTTAATTTT
684538 TTTTATTTTAATTTT
1 TTTT-TTTTAATTTT
684553 T
1 T
684554 CAAGTTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTAATTTT
Found at i:685642 original size:14 final size:14
Alignment explanation
Indices: 685623--685652 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
685613 TTTAGATTTT
*
685623 TTAAAATTACATTA
1 TTAAAAATACATTA
685637 TTAAAAATACATTA
1 TTAAAAATACATTA
685651 TT
1 TT
685653 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:685746 original size:23 final size:23
Alignment explanation
Indices: 685709--685755 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
685699 ATTTTTGTAG
*
685709 GTTCAAATTCGAGCTTGAATCGA
1 GTTCAAAATCGAGCTTGAATCGA
* *
685732 GTTCAAAATCTAGCTTTAATCGA
1 GTTCAAAATCGAGCTTGAATCGA
685755 G
1 G
685756 CTCGAGTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (23 bp):
GTTCAAAATCGAGCTTGAATCGA
Found at i:686027 original size:2 final size:2
Alignment explanation
Indices: 686020--686077 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
686010 TCTCCAGTAG
686020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
686062 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
686078 CATTTTTTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:687151 original size:17 final size:17
Alignment explanation
Indices: 687124--687162 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
687114 AATTTACAAT
687124 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
687140 TAATTATAAATAATATC
1 TAATTATAAATAATATC
687157 TAATTA
1 TAATTA
687163 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:699192 original size:2 final size:2
Alignment explanation
Indices: 699185--699214 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
699175 ATATAACACA
699185 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
699215 TTGTAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:699413 original size:19 final size:20
Alignment explanation
Indices: 699389--699432 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
699379 CAGAAGTCTC
*
699389 GAAAC-TTTACAAGATTTTT
1 GAAACTTTTACAAGAGTTTT
*
699408 GAAACTTTTATAAGAGTTTT
1 GAAACTTTTACAAGAGTTTT
699428 GAAAC
1 GAAAC
699433 GCCCATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (20 bp):
GAAACTTTTACAAGAGTTTT
Found at i:700857 original size:18 final size:18
Alignment explanation
Indices: 700832--700873 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
700822 AATGATAAAG
700832 GAAG-AAGAAGAACAAAA
1 GAAGAAAGAAGAACAAAA
* **
700849 GAAGAAAGATGAGGAAAA
1 GAAGAAAGAAGAACAAAA
700867 GAAGAAA
1 GAAGAAA
700874 ATGGAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.67, C:0.02, G:0.29, T:0.02
Consensus pattern (18 bp):
GAAGAAAGAAGAACAAAA
Found at i:700879 original size:15 final size:16
Alignment explanation
Indices: 700845--700889 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
700835 GAAGAAGAAC
700845 AAAAGAAGAAAGATGAGG
1 AAAAGAAGAAA-AT-AGG
700863 AAAAGAAGAAAAT-GG
1 AAAAGAAGAAAATAGG
700878 AAAAGAAGAAAA
1 AAAAGAAGAAAA
700890 AGATTGGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.52
17 2 0.07
18 11 0.41
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (16 bp):
AAAAGAAGAAAATAGG
Found at i:705289 original size:20 final size:20
Alignment explanation
Indices: 705266--705319 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
705256 AGCTACTTTA
705266 AAAGTTTCGAAATT-TTGCAT
1 AAAGTTTCGAAATTCTTGC-T
* * *
705286 AAAGTATCGATATTCTTTCT
1 AAAGTTTCGAAATTCTTGCT
*
705306 AAAGTTTCAAAATT
1 AAAGTTTCGAAATT
705320 GTAAAAAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (20 bp):
AAAGTTTCGAAATTCTTGCT
Found at i:705630 original size:21 final size:21
Alignment explanation
Indices: 705606--705646 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
705596 TTTAGAAGGT
*
705606 AAATTTCGCATAGACCCTAAC
1 AAATTTCGCATAGAACCTAAC
*
705627 AAATTTTGCATAGAACCTAA
1 AAATTTCGCATAGAACCTAA
705647 TACTCTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (21 bp):
AAATTTCGCATAGAACCTAAC
Found at i:707204 original size:18 final size:18
Alignment explanation
Indices: 707181--707246 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 18
707171 TATTATTGCA
707181 TTTGGATGTTTTGGTTAT
1 TTTGGATGTTTTGGTTAT
707199 TTTGGAT-TTTTAGGACTTCATAT
1 TTTGGATGTTTT-GG---T--TAT
707222 TTTGGATGTTTTGGTTAT
1 TTTGGATGTTTTGGTTAT
707240 TTTGGAT
1 TTTGGAT
707247 ATTTCACTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
17 4 0.10
18 19 0.46
20 1 0.02
21 1 0.02
23 12 0.29
24 4 0.10
ACGTcount: A:0.15, C:0.03, G:0.24, T:0.58
Consensus pattern (18 bp):
TTTGGATGTTTTGGTTAT
Found at i:707842 original size:20 final size:20
Alignment explanation
Indices: 707813--707864 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
707803 TTTGACCAGA
*
707813 AGTTTTGAAACTTCTGCAAG
1 AGTTTCGAAACTTCTGCAAG
* *
707833 AGTTTCGAAACTTTTGTAAG
1 AGTTTCGAAACTTCTGCAAG
707853 AGTTTCGAAACT
1 AGTTTCGAAACT
707865 ATCCAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
AGTTTCGAAACTTCTGCAAG
Found at i:707908 original size:19 final size:19
Alignment explanation
Indices: 707884--707933 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
707874 AAAAGACTTT
707884 AGAGTTTCGAAACTTTACA
1 AGAGTTTCGAAACTTTACA
707903 AGAGTTTCGAAACTTTACA
1 AGAGTTTCGAAACTTTACA
707922 AGAGTTTCGAAA
1 AGAGTTTCGAAA
707934 TGTCCATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (19 bp):
AGAGTTTCGAAACTTTACA
Found at i:708012 original size:21 final size:21
Alignment explanation
Indices: 707986--708030 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
707976 TTTTTAATTC
*
707986 CTTTTTTGAAGAGTTTCGAAA
1 CTTTTTTCAAGAGTTTCGAAA
* *
708007 C-TTTTTCCATAGTTTCGAAA
1 CTTTTTTCAAGAGTTTCGAAA
708027 CTTT
1 CTTT
708031 GTGTGCATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (21 bp):
CTTTTTTCAAGAGTTTCGAAA
Found at i:709954 original size:22 final size:22
Alignment explanation
Indices: 709929--709981 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
709919 TAAAAGATTG
*
709929 GTATTTAAATTATTAGATGGAT
1 GTATTTAAAATATTAGATGGAT
** *
709951 GTATAAAAAAATATTAGATGGGT
1 GTAT-TTAAAATATTAGATGGAT
709974 -TATTTAAA
1 GTATTTAAA
709982 CAGTTACAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 3 0.12
22 7 0.29
23 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (22 bp):
GTATTTAAAATATTAGATGGAT
Found at i:711265 original size:31 final size:31
Alignment explanation
Indices: 711225--711302 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
711215 CAATTACGTC
**
711225 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACAAACTAAATGTTG
*
711256 ATGGACCATATTGCAAACAAACTAAATGTTG
1 AGGGACCATATTGCAAACAAACTAAATGTTG
**
711287 AGGGATTATATTGCAA
1 AGGGACCATATTGCAA
711303 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (31 bp):
AGGGACCATATTGCAAACAAACTAAATGTTG
Found at i:713195 original size:31 final size:31
Alignment explanation
Indices: 713123--713188 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
713113 AGTTACGTCG
* *
713123 GGGACCATATTGCAAATGGACTAAATGTTGA
1 GGGACCATATTGCAAATAGACTAAATATTGA
*
713154 GGGACCATATTGCAAATAGACTAAATATTGG
1 GGGACCATATTGCAAATAGACTAAATATTGA
713185 GGGA
1 GGGA
713189 TTATATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (31 bp):
GGGACCATATTGCAAATAGACTAAATATTGA
Found at i:720696 original size:21 final size:21
Alignment explanation
Indices: 720667--720719 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
720657 ATTTTGACTA
720667 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
720688 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
720709 TCGCAATGCGA
1 TCGCATTGCGA
720720 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:720784 original size:20 final size:20
Alignment explanation
Indices: 720709--720775 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
720699 TTTTCCGAAT
720709 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
720729 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
720749 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
720769 TCGCAAT
1 TCGCAAT
720776 ACGATTATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:720791 original size:20 final size:20
Alignment explanation
Indices: 720768--720897 Score: 172
Period size: 20 Copynumber: 6.5 Consensus size: 20
720758 GAATATGTAA
* *
720768 ATCGCAATACGATTATGACT
1 ATCGCAACACGATTCTGACT
***
720788 ATCGCAATGTGATTCTGACT
1 ATCGCAACACGATTCTGACT
* *
720808 ATCGCAACGCGATTCTGATT
1 ATCGCAACACGATTCTGACT
720828 ATCGCAACGA-GATTCTGACT
1 ATCGCAAC-ACGATTCTGACT
720848 ATCGCAACACGATTCTGACT
1 ATCGCAACACGATTCTGACT
720868 ATCGCAACACGATTCTGACT
1 ATCGCAACACGATTCTGACT
*
720888 GTCGCAACAC
1 ATCGCAACAC
720898 TGAATTTCAA
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 98 0.99
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGCAACACGATTCTGACT
Found at i:720796 original size:40 final size:40
Alignment explanation
Indices: 720709--720784 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
720699 TTTTCCGAAT
*
720709 TCGCAATGCGAATATGTAAATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAATCGCAATACGAATATGTAAA
*
720749 TCGCAATGCGAATATGTAAATCGCAATACGATTATG
1 TCGCAATGCGAATATGTAAATCGCAATACGAATATG
720785 ACTATCGCAA
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:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGAATATGTAAATCGCAATACGAATATGTAAA
Found at i:720812 original size:60 final size:60
Alignment explanation
Indices: 720748--720875 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
720738 GAATATGTAA
* * ***
720748 ATCGCAATGCGAATATG-TAAATCGCAA-TACGATTATGACTATCGCAATGTGATTCTGACT
1 ATCGCAACGCGAATATGAT-AATCGCAACGA-GATTATGACTATCGCAACACGATTCTGACT
* * * *
720808 ATCGCAACGCGATTCTGATTATCGCAACGAGATTCTGACTATCGCAACACGATTCTGACT
1 ATCGCAACGCGAATATGATAATCGCAACGAGATTATGACTATCGCAACACGATTCTGACT
720868 ATCGCAAC
1 ATCGCAAC
720876 ACGATTCTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 55 0.96
61 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (60 bp):
ATCGCAACGCGAATATGATAATCGCAACGAGATTATGACTATCGCAACACGATTCTGACT
Found at i:721742 original size:24 final size:24
Alignment explanation
Indices: 721715--721768 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
721705 GTATTCGAAA
721715 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
721739 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
721763 TTTGAT
1 TTTGAT
721769 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:724370 original size:140 final size:140
Alignment explanation
Indices: 724118--724400 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
724108 GTAAACGTTG
*
724118 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAATAACTTGAGT
*
724183 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTACTACACATTCATTTGAATATCGCAACG
724248 CGAATTTGAC
131 CGAATTTGAC
724258 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAATAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAATAACTTGAGT
724323 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTACTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTACTACACATTCATTTGAATATCGCAACG
*
724388 TGAATTTGAC
131 CGAATTTGAC
724398 TAT
1 TAT
724401 CGCAACGCGA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAATAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTACTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:724396 original size:20 final size:20
Alignment explanation
Indices: 724371--724553 Score: 167
Period size: 20 Copynumber: 9.8 Consensus size: 20
724361 CTACACATTC
*
724371 ATTTGAATATCGCAACGTGA
1 ATTTGAATATCGCAACGCGA
*
724391 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
724411 ATTTGATTATCGCAACTC-A
1 ATTTGAATATCGCAACGCGA
724430 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
724445 ATTT-AACTATCGTAACGCGA
1 ATTTGAA-TATCGCAACGCGA
*
724465 ATTTGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
724484 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
724499 ATTTGACTATCACAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
724519 ATTTGACTATCGCAACGTGA
1 ATTTGAATATCGCAACGCGA
*
724539 ATTTGATTATCGCAA
1 ATTTGAATATCGCAA
724554 TGGGTATTTG
Statistics
Matches: 135, Mismatches: 15, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 6 0.04
18 2 0.01
19 5 0.04
20 102 0.76
21 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:724462 original size:54 final size:54
Alignment explanation
Indices: 724379--724535 Score: 260
Period size: 54 Copynumber: 2.9 Consensus size: 54
724369 TCATTTGAAT
* * *
724379 ATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* *
724433 ATCGCAACGCGAATTTAACTATCGTAACGCGAATTTGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
*
724487 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
724536 TGAATTTGAT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:724562 original size:20 final size:20
Alignment explanation
Indices: 724371--724575 Score: 137
Period size: 20 Copynumber: 10.8 Consensus size: 20
724361 CTACACATTC
* *
724371 ATTTGAATATCGCAACGTGA
1 ATTTGACTATCGCAACGGGA
*
724391 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGGGA
* **
724411 ATTTGATTATCGCAAC-TCA
1 ATTTGACTATCGCAACGGGA
* *
724430 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGGGA
* * *
724445 ATTTAACTATCGTAACGCGA
1 ATTTGACTATCGCAACGGGA
*
724465 ATTTGACTATCGCAAC-GCA
1 ATTTGACTATCGCAACGGGA
* *
724484 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGGGA
* *
724499 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGGGA
*
724519 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGGGA
* * *
724539 ATTTGATTATCGCAATGGGT
1 ATTTGACTATCGCAACGGGA
*
724559 ATTTGACTATTGCAACG
1 ATTTGACTATCGCAACG
724576 AGAAAATCAC
Statistics
Matches: 145, Mismatches: 28, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
14 16 0.11
15 6 0.04
19 6 0.04
20 117 0.81
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGGGA
Found at i:724563 original size:40 final size:40
Alignment explanation
Indices: 724371--724575 Score: 164
Period size: 40 Copynumber: 5.4 Consensus size: 40
724361 CTACACATTC
* * *
724371 ATTTGAATATCGCAACGTGAATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGA
* * * *
724411 ATTTGATTATCGCAACTC-AA----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGA
* * *
724445 ATTTAACTATCGTAACGCGAATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGA
*
724484 A----A-AATCGCAACGCGAATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGA
* * * * * *
724519 ATTTGACTATCGCAACGTGAATTTGATTATCGCAATGGGT
1 ATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGA
*
724559 ATTTGACTATTGCAACG
1 ATTTGACTATCGCAACG
724576 AGAAAATCAC
Statistics
Matches: 133, Mismatches: 20, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
34 54 0.41
35 6 0.05
39 6 0.05
40 67 0.50
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (40 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGA
Found at i:724716 original size:14 final size:14
Alignment explanation
Indices: 724655--724716 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
724645 CGCAAATAAG
*
724655 AATTATTTACATATC
1 AATT-TTTACAAATC
**
724670 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
724685 AACTTTTACAAATC
1 AATTTTTACAAATC
*
724699 AATTTTTACAAATT
1 AATTTTTACAAATC
724713 AATT
1 AATT
724717 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:726174 original size:21 final size:21
Alignment explanation
Indices: 726141--726190 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
726131 TGACAGTGGC
*
726141 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGAGAGGGGA
** * *
726162 CTCTTGAGGGGTGATAGGGGC
1 CTCTTGAACGGTGAGAGGGGA
726183 CTCTTGAA
1 CTCTTGAA
726191 TGATAGGGGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.42, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGA
Found at i:726730 original size:18 final size:18
Alignment explanation
Indices: 726707--726773 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 18
726697 GAAACTTAAA
*
726707 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
726725 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
*
726745 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
726765 ATCGCAACG
1 ATCGCAACG
726774 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.29
20 30 0.71
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:726743 original size:20 final size:20
Alignment explanation
Indices: 726718--726773 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
726708 TCGCAACACG
726718 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
726738 AATGACTATCGCAATGCGAA
1 AATGACTATCGCAACGCGAA
**
726758 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
726774 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:726841 original size:20 final size:20
Alignment explanation
Indices: 726816--726859 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
726806 GCGATTCTTT
726816 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
726836 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
726856 CGTT
1 CGTT
726860 ACGAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:727224 original size:21 final size:21
Alignment explanation
Indices: 727197--727249 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
727187 TGCACCATTG
*
727197 TCATCACGTAAAGTATCGACC
1 TCATCACGTAAAGCATCGACC
* * *
727218 TCCTCACGTAAGGCATTGACC
1 TCATCACGTAAAGCATCGACC
727239 TCATCACGTAA
1 TCATCACGTAA
727250 CTCCCCTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (21 bp):
TCATCACGTAAAGCATCGACC
Found at i:728799 original size:20 final size:20
Alignment explanation
Indices: 728776--728848 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
728766 GAAACTTAAA
*
728776 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
728796 ATCGCAACGC-AAATTTGACT
1 ATCGCAACGCGAAA-ATGACT
**
728816 ATCGCAACGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
728835 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
728849 CTAAAATCGC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 17 0.38
20 28 0.62
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:728840 original size:19 final size:20
Alignment explanation
Indices: 728773--728859 Score: 81
Period size: 19 Copynumber: 4.5 Consensus size: 20
728763 TCTGAAACTT
* *
728773 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAATTG
**
728793 ACTATCGCAACGC-AAATTTG
1 AAAATCGCAACGCGAAA-TTG
**
728813 ACTATCGCAACGCGAAA-TG
1 AAAATCGCAACGCGAAATTG
*
728832 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAATTG
728851 AAAATCGCA
1 AAAATCGCA
728860 TTGCGATTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
19 29 0.50
20 26 0.45
21 3 0.05
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAATTG
Found at i:729270 original size:22 final size:22
Alignment explanation
Indices: 729240--729297 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
729230 AGATGGAGAT
729240 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* * *
729262 AGACTGATTCCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* *
729284 GGACGGATGTCGCC
1 AGACGGATTTCGCC
729298 TTAGAGAGTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.19
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:729492 original size:20 final size:20
Alignment explanation
Indices: 729460--729535 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
729450 TGGCGCTTTG
729460 AAAATCGCATTGCGATAGTC
1 AAAATCGCATTGCGATAGTC
** *
729480 AGCATCGCGTTGCGATAGTC
1 AAAATCGCATTGCGATAGTC
* *
729500 AAAATCTCGTTGCGATAGTC
1 AAAATCGCATTGCGATAGTC
*
729520 ATAATCGCATTGCGAT
1 AAAATCGCATTGCGAT
729536 TTACATATTC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (20 bp):
AAAATCGCATTGCGATAGTC
Found at i:729515 original size:40 final size:40
Alignment explanation
Indices: 729460--729613 Score: 116
Period size: 40 Copynumber: 3.8 Consensus size: 40
729450 TGGCGCTTTG
* *
729460 AAAATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTC
1 AAAATCGCATTGCGATAGTCAGAATCGCATTGCGATAGTC
* * * *
729500 AAAATCTCGTTGCGATAGTCATAATCGCATTGCGAT-TTAC
1 AAAATCGCATTGCGATAGTCAGAATCGCATTGCGATAGT-C
* * * ** * *
729540 ATATTCGCATTGCGA-ATTCAGAAAATCGCAACGCGA-ATTTGG
1 AAAATCGCATTGCGATAGTCAG--AATCGCATTGCGATA-GT-C
*
729582 AAAATCGCAATGCGATAGTCAGAATCGCATTG
1 AAAATCGCATTGCGATAGTCAGAATCGCATTG
729614 AGAATCTAGA
Statistics
Matches: 86, Mismatches: 22, Indels: 11
0.72 0.18 0.09
Matches are distributed among these distances:
39 5 0.06
40 43 0.50
41 19 0.22
42 14 0.16
43 5 0.06
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (40 bp):
AAAATCGCATTGCGATAGTCAGAATCGCATTGCGATAGTC
Found at i:729575 original size:21 final size:21
Alignment explanation
Indices: 729551--729605 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
729541 TATTCGCATT
729551 GCGAATTCAGAAAATCGCAAC
1 GCGAATTCAGAAAATCGCAAC
** *
729572 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCAGAAAATCGCAAC
*
729593 GCGATAGTCAGAA
1 GCGA-ATTCAGAA
729606 TCGCATTGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
GCGAATTCAGAAAATCGCAAC
Found at i:736010 original size:22 final size:25
Alignment explanation
Indices: 735956--736005 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
735946 ATGATTCAAC
735956 ACAGAAGTACATTCTGAATGATTTAGT
1 ACAGAAGTACATTCTGAATGA-TTA-T
*
735983 ACAGAAGTACATTCTGATTGATT
1 ACAGAAGTACATTCTGAATGATT
736006 CAGAATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (25 bp):
ACAGAAGTACATTCTGAATGATTAT
Found at i:737087 original size:20 final size:22
Alignment explanation
Indices: 737062--737103 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
737052 TTTTATTTAG
737062 AATAAAAAA-TC-TAAAATTTT
1 AATAAAAAATTCTTAAAATTTT
737082 AATAAAAAATTCTTAAAATTTT
1 AATAAAAAATTCTTAAAATTTT
737104 CTCAATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAAAAATTCTTAAAATTTT
Found at i:746141 original size:17 final size:19
Alignment explanation
Indices: 746119--746153 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
746109 AGTTATGGCT
746119 AGGATT-TGGGG-ATTTTA
1 AGGATTGTGGGGCATTTTA
746136 AGGATTGTGGGGCATTTT
1 AGGATTGTGGGGCATTTT
746154 TTGTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.20, C:0.03, G:0.37, T:0.40
Consensus pattern (19 bp):
AGGATTGTGGGGCATTTTA
Found at i:746278 original size:15 final size:15
Alignment explanation
Indices: 746239--746278 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
746229 ATATTAATTA
746239 TTTAAAAAT-TAAAT
1 TTTAAAAATATAAAT
*
746253 TTTATAAAATATATAT
1 TTTA-AAAATATAAAT
746269 TTTAAAAATA
1 TTTAAAAATA
746279 CTTAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAAAAATATAAAT
Found at i:749498 original size:231 final size:233
Alignment explanation
Indices: 749081--749546 Score: 900
Period size: 231 Copynumber: 2.0 Consensus size: 233
749071 TAAATAGCTC
749081 TCTCCCAGTAAACTCTCTCACAATTTCCTCTCAACCGATAAATTAATACAACAATCCTTTCAACC
1 TCTCCCAGTAAAC-CTCTCACAATTTCCTCTCAACCGATAAATTAATACAACAATCCTTTCAACC
749146 AGCAAATAACACCCGACAATCCTCTTATATTTGATTCAGAAGTTCGTTCGATATTTCTTTATAAA
65 AGCAAATAACACCCGACAATCCTCTTATATTTGATTCAGAAGTTCGTTCGATATTTCTTTATAAA
749211 GTAATTTTGTTATAATATTTTTTAATTATACTTATTGTTTATTATGATTATTTGAAAAAATATTA
130 GTAATTTTGTTATAATATTTTTTAATTATACTTATTGTTTATTATGATTATTTGAAAAAATATTA
749276 TACTAATTGTTTTCAATTAATTTC-TGCCAGTTCAAGGA
195 TACTAATTGTTTTCAATTAATTTCGTGCCAGTTCAAGGA
749314 TCTCCCAGTAAA-CTCTCACAATTTCCTCTCAACCGATAAATTAATACAACAATCCTTTCAACCA
1 TCTCCCAGTAAACCTCTCACAATTTCCTCTCAACCGATAAATTAATACAACAATCCTTTCAACCA
749378 GCAAATAACACCCGACAATCCTCTTATATTTGATTCAGAAGTTCGTTCGATATTTCTTTATAAAG
66 GCAAATAACACCCGACAATCCTCTTATATTTGATTCAGAAGTTCGTTCGATATTTCTTTATAAAG
749443 TAATTTTGTTATAATATTTTTTAATTATACTTATTGTTTATTATGATTATTTGAAAAAATATTAT
131 TAATTTTGTTATAATATTTTTTAATTATACTTATTGTTTATTATGATTATTTGAAAAAATATTAT
749508 ACTAATTGTTTTCAATTAATTTCTGTGCCAGTTCAAGGA
196 ACTAATTGTTTTCAATTAATTTC-GTGCCAGTTCAAGGA
749547 GAAAGCGGGA
Statistics
Matches: 231, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
231 205 0.89
233 26 0.11
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (233 bp):
TCTCCCAGTAAACCTCTCACAATTTCCTCTCAACCGATAAATTAATACAACAATCCTTTCAACCA
GCAAATAACACCCGACAATCCTCTTATATTTGATTCAGAAGTTCGTTCGATATTTCTTTATAAAG
TAATTTTGTTATAATATTTTTTAATTATACTTATTGTTTATTATGATTATTTGAAAAAATATTAT
ACTAATTGTTTTCAATTAATTTCGTGCCAGTTCAAGGA
Found at i:752836 original size:23 final size:23
Alignment explanation
Indices: 752804--752849 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
752794 TAAAAAATTT
*
752804 AAATACTTAAATATATTACAAATA
1 AAATACTTAAATATAATA-AAATA
752828 AAATA-TTAAATATAATAAAATA
1 AAATACTTAAATATAATAAAATA
752850 TATCTTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATACTTAAATATAATAAAATA
Found at i:752890 original size:10 final size:10
Alignment explanation
Indices: 752884--752910 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
752874 ATAAGAGTAT
752884 TTGAGAGAAG
1 TTGAGAGAAG
752894 TTGAGAGAAG
1 TTGAGAGAAG
752904 TTGAGAG
1 TTGAGAG
752911 GATTTGGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:758174 original size:21 final size:21
Alignment explanation
Indices: 758116--758174 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
758106 TACTACGATA
*
758116 GGTTTAGGGTTTATAA-TTTAT
1 GGTTTAGGGTTT-TAAGGTTAT
* * *
758137 GATTTAAAGGTTATAAGGTTAT
1 GGTTT-AGGGTTTTAAGGTTAT
758159 GGTTTAGGGTTTTAAG
1 GGTTTAGGGTTTTAAG
758175 TTAATTGAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
GGTTTAGGGTTTTAAGGTTAT
Found at i:759369 original size:2 final size:2
Alignment explanation
Indices: 759362--759390 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
759352 ATATTTTTAT
759362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
759391 TTGTGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:759464 original size:32 final size:28
Alignment explanation
Indices: 759424--759493 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
759414 TTTTGAGTCT
759424 TTTATTTTACTATATATACGTGTATATATTTA
1 TTTATTTTA-TAT-TATA--TGTATATATTTA
*
759456 TTTATTTTATATTTTATGTATATATTTA
1 TTTATTTTATATTATATGTATATATTTA
* *
759484 ATTATATTAT
1 TTTATTTTAT
759494 TCTATTCGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 20 0.57
30 3 0.09
31 3 0.09
32 9 0.26
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (28 bp):
TTTATTTTATATTATATGTATATATTTA
Found at i:759602 original size:2 final size:2
Alignment explanation
Indices: 759595--759627 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
759585 GTGTCTTTAT
759595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
759628 TGTATTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:771097 original size:94 final size:94
Alignment explanation
Indices: 770857--771456 Score: 797
Period size: 106 Copynumber: 6.1 Consensus size: 94
770847 TTACCCAGAG
* * *
770857 CCAATTTCAACTTCATAATGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
770922 GGGACCACTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAACAAACAATTTC
*
770951 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
771016 CGAAGGGACCGCTGGTTGTCAACAAACAATTTC
62 CGAAGGGACCGCTGGTTGTCAACAAACAATTTC
* *
771049 CCAATCTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
771114 GGGACCGCTGGTTGTCAATC-AACAATTTC
66 GGGACCGCTGGTTGTCAA-CAAACAATTTC
* *
771143 CCAATTTCAACTTCACAATGGAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
771208 GGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 GGGACCGCTGGTTGTCAAC--A-AA-----CAATTTC
*
771245 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
771310 TGAAGGGACCGCTGATTGTCAACAAACAACTTCTCAATTTC
62 CGAAGGGACCGCTGGTTGTCAAC--A-AA-----CAATTTC
*
771351 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
771416 CGAAGGGACCGCTGGTTGTCAACAAATAATTTC
62 CGAAGGGACCGCTGGTTGTCAACAAACAATTTC
771449 CCAATTTC
1 CCAATTTC
771457 GGAGCCAATT
Statistics
Matches: 462, Mismatches: 26, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
93 1 0.00
94 176 0.38
95 1 0.00
97 2 0.00
98 94 0.20
102 7 0.02
103 2 0.00
104 1 0.00
106 178 0.39
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (94 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAATTTC
Found at i:771329 original size:106 final size:106
Alignment explanation
Indices: 771143--771491 Score: 583
Period size: 106 Copynumber: 3.3 Consensus size: 106
771133 CAACAATTTC
** *
771143 CCAATTTCAACTTCACAATGGAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
771208 GGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAG
66 GGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAG
*
771249 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
771314 GGGACCGCTGATTGTCAACAAACAACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAG
771355 CCAATTTCAACTTCAC-GACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 CCAATTTCAACTTCACAG-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
771419 AGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAG
65 AGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAG
* *
771461 CCAATTTCAACTTCATAGCGAAAGATATTGG
1 CCAATTTCAACTTCACAGCGAAGGATATTGG
771492 CCTCGAAACA
Statistics
Matches: 225, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
105 1 0.00
106 223 0.99
107 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAG
Found at i:773060 original size:2 final size:2
Alignment explanation
Indices: 773053--773101 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
773043 TTTTATTATT
773053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
773095 TA TA TA T
1 TA TA TA T
773102 TTGTGTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:773175 original size:32 final size:28
Alignment explanation
Indices: 773135--773204 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
773125 TTTTGAGTCT
773135 TTTATTTTACTATATATACGTGTATATATTTA
1 TTTATTTTA-TAT-TATA--TGTATATATTTA
*
773167 TTTATTTTATATTTTATGTATATATTTA
1 TTTATTTTATATTATATGTATATATTTA
* *
773195 ATTATATTAT
1 TTTATTTTAT
773205 TCTATTCGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 20 0.57
30 3 0.09
31 3 0.09
32 9 0.26
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (28 bp):
TTTATTTTATATTATATGTATATATTTA
Found at i:773326 original size:17 final size:17
Alignment explanation
Indices: 773304--773336 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
773294 TTTTTGTCTT
773304 TATTATT-TATATATATA
1 TATTATTGTAT-TATATA
773321 TATTATTGTATTATAT
1 TATTATTGTATTATAT
773337 TACATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTATTGTATTATATA
Found at i:779721 original size:23 final size:25
Alignment explanation
Indices: 779676--779721 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
779666 CCCATATTTT
* *
779676 AAAAAATTTAAATATAATTTTAATA
1 AAAAAATATAAATATAATATTAATA
779701 AAAAAATATAAAT-T-ATATTAA
1 AAAAAATATAAATATAATATTAA
779722 AAATTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 1 0.05
25 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAAAATATAAATATAATATTAATA
Found at i:779722 original size:20 final size:19
Alignment explanation
Indices: 779685--779724 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
779675 TAAAAAATTT
*
779685 AAATATAATTTTAATAAAA
1 AAATATAATTATAATAAAA
*
779704 AAATATAAATTATATTAAAA
1 AAATAT-AATTATAATAAAA
779724 A
1 A
779725 TTATATTCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATAATTATAATAAAA
Found at i:780813 original size:33 final size:33
Alignment explanation
Indices: 780766--780869 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
780756 ACAAAGTTTA
* * *
780766 CGAT-AATTGAAATACTTAAATACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTACAAGTT
*
780798 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTACAAGTT
780831 CGATAAATTCAAATACTTAAAAACTTACAAGTT
1 CGATAAATTCAAATACTTAAAAACTTACAAGTT
780864 CGATAA
1 CGATAA
780870 TTGAAACAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 4 0.06
33 63 0.94
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTACAAGTT
Found at i:783781 original size:23 final size:23
Alignment explanation
Indices: 783745--783800 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
783735 ATTTTGATCA
783745 AAAATATTATTTATTAAAATATTT
1 AAAATA-TATTTATTAAAATATTT
* *
783769 AAAATATATTTATTAATATTTTT
1 AAAATATATTTATTAAAATATTT
783792 AATAATATA
1 AA-AATATA
783801 ATATTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAAATATATTTATTAAAATATTT
Found at i:783786 original size:12 final size:12
Alignment explanation
Indices: 783747--783800 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
783737 TTTGATCAAA
783747 AATATTATTTATT
1 AATA-TATTTATT
* *
783760 AAAATATTTA-A
1 AATATATTTATT
783771 AATATATTTATT
1 AATATATTTATT
* *
783783 AATATTTTTAAT
1 AATATATTTATT
783795 AATATA
1 AATATA
783801 ATATTATATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 9 0.27
12 21 0.64
13 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATATTTATT
Found at i:783805 original size:23 final size:24
Alignment explanation
Indices: 783747--783817 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
783737 TTTGATCAAA
* * *
783747 AATATTATTTATTAAAATATTTAA-
1 AATA-TATATATTAATATTTTTAAT
*
783771 AATATATTTATTAATATTTTTAAT
1 AATATATATATTAATATTTTTAAT
*
783795 AATATA-ATATT-ATATTTTAAAT
1 AATATATATATTAATATTTTTAAT
783817 A
1 A
783818 TTATTACTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.26
23 21 0.50
24 10 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATATATATTAATATTTTTAAT
Done.