Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003252.1 Hibiscus syriacus cultivar Beakdansim tig00006835_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: 68337
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:83 original size:20 final size:20
Alignment explanation
Indices: 52--133 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
42 GTATGATGAT
52 TTATTTTAAAATATGGATTGA
1 TTATTTT-AAATATGGATTGA
*
73 TTATTTTAAATAATTTAGTATATATTGA
1 TTATTTTAAAT-A--T-G--GAT--TGA
101 TTTATTTTAAATATGGATTGA
1 -TTATTTTAAATATGGATTGA
122 TTATTTTAAATA
1 TTATTTTAAATA
134 ATTTATTAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
20 16 0.32
21 11 0.22
23 3 0.06
24 1 0.02
25 1 0.02
26 3 0.06
28 4 0.08
29 11 0.22
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
TTATTTTAAATATGGATTGA
Found at i:225 original size:30 final size:31
Alignment explanation
Indices: 202--287 Score: 113
Period size: 30 Copynumber: 2.8 Consensus size: 31
192 AAATAATTAT
202 AGTATCGATTGATTTATTTTAAATAATTTATT
1 AGTAT-GATTGATTTATTTTAAATAATTTATT
*
234 AGTAT-ATTGGTTTATTTTAAATAATTTATT
1 AGTATGATTGATTTATTTTAAATAATTTATT
* *
264 TGTATGGA-TGATTTATTTAAAATA
1 AGTAT-GATTGATTTATTTTAAATA
288 TGGATTGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 28 0.58
31 14 0.29
32 6 0.12
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (31 bp):
AGTATGATTGATTTATTTTAAATAATTTATT
Found at i:229 original size:61 final size:63
Alignment explanation
Indices: 16--287 Score: 239
Period size: 61 Copynumber: 4.8 Consensus size: 63
6 TTAAAATATG
16 GATTGATTTA-TTTAAATAATTTATTAGTAT-GA-TGATTTATTTT-AA-AA--TA-T-G---
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTAT
*
67 GATTGA-TTATTTTAAATAATTTAGTA-TAT--ATTGATTTATTTT--A-AA--TA-T-G---
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTAT
* * *
116 GATTGA-TTATTTTAAATAATTTATTAGTATGAATTAATTTATTTTAAATAATTTATTTGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTAT
*
178 GGATTGATTTA-TTTAAATAA-TTA-TAGTATCGATTGATTTATTTTAAATAATTTATTAGTAT
1 -GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTAT
* * *
239 -ATTGGTTTATTTTAAATAATTTATTTGTATGGA-TGATTTATTTAAAATA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATA
288 TGGATTGATT
Statistics
Matches: 190, Mismatches: 11, Indels: 30
0.82 0.05 0.13
Matches are distributed among these distances:
49 33 0.17
50 20 0.11
51 21 0.11
52 12 0.06
54 1 0.01
55 2 0.01
57 2 0.01
58 1 0.01
59 9 0.05
60 9 0.05
61 52 0.27
62 10 0.05
63 15 0.08
64 3 0.02
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (63 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTAT
Found at i:443 original size:31 final size:31
Alignment explanation
Indices: 408--466 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
398 AGTTGTATGG
* *
408 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
439 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
467 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:505 original size:16 final size:16
Alignment explanation
Indices: 484--526 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
474 GTTTAAAAAA
484 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
500 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
*
516 TCAATTTATTT
1 TCAGTTTATTT
527 TAGCAGTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.63
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:16826 original size:63 final size:63
Alignment explanation
Indices: 16748--16883 Score: 218
Period size: 63 Copynumber: 2.2 Consensus size: 63
16738 ATTCTAAGTA
* * * *
16748 GAGTGCATCGATGCATCCTCAATTAATTGAACATCGAATGTCGTTAGTGCATCGATGCATAAG
1 GAGTGCATCGATGCATCCTCAATTAAATGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
**
16811 GAGTGCATCGATGCATTTTCAATTAAATGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
1 GAGTGCATCGATGCATCCTCAATTAAATGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
16874 GAGTGCATCG
1 GAGTGCATCG
16884 GTGTACCTCC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (63 bp):
GAGTGCATCGATGCATCCTCAATTAAATGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
Found at i:16966 original size:24 final size:23
Alignment explanation
Indices: 16939--16996 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
16929 ATGCACAGTT
16939 AGTGCATCGATGCACACACTGTAG
1 AGTGCATCGATGCA-ACACTGTAG
*
16963 AGTGCATCGAT---ATACTGTAG
1 AGTGCATCGATGCAACACTGTAG
16983 AGTGCATCGATGCA
1 AGTGCATCGATGCA
16997 TACCTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 19 0.63
24 11 0.37
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (23 bp):
AGTGCATCGATGCAACACTGTAG
Found at i:17405 original size:30 final size:28
Alignment explanation
Indices: 17343--17406 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
17333 TATGAGTTAT
* *
17343 GTGATAAAGGTATGGAAATGATGTCTAT
1 GTGATAAAGGTATGAAAATGATGTCTAC
*
17371 GTGATAAAGGTATGAAAATAATATGTCTAC
1 GTGATAAAGGTATGAAAAT--GATGTCTAC
17401 GTGATA
1 GTGATA
17407 CAAATTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 18 0.58
30 13 0.42
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (28 bp):
GTGATAAAGGTATGAAAATGATGTCTAC
Found at i:17646 original size:23 final size:23
Alignment explanation
Indices: 17613--17680 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
17603 ATTATTATAT
*
17613 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* * **
17636 GGCACTCCGGTGCAATTTTACAT
1 GGCACTACGGTGCAATTATACGC
*
17659 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
17681 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:17775 original size:14 final size:14
Alignment explanation
Indices: 17756--17788 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17746 TCATGGGCTA
17756 GTGAACTTAAT-AAT
1 GTGAACTT-ATGAAT
17770 GTGAACTTATGAAT
1 GTGAACTTATGAAT
17784 GTGAA
1 GTGAA
17789 TTTGATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (14 bp):
GTGAACTTATGAAT
Found at i:24303 original size:30 final size:30
Alignment explanation
Indices: 24269--24330 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
24259 TTATATGAGT
* *
24269 TATGTGATAAAGGTATGTAAATGATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
24299 TATGTGATAAAGGTATGAAAATAATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
24329 TA
1 TA
24331 CATGATACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.35
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:24337 original size:30 final size:30
Alignment explanation
Indices: 24273--24337 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
24263 ATGAGTTATG
* * **
24273 TGATAAAGGTATGTAAATGATATGTCTATG
1 TGATAAAGGTATGAAAATAATATGTCTACA
24303 TGATAAAGGTATGAAAATAATATGTCTACA
1 TGATAAAGGTATGAAAATAATATGTCTACA
24333 TGATA
1 TGATA
24338 CAAACTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.34
Consensus pattern (30 bp):
TGATAAAGGTATGAAAATAATATGTCTACA
Found at i:24580 original size:23 final size:23
Alignment explanation
Indices: 24547--24614 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
24537 ATTATTATAT
24547 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
24570 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
24593 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
24615 AGTTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:24709 original size:14 final size:14
Alignment explanation
Indices: 24690--24722 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24680 TCATGGGCTA
24690 GTGAACTTAAT-AAT
1 GTGAACTT-ATGAAT
24704 GTGAACTTATGAAT
1 GTGAACTTATGAAT
24718 GTGAA
1 GTGAA
24723 TTTGATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (14 bp):
GTGAACTTATGAAT
Found at i:25440 original size:32 final size:32
Alignment explanation
Indices: 25390--25487 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 32
25380 TTGAGCATAG
* * * *
25390 GAGCCAATCTAAGGGAGTACCTTGGGGCCTTA
1 GAGCCTATCAAAGAGAGTACCTTGGGGCCTAA
* **
25422 GAGCCTATCCAAGAGAGTACCTT-GAACCTAA
1 GAGCCTATCAAAGAGAGTACCTTGGGGCCTAA
*
25453 AAGCCTACTCAAAGA-AGTACCTTGGGGCCTAA
1 GAGCCTA-TCAAAGAGAGTACCTTGGGGCCTAA
25485 GAG
1 GAG
25488 TATACCCATG
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 19 0.36
32 34 0.64
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (32 bp):
GAGCCTATCAAAGAGAGTACCTTGGGGCCTAA
Found at i:27492 original size:17 final size:17
Alignment explanation
Indices: 27472--27506 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27462 ATAAAATATG
27472 ACTTTTCGAAAAAGTTA
1 ACTTTTCGAAAAAGTTA
* *
27489 ACTTTTGGTAAAAGTTA
1 ACTTTTCGAAAAAGTTA
27506 A
1 A
27507 TGTTGGTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (17 bp):
ACTTTTCGAAAAAGTTA
Found at i:27518 original size:16 final size:17
Alignment explanation
Indices: 27481--27524 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
27471 GACTTTTCGA
*
27481 AAAAGTTAACTTTTGGT
1 AAAAGTTAACTGTTGGT
27498 AAAAGTTAA-TGTTGGT
1 AAAAGTTAACTGTTGGT
* *
27514 CAAAGTCAACT
1 AAAAGTTAACT
27525 CTGATCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (17 bp):
AAAAGTTAACTGTTGGT
Found at i:30119 original size:26 final size:26
Alignment explanation
Indices: 30087--30147 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
30077 CCAAGGCTCT
* *
30087 TCTTTAATTCTAGGACTTTCCTAGCT
1 TCTTTAATTCTAAGACTTTCCTAGCC
*
30113 TTTTTAATTCTAAGACTTTCCTAGCC
1 TCTTTAATTCTAAGACTTTCCTAGCC
30139 TCTTTAATT
1 TCTTTAATT
30148 TGTTTTTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.49
Consensus pattern (26 bp):
TCTTTAATTCTAAGACTTTCCTAGCC
Found at i:30980 original size:36 final size:35
Alignment explanation
Indices: 30909--31105 Score: 261
Period size: 36 Copynumber: 5.5 Consensus size: 35
30899 ATGAACACTC
* * * *
30909 GAATCGAAAGTGCGATACATCCTTCCGTTCAACTT
1 GAATCGGAAGTGCGATGCTTCCTTCCGTTCGACTT
*
30944 GAATCGGAAGTGCTGATGCTTCATTCCGTTCGACTT
1 GAATCGGAAGTGC-GATGCTTCCTTCCGTTCGACTT
* *
30980 GAATCGAAAGTGCCGATGCTTCCCTCCGTTCGACTT
1 GAATCGGAAGTG-CGATGCTTCCTTCCGTTCGACTT
* *
31016 GAATCGGGAGTGCCGACGCTTTCC-TCCGTTCGACTT
1 GAATCGGAAGTG-CGATGC-TTCCTTCCGTTCGACTT
31052 GAATCGGAAGTGTCGATGCTTCCTTCCGTTCGACTT
1 GAATCGGAAGTG-CGATGCTTCCTTCCGTTCGACTT
31088 GAATCGGAAGTGCGATGC
1 GAATCGGAAGTGCGATGC
31106 ATTCTTTCGT
Statistics
Matches: 144, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
35 22 0.15
36 117 0.81
37 5 0.03
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (35 bp):
GAATCGGAAGTGCGATGCTTCCTTCCGTTCGACTT
Found at i:32884 original size:29 final size:29
Alignment explanation
Indices: 32841--32898 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
32831 AATAAACGAC
*
32841 ATATTCTCTGCTTTATTTTTCATTATGAT
1 ATATTCTCTGCTTTATTTTTCAATATGAT
*
32870 ATATTCTCTGTTTTATTTTTCAATATGAT
1 ATATTCTCTGCTTTATTTTTCAATATGAT
32899 GAACTGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (29 bp):
ATATTCTCTGCTTTATTTTTCAATATGAT
Found at i:38091 original size:40 final size:39
Alignment explanation
Indices: 38010--38153 Score: 189
Period size: 39 Copynumber: 3.6 Consensus size: 39
38000 TACTCTAGAT
* * * * *
38010 ATTTCAAATTATTATATAATTTTAAAAAATTTCATTGAG
1 ATTTTAAATTATTATATAATATTAAAAAAATTAAATGAG
38049 ATTTTAAATTATTATATAATATTAAAAAAATTAAATGTAG
1 ATTTTAAATTATTATATAATATTAAAAAAATTAAATG-AG
* * *
38089 ATTTTAAATTATTATATAATTTTAAAAAACTTAAATGAT
1 ATTTTAAATTATTATATAATATTAAAAAAATTAAATGAG
*
38128 ATTTTAAATTATTATAATTATATTAA
1 ATTTTAAATTATTAT-ATAATATTAA
38154 TTACAAGTTA
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 48 0.52
40 45 0.48
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (39 bp):
ATTTTAAATTATTATATAATATTAAAAAAATTAAATGAG
Found at i:38104 original size:79 final size:82
Alignment explanation
Indices: 38005--38153 Score: 232
Period size: 79 Copynumber: 1.9 Consensus size: 82
37995 GTTAGTACTC
* * *
38005 TAGATATTTCAAATTATTATATAATTTTAAAAAATTTCATTGAGATTTTAAATTATTAT-ATAAT
1 TAGATATTTCAAATTATTATATAATTTTAAAAAACTTAAATGAGATTTTAAATTATTATAATAAT
38069 ATTAAAAAAATTAAATG
66 ATTAAAAAAATTAAATG
* *
38086 TAGAT-TTT-AAATTATTATATAATTTTAAAAAACTTAAATGATATTTTAAATTATTATAATTAT
1 TAGATATTTCAAATTATTATATAATTTTAAAAAACTTAAATGAGATTTTAAATTATTATAATAAT
38149 ATTAA
66 ATTAA
38154 TTACAAGTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
79 45 0.73
80 12 0.19
81 5 0.08
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (82 bp):
TAGATATTTCAAATTATTATATAATTTTAAAAAACTTAAATGAGATTTTAAATTATTATAATAAT
ATTAAAAAAATTAAATG
Found at i:38758 original size:2 final size:2
Alignment explanation
Indices: 38751--38815 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
38741 TTGTTTGCTT
38751 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
38793 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
38816 TTGAAAATGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38916 original size:36 final size:35
Alignment explanation
Indices: 38796--39075 Score: 187
Period size: 36 Copynumber: 7.6 Consensus size: 35
38786 ATATATATAT
* **
38796 ATATATATATATATATATATTTGAAAATGTTTTAGAAA
1 ATATATATAT-TATATAT-TTTTAAAACATTTT-GAAA
* *
38834 A-ATATAGTA-TATA-ATTTCCATAAATCAGTTTTCGAAA
1 ATATATA-TATTATATATTT--TTAAAACA-TTTT-GAAA
* *
38871 ATA-AGTATATTATATGATTTTTGAAATCATTTTTAAA
1 ATATA-TATATTATAT-ATTTTT-AAAACATTTTGAAA
*
38908 TATATATATATAATATATAGTTTTAAAAACATGTTTGAAA
1 -ATATATATAT--TATATA-TTTTTAAAACAT-TTTGAAA
38948 ATATTTATATATTATATAATTTTTAAAACATTTTGAAA
1 ATA--TATATATTATAT-ATTTTTAAAACATTTTGAAA
* ** *
38986 ATAAATATAACATATAGTTTTTAAAACATTTTTAAA
1 ATATATATATTATATA-TTTTTAAAACATTTTGAAA
* *
39022 A-ATATATATTATATAATTTTTAAAATATTTTGGAA
1 ATATATATATTATAT-ATTTTTAAAACATTTTGAAA
*
39057 ATATATA-A-TACATATTTTT
1 ATATATATATTATATATTTTT
39076 TCAAAGTTTT
Statistics
Matches: 197, Mismatches: 23, Indels: 49
0.73 0.09 0.18
Matches are distributed among these distances:
33 6 0.03
34 6 0.03
35 31 0.16
36 41 0.21
37 20 0.10
38 33 0.17
39 33 0.17
40 20 0.10
41 7 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (35 bp):
ATATATATATTATATATTTTTAAAACATTTTGAAA
Found at i:39059 original size:71 final size:71
Alignment explanation
Indices: 38876--39106 Score: 225
Period size: 71 Copynumber: 3.2 Consensus size: 71
38866 CGAAAATAAG
* * * * *
38876 TATATTATATGATTTTTGAAATCATTTTTAAATATATATATATAATATATAGTTTTAAAAACATG
1 TATATTATATAATTTTTAAAAT-ATTTTGAAA-ATA-A-ATATAACATATAGTTTTTAAAACAT-
*
38941 TTTGAAAATATTTA
61 TTTTAAAA-A--TA
*
38955 TATATTATATAATTTTTAAAACATTTTGAAAATAAATATAACATATAGTTTTTAAAACATTTTTA
1 TATATTATATAATTTTTAAAATATTTTGAAAATAAATATAACATATAGTTTTTAAAACATTTTTA
39020 AAAATA
66 AAAATA
* * ***
39026 TATATTATATAATTTTTAAAATATTTTGGAAATATATA-ATACATAT--TTTTTCAAAGTTTTTT
1 TATATTATATAATTTTTAAAATATTTTGAAAATAAATATA-ACATATAGTTTTT-AAAACATTTT
* *
39088 TGAAAGTA
64 TAAAAATA
39096 TATATTATATA
1 TATATTATATA
39107 GTTTGAAAAA
Statistics
Matches: 135, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
69 5 0.04
70 25 0.19
71 43 0.32
73 1 0.01
74 7 0.05
75 23 0.17
76 1 0.01
77 3 0.02
78 8 0.06
79 19 0.14
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (71 bp):
TATATTATATAATTTTTAAAATATTTTGAAAATAAATATAACATATAGTTTTTAAAACATTTTTA
AAAATA
Found at i:39190 original size:21 final size:22
Alignment explanation
Indices: 39166--39209 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
39156 ATATATTTGT
39166 TTTTTTA-TATTATTTGTTCTA
1 TTTTTTATTATTATTTGTTCTA
* *
39187 -TTTTTATTTTTATTTGTTTTA
1 TTTTTTATTATTATTTGTTCTA
39208 TT
1 TT
39210 AATTTTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 6 0.32
21 12 0.63
22 1 0.05
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTTTTATTATTATTTGTTCTA
Found at i:40323 original size:20 final size:20
Alignment explanation
Indices: 40278--40323 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
40268 TATTTTATTT
40278 TATTTATTTATTATTATCATG
1 TATTT-TTTATTATTATCATG
*
40299 T-TTTTTTAATTATTATTA-G
1 TATTTTTT-ATTATTATCATG
40318 TATTTT
1 TATTTT
40324 ATTTACCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TATTTTTTATTATTATCATG
Found at i:40598 original size:13 final size:13
Alignment explanation
Indices: 40580--40609 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40570 CGAACCGAAT
40580 TTTTAAATTTTAA
1 TTTTAAATTTTAA
40593 TTTTAAATTTTAA
1 TTTTAAATTTTAA
40606 TTTT
1 TTTT
40610 CGCAACTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:42386 original size:125 final size:125
Alignment explanation
Indices: 42164--42415 Score: 495
Period size: 125 Copynumber: 2.0 Consensus size: 125
42154 CAGAATATTC
*
42164 TTGTCTCTTAAAAGATAAAACACTTTTGTCCCCAATAAGGATTATTTTTAATAACATATACATTT
1 TTGTCTCTTAAAAGATAAAACACTTTTGTCCCCAATAAGGATTATTTTTAATAACAGATACATTT
42229 TTGGATTAATGCCTCGATCATTTCATGCATCATATATTTAGACATTTAGACATTTTGCAT
66 TTGGATTAATGCCTCGATCATTTCATGCATCATATATTTAGACATTTAGACATTTTGCAT
42289 TTGTCTCTTAAAAGATAAAACACTTTTGTCCCCAATAAGGATTATTTTTAATAACAGATACATTT
1 TTGTCTCTTAAAAGATAAAACACTTTTGTCCCCAATAAGGATTATTTTTAATAACAGATACATTT
42354 TTGGATTAATGCCTCGATCATTTCATGCATCATATATTTAGACATTTAGACATTTTGCAT
66 TTGGATTAATGCCTCGATCATTTCATGCATCATATATTTAGACATTTAGACATTTTGCAT
42414 TT
1 TT
42416 TTATTTTCTT
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (125 bp):
TTGTCTCTTAAAAGATAAAACACTTTTGTCCCCAATAAGGATTATTTTTAATAACAGATACATTT
TTGGATTAATGCCTCGATCATTTCATGCATCATATATTTAGACATTTAGACATTTTGCAT
Found at i:42440 original size:19 final size:18
Alignment explanation
Indices: 42407--42450 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
42397 ATTTAGACAT
42407 TTTGCA-TTTTTATTTTC
1 TTTGCATTTTTTATTTTC
42424 TTTGCATTTTGTTATTTTC
1 TTTGCATTTT-TTATTTTC
42443 TTTGCATT
1 TTTGCATT
42451 CACATTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 6 0.24
18 3 0.12
19 16 0.64
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.68
Consensus pattern (18 bp):
TTTGCATTTTTTATTTTC
Found at i:46051 original size:84 final size:82
Alignment explanation
Indices: 45881--47352 Score: 1416
Period size: 84 Copynumber: 17.8 Consensus size: 82
45871 AGCTCAAGGT
* * * *
45881 GAGAAGGGCTATCTG--CCAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCACATCAT
1 GAGAAGGGTTATCTGCACCAAAGA-CCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCAT
* ** *
45943 TTACAGCATAACCCAAGGC
64 TTGCAGCATAACTTAAGTC
* * * * *
45962 TAGAAGAGTTATATGTCACCAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAT
1 GAGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
* *
46027 TTACAGCATAGCTTAAGTC
64 TTGCAGCATAACTTAAGTC
* ** * * *
46046 GAGAAGGGCTATCTG--CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 GAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATT
* * *
46109 TACAGCATAACTCAAGGC
65 TGCAGCATAACTTAAGTC
* * * * *
46127 TAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
1 GAGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
*
46192 TTGCAGCATAGCTTAAGTC
64 TTGCAGCATAACTTAAGTC
* ** * * *
46211 GAGAAGGGCTATCTG--CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 GAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATT
46274 TGCAGCATAACTTAAGTC
65 TGCAGCATAACTTAAGTC
* *
46292 GAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCAT
1 GAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
* *
46357 TTGCAACACAACTTAAGTC
64 TTGCAGCATAACTTAAGTC
* * * *
46376 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCA
1 GAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCA
* * *
46440 TTCGCAGCATAGCTTAACTC
63 TTTGCAGCATAACTTAAGTC
* ** * * * *
46460 GAGAAGGGCTATCTG--CCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATT
1 GAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATT
* * *
46523 TACAGCATAACTCAAGGC
65 TGCAGCATAACTTAAGTC
* * * * * **
46541 TAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGATTACGCTCAGCATAAAAGGCACATCA
1 GAGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCA
*
46606 TTTGCAGCATAGCTTAAGTC
63 TTTGCAGCATAACTTAAGTC
* * ** * * * *
46626 GATAAGGGCTATCTG--CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATT
1 GAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATT
46689 TGCAGCATAACTTAAGTC
65 TGCAGCATAACTTAAGTC
* * * * *
46707 GAAAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTGCGCTCAGCTCCAAGGCACATCAT
1 GAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
**
46772 TTGCAGCATAGTTTAAGTC
64 TTGCAGCATAACTTAAGTC
* ** * *
46791 GAGAAGGGCTATCTG--CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATT
1 GAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCATT
* * *
46854 TACAGCATAACTCAAGGC
65 TGCAGCATAACTTAAGTC
* * * * *
46872 TAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
1 GAGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
*
46937 TTGCAGCATAGCTTAAGTC
64 TTGCAGCATAACTTAAGTC
* ** * ** *
46956 GAGAAGGGCTATCTG--CCAAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATT
1 GAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATT
47019 TGCAGCATAACTTAAGTC
65 TGCAGCATAACTTAAGTC
* *
47037 GAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCAT
1 GAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
* *
47102 TTGCAACACAACTTAAGTC
64 TTGCAGCATAACTTAAGTC
* *
47121 GAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCAT
1 GAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
* *
47186 TTGCAACACAACTTAAGTC
64 TTGCAGCATAACTTAAGTC
* * * * *
47205 TAGAAGGGTTGTCTGCTAACAAAAGACCTTTGAGTTCGACTACACTCAGCT-CAACGACACATCA
1 GAGAAGGGTTATCTGC--ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCA
* * * *
47269 TTTACAGTATAACTCAAGGC
63 TTTGCAGCATAACTTAAGTC
* * * *
47289 GAGAAGGGTTATCTGTTA-CAAAGACATTCGAGTTCGACTACGA-TCAGCTCCATGACACATCAT
1 GAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTAC-ACTCAGCTCCAAGGCACATCAT
47352 T
64 T
47353 CACTACTGTT
Statistics
Matches: 1154, Mismatches: 196, Indels: 81
0.81 0.14 0.06
Matches are distributed among these distances:
80 127 0.11
81 287 0.25
82 40 0.03
83 11 0.01
84 470 0.41
85 219 0.19
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (82 bp):
GAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTC
Found at i:46153 original size:165 final size:165
Alignment explanation
Indices: 45881--47352 Score: 1438
Period size: 165 Copynumber: 8.9 Consensus size: 165
45871 AGCTCAAGGT
* * * * * *
45881 GAGAAGGGCTATCTG-CC-AAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCACATCATT
1 GAGAAGGGTTATCTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATT
* ** * * * * *
45944 TACAGCATAACCCAAGGCTAGAAGAGTTATATGTCACCAAAAGACCTTCGAGTTCGATTACACTC
65 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTACACTC
* * *
46009 AGCTCAAAGGCACATCATTTACAGCATAGCTTAAGTC
129 AGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *** * * * *
46046 GAGAAGGGCTATCTG-CC-AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 GAGAAGGGTTATCTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATT
* * * * * * * *
46109 TACAGCATAACTCAAGGCTAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTC
65 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTACACTC
*
46174 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
129 AGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *** * * * *
46211 GAGAAGGGCTATCTG-CC-AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 GAGAAGGGTTATCTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATT
** * *
46274 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
65 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGATTACACTC
* * *
46339 AGCTCCAAGGCATATCATTTGCAACACAACTTAAGTC
129 AGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * *
46376 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCAT
1 GAGAAGGGTTATCTG--ACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCAT
* * * * ** *
46441 TCGCAGCATAGCTTAACTCGAGAAGGGCTATC--TG-CCAAAGACCCCCGAGTTTGATTACACTC
64 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACACTC
* * * * *
46503 AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGC
129 AGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * *
46541 TAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGATTACGCTCAGCATAAAAGGCACATCA
1 GAGAAGGGTTATC--TGACCAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAAAGGCACATCA
* * * **
46606 TTTGCAGCATAGCTTAAGTCGATAAGGGCTATC--TG-CCAAAGACCCCCGAGTTCGATTACACT
63 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACACT
* * *
46668 CAGCTTCGAGGGCATATCATTTGCAGCATAACTTAAGTC
128 CAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * * *
46707 GAAAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTGCGCTCAGCTCCAAGGCACATCAT
1 GAGAAGGGTTATCTG--ACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCAT
** * **
46772 TTGCAGCATAGTTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCCCGAGTTCGATTACACTC
64 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACACTC
* * * *
46834 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGC
129 AGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTC
* * *
46872 TAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
1 GAGAAGGGTTATC--TGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCAT
* * **
46937 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCCCGAGTTCGATTACACTC
64 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACACTC
** *
46999 AGCTTTGAGGGCACATCATTTGCAGCATAACTTAAGTC
129 AGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * *
47037 GAGAAGGGTTATCTG-CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA
1 GAGAAGGGTTATCTGACC-A--AAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
* * ** * *
47101 TTTGCAACACAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGC
63 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGATTACAC
* * *
47166 TCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTC
127 TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * * * * *
47205 TAGAAGGGTTGTCTGCTAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCAACGACACATCAT
1 GAGAAGGGTTATCTG--ACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCAT
* * * * * * *
47270 TTACAGTATAACTCAAGGCGAGAAGGGTTATCTGTTA-CAAAGACATTCGAGTTCGACTACGA-T
64 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTAC-ACT
* *
47333 CAGCTCCATGACACATCATT
128 CAGCTCCAAGGCACATCATT
47353 CACTACTGTT
Statistics
Matches: 1145, Mismatches: 136, Indels: 51
0.86 0.10 0.04
Matches are distributed among these distances:
162 2 0.00
163 3 0.00
164 30 0.03
165 711 0.62
166 192 0.17
167 5 0.00
168 149 0.13
169 51 0.04
170 1 0.00
171 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (165 bp):
GAGAAGGGTTATCTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTT
GCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACACTCAG
CTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
Found at i:47352 original size:745 final size:745
Alignment explanation
Indices: 45860--47336 Score: 2370
Period size: 745 Copynumber: 2.0 Consensus size: 745
45850 TAAACAAACT
* **
45860 ATTTGCAGCTTAGCTCAAGGTGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTCAAGGTGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * *
45925 GCTTCAAGGGCACATCATTTACAGCATAACCCAAGGCTAGAAGAGTTATATGTCACCAAAAGACC
66 GCTTCAAGGGCACATCATTTACAGCATAACCCAAGGCGAAAAGAGTTATATGCCAACAAAAGACC
*
45990 TTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGC
131 TTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGC
*
46055 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
196 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAAC
46120 TCAAGGCTAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
261 TCAAGGCTAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
46185 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
326 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
46250 ACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA
391 ACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA
*
46315 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCTAGA
456 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCGAGA
*
46380 AGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTCGC
521 AGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTCGC
* * * * * *
46445 AGCATAGCTTAACTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCAGCTTCG
586 AACACAACTTAACTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAGCTTCA
* * * * *
46510 AGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAG
651 ACGACACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACCAAAAGACATTCGAG
* * *
46575 TTCGATTACGCTCAGCATAAAAGGCACATC
716 TTCGACTACGATCAGCATAAAAGACACATC
* * *
46605 ATTTGCAGCATAGCTTAA-GTCGATAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTCAAGGT-GAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTC
* * * ** * * *
46669 AGCTTCGAGGGCATATCATTTGCAGCATAACTTAAGTCGAAAAGGGTTATCTGCCAACAAAAGAC
65 AGCTTCAAGGGCACATCATTTACAGCATAACCCAAGGCGAAAAGAGTTATATGCCAACAAAAGAC
* * * * * *
46734 CTTTGAGTTCGACTGCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGTTTAAGTCGAGAAGGG
130 CTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGG
46799 CTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAA
195 CTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAA
46864 CTCAAGGCTAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
260 CTCAAGGCTAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
46929 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
325 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
*
46994 CACTCAGCTTTGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
390 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
47059 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCGAG
455 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCGAG
* * *
47124 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTT
520 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTC
* * * * ***
47188 GCAACACAACTTAAGTCTAGAAGGGTTGTCTGCTAACAAAAGACCTTTGAGTTCGACTACACTCA
584 GCAACACAACTTAACTCGAGAAGGGCTATCTGC---C-AAAGACCCCCGAGTTCGACTACACTCA
* *
47253 GC-TCAACGACACATCATTTACAGTATAACTCAAGGCGAGAAGGGTTATCTGTTA-C-AAAGACA
645 GCTTCAACGACACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACCAAAAGACA
47315 TTCGAGTTCGACTACGATCAGC
710 TTCGAGTTCGACTACGATCAGC
47337 TCCATGACAC
Statistics
Matches: 672, Mismatches: 54, Indels: 11
0.91 0.07 0.01
Matches are distributed among these distances:
744 2 0.00
745 570 0.85
746 28 0.04
747 1 0.00
748 47 0.07
749 24 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (745 bp):
ATTTGCAGCATAGCTCAAGGTGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
GCTTCAAGGGCACATCATTTACAGCATAACCCAAGGCGAAAAGAGTTATATGCCAACAAAAGACC
TTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGC
TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAAC
TCAAGGCTAGGAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
ACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA
AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCGAGA
AGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTCGC
AACACAACTTAACTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAGCTTCA
ACGACACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACCAAAAGACATTCGAG
TTCGACTACGATCAGCATAAAAGACACATC
Found at i:47854 original size:2 final size:2
Alignment explanation
Indices: 47847--47897 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
47837 TTGTTTGCTT
* * **
47847 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TG TA TA TA CG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47889 TA TA -A TA TA
1 TA TA TA TA TA
47898 ATCTTTGAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:48032 original size:75 final size:72
Alignment explanation
Indices: 47953--48137 Score: 228
Period size: 75 Copynumber: 2.5 Consensus size: 72
47943 ATCAGTTTTC
* * * * *
47953 GAAAATAAGTATATTATATGATTTTTGAAACCATTTTTAAATATATATATAATATATAGTTTTGA
1 GAAAATAA-TATATTATATAATTTTT-AAAACATTTTGAAA-ATAAATATAACATATAGTTTTGA
48018 AAACATGTTT
63 AAACATGTTT
*
48028 GAAAATATTTATATATTATATAATTTTTAAAACATTTTGAAAATAAATATAACATATAGTTTTTA
1 GAAAATA---ATATATTATATAATTTTTAAAACATTTTGAAAATAAATATAACATATAGTTTTGA
*
48093 AAACATTTTT
63 AAACATGTTT
* *
48103 AAAAAT-ATATATTATATAATTTTTAAAATATTTTG
1 GAAAATAATATATTATATAATTTTTAAAACATTTTG
48138 GAAACATATA
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
71 28 0.29
75 41 0.42
76 12 0.12
77 16 0.16
78 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (72 bp):
GAAAATAATATATTATATAATTTTTAAAACATTTTGAAAATAAATATAACATATAGTTTTGAAAA
CATGTTT
Found at i:49395 original size:23 final size:22
Alignment explanation
Indices: 49357--49412 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
49347 ATTCTTATTT
* *
49357 TATTTTATTTATTTATTATTA-
1 TATTTTTTTTAATTATTATTAG
49378 TCATGTTTTTTTAATTATTATTAG
1 T-AT-TTTTTTTAATTATTATTAG
49402 TATTTTTTTTA
1 TATTTTTTTTA
49413 CCTCATATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 18 0.60
24 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
TATTTTTTTTAATTATTATTAG
Found at i:49407 original size:20 final size:20
Alignment explanation
Indices: 49362--49409 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
49352 TATTTTATTT
49362 TATTTATTTATTATTATCATG
1 TATTT-TTTATTATTATCATG
*
49383 T-TTTTTTAATTATTATTA-G
1 TATTTTTT-ATTATTATCATG
49402 TATTTTTT
1 TATTTTTT
49410 TTACCTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TATTTTTTATTATTATCATG
Found at i:49510 original size:5 final size:5
Alignment explanation
Indices: 49469--49510 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
49459 TTAATACTTC
* *
49469 TTTAT TTT-T TTTAT TTAAT TTTAAT TTTAT TGTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT TT
49511 CTTTGGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:49682 original size:13 final size:13
Alignment explanation
Indices: 49664--49693 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
49654 CGAACCGAAT
49664 TTTTAAATTTCAA
1 TTTTAAATTTCAA
*
49677 TTTTAAATTTTAA
1 TTTTAAATTTCAA
49690 TTTT
1 TTTT
49694 CGCAACTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAAATTTCAA
Found at i:50403 original size:20 final size:20
Alignment explanation
Indices: 50368--50405 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50358 TATAAATCCA
50368 CATATTATTTTGTATCAAAT
1 CATATTATTTTGTATCAAAT
50388 CATATATATTTT-TATCAA
1 CATAT-TATTTTGTATCAA
50406 CATAGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (20 bp):
CATATTATTTTGTATCAAAT
Found at i:55552 original size:38 final size:38
Alignment explanation
Indices: 55509--55604 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
55499 TACGAGACAT
* * *
55509 ATGATAGGTCTTTCGGGACACATATTACATCCTTCGAG
1 ATGATAGGTCATTCGGGACACAGATGACATCCTTCGAG
* *
55547 ATGATAGGTCATTCGGGACACAGATGACATCCTTTGGG
1 ATGATAGGTCATTCGGGACACAGATGACATCCTTCGAG
*
55585 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCATTCGGGACA
55605 TAGTTTATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (38 bp):
ATGATAGGTCATTCGGGACACAGATGACATCCTTCGAG
Done.