Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004819.1 Hibiscus syriacus cultivar Beakdansim tig00010861_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: 83788
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:11382 original size:11 final size:11
Alignment explanation
Indices: 11366--11423 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
11356 AGGTAACCTA
*
11366 TTTCGTTTTAT
1 TTTCATTTTAT
* *
11377 TTTCGTTTTTAA
1 TTTC-ATTTTAT
11389 TTTCATTTTAT
1 TTTCATTTTAT
11400 TTTCATTTTAAT
1 TTTCATTTT-AT
11412 TTTC--TTTAT
1 TTTCATTTTAT
11421 TTT
1 TTT
11424 TAGCAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 5 0.12
10 3 0.07
11 18 0.44
12 15 0.37
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:11397 original size:23 final size:22
Alignment explanation
Indices: 11365--11413 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
11355 GAGGTAACCT
* *
11365 ATTTCGTTTTATTTTCGTTTTTA
1 ATTTCATTTTATTTTC-ATTTTA
11388 ATTTCATTTTATTTTCATTTTA
1 ATTTCATTTTATTTTCATTTTA
11410 ATTT
1 ATTT
11414 TCTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.69
Consensus pattern (22 bp):
ATTTCATTTTATTTTCATTTTA
Found at i:11415 original size:23 final size:22
Alignment explanation
Indices: 11365--11423 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
11355 GAGGTAACCT
*
11365 ATTTCGTTTTATTTTCGTTTTTA
1 ATTTC-TTTTATTTTCGATTTTA
11388 ATTTCATTTTATTTTC-ATTTTA
1 ATTTC-TTTTATTTTCGATTTTA
11410 ATTT-TCTTTATTTT
1 ATTTCT-TTTATTTT
11424 TAGCAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 8 0.24
22 9 0.27
23 15 0.45
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.71
Consensus pattern (22 bp):
ATTTCTTTTATTTTCGATTTTA
Found at i:13959 original size:29 final size:29
Alignment explanation
Indices: 13914--13990 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
13904 CCGTTGACCA
*
13914 GGTGCTATTTTGAGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
13943 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* *
13972 GCTGCTATTTTGGTAATTA
1 GGTGCTATTTTGGGAATTA
13991 TTTTAAAAAA
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:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATG
Found at i:14006 original size:29 final size:28
Alignment explanation
Indices: 13913--14010 Score: 88
Period size: 29 Copynumber: 3.4 Consensus size: 28
13903 ACCGTTGACC
* * *
13913 AGGTGCTATTTTGAGAATTAATTCGAAAT
1 AGGTGCTATTTTGGGAATTAATT-AAAAA
* **
13942 GGGTGCTATTTTGGGAATTAATTCGAAA
1 AGGTGCTATTTTGGGAATTAATTAAAAA
* * *
13970 TGGCTGCTATTTTGGTAATTATTTTAAAAA
1 AGG-TGCTATTTTGGGAATTA-ATTAAAAA
14000 AGGTGCTATTT
1 AGGTGCTATTT
14011 CTGTAAAATG
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 4 0.07
29 45 0.80
30 7 0.12
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (28 bp):
AGGTGCTATTTTGGGAATTAATTAAAAA
Found at i:14989 original size:42 final size:41
Alignment explanation
Indices: 14942--15107 Score: 260
Period size: 42 Copynumber: 4.0 Consensus size: 41
14932 GAAGTATTAT
* *
14942 CAGGTCCCTTTGTTGTGTACGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
14984 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
15026 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
*
15068 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
15108 TCCTAGTCTC
Statistics
Matches: 117, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
41 4 0.03
42 113 0.97
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:16829 original size:41 final size:42
Alignment explanation
Indices: 16776--16857 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 42
16766 AAAAAAAGTC
*
16776 AAATTTCATTGTTTCGAAAATAGAAA-AAAGAGAAAAAGAAA
1 AAATTTCATTGTTTCGAAAATAGAAAGAAAAAGAAAAAGAAA
* * *
16817 AAATATTC-TTGTTTTGAATATAGAAAGAAAAAGAAGAAGAA
1 AAAT-TTCATTGTTTCGAAAATAGAAAGAAAAAGAAAAAGAA
16858 GGAAAATCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (42 bp):
AAATTTCATTGTTTCGAAAATAGAAAGAAAAAGAAAAAGAAA
Found at i:17832 original size:73 final size:73
Alignment explanation
Indices: 17737--17876 Score: 226
Period size: 73 Copynumber: 1.9 Consensus size: 73
17727 TTATTTTAAA
* * *
17737 TATTATATTTTATCTTTGTTTTAGGTAGTTTAGTTTAAATAGCTTTAAGTGTTTTAATTAGGATT
1 TATTATATCTTATCCTTGTTTTAGGTAGTTTAGTTTAAATAGCTTTAAGTATTTTAATTAGGATT
17802 TAGGATAT
66 TAGGATAT
* * *
17810 TATTTTATCTTATCCTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
1 TATTATATCTTATCCTTGTTTTAGGTAGTTTAGTTTAAATAGCTTTAAGTATTTTAATTAGGATT
17875 TA
66 TA
17877 TTGTTTCTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (73 bp):
TATTATATCTTATCCTTGTTTTAGGTAGTTTAGTTTAAATAGCTTTAAGTATTTTAATTAGGATT
TAGGATAT
Found at i:23539 original size:22 final size:22
Alignment explanation
Indices: 23484--23539 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
23474 TTTCTCTTTT
*
23484 CTTTTCTATTTTTGTTTCAATTC
1 CTTTTCT-TTTTTGTTTCAATCC
*
23507 TTTTTC-TTTTTGTTTTC-ATCC
1 CTTTTCTTTTTTG-TTTCAATCC
23528 CTTTTCTTTTTT
1 CTTTTCTTTTTT
23540 CTTCTACCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 14 0.50
22 9 0.32
23 5 0.18
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (22 bp):
CTTTTCTTTTTTGTTTCAATCC
Found at i:24405 original size:44 final size:44
Alignment explanation
Indices: 24261--24409 Score: 169
Period size: 44 Copynumber: 3.4 Consensus size: 44
24251 TCTGGTGCTA
*
24261 ATCCAACTTCTTATGTGATGGAATCGAGCGAAAAATATAATGTTG
1 ATCCAACTCCTTATGTGATGGAATCGAGCGAAAAAT-TAATGTTG
** * *
24306 GGCCAACTCCTTATGTGATGG-A-CGAGCGAAACGA-TGATGTTG
1 ATCCAACTCCTTATGTGATGGAATCGAGCGAAA-AATTAATGTTG
** * * *
24348 ATCCAACTCCTTATGTGATGGAATAAAGTGAAATATTCATGTTG
1 ATCCAACTCCTTATGTGATGGAATCGAGCGAAAAATTAATGTTG
24392 ATCCAACTCCTTATGTGA
1 ATCCAACTCCTTATGTGA
24410 AGGATTTGAA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 26 0.30
43 11 0.12
44 33 0.38
45 18 0.20
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (44 bp):
ATCCAACTCCTTATGTGATGGAATCGAGCGAAAAATTAATGTTG
Found at i:25996 original size:54 final size:53
Alignment explanation
Indices: 25938--26535 Score: 671
Period size: 54 Copynumber: 11.1 Consensus size: 53
25928 TTTTTTTAAA
* * * * *
25938 AAAATTCATTTGAAGATATTAAGAAACCCCTAAAAATCAGGCTTATCTTCTTT
1 AAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
* * * * * * *
25991 CAAAATCCATTTGTAAACATAAAAAAACCCTTGAAAATTAGGCTTAGCTCCTTTT
1 -AAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCC-TTT
* * *
26046 AAAATTCATTTGAAAACATCAAAAAACCCTTAAAAATTAGGCTTAGCTCCTTT
1 AAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
* * * **
26099 AAACATTCATTTGAAAACATCAAGAAACCCTTAAAAATTAGGCGTAGCTTATTT
1 AAA-ATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
* *
26153 CAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATTAGGCTTAGCTCCTTT
1 --AAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
* * *
26208 AAACAATCATTTGAAAACATCAAGAAATCCCTAAAAATCAGGCTTAGCTTCTATT
1 AAA-ATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCT-TT
*
26263 AAAATTCATTTGCAAAA-ATCAAGAAACCCCAAAAAATCAGGCTTAGCTCCTTT
1 AAAATTCATTTG-AAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
* * * *
26316 AAAAATTCATTTAAAAACATCAAGAAACTCATAAAAATCAGGCTTAACTCCTTT
1 -AAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
* *
26370 AAAAATTCATTTGAAGACATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT
1 -AAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
* * * * * *
26424 CAAAATCCATTTGTAAACAT-AA-AACCCCCCCTGAAAATTAGGCTTAGCTACTTT
1 -AAAATTCATTTGAAAACATCAAGAA--ACCCCTAAAAATCAGGCTTAGCTCCTTT
* * * *
26478 AAAATTTCATTTGAAAACATCAAGAAATCCCTGAAAATCAGGCTTGGCTTCTTT
1 AAAA-TTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
26532 AAAA
1 AAAA
26536 ATTCTTTTAA
Statistics
Matches: 471, Mismatches: 59, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.00
53 21 0.04
54 384 0.82
55 59 0.13
56 5 0.01
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.29
Consensus pattern (53 bp):
AAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGCTCCTTT
Found at i:35616 original size:7 final size:8
Alignment explanation
Indices: 35588--35615 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
35578 AAAGATTACA
35588 TTTTTATT
1 TTTTTATT
35596 TTTTTATT
1 TTTTTATT
35604 TTTTTATT
1 TTTTTATT
35612 TTTT
1 TTTT
35616 AATAAGTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:36352 original size:35 final size:35
Alignment explanation
Indices: 36313--36381 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
36303 CTTTAGTTTA
36313 GGGTTTAGAATATAATTAAAGTATTTTGGAATTTG
1 GGGTTTAGAATATAATTAAAGTATTTTGGAATTTG
* * *
36348 GGGTTTAGAATGTAATTGAAGTGTTTTGGAATTT
1 GGGTTTAGAATATAATTAAAGTATTTTGGAATTT
36382 TGAACATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.43
Consensus pattern (35 bp):
GGGTTTAGAATATAATTAAAGTATTTTGGAATTTG
Found at i:37746 original size:3 final size:3
Alignment explanation
Indices: 37738--37861 Score: 115
Period size: 3 Copynumber: 39.0 Consensus size: 3
37728 TTACCCTTAA
* *
37738 TAT TAT TAT TAT CAT TAT TAT TAAT T-T TAT TAT TAAA TAT TAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T-AT TAT TAT TA-T
* *
37785 TAT TAT TAT TAT TGAC TAT TAT TAT TAT TAAT TAG TAT TAT TAT TAGT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA-T
* *
37833 TGT TAT TAT TAAT TAT TAA TATT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TA-T TAT TAT
37862 AAATAAAATA
Statistics
Matches: 100, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
2 2 0.02
3 78 0.78
4 20 0.20
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:37782 original size:13 final size:12
Alignment explanation
Indices: 37734--37889 Score: 107
Period size: 13 Copynumber: 12.2 Consensus size: 12
37724 TACTTTACCC
37734 TTAATATTATTA
1 TTAATATTATTA
37746 TT-ATCATTATTA
1 TTAAT-ATTATTA
*
37758 TTAATTTTATTA
1 TTAATATTATTA
37770 TTAAATATTATTA
1 TT-AATATTATTA
*
37783 GTTATTATTATTA
1 -TTAATATTATTA
*
37796 TTGACTATTATTA
1 TT-AATATTATTA
* *
37809 TTATTAATTAGTA
1 TTAAT-ATTATTA
* *
37822 TTATTATTAGTTG
1 TTAATATTA-TTA
*
37835 TTATTATTAATTA
1 TTAATATT-ATTA
37848 TTAATATTTATTA
1 TTAATA-TTATTA
* **
37861 TAAATAAAATATA
1 TTAATATTAT-TA
*
37874 TGTAATATTTTTA
1 T-TAATATTATTA
37887 TTA
1 TTA
37890 TTATATTTTA
Statistics
Matches: 116, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
11 2 0.02
12 31 0.27
13 73 0.63
14 10 0.09
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (12 bp):
TTAATATTATTA
Found at i:37796 original size:16 final size:15
Alignment explanation
Indices: 37738--37861 Score: 115
Period size: 16 Copynumber: 7.8 Consensus size: 15
37728 TTACCCTTAA
*
37738 TATTATTATTATCAT
1 TATTATTATTATTAT
37753 TATTATTAATT-TTAT
1 TATTATT-ATTATTAT
*
37768 TATTAAATATTATTAGT
1 TATT-ATTATTATTA-T
*
37785 TATTATTATTATTGAC
1 TATTATTATTATT-AT
37801 TATTATTATTATTAAT
1 TATTATTATTATT-AT
*
37817 TAGTATTATTATTAGT
1 TATTATTATTATTA-T
*
37833 TGTTATTATTAATTAT
1 TATTATTATT-ATTAT
*
37849 TAATATTTATTAT
1 TATTA-TTATTAT
37862 AAATAAAATA
Statistics
Matches: 90, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
15 18 0.20
16 57 0.63
17 15 0.17
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAT
Found at i:39431 original size:2 final size:2
Alignment explanation
Indices: 39424--39501 Score: 56
Period size: 2 Copynumber: 39.0 Consensus size: 2
39414 ACTGTTTATT
* *
39424 TA TA TA TA TA TA TA TA TA TA TA TA TT TCA TA CA TCA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA TA
* *
39466 T- TA -A TT TT TA CTA CTA 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
39502 CATGTATACA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
1 4 0.06
2 51 0.81
3 8 0.13
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43938 original size:17 final size:17
Alignment explanation
Indices: 43918--43977 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
43908 TGGATGTTTC
43918 GGGTACCCGGATTTTGT
1 GGGTACCCGGATTTTGT
*
43935 GGGTACCCAGATTTTGT
1 GGGTACCCGGATTTTGT
** *
43952 GGGTACCCGGATCATAT
1 GGGTACCCGGATTTTGT
43969 GGGTACCCG
1 GGGTACCCG
43978 ATACCCAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (17 bp):
GGGTACCCGGATTTTGT
Found at i:44207 original size:14 final size:16
Alignment explanation
Indices: 44176--44206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44166 GAATAATTAT
44176 TGATAATATAAATATA
1 TGATAATATAAATATA
*
44192 TGATAATAAAAATAT
1 TGATAATATAAATAT
44207 GTTTAGTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TGATAATATAAATATA
Found at i:45749 original size:2 final size:2
Alignment explanation
Indices: 45744--45788 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
45734 AAAAAAAATA
* *
45744 AT AT AT TT AT AT -T A- AT AT AT AG 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
45784 AT AT A
1 AT AT A
45789 ATTATCAACG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48818 original size:30 final size:30
Alignment explanation
Indices: 48761--48818 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
48751 ACTAAATTAC
* **
48761 AAATTTGTATAAGTTATGGGTATGAAATGG
1 AAATTGGTATAAGTTATAAGTATGAAATGG
48791 AAATTGGTATAAGTTAATAAGTA-GAAAT
1 AAATTGGTATAAGTT-ATAAGTATGAAAT
48819 TACACGTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.34
Consensus pattern (30 bp):
AAATTGGTATAAGTTATAAGTATGAAATGG
Found at i:50565 original size:17 final size:17
Alignment explanation
Indices: 50545--50606 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
50535 AAAAGAAGGA
50545 TACAGGAAAAAGAATAG
1 TACAGGAAAAAGAATAG
* *
50562 TACAGTG-AAAGGATTAG
1 TACAG-GAAAAAGAATAG
* *
50579 TACAGAAAAAAGAGTAAG
1 TACAGGAAAAAGAAT-AG
*
50597 TATAGGAAAA
1 TACAGGAAAA
50607 GAAACGATAC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
17 24 0.69
18 11 0.31
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.16
Consensus pattern (17 bp):
TACAGGAAAAAGAATAG
Found at i:51930 original size:20 final size:20
Alignment explanation
Indices: 51889--51944 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
51879 GATACTATAA
*
51889 GAACAATATTGATACTTGAC
1 GAACAATATCGATACTTGAC
*
51909 GAACAATATCGGTA-TTGTAC
1 GAACAATATCGATACTTG-AC
*
51929 GAACAATATCAATACT
1 GAACAATATCGATACT
51945 AAATGCACGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (20 bp):
GAACAATATCGATACTTGAC
Found at i:54825 original size:42 final size:42
Alignment explanation
Indices: 54766--54857 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
54756 GTGAATCGAG
*
54766 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAGGGGC
* ** *
54808 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
54850 CTCTTGAA
1 CTCTTGAA
54858 TGATAGGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 40 0.91
43 4 0.09
ACGTcount: A:0.21, C:0.18, G:0.38, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
Found at i:54826 original size:21 final size:21
Alignment explanation
Indices: 54766--54857 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
54756 GTGAATCGAG
* * *
54766 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGAGAGGGGC
* * *
54787 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGAGAGGGGC
* *
54808 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGAGAGGGGC
* *
54829 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGAGAGGGGC
54850 CTCTTGAA
1 CTCTTGAA
54858 TGATAGGAGA
Statistics
Matches: 54, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.06
21 50 0.93
22 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.38, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGC
Found at i:54877 original size:42 final size:42
Alignment explanation
Indices: 54796--54877 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
54786 CCTCTTCAAC
* * * *
54796 GATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGGAGAGGACACTTGAGG
* * *
54838 GATGATAGGGGCCTCTTGAATGATAGGAGAGGCCACTTGA
1 GATGACAGGGGCCTCTTGAACGATAGGAGAGGACACTTGA
54878 ATGATGAAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGGAGAGGACACTTGAGG
Found at i:55402 original size:20 final size:20
Alignment explanation
Indices: 55379--55427 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
55369 GAAACTTAAA
55379 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
55399 ATCGCAGCGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
55419 ATCGCAACG
1 ATCGCAACG
55428 GGATAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:55456 original size:33 final size:34
Alignment explanation
Indices: 55419--55494 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
55409 GGAAATGACT
*
55419 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* *
55452 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
55486 ATCGCAACG
1 ATCGCAACG
55495 CGAATTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:55484 original size:20 final size:20
Alignment explanation
Indices: 55461--55498 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55451 AATCGCAACG
*
55461 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
55481 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
55499 TTTTGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:55536 original size:19 final size:19
Alignment explanation
Indices: 55494--55537 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
55484 AAATCGCAAC
* * *
55494 GCGAATTTTGTTTCGCGTT
1 GCGATTTTTATTTCGCATT
55513 GCGATTTTTATTTCGCATT
1 GCGATTTTTATTTCGCATT
55532 GCGATT
1 GCGATT
55538 ATCTTGTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTTTTATTTCGCATT
Found at i:55587 original size:20 final size:20
Alignment explanation
Indices: 55564--55611 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
55554 CAAATTCGCA
55564 TTGCGATTGTCATTTCCGCG
1 TTGCGATTGTCATTTCCGCG
* **
55584 TTGCGATAGTCATTTTTGCG
1 TTGCGATTGTCATTTCCGCG
55604 TTGCGATT
1 TTGCGATT
55612 TTAAGTTTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (20 bp):
TTGCGATTGTCATTTCCGCG
Found at i:55626 original size:20 final size:20
Alignment explanation
Indices: 55603--55640 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
55593 TCATTTTTGC
55603 GTTGCGATTTTAAGTTTCGT
1 GTTGCGATTTTAAGTTTCGT
55623 GTTGCGATTTTAAGTTTC
1 GTTGCGATTTTAAGTTTC
55641 AAAAACTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.24, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCGT
Found at i:59535 original size:6 final size:6
Alignment explanation
Indices: 59524--59575 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
59514 GGCCTGCAAA
* * *
59524 AATATT AATATT AATATT AATATT AATATT AATAAT AATAAT AATAAT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
59572 AATA
1 AATA
59576 ATATAATGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATATT
Found at i:59576 original size:6 final size:6
Alignment explanation
Indices: 59524--59582 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
59514 GGCCTGCAAA
* * * * *
59524 AATATT AATATT AATATT AATATT AATATT AATAAT AATAAT AATAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
59572 AATAAT -ATAAT
1 AATAAT AATAAT
59583 GTTTTATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 5 0.10
6 47 0.90
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATAAT
Found at i:60094 original size:9 final size:8
Alignment explanation
Indices: 60068--60116 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
60058 TTAAATTTAG
60068 TTATAATT
1 TTATAATT
60076 TTATAATT
1 TTATAATT
60084 TTATAAATT
1 TTAT-AATT
* *
60093 TTTTATTT
1 TTATAATT
60101 TTAT-ATT
1 TTATAATT
*
60108 ATATAATT
1 TTATAATT
60116 T
1 T
60117 GAATTTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 5 0.15
8 21 0.64
9 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATAATT
Found at i:60094 original size:17 final size:17
Alignment explanation
Indices: 60068--60105 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
60058 TTAAATTTAG
60068 TTAT-AATTTTATAATT
1 TTATAAATTTTATAATT
* *
60084 TTATAAATTTTTTATTT
1 TTATAAATTTTATAATT
60101 TTATA
1 TTATA
60106 TTATATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATAAATTTTATAATT
Found at i:60826 original size:60 final size:60
Alignment explanation
Indices: 60752--60900 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 60
60742 GAATTGCTAA
** ** * *
60752 AAAAGTTTGGGGACTAATTTAGAATGAAAGTCATAGGTTAGGGATGAAATTAAATTGTTT
1 AAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGGTTAAAGATGAAATTAAAATATTT
* * * * *
60812 AAAAGTTTAAGGACTACTTTAGAATAAAAGTTATAGTTTAAATATGAAATTAAAATATTT
1 AAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGGTTAAAGATGAAATTAAAATATTT
* * *
60872 AAAGGATTAAGGA-TCAATTTAAAATGAAA
1 AAAAGTTTAAGGACT-AATTTAGAATGAAA
60901 TTCGTACATT
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 1 0.01
60 71 0.99
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (60 bp):
AAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAGGTTAAAGATGAAATTAAAATATTT
Found at i:61793 original size:22 final size:23
Alignment explanation
Indices: 61752--61802 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
61742 CACAACCACA
*
61752 CCCAATTCATAACCTGGTTCAGG
1 CCCAATTCATAACCTGGTTCAAG
61775 CCCAATTACA-AA-CTGGTTCAAG
1 CCCAATT-CATAACCTGGTTCAAG
61797 CCCAAT
1 CCCAAT
61803 AACCCAACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 15 0.58
23 9 0.35
24 2 0.08
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (23 bp):
CCCAATTCATAACCTGGTTCAAG
Found at i:67232 original size:16 final size:16
Alignment explanation
Indices: 67211--67257 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
67201 CATAACAAAA
67211 AGGCAAGAAAGCAACC
1 AGGCAAGAAAGCAACC
*
67227 AGGCAAGAATGCAACC
1 AGGCAAGAAAGCAACC
*
67243 AGTCAAGAAAGCAAC
1 AGGCAAGAAAGCAAC
67258 TAGTCAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.49, C:0.23, G:0.23, T:0.04
Consensus pattern (16 bp):
AGGCAAGAAAGCAACC
Found at i:67262 original size:16 final size:16
Alignment explanation
Indices: 67214--67264 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
67204 AACAAAAAGG
*
67214 CAAGAAAGCAACCAGG
1 CAAGAAAGCAACCAGT
*
67230 CAAGAATGCAACCAGT
1 CAAGAAAGCAACCAGT
*
67246 CAAGAAAGCAACTAGT
1 CAAGAAAGCAACCAGT
67262 CAA
1 CAA
67265 AGAGGAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.20, T:0.08
Consensus pattern (16 bp):
CAAGAAAGCAACCAGT
Found at i:69081 original size:20 final size:20
Alignment explanation
Indices: 69053--69176 Score: 153
Period size: 20 Copynumber: 6.2 Consensus size: 20
69043 TCAAGAAAAA
*
69053 TAAATCCTCAGGGTAATTTG
1 TAAAACCTCAGGGTAATTTG
*
69073 TAAAACCTCCGGGTAATTTG
1 TAAAACCTCAGGGTAATTTG
* *
69093 TAAAACCTCTGGGTAATTTA
1 TAAAACCTCAGGGTAATTTG
69113 TAAAACCTTCA-GGTAATTTG
1 TAAAACC-TCAGGGTAATTTG
* *
69133 TAAAACCTCCGGGTCATTTG
1 TAAAACCTCAGGGTAATTTG
*
69153 TAAAACCTTC-GAGTAATTTG
1 TAAAACC-TCAGGGTAATTTG
69173 TAAA
1 TAAA
69177 TCCTTAGAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 85 0.93
21 4 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATTTG
Found at i:69118 original size:40 final size:40
Alignment explanation
Indices: 69053--69176 Score: 176
Period size: 40 Copynumber: 3.1 Consensus size: 40
69043 TCAAGAAAAA
* *
69053 TAAATCCTCAGGGTAATTTGTAAAACCTCCGGGTAATTTG
1 TAAAACCTCAGGGTAATTTGTAAAACCTTCGGGTAATTTG
* * *
69093 TAAAACCTCTGGGTAATTTATAAAACCTTCAGGTAATTTG
1 TAAAACCTCAGGGTAATTTGTAAAACCTTCGGGTAATTTG
* * *
69133 TAAAACCTCCGGGTCATTTGTAAAACCTTCGAGTAATTTG
1 TAAAACCTCAGGGTAATTTGTAAAACCTTCGGGTAATTTG
69173 TAAA
1 TAAA
69177 TCCTTAGAGT
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (40 bp):
TAAAACCTCAGGGTAATTTGTAAAACCTTCGGGTAATTTG
Found at i:69193 original size:40 final size:39
Alignment explanation
Indices: 69063--69195 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 39
69053 TAAATCCTCA
* * *
69063 GGGTAATTTGTAAAACCTCCGGGTAATTTGTAAAACCTCT
1 GGGTCATTTGTAAAACCTTCGAGTAATTTGTAAAACCT-T
* * *
69103 GGGTAATTTATAAAACCTTC-AGGTAATTTGTAAAACCTCC
1 GGGTCATTTGTAAAACCTTCGA-GTAATTTGTAAAACCT-T
*
69143 GGGTCATTTGTAAAACCTTCGAGTAATTTGTAAATCCTT
1 GGGTCATTTGTAAAACCTTCGAGTAATTTGTAAAACCTT
* *
69182 AGAGTCTTTTGTAA
1 -GGGTCATTTGTAA
69196 GTCTTTCGAG
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
40 79 0.99
41 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (39 bp):
GGGTCATTTGTAAAACCTTCGAGTAATTTGTAAAACCTT
Found at i:69195 original size:60 final size:60
Alignment explanation
Indices: 69064--69181 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
69054 AAATCCTCAG
*
69064 GGTAATTTGTAAAACCTCCGGGTAATTTGTAAAACCTCTGGGTAATTTATAAAACCTTCA
1 GGTAATTTGTAAAACCTCCGGGTAATTTGTAAAACCTCTGAGTAATTTATAAAACCTTCA
* * *
69124 GGTAATTTGTAAAACCTCCGGGTCATTTGTAAAACCT-TCGAGTAATTTGTAAATCCTT
1 GGTAATTTGTAAAACCTCCGGGTAATTTGTAAAACCTCT-GAGTAATTTATAAAACCTT
69182 AGAGTCTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (60 bp):
GGTAATTTGTAAAACCTCCGGGTAATTTGTAAAACCTCTGAGTAATTTATAAAACCTTCA
Found at i:69357 original size:35 final size:34
Alignment explanation
Indices: 69276--69544 Score: 272
Period size: 35 Copynumber: 7.7 Consensus size: 34
69266 GCAACGTATC
*
69276 CAGCCTTCACGAAAGAGTAGTGAAGTAAATCATT
1 CAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
* *
69310 CAGCCTTTACGGAAGAGTAGTGAAGTAAAATTATT
1 CAGCCTTCACGGAAGAGTAGTGAAGT-AAATCATT
69345 CAGCCTTCACGGAAGAGTAGTGAAGT-AATGCATCT
1 CAGCCTTCACGGAAGAGTAGTGAAGTAAAT-CAT-T
* ** *
69380 CAACCTTCACAAAAGAGTAGTGAAGTAATTCATCT
1 CAGCCTTCACGGAAGAGTAGTGAAGTAAATCAT-T
*
69415 CAACCTTCACGGAAGAGTAGTGAAGTAAAATCA-T
1 CAGCCTTCACGGAAGAGTAGTGAAGT-AAATCATT
* * ** * **
69449 CCGATCTTCGTGAAAGAGTAGTGAAGTAAGGCAATCT
1 CAG-CCTTCACGGAAGAGTAGTGAAGTAAATC-AT-T
* * * *
69486 CAGCCTTCACAGAAGAGTAGTGAAGTGATTCAAT
1 CAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
69520 CTAGCCTTCACGGAAGAGTAGTGAA
1 C-AGCCTTCACGGAAGAGTAGTGAA
69545 ACAAGATCAG
Statistics
Matches: 194, Mismatches: 31, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
33 3 0.02
34 33 0.17
35 128 0.66
36 27 0.14
37 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (34 bp):
CAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
Found at i:69529 original size:106 final size:105
Alignment explanation
Indices: 69276--69544 Score: 348
Period size: 105 Copynumber: 2.6 Consensus size: 105
69266 GCAACGTATC
* * *
69276 CAGCCTTCAC-GAAAGAGTAGTGAAGTAAATCATTC-AGCCTTTACGGAAGAGTAGTGAAGTAAA
1 CAGCCTTCACAG-AAGAGTAGTGAAGTAATTCAATCTAGCCTTCACGGAAGAGTAGTGAAGTAAA
* * * *
69339 ATTATTCAGCCTTCACGGAAGAGTAGTGAAGTAATGCATCT
65 ATCATCCAGCCTTCACGAAAGAGTAGTGAAGTAAGGCATCT
* * *
69380 CAACCTTCACAAAAGAGTAGTGAAGTAATTC-ATCTCAACCTTCACGGAAGAGTAGTGAAGTAAA
1 CAGCCTTCACAGAAGAGTAGTGAAGTAATTCAATCT-AGCCTTCACGGAAGAGTAGTGAAGTAAA
* **
69444 ATCATCC-GATCTTCGTGAAAGAGTAGTGAAGTAAGGCAATCT
65 ATCATCCAG-CCTTCACGAAAGAGTAGTGAAGTAAGGC-ATCT
*
69486 CAGCCTTCACAGAAGAGTAGTGAAGTGATTCAATCTAGCCTTCACGGAAGAGTAGTGAA
1 CAGCCTTCACAGAAGAGTAGTGAAGTAATTCAATCTAGCCTTCACGGAAGAGTAGTGAA
69545 ACAAGATCAG
Statistics
Matches: 142, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
103 2 0.01
104 28 0.20
105 54 0.38
106 54 0.38
107 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (105 bp):
CAGCCTTCACAGAAGAGTAGTGAAGTAATTCAATCTAGCCTTCACGGAAGAGTAGTGAAGTAAAA
TCATCCAGCCTTCACGAAAGAGTAGTGAAGTAAGGCATCT
Found at i:69764 original size:12 final size:12
Alignment explanation
Indices: 69724--69774 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
69714 AGTGTCATTT
69724 CTATTATTTATTA
1 CTATTA-TTATTA
69737 -TA-TA-TATTA
1 CTATTATTATTA
*
69746 ATA-TATTATTA
1 CTATTATTATTA
69757 CTATTATTATTA
1 CTATTATTATTA
69769 CTATTA
1 CTATTA
69775 AATTATTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 5 0.15
10 4 0.12
11 9 0.26
12 16 0.47
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (12 bp):
CTATTATTATTA
Found at i:70791 original size:13 final size:13
Alignment explanation
Indices: 70773--70799 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70763 CAGGTTTTTA
70773 TGTCTTTGAATTT
1 TGTCTTTGAATTT
70786 TGTCTTTGAATTT
1 TGTCTTTGAATTT
70799 T
1 T
70800 ATTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (13 bp):
TGTCTTTGAATTT
Found at i:71153 original size:30 final size:30
Alignment explanation
Indices: 71119--71180 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
71109 TATAATTATT
71119 ATTTGTAATATAGATATTTTATTTTATACA
1 ATTTGTAATATAGATATTTTATTTTATACA
71149 ATTTGTAATATAGATATTTTATTTTATACA
1 ATTTGTAATATAGATATTTTATTTTATACA
71179 AT
1 AT
71181 AAGTCATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.53
Consensus pattern (30 bp):
ATTTGTAATATAGATATTTTATTTTATACA
Found at i:73901 original size:163 final size:155
Alignment explanation
Indices: 73689--74086 Score: 493
Period size: 163 Copynumber: 2.5 Consensus size: 155
73679 TCCTTTAATT
* *
73689 CATCATTTATTTTAAGTTTGTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGAATG
1 CATCATTTATTTTAAGTCTGTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGAATA
* *
73754 CATATGTACTTTCAATTTCTCTTTTTGATAACAAATTTTTCT-A-TTTTCAATTTAGTCCCTCAA
66 CATATGTACTTTCAATTTCTATTTTTGAT----AATTTTT-TAATTTTTCAATCTAGTCCCTCAA
* *
73817 TTTTGTTTTATAATTTGATTATTTCTTCAATC
126 -ATT-TTTTATAATTTGATTATTTCTTCAATA
* *
73849 CATCATTTTATTTTAAGTCTGTTGTTTTATCAACTTTGAACCACATGCTCCTAAACCATCATAGA
1 CATCA-TTTATTTTAAGTCTG-T-TTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGA
* *
73914 CTACATATGTTCTTTCAA-TTCTATTTTTGATAATTTTTTAATTTTTCAATCTAGTCCCTCAAAT
63 ATACATATGTACTTTCAATTTCTATTTTTGATAATTTTTTAATTTTTCAATCTAGTCCCTCAAAT
**
73978 TTTTTATAATTTTCTTATTTCTTCAATA
128 TTTTTATAATTTGATTATTTCTTCAATA
* * * *
74006 CATC-GTTATTTTAAGTCTGTTTTTACCAAATTTGAACCACGTGCTCATATACCA-CAATAGAAT
1 CATCATTTATTTTAAGTCTGTTTTTACCAAATTTGAACCACATGCTCCTAAACCATC-ATAGAAT
*
74069 ACCTATGTAAC-TTCAATT
65 ACATATGT-ACTTTCAATT
74087 CTTACTTTTT
Statistics
Matches: 209, Mismatches: 21, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
152 1 0.00
153 47 0.22
154 3 0.01
155 14 0.07
157 29 0.14
158 10 0.05
159 19 0.09
160 5 0.02
161 14 0.07
162 13 0.06
163 54 0.26
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (155 bp):
CATCATTTATTTTAAGTCTGTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGAATA
CATATGTACTTTCAATTTCTATTTTTGATAATTTTTTAATTTTTCAATCTAGTCCCTCAAATTTT
TTATAATTTGATTATTTCTTCAATA
Found at i:74964 original size:25 final size:25
Alignment explanation
Indices: 74930--74987 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
74920 CCATAGTAAG
*
74930 GACATGACGGTCCATGATGACTGGC
1 GACATGACGGTCCATGATGACTGGA
*
74955 GACATGACGGTCCATGATGGCTGGA
1 GACATGACGGTCCATGATGACTGGA
*
74980 AACATGAC
1 GACATGAC
74988 ATATATATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (25 bp):
GACATGACGGTCCATGATGACTGGA
Found at i:76642 original size:22 final size:19
Alignment explanation
Indices: 76573--76662 Score: 81
Period size: 19 Copynumber: 4.4 Consensus size: 19
76563 AACGCGATTT
*
76573 TGAAAAATGTGTTGCAATAG
1 TGAAAAA-GTGTTGCGATAG
* * *
76593 TTAAAATGTGTTGCGAGAG
1 TGAAAAAGTGTTGCGATAG
76612 TTTGAAAAACGTGTTGTTACGATAG
1 --TGAAAAA-GTGTTG---CGATAG
76637 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
76656 TGAAAAA
1 TGAAAAA
76663 TCCAAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
19 23 0.40
20 5 0.09
21 5 0.09
22 12 0.21
23 7 0.12
25 5 0.09
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.30
Consensus pattern (19 bp):
TGAAAAAGTGTTGCGATAG
Found at i:76964 original size:5 final size:5
Alignment explanation
Indices: 76956--76996 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
76946 CCGTCCCGTC
76956 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
76997 TGGTAATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:76985 original size:6 final size:6
Alignment explanation
Indices: 76959--77000 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
76949 TCCCGTCTCG
76959 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
77001 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:77112 original size:21 final size:21
Alignment explanation
Indices: 77086--77126 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
77076 CAGTCGTTGC
77086 GAACTTCGACTAACGCAACGT
1 GAACTTCGACTAACGCAACGT
* *
77107 GAACTTGGACTATCGCAACG
1 GAACTTCGACTAACGCAACG
77127 AATTTGGAAA
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:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (21 bp):
GAACTTCGACTAACGCAACGT
Found at i:77183 original size:53 final size:53
Alignment explanation
Indices: 77102--77208 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
77092 CGACTAACGC
77102 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
1 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
*
77155 AACGTGAACTTGGACTATCGCAATGAATTTGGAAAATCGCAACGCGAACTTCG
1 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
77208 A
1 A
77209 CTATCGCAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (53 bp):
AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
Found at i:77215 original size:40 final size:40
Alignment explanation
Indices: 77155--77299 Score: 245
Period size: 40 Copynumber: 3.6 Consensus size: 40
77145 GCGAACTTCG
* *
77155 AACGTGAACTTGGACTATCGCAATGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
*
77195 AACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
*
77235 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
*
77275 AACGCGAACTTTGACTATCGCAACG
1 AACGCGAACTTGGACTATCGCAACG
77300 TGAACTTGGA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
AACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
Found at i:77216 original size:21 final size:21
Alignment explanation
Indices: 77155--77320 Score: 146
Period size: 21 Copynumber: 8.2 Consensus size: 21
77145 GCGAACTTCG
*
77155 AACGTGAACTTGGACTATCGC
1 AACGCGAACTTGGACTATCGC
* * **
77176 AA--TGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGC
*
77195 AACGCGAACTTCGACTATCGC
1 AACGCGAACTTGGACTATCGC
* **
77216 AA--CGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGC
*
77235 AACGTGAACTTGGACTATCGC
1 AACGCGAACTTGGACTATCGC
* **
77256 AA--CGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGC
*
77275 AACGCGAACTTTGACTATCGC
1 AACGCGAACTTGGACTATCGC
* *
77296 AACGTGAACTTGGACTATCGT
1 AACGCGAACTTGGACTATCGC
77317 AACG
1 AACG
77321 AATTTGGACT
Statistics
Matches: 112, Mismatches: 27, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
19 46 0.41
21 66 0.59
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (21 bp):
AACGCGAACTTGGACTATCGC
Found at i:77328 original size:80 final size:79
Alignment explanation
Indices: 77155--77393 Score: 267
Period size: 80 Copynumber: 3.0 Consensus size: 79
77145 GCGAACTTCG
*
77155 AACGTGAACTTGGACTATCGCAATGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC-
1 AACG-GAACTTGGACTATCGCAA-GAATTTGGAAAATCGCAACGCGAACTTTGACTATCGCAACG
* **
77219 GAATTTGGAAAATCGC
64 GAACTTGGACTATCGC
77235 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTTGACTATCGCAACG
1 AACG-GAACTTGGACTATCGCAA-GAATTTGGAAAATCGCAACGCGAACTTTGACTATCGCAACG
*
77300 TGAACTTGGACTATCGT
64 -GAACTTGGACTATCGC
* * * **
77317 AAC-GAATTTGGACTAACG-TA-AATTTGGAAAATCGCAA--CGAA-TTTGGAAAATCGCAACGC
1 AACGGAACTTGGACTATCGCAAGAATTTGGAAAATCGCAACGCGAACTTT-GACTATCGCAACG-
*
77376 GAACTTGGACTATAGC
64 GAACTTGGACTATCGC
77392 AA
1 AA
77394 AATCGCGTTG
Statistics
Matches: 142, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
74 3 0.02
75 31 0.22
77 17 0.12
79 1 0.01
80 75 0.53
82 15 0.11
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (79 bp):
AACGGAACTTGGACTATCGCAAGAATTTGGAAAATCGCAACGCGAACTTTGACTATCGCAACGGA
ACTTGGACTATCGC
Found at i:77344 original size:35 final size:35
Alignment explanation
Indices: 77296--77363 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
77286 TGACTATCGC
* ** *
77296 AACGTGAACTTGGACTATCGTAACGAATTTGGACT
1 AACGTAAACTTGGAAAATCGCAACGAATTTGGACT
*
77331 AACGTAAATTTGGAAAATCGCAACGAATTTGGA
1 AACGTAAACTTGGAAAATCGCAACGAATTTGGA
77364 AAATCGCAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (35 bp):
AACGTAAACTTGGAAAATCGCAACGAATTTGGACT
Found at i:77361 original size:19 final size:19
Alignment explanation
Indices: 77171--77374 Score: 139
Period size: 19 Copynumber: 10.5 Consensus size: 19
77161 AACTTGGACT
*
77171 ATCGCAATGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* * **
77190 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAATTTGGAAA
77211 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* **
77230 ATCGCAACGTGAACTTGGACT
1 ATCGCAAC--GAATTTGGAAA
77251 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
**
77270 ATCGCAACGCGAACTTT-GACT
1 ATCGCAA--CGAA-TTTGGAAA
* **
77291 ATCGCAACGTGAACTTGGACT
1 ATCGCAAC--GAATTTGGAAA
* *
77312 ATCGTAACGAATTTGGACTA
1 ATCGCAACGAATTTGGA-AA
*
77332 A-CG-TA--AATTTGGAAA
1 ATCGCAACGAATTTGGAAA
77347 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
77366 ATCGCAACG
1 ATCGCAACG
77375 CGAACTTGGA
Statistics
Matches: 145, Mismatches: 25, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.01
16 10 0.07
17 1 0.01
18 1 0.01
19 68 0.47
20 3 0.02
21 57 0.39
22 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:77371 original size:96 final size:99
Alignment explanation
Indices: 77190--77393 Score: 279
Period size: 96 Copynumber: 2.1 Consensus size: 99
77180 AATTTGGAAA
* **
77190 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCG
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG--AATCGCAACGTAAACTTGGAAAATCG
*
77255 CAACGAATTTGGAAAATCGCAACGCGAACTTTGACT
64 CAACGAATTTGGAAAATCGCAACGCGAACTTGGACT
* * * * *
77291 ATCGCAACGTGAACTTGGACTATCGTAACGAATTTGG-A-C-TAACGTAAATTTGGAAAATCGCA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATCGCAACGTAAACTTGGAAAATCGCA
77353 ACGAATTTGGAAAATCGCAACGCGAACTTGGACT
66 ACGAATTTGGAAAATCGCAACGCGAACTTGGACT
*
77387 ATAGCAA
1 ATCGCAA
77394 AATCGCGTTG
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
96 57 0.61
97 1 0.01
98 1 0.01
101 34 0.37
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (99 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATCGCAACGTAAACTTGGAAAATCGCA
ACGAATTTGGAAAATCGCAACGCGAACTTGGACT
Found at i:77383 original size:21 final size:19
Alignment explanation
Indices: 77107--77384 Score: 126
Period size: 19 Copynumber: 14.5 Consensus size: 19
77097 AACGCAACGT
**
77107 GAACTTGGACTATCGCAAC
1 GAACTTGGAAAATCGCAAC
*
77126 GAATTTGGAAAATCGCAACGC
1 GAACTTGGAAAATCGCAA--C
* *
77147 GAACTTCG--AA-CG---T
1 GAACTTGGAAAATCGCAAC
** *
77160 GAACTTGGACTATCGCAAT
1 GAACTTGGAAAATCGCAAC
*
77179 GAATTTGGAAAATCGCAACGC
1 GAACTTGGAAAATCGCAA--C
* **
77200 GAACTTCGACTATCGCAAC
1 GAACTTGGAAAATCGCAAC
*
77219 GAATTTGGAAAATCGCAAC
1 GAACTTGGAAAATCGCAAC
**
77238 GTGAACTTGGACTATCGCAAC
1 --GAACTTGGAAAATCGCAAC
*
77259 GAATTTGGAAAATCGCAACGC
1 GAACTTGGAAAATCGCAA--C
* **
77280 GAACTTTGACTATCGCAAC
1 GAACTTGGAAAATCGCAAC
** *
77299 GTGAACTTGGACTATCGTAAC
1 --GAACTTGGAAAATCGCAAC
* * *
77320 GAATTTGGACTAA-CG-TA-
1 GAACTTGGA-AAATCGCAAC
*
77337 -AATTTGGAAAATCGCAAC
1 GAACTTGGAAAATCGCAAC
*
77355 GAATTTGGAAAATCGCAACGC
1 GAACTTGGAAAATCGCAA--C
77376 GAACTTGGA
1 GAACTTGGA
77385 CTATAGCAAA
Statistics
Matches: 197, Mismatches: 39, Indels: 44
0.70 0.14 0.16
Matches are distributed among these distances:
13 7 0.04
15 3 0.02
16 12 0.06
17 1 0.01
18 3 0.02
19 92 0.47
20 1 0.01
21 78 0.40
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (19 bp):
GAACTTGGAAAATCGCAAC
Found at i:78148 original size:3 final size:3
Alignment explanation
Indices: 78140--78182 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
78130 CGTCCGTAGA
* * * *
78140 TAT TAT TAT TAT TAT TAT TAT TGT TGT TGT TGT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
78183 TACTTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:78202 original size:10 final size:10
Alignment explanation
Indices: 78175--78213 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
78165 GTTGTTGTTA
78175 TTATTATTTACT
1 TTATT-TTTA-T
78187 TATATTTTTAT
1 T-TATTTTTAT
78198 TTATTTTTAT
1 TTATTTTTAT
78208 TTATTT
1 TTATTT
78214 CTGTGGCACG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 5 0.19
13 4 0.15
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTTTTAT
Done.