Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008420.1 Hibiscus syriacus cultivar Beakdansim tig00111200_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: 1020524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:15303 original size:50 final size:49
Alignment explanation
Indices: 15221--15396 Score: 228
Period size: 50 Copynumber: 3.5 Consensus size: 49
15211 CCTAGTTGTA
* **
15221 AGTATATGTTAAGTGCTACACTTTTTTATTTTATTCACTTACATTGGTGT
1 AGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTCACTTACACCGGTGT
* * *
15271 AGTACGTGTTAAGTGCTACACTTTTTTGTTTTATTCACTTACACCAGTG-
1 AGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTCACTTACACCGGTGT
* * *
15320 AGTATGTGTTAATTGCTACATTTGTTTATTTTATTCATTTACACCGGTAT
1 AGTATGTGTTAAGTGCTACATTT-TTTATTTTATTCACTTACACCGGTGT
15370 AAGTATGTGTTAAGTGCTACATTTTTT
1 -AGTATGTGTTAAGTGCTACATTTTTT
15397 GTAGTATGAA
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
48 3 0.03
49 39 0.35
50 46 0.42
51 22 0.20
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (49 bp):
AGTATGTGTTAAGTGCTACATTTTTTATTTTATTCACTTACACCGGTGT
Found at i:17388 original size:20 final size:22
Alignment explanation
Indices: 17363--17403 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17353 TTGACTCGAA
*
17363 CTCG-AAA-TCATGAACTGAAG
1 CTCGAAAAGTCATGAAATGAAG
17383 CTCGAAAAGTCATGAAATGAA
1 CTCGAAAAGTCATGAAATGAA
17404 AAAACCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (22 bp):
CTCGAAAAGTCATGAAATGAAG
Found at i:29518 original size:15 final size:16
Alignment explanation
Indices: 29490--29519 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29480 ACGACTAACT
29490 AAATTAAAATATGATA
1 AAATTAAAATATGATA
29506 AAATTAAAA-ATGAT
1 AAATTAAAATATGAT
29520 CATCAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
AAATTAAAATATGATA
Found at i:32857 original size:25 final size:25
Alignment explanation
Indices: 32784--32857 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
32774 GATAATTAAA
* * *
32784 AAACATAATAAGTTTCGACTAATCC
1 AAACATTATAAGTCTCGACTAATTC
* * *
32809 AAAAATTATAAATCTTGACTAATTC
1 AAACATTATAAGTCTCGACTAATTC
32834 AAACATTATAAGTCTCGACTAATT
1 AAACATTATAAGTCTCGACTAATT
32858 TAGTATAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (25 bp):
AAACATTATAAGTCTCGACTAATTC
Found at i:33115 original size:24 final size:24
Alignment explanation
Indices: 33088--33144 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
33078 TATTTAAATT
*
33088 TTTAAATATTCAAAT-ATTTTTATA
1 TTTAAA-ATTAAAATAATTTTTATA
* *
33112 TTTAGAACTTAAAATAATTTTTATT
1 TTTA-AAATTAAAATAATTTTTATA
33137 TTTAAAAT
1 TTTAAAAT
33145 AAATTAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAAAATTAAAATAATTTTTATA
Found at i:33584 original size:26 final size:26
Alignment explanation
Indices: 33551--33604 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
33541 TAAGTCCAAT
33551 ATTTTTCAATATTTGTTATAAGAGGC
1 ATTTTTCAATATTTGTTATAAGAGGC
33577 ATTTTTCAATATTTGTTATAAGAGGC
1 ATTTTTCAATATTTGTTATAAGAGGC
33603 AT
1 AT
33605 ACTTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (26 bp):
ATTTTTCAATATTTGTTATAAGAGGC
Found at i:41294 original size:45 final size:45
Alignment explanation
Indices: 41209--41294 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
41199 TATTTTATAT
* * *
41209 TTTTATAATTGAAACTCTTAAATTTTTTAGTTTTACTTTTTTTAC
1 TTTTATAATTGAAACTCTTAAATTTTTTAATCTCACTTTTTTTAC
* *
41254 TTTTGTAATTGAGACTCTT-AATTTTTGTAATCTCA-TTTTTT
1 TTTTATAATTGAAACTCTTAAATTTTT-TAATCTCACTTTTTT
41295 ATGTTTTGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 13 0.37
45 22 0.63
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.59
Consensus pattern (45 bp):
TTTTATAATTGAAACTCTTAAATTTTTTAATCTCACTTTTTTTAC
Found at i:42483 original size:42 final size:43
Alignment explanation
Indices: 42351--42489 Score: 156
Period size: 44 Copynumber: 3.2 Consensus size: 43
42341 TTTTTATTGA
* *
42351 TATAATT-AGATCCTTAATTTTTTTCAATCACAATTTTTACCTT
1 TATAATTGAGATCTTTAATTTTTTTCAATCTCAA-TTTTACCTT
* * ** * *
42394 TATAATTAAGATCTCTGTTTTTTTTCAATCTTATATTTTACTTT
1 TATAATTGAGATCTTTAATTTTTTTCAATCTCA-ATTTTACCTT
* *
42438 TATAATTGAGATCTTTAATTTTTTT-AATCTCACTTCTACCTT
1 TATAATTGAGATCTTTAATTTTTTTCAATCTCAATTTTACCTT
42480 TATAATTGAG
1 TATAATTGAG
42490 GTTCCTGTTT
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
42 17 0.22
43 13 0.16
44 48 0.61
45 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (43 bp):
TATAATTGAGATCTTTAATTTTTTTCAATCTCAATTTTACCTT
Found at i:42558 original size:43 final size:42
Alignment explanation
Indices: 42511--42625 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 42
42501 CTTATATTAC
42511 TGAGGTCCCTAATTTTTTTAATATCACTTTTTACCA-TTATAAT
1 TGAGG-CCCTAATTTTTTTAATATCACTTTTTA-CATTTATAAT
* ** *
42554 TGAGG-CCTCAAATTTTTTAATCGCACTTTTTACATTTATTAT
1 TGAGGCCCT-AATTTTTTTAATATCACTTTTTACATTTATAAT
* *
42596 TGAGACCCCTAATTTTTTTCAATGTCACTT
1 TGAG-GCCCTAATTTTTTT-AATATCACTT
42626 ATATTTGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
41 5 0.08
42 30 0.51
43 13 0.22
44 11 0.19
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (42 bp):
TGAGGCCCTAATTTTTTTAATATCACTTTTTACATTTATAAT
Found at i:45162 original size:37 final size:38
Alignment explanation
Indices: 45107--45190 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
45097 TGGTAACCAA
45107 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
45144 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
45181 -GTTGAAAAAT
1 CTTTGAAAAAT
45191 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:49751 original size:37 final size:38
Alignment explanation
Indices: 49696--49779 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
49686 TGGTAACCAA
49696 CTTTGAAAAA-ATGGTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
* * *
49733 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
*
49770 -GTTGAAAAAT
1 CTTTGAAAAAT
49780 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
Found at i:62251 original size:18 final size:18
Alignment explanation
Indices: 62228--62270 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
62218 TTAAAGTACT
62228 CTCGTTGTTTAGGTTCTA
1 CTCGTTGTTTAGGTTCTA
62246 CTCGTTGTTTAGGTTCTA
1 CTCGTTGTTTAGGTTCTA
*
62264 ATCGTTG
1 CTCGTTG
62271 GTATTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.49
Consensus pattern (18 bp):
CTCGTTGTTTAGGTTCTA
Found at i:71887 original size:22 final size:21
Alignment explanation
Indices: 71845--71884 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
71835 AAGACAATTT
71845 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
71866 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
71885 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:75685 original size:12 final size:12
Alignment explanation
Indices: 75668--75709 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
75658 AATTTTTCAT
75668 TGTTCATGGTAC
1 TGTTCATGGTAC
* *
75680 TGTTCACGGTAT
1 TGTTCATGGTAC
75692 TGTTCAT--TAC
1 TGTTCATGGTAC
75702 TGTTCATG
1 TGTTCATG
75710 ATATTGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.45
Consensus pattern (12 bp):
TGTTCATGGTAC
Found at i:75705 original size:22 final size:22
Alignment explanation
Indices: 75666--75725 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
75656 GAAATTTTTC
*
75666 ATTGTTCATGGTACTGTTCACGGT
1 ATTGTTCAT--TACTGTTCACGAT
*
75690 ATTGTTCATTACTGTTCATGAT
1 ATTGTTCATTACTGTTCACGAT
*
75712 ATTGTTTA-TACTGT
1 ATTGTTCATTACTGT
75726 ATAGTACTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.18
22 18 0.55
24 9 0.27
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.48
Consensus pattern (22 bp):
ATTGTTCATTACTGTTCACGAT
Found at i:77648 original size:37 final size:36
Alignment explanation
Indices: 77526--77830 Score: 157
Period size: 37 Copynumber: 8.6 Consensus size: 36
77516 TCTTATTTTT
* * * *
77526 TTTTAAAAACGTATAATATATGGTTTT-TAAAACGG
1 TTTTGAAAACGTATAATATATAGTTTTAAAAAACAG
*
77561 TTTTGAAAAC-----ATATATAGTTTTTAAAATA-A-
1 TTTTGAAAACGTATAATATATAG-TTTTAAAAAACAG
* * *
77591 TTTTAAAAAACGTATAAATATATAATTTTAAAAAAATAG
1 TTTT-GAAAACGTAT-AATATATAGTTTT-AAAAAACAG
* *
77630 TTTTGAAAACGTATAATATATAGTTTT-TAAAACGG
1 TTTTGAAAACGTATAATATATAGTTTTAAAAAACAG
* ** ** * *
77665 TTTTTGAAAACATATAGCATATAGTTTTTTAAAATAT
1 -TTTTGAAAACGTATAATATATAGTTTTAAAAAACAG
* * *
77702 TTTTGAAAATGTATAATATATAGTTTTTTAAAAACGG
1 TTTTGAAAACGTATAATATATAG-TTTTAAAAAACAG
* * * *
77739 TTTTTAAAACATATAGTATATAGTTTTTAAAATA-A-
1 TTTTGAAAACGTATAATATATAG-TTTTAAAAAACAG
* ** * * * *
77774 TTTTAAAAAAAATTATAATAAATAGTTTT-TAAAATAT
1 TTTT--GAAAACGTATAATATATAGTTTTAAAAAACAG
*
77811 TTTTGAAAACTTATAATATA
1 TTTTGAAAACGTATAATATA
77831 GTTTTTGAAA
Statistics
Matches: 207, Mismatches: 44, Indels: 38
0.72 0.15 0.13
Matches are distributed among these distances:
30 11 0.05
31 9 0.04
32 3 0.01
35 34 0.16
36 52 0.25
37 84 0.41
38 10 0.05
39 4 0.02
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (36 bp):
TTTTGAAAACGTATAATATATAGTTTTAAAAAACAG
Found at i:77655 original size:74 final size:72
Alignment explanation
Indices: 77571--77734 Score: 184
Period size: 74 Copynumber: 2.2 Consensus size: 72
77561 TTTTGAAAAC
* * *
77571 ATATATAGTTTTTAAAATAATTTTAAAAAACGTATAAATATATAATTTTAAAAAAATAGTTTTGA
1 ATATATAGTTTTTAAAACAATTTTAAAAAACATAT-AACATATAATTTT-AAAAAATAGTTTTGA
77636 AAACGTATA
64 AAACGTATA
** ** * * ** *
77645 ATATATAGTTTTTAAAACGGTTTTTGAAAACATATAGCATATAGTTTTTTAAAATATTTTTGAAA
1 ATATATAGTTTTTAAAACAATTTTAAAAAACATATAACATATAATTTTAAAAAATAGTTTTGAAA
*
77710 ATGTATA
66 ACGTATA
77717 ATATATAGTTTTTTAAAA
1 ATATATAG-TTTTTAAAA
77735 ACGGTTTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
72 28 0.37
73 19 0.25
74 29 0.38
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (72 bp):
ATATATAGTTTTTAAAACAATTTTAAAAAACATATAACATATAATTTTAAAAAATAGTTTTGAAA
ACGTATA
Found at i:77687 original size:36 final size:36
Alignment explanation
Indices: 77525--77859 Score: 244
Period size: 36 Copynumber: 9.4 Consensus size: 36
77515 ATCTTATTTT
* * *
77525 TTTTTAAAAACGTATAATATATGGTTTTTAAAACG-
1 TTTTTGAAAACATATAATATATAGTTTTTAAAACGA
* **
77560 GTTTTGAAAAC-----ATATATAGTTTTTAAAATAA
1 TTTTTGAAAACATATAATATATAGTTTTTAAAACGA
** * * **
77591 TTTTAAAAAACGTATAAATATATA-ATTTTAAAAAAA
1 TTTTTGAAAACATAT-AATATATAGTTTTTAAAACGA
* *
77627 TAGTTTTGAAAACGTATAATATATAGTTTTTAAAACGG
1 T--TTTTGAAAACATATAATATATAGTTTTTAAAACGA
** *
77665 TTTTTGAAAACATATAGCATATAGTTTTTTAAAA-TA
1 TTTTTGAAAACATATAATATATAG-TTTTTAAAACGA
** *
77701 TTTTTGAAAATGTATAATATATAGTTTTTTAAAAACGG
1 TTTTTGAAAACATATAATATATAG-TTTTT-AAAACGA
* **
77739 TTTTT-AAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTTGAAAACATATAATATATAGTTTTTAAAACGA
** * * *
77774 TTTTAAAAAAAATTATAATAAATAGTTTTTAAAA-TA
1 TTTTTGAAAACA-TATAATATATAGTTTTTAAAACGA
*
77810 TTTTTGAAAACTTAT-A-ATATAGTTTTTGAAAACGTA
1 TTTTTGAAAACATATAATATATAGTTTTT-AAAACG-A
77846 TTTTTGAAAACATA
1 TTTTTGAAAACATA
77860 GTATATGATT
Statistics
Matches: 237, Mismatches: 45, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
30 16 0.07
31 8 0.03
33 10 0.04
34 5 0.02
35 20 0.08
36 90 0.38
37 62 0.26
38 26 0.11
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (36 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAACGA
Found at i:77716 original size:72 final size:71
Alignment explanation
Indices: 77623--77855 Score: 269
Period size: 72 Copynumber: 3.2 Consensus size: 71
77613 TAATTTTAAA
* *
77623 AAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAACGGTTTTTGAAAACATATAGCATATA
1 AAAATATTTTTGAAAATGTATAATATATAGTTTTTAAAACGGTTTTTGAAAACATATAG-ATATA
77688 GTTTTTT
65 GTTTTTT
77695 AAAATATTTTTGAAAATGTATAATATATAGTTTTTTAAAAACGGTTTTT-AAAACATATAGTATA
1 AAAATATTTTTGAAAATGTATAATATATAG-TTTTT-AAAACGGTTTTTGAAAACATATAG-ATA
77759 TAG-TTTTT
63 TAGTTTTTT
** * ** *
77767 AAAATAATTTTAAAAAAAAT-TATAATAAATAGTTTTTAAAA-TATTTTTGAAAACTTATA-ATA
1 AAAAT-ATTTT--TGAAAATGTATAATATATAGTTTTTAAAACGGTTTTTGAAAACATATAGATA
*
77829 TAGTTTTTG
63 TAGTTTTTT
77838 AAAACGTATTTTTGAAAA
1 AAAA--TATTTTTGAAAA
77856 CATAGTATAT
Statistics
Matches: 140, Mismatches: 12, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
70 10 0.07
71 13 0.09
72 56 0.40
73 33 0.24
74 23 0.16
75 5 0.04
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.43
Consensus pattern (71 bp):
AAAATATTTTTGAAAATGTATAATATATAGTTTTTAAAACGGTTTTTGAAAACATATAGATATAG
TTTTTT
Found at i:79195 original size:26 final size:26
Alignment explanation
Indices: 79073--79196 Score: 64
Period size: 26 Copynumber: 4.9 Consensus size: 26
79063 GATTTTCTCC
* *
79073 ATTT-TTTTAGAAACTTATTATTTTTT
1 ATTTCTTTTA-AAATTTAATATTTTTT
* *
79099 ATTTCTTCTAGAATTTAATA---TTT
1 ATTTCTTTTAAAATTTAATATTTTTT
* ** *
79122 ATTTCCTTTT--ATTTTGTTCTTTATTT
1 ATTT-CTTTTAAAATTTAATATTT-TTT
* * **
79148 -TTTATTTTAAAAATTAGCATTTTTT
1 ATTTCTTTTAAAATTTAATATTTTTT
79173 ATTTCTTTTAAAATTTAATATTTT
1 ATTTCTTTTAAAATTTAATATTTT
79197 CTTCATTTTT
Statistics
Matches: 69, Mismatches: 20, Indels: 18
0.64 0.19 0.17
Matches are distributed among these distances:
22 5 0.07
23 7 0.10
24 8 0.12
25 6 0.09
26 39 0.57
27 4 0.06
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTTCTTTTAAAATTTAATATTTTTT
Found at i:79251 original size:15 final size:16
Alignment explanation
Indices: 79211--79263 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 16
79201 ATTTTTTTGT
* *
79211 TTATTTCTCTTTTAATA
1 TTATTTCAC-TTTATTA
79228 TTATTTCACTTTATTA
1 TTATTTCACTTTATTA
*
79244 TT-TTTCACTTTATTT
1 TTATTTCACTTTATTA
79259 TTATT
1 TTATT
79264 CTTATTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 14 0.44
16 10 0.31
17 8 0.25
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTCACTTTATTA
Found at i:80156 original size:21 final size:21
Alignment explanation
Indices: 80126--80199 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
80116 GCGTTGCATT
80126 TCGCGTTGCGATAGTTCAAAA
1 TCGCGTTGCGATAGTTCAAAA
* * * **
80147 TCGTGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTCAAAA
*
80167 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAA
80188 TCGCGTTGCGAT
1 TCGCGTTGCGAT
80200 TTTCCAGTTC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCAAAA
Found at i:80172 original size:41 final size:43
Alignment explanation
Indices: 80125--80410 Score: 263
Period size: 41 Copynumber: 7.1 Consensus size: 43
80115 CGCGTTGCAT
*
80125 TTCGCGTTGCGATAGT-TCAAAATCGT-GTTGCGATTTTCC-AG
1 TTCGCGTTGCGATAGTCT-AAAATCGTCGTTGCGATTTTCCAAA
*
80166 TTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AG
1 TTCGCGTTGCGATAGTCT-AAAATCGTCGTTGCGATTTTCCAAA
* * * *
80207 TTCGTGTTGCGATAGTCTACAGTAGTCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAA
* * *
80250 TT--CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAA
*
80291 TT--CGTTGC----G---AAAATCG-CGTTGCGATTTTCC-AG
1 TTCGCGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAA
* *
80323 TTCGCGTTGCGATAGTCTACAATTGTCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAA
* * **
80366 TT--CGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAA
80407 TTCG
1 TTCG
80411 TTGCGAAAAG
Statistics
Matches: 211, Mismatches: 17, Indels: 32
0.81 0.07 0.12
Matches are distributed among these distances:
32 3 0.01
33 14 0.07
34 10 0.05
37 1 0.00
38 1 0.00
41 147 0.70
42 29 0.14
43 6 0.03
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (43 bp):
TTCGCGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAA
Found at i:80176 original size:20 final size:20
Alignment explanation
Indices: 80151--80219 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
80141 TCAAAATCGT
80151 GTTGCGATTTTCCAGTTCGC
1 GTTGCGATTTTCCAGTTCGC
* ** **
80171 GTTGCGATAGTTGAAAATCGC
1 GTTGCGAT-TTTCCAGTTCGC
*
80192 GTTGCGATTTTCCAGTTCGT
1 GTTGCGATTTTCCAGTTCGC
80212 GTTGCGAT
1 GTTGCGAT
80220 AGTCTACAGT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 22 0.59
21 15 0.41
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTTCCAGTTCGC
Found at i:80237 original size:22 final size:22
Alignment explanation
Indices: 80212--80282 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
80202 TCCAGTTCGT
80212 GTTGCGATAGTCTACAGTAGTC
1 GTTGCGATAGTCTACAGTAGTC
* * * *
80234 GTTGCGAT--TTTCCA-AATTC
1 GTTGCGATAGTCTACAGTAGTC
*
80253 GTTGCGATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTAGTC
80275 GTTGCGAT
1 GTTGCGAT
80283 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 11 0.30
20 4 0.11
21 4 0.11
22 18 0.49
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (22 bp):
GTTGCGATAGTCTACAGTAGTC
Found at i:80312 original size:116 final size:116
Alignment explanation
Indices: 80183--80419 Score: 438
Period size: 116 Copynumber: 2.0 Consensus size: 116
80173 TGCGATAGTT
* *
80183 GAAAATCGCGTTGCGATTTTCCAGTTCGTGTTGCGATAGTCTACAGTAGTCGTTGCGATTTTCCA
1 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAATAGTCGTTGCGATTTTCCA
*
80248 AATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
66 AATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTCGTTGC
*
80299 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAATTGTCGTTGCGATTTTCCA
1 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAATAGTCGTTGCGATTTTCCA
80364 AATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTCGTTGC
66 AATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTCGTTGC
80415 GAAAA
1 GAAAA
80420 GTCGTTGTGA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (116 bp):
GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAATAGTCGTTGCGATTTTCCA
AATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTCGTTGC
Found at i:80355 original size:22 final size:21
Alignment explanation
Indices: 80327--80398 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
80317 TTCCAGTTCG
80327 CGTTGCGATAGTCTACAATTGT
1 CGTTGCGATAGTCTACAATT-T
* * *
80349 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAATTT
*
80368 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAATT-T
80390 CGTTGCGAT
1 CGTTGCGAT
80399 TTTCCAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 10 0.25
20 6 0.15
21 5 0.12
22 19 0.47
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAATTT
Found at i:80355 original size:75 final size:74
Alignment explanation
Indices: 80233--80375 Score: 243
Period size: 75 Copynumber: 1.9 Consensus size: 74
80223 CTACAGTAGT
*
80233 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTG
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAATTGTCGTTGCGATTTTCCAAATTCGTTG
80298 CGAAAATCG
66 CGAAAATCG
*
80307 CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTACAATTGTCGTTGCGATTTTCCAAATTCGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAATTGTCGTTGCGATTTTCCAAATTCGT
80371 TGCGA
64 TGCGA
80376 TAGTCTACAG
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
73 3 0.05
74 14 0.22
75 48 0.74
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (74 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAATTGTCGTTGCGATTTTCCAAATTCGTTG
CGAAAATCG
Found at i:80519 original size:6 final size:6
Alignment explanation
Indices: 80509--80556 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
80499 GACACGTATT
*
80509 ACCACT ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
80554 ACC
1 ACC
80557 CGAGACAGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 15 0.37
6 26 0.63
ACGTcount: A:0.29, C:0.54, G:0.15, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:80547 original size:5 final size:5
Alignment explanation
Indices: 80519--80559 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
80509 ACCACTACCA
80519 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
80560 GACAGACAAA
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:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:81085 original size:12 final size:12
Alignment explanation
Indices: 81063--81094 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
81053 GGTCGGGTCG
81063 GGTCG-GGTCAT
1 GGTCGTGGTCAT
81074 GGTCGTGGTCAT
1 GGTCGTGGTCAT
81086 GGTCGTGGT
1 GGTCGTGGT
81095 AATACGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (12 bp):
GGTCGTGGTCAT
Found at i:81220 original size:22 final size:22
Alignment explanation
Indices: 81195--81244 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
81185 TGGAAAATCG
*
81195 CAACGACAACTGTAGACTTTCC
1 CAACGACAACTGTAGACTATCC
* *
81217 CAACAACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCC
81239 CAACGA
1 CAACGA
81245 ATTTGGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (22 bp):
CAACGACAACTGTAGACTATCC
Found at i:81282 original size:21 final size:21
Alignment explanation
Indices: 81232--81368 Score: 111
Period size: 21 Copynumber: 6.7 Consensus size: 21
81222 ACAACTGTAG
* *
81232 ACTATCGCAACG-AATTTGGA
1 ACTATCGCAACGCGATTTGCA
* *
81252 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTGCA
* ** *
81272 ACTATAGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTGCA
* *
81293 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTGCA
** *
81313 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTGCA
* *
81334 A-AATCGCAACGCGATTTCCA
1 ACTATCGCAACGCGATTTGCA
81354 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
81369 AATGCAACGC
Statistics
Matches: 86, Mismatches: 27, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
19 9 0.10
20 36 0.42
21 41 0.48
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTGCA
Found at i:81299 original size:41 final size:41
Alignment explanation
Indices: 81232--81372 Score: 232
Period size: 41 Copynumber: 3.5 Consensus size: 41
81222 ACAACTGTAG
*
81232 ACTATCGCAA--CGAATTTGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACGCGATTTTCA
*
81272 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
81313 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
81354 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
81373 CAACGCGAAT
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
40 9 0.09
41 82 0.86
42 4 0.04
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:81303 original size:20 final size:20
Alignment explanation
Indices: 81278--81347 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
81268 TTCAACTATA
81278 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
** ** *
81298 GCAACGCGATTTTCAACTATC
1 GCAACGCGAAATGGAA-AATC
81319 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
81339 GCAACGCGA
1 GCAACGCGA
81348 TTTCCAACTA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 24 0.62
21 15 0.38
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAATGGAAAATC
Found at i:82012 original size:38 final size:38
Alignment explanation
Indices: 81970--82051 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 38
81960 TTCATTAAAC
* * *
81970 ATTTTTAT-ATTTTCAATTTTGTAAAAAAAATTATATGA
1 ATTTTTATGAATTTAAATTTTGTAAAAAAAA-TATATAA
* *
82008 A-TTTTATGAATTTAAATTTTTTAAAGAAAATATATAA
1 ATTTTTATGAATTTAAATTTTGTAAAAAAAATATATAA
82045 ATATTTT
1 AT-TTTT
82052 CCAACTTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
37 13 0.36
38 19 0.53
39 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (38 bp):
ATTTTTATGAATTTAAATTTTGTAAAAAAAATATATAA
Found at i:82220 original size:18 final size:19
Alignment explanation
Indices: 82197--82240 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
82187 CCAGTAATCC
*
82197 TATTCC-CTAGTAATCTTT
1 TATTCCACTAGTAATCTTA
*
82215 TATTCCCACTGGTAATCTTA
1 TATT-CCACTAGTAATCTTA
82235 TATTCC
1 TATTCC
82241 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (19 bp):
TATTCCACTAGTAATCTTA
Found at i:84687 original size:13 final size:13
Alignment explanation
Indices: 84671--84695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84661 AGACCATCCA
84671 ATTGATTTGCATG
1 ATTGATTTGCATG
84684 ATTGATTTGCAT
1 ATTGATTTGCAT
84696 CAAACGAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
ATTGATTTGCATG
Found at i:88244 original size:2 final size:2
Alignment explanation
Indices: 88239--88267 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
88229 AAAATAATTA
88239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88268 CGTATAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88292 original size:18 final size:17
Alignment explanation
Indices: 88271--88313 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
88261 ATATATACGT
88271 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
88289 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
88306 ATAA-AATA
1 ATAATAATA
88314 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:89788 original size:106 final size:106
Alignment explanation
Indices: 89603--90134 Score: 836
Period size: 106 Copynumber: 5.0 Consensus size: 106
89593 AGTATTGTTC
* *
89603 CGAGTCCAATATCC-TCCTTCGTGAAGTTGAAATTGGTTCT-AGAACTGGGAAATTGTTTGTTGA
1 CGAGTCCAATATCCTTCGTT-GTGAAGTTGAAATTGGTTCTGA-AATTGGGAAATTGTTTGTTGA
*
89666 CAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
89709 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
* *
89774 ACCACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTGT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * *
89815 CGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
89880 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** *
89921 CGAGTCCAATGCCCTTCGTTGTGAAGTTGAAATCGGCTT-TGAAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-TTCTGAAATTGGGAAATTGTTTGTTGAC
* *
89985 AACCGGCCGTCCCTTCGTTGTGAAGTTGAACTTGTATTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
90027 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
90092 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
90133 CG
1 CG
90135 GGTGGCGCGA
Statistics
Matches: 393, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
105 1 0.00
106 386 0.98
107 6 0.02
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:90831 original size:37 final size:36
Alignment explanation
Indices: 90749--90863 Score: 97
Period size: 37 Copynumber: 3.1 Consensus size: 36
90739 GTTTCATGAG
* * * **
90749 AAACGGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAGAA
90786 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAGAA
* * ** *
90822 GAAATTGTCTCACGGAGAGATGAAATTAGTTCCAAGGA
1 -AAACTGTCTCA-AGAGAGACAAAATTAGTTCCAAGAA
90860 AAAC
1 AAAC
90864 ATATTCAAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
36 2 0.03
37 51 0.81
38 10 0.16
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.23
Consensus pattern (36 bp):
AAACTGTCTCAAGAGAGACAAAATTAGTTCCAAGAA
Found at i:90918 original size:36 final size:36
Alignment explanation
Indices: 90876--90945 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
90866 ATTCAAAGAT
*
90876 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAG
*
90912 TTTGTTTCAAGGTAAACTGTCTCAAGAGAGACAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
90946 TGGTGAGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAG
Found at i:92764 original size:14 final size:14
Alignment explanation
Indices: 92745--92799 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
92735 ATCTTTTTAA
92745 ATATATATATTATT
1 ATATATATATTATT
*
92759 ATATATATATTTTT
1 ATATATATATTATT
* *
92773 TTTTAT-TATTATT
1 ATATATATATTATT
*
92786 ATATGTATATTATT
1 ATATATATATTATT
92800 TTTATTTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 9 0.27
14 24 0.73
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
ATATATATATTATT
Found at i:92789 original size:27 final size:26
Alignment explanation
Indices: 92752--92815 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
92742 TAAATATATA
*
92752 TATTATTATATATATATTTTTTTTTAT
1 TATTATTATATATATA-TTATTTTTAT
*
92779 TATTATTATATGTATATTATTTTTAT
1 TATTATTATATATATATTATTTTTAT
92805 T-TTATT-TATAT
1 TATTATTATATAT
92816 TTATCTTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.12
25 5 0.15
26 10 0.29
27 15 0.44
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TATTATTATATATATATTATTTTTAT
Found at i:92937 original size:9 final size:9
Alignment explanation
Indices: 92909--92964 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
92899 TTATCATCGG
92909 TTTTCTTTA
1 TTTTCTTTA
*
92918 TTTTATATTA
1 TTTTCT-TTA
92928 TTTTCTTTA
1 TTTTCTTTA
*
92937 -TTTCATTTG
1 TTTTC-TTTA
*
92946 TTTT-TGTA
1 TTTTCTTTA
92954 TTTTCTTTA
1 TTTTCTTTA
92963 TT
1 TT
92965 ATTTATTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
8 10 0.27
9 16 0.43
10 11 0.30
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTCTTTA
Found at i:103386 original size:16 final size:16
Alignment explanation
Indices: 103368--103397 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
103358 AAAAAATTGA
103368 AAAAGAAAAA-AGAAC
1 AAAAGAAAAAGAGAAC
103383 AAAAGAAAAAGAGAA
1 AAAAGAAAAAGAGAA
103398 AGAACAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAGAAC
Found at i:103399 original size:20 final size:21
Alignment explanation
Indices: 103368--103406 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
103358 AAAAAATTGA
103368 AAAAGAAAAAAGAACAAAAGA
1 AAAAGAAAAAAGAACAAAAGA
*
103389 AAAAG-AGAAAGAACAAAA
1 AAAAGAAAAAAGAACAAAA
103407 ATGTGGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAGAACAAAAGA
Found at i:104006 original size:14 final size:14
Alignment explanation
Indices: 103987--104013 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
103977 GATCAAAACT
103987 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
104001 TCAAGATTCCAGA
1 TCAAGATTCCAGA
104014 TAGGCAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:104505 original size:106 final size:106
Alignment explanation
Indices: 104382--104686 Score: 336
Period size: 100 Copynumber: 2.9 Consensus size: 106
104372 GTGTCACTCG
* * **
104382 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACACAAGCTCAACTTCACAACGAAGGGGCGGTTGGTTGTCAACAAACAATTTCCCAATTT
* *
104447 CAGAGCCAATTTCAACTTCCCAACGAAGGATCTT-GAACCCA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAG-ACCCA
** *
104488 AGACAACACAAGCTCAACTTCATGACGAAGGGGCGGTTGATTGTCAAC-AA-AATTT--C-A-TT
1 AGACAACACAAGCTCAACTTCACAACGAAGGGGCGGTTGGTTGTCAACAAACAATTTCCCAATTT
* * * * *
104547 CAGAGTCGATTTCAACTTCACATCGAAGGATATTAGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACCCA
* * * * * * **
104588 AGATAGCACAAGCACAACTTCACAACGAAGGGGCGGTTGGCTGTTAACAAACAATTTCCCAGTCC
1 AGACAACACAAGCTCAACTTCACAACGAAGGGGCGGTTGGTTGTCAACAAACAATTTCCCAATTT
* *
104653 CAGAACCAATTTCAACTTCACGACGAAGGATATT
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATT
104687 GGACTCGGAG
Statistics
Matches: 162, Mismatches: 30, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
100 74 0.46
101 4 0.02
102 6 0.04
104 6 0.04
105 2 0.01
106 70 0.43
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
AGACAACACAAGCTCAACTTCACAACGAAGGGGCGGTTGGTTGTCAACAAACAATTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACCCA
Found at i:106484 original size:20 final size:21
Alignment explanation
Indices: 106441--106484 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
106431 ATATATACAT
* *
106441 TTTTTTAAATTGATTTTCATC
1 TTTTTTAAATTCATTTTCACC
*
106462 TTTTTTAAA-TCATTTTTACC
1 TTTTTTAAATTCATTTTCACC
106482 TTT
1 TTT
106485 ACCTTATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTTAAATTCATTTTCACC
Found at i:106538 original size:9 final size:9
Alignment explanation
Indices: 106510--106565 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
106500 TTATCATCGG
106510 TTTTCTTTA
1 TTTTCTTTA
*
106519 TTTTATATTA
1 TTTTCT-TTA
106529 TTTTCTTTA
1 TTTTCTTTA
*
106538 -TTTCATTTG
1 TTTTC-TTTA
*
106547 TTTT-TGTA
1 TTTTCTTTA
106555 TTTTCTTTA
1 TTTTCTTTA
106564 TT
1 TT
106566 ATTTATTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
8 10 0.27
9 16 0.43
10 11 0.30
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTCTTTA
Found at i:108025 original size:21 final size:19
Alignment explanation
Indices: 108008--108064 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
107998 TTCCTTTTGA
108008 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
* * *
108027 TTGTT-CTTGTTTT-TTCT
1 TTTTTGCTTCTTTTCTTTT
108044 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
108063 TT
1 TT
108065 GTTCTTGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 7 0.23
18 14 0.47
19 9 0.30
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTGCTTCTTTTCTTTT
Found at i:108026 original size:36 final size:35
Alignment explanation
Indices: 107986--108063 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
107976 TTTGCATGTG
*
107986 CTTTTTGTCCGTT-TCCTTTTGATTTTTGCTTCTTTT
1 CTTTTTGTCC-TTGT-CTTTTCATTTTTGCTTCTTTT
* * *
108022 CTTTTTTGTTCTTGTTTTTTCTTTTTTGCTTCTTTT
1 C-TTTTTGTCCTTGTCTTTTCATTTTTGCTTCTTTT
108058 CTTTTT
1 CTTTTT
108064 TGTTCTTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 5 0.14
36 22 0.61
37 9 0.25
ACGTcount: A:0.01, C:0.17, G:0.09, T:0.73
Consensus pattern (35 bp):
CTTTTTGTCCTTGTCTTTTCATTTTTGCTTCTTTT
Found at i:108033 original size:15 final size:16
Alignment explanation
Indices: 108008--108070 Score: 74
Period size: 16 Copynumber: 3.8 Consensus size: 16
107998 TTCCTTTTGA
108008 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
*
108024 TTTTTGTTCTTGTTTTTTCT
1 TTTTTG--C-T-TCTTTTCT
108044 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
108060 TTTTTG-TTCTT
1 TTTTTGCTTCTT
108071 GATTGAATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.12
16 19 0.46
17 1 0.02
18 2 0.05
19 1 0.02
20 13 0.32
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTTGCTTCTTTTCT
Found at i:108070 original size:10 final size:10
Alignment explanation
Indices: 108020--108057 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
108010 TTTGCTTCTT
108020 TTCTTTTTTG
1 TTCTTTTTTG
108030 TTCTTGTTTT-
1 TTCTT-TTTTG
108040 TTCTTTTTTG
1 TTCTTTTTTG
108050 CTTCTTTT
1 -TTCTTTT
108058 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:112659 original size:38 final size:40
Alignment explanation
Indices: 112593--112669 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
112583 AATGAAAAAA
*
112593 ATATATATACATCAAAGTATTAATAAAATA-AATAAGCTAT
1 ATATATATACAACAAAGTATTAATAAAATAGAA-AAGCTAT
*
112633 ATATATATACAACAAA-TATTTA-AAAATAGAAAAGCTA
1 ATATATATACAACAAAGTATTAATAAAATAGAAAAGCTA
112670 CCCTCTCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.35
39 7 0.21
40 15 0.44
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (40 bp):
ATATATATACAACAAAGTATTAATAAAATAGAAAAGCTAT
Found at i:113007 original size:20 final size:19
Alignment explanation
Indices: 112982--113019 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
112972 ATAATAGGTA
112982 TATAAATAAACTAT-TATAAG
1 TATAAA-AAA-TATATATAAG
113002 TATAAAAAATATATATAA
1 TATAAAAAATATATATAA
113020 CTAGATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 8 0.47
20 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (19 bp):
TATAAAAAATATATATAAG
Found at i:113180 original size:18 final size:17
Alignment explanation
Indices: 113157--113199 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
113147 ATATATACGT
113157 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
113175 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
113192 ATAA-AATA
1 ATAATAATA
113200 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:114954 original size:37 final size:37
Alignment explanation
Indices: 114881--114955 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
114871 GTTGGAAAAT
* *
114881 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
114918 ATTTATATAAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT--ATTTTCTTTAAAAAATTGAAAATCATAAA
114955 A
1 A
114956 AATGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 14 0.42
39 5 0.15
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:116224 original size:23 final size:23
Alignment explanation
Indices: 116170--116224 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
116160 TTCATATTCA
* *
116170 ATTCATTTCATGTTTATAAATAT
1 ATTCATTTAAAGTTTATAAATAT
*
116193 ATTTATTTAAAGTTTATAAATAT
1 ATTCATTTAAAGTTTATAAATAT
*
116216 ATTCGTTTA
1 ATTCATTTA
116225 CCATTCGTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (23 bp):
ATTCATTTAAAGTTTATAAATAT
Found at i:117246 original size:23 final size:23
Alignment explanation
Indices: 117216--117261 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
117206 TATTAATTCC
117216 CTTTTATTTTATTTACATTATTA
1 CTTTTATTTTATTTACATTATTA
*
117239 CTTTTATTTTATTTATATTATTA
1 CTTTTATTTTATTTACATTATTA
117262 TTCTTTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (23 bp):
CTTTTATTTTATTTACATTATTA
Found at i:122770 original size:14 final size:13
Alignment explanation
Indices: 122753--122798 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
122743 TTCAATTTAG
122753 TATTTTAATAATTT
1 TATTTTAAT-ATTT
*
122767 TATTTCAATATTT
1 TATTTTAATATTT
* *
122780 TAATTTAGTATTT
1 TATTTTAATATTT
122793 TATTTT
1 TATTTT
122799 TTTTCTATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 19 0.70
14 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (13 bp):
TATTTTAATATTT
Found at i:123186 original size:2 final size:2
Alignment explanation
Indices: 123179--123214 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
123169 TTTAAAATAC
123179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123215 TTTATTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123265 original size:20 final size:19
Alignment explanation
Indices: 123222--123265 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
123212 TATTTTATTA
123222 TTATTTTATTAAAATATAT
1 TTATTTTATTAAAATATAT
* * *
123241 ATATTCTTATTAATATTTAT
1 TTATT-TTATTAAAATATAT
123261 TTATT
1 TTATT
123266 AATTAATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTTATTAAAATATAT
Found at i:132311 original size:22 final size:22
Alignment explanation
Indices: 132283--132386 Score: 181
Period size: 22 Copynumber: 4.7 Consensus size: 22
132273 TCTACATCTG
132283 CTCTTTTCAAAGATGATAGATT
1 CTCTTTTCAAAGATGATAGATT
132305 CTCTTTTCAAAGATGATAGATT
1 CTCTTTTCAAAGATGATAGATT
*
132327 CTCTCTTCAAAGATGATAGATT
1 CTCTTTTCAAAGATGATAGATT
* *
132349 CTCTCTTCAAAGATGATAAATT
1 CTCTTTTCAAAGATGATAGATT
132371 CTCTTTTCAAAGATGA
1 CTCTTTTCAAAGATGA
132387 AAGCTTTATT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 79 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
CTCTTTTCAAAGATGATAGATT
Found at i:133344 original size:45 final size:45
Alignment explanation
Indices: 133044--133341 Score: 544
Period size: 45 Copynumber: 6.6 Consensus size: 45
133034 CTATTTCCCA
*
133044 CATCTATAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
133089 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
*
133134 CATCTGTAACCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
*
133179 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
*
133224 CATCTGTAAGCCCTTCAGTGCATGATGTTATC-AAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
*
133268 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
133313 CATCTGTAAGCCCTTCAGTGCATGATGTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTT
133342 TTCGAGACCT
Statistics
Matches: 244, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
44 42 0.17
45 202 0.83
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
Found at i:134786 original size:21 final size:21
Alignment explanation
Indices: 134761--134806 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
134751 TTATTTCGAA
*
134761 TTAATACCTTAATTTTAATAT
1 TTAATACCTTAATTATAATAT
**
134782 TTAATATTTTAATTATAATAT
1 TTAATACCTTAATTATAATAT
134803 TTAA
1 TTAA
134807 ATAATTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATACCTTAATTATAATAT
Found at i:134802 original size:14 final size:15
Alignment explanation
Indices: 134772--134809 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
134762 TAATACCTTA
*
134772 ATTTTAATATTTAAT
1 ATTTTAATATATAAT
134787 ATTTTAAT-TATAAT
1 ATTTTAATATATAAT
*
134801 ATTTAAATA
1 ATTTTAATA
134810 ATTTTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAATATATAAT
Found at i:134908 original size:22 final size:22
Alignment explanation
Indices: 134883--134930 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
134873 ATTAATTGCC
134883 CTTTTATTTTATTTACATTATA
1 CTTTTATTTTATTTACATTATA
* *
134905 CTTTTATTTTATTTATATTATT
1 CTTTTATTTTATTTACATTATA
134927 CTTT
1 CTTT
134931 AAGTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (22 bp):
CTTTTATTTTATTTACATTATA
Found at i:134937 original size:22 final size:22
Alignment explanation
Indices: 134890--134937 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
134880 GCCCTTTTAT
* *
134890 TTTATTTACATTATACTTTTAT
1 TTTATTTACATTATACTTTAAG
* *
134912 TTTATTTATATTATTCTTTAAG
1 TTTATTTACATTATACTTTAAG
134934 TTTA
1 TTTA
134938 AATATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATTTACATTATACTTTAAG
Found at i:135539 original size:13 final size:13
Alignment explanation
Indices: 135482--135547 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 13
135472 TTATTATCCC
135482 TTTAATTTCAATAT
1 TTTAATTT-AATAT
*
135496 TTTCAATTTAGTAT
1 TTT-AATTTAATAT
135510 TTTAA--TAAT-T
1 TTTAATTTAATAT
135520 TTT--TTTAATAT
1 TTTAATTTAATAT
*
135531 TTTAATTTAGTAT
1 TTTAATTTAATAT
135544 TTTA
1 TTTA
135548 TTTTTTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
10 8 0.19
11 7 0.16
13 13 0.30
14 10 0.23
15 5 0.12
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTAATTTAATAT
Found at i:138368 original size:19 final size:19
Alignment explanation
Indices: 138317--138371 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
138307 CTTAATATTG
*
138317 AAAAATAAATAAAT-A-TT
1 AAAAATAATTAAATAAGTT
138334 AAAACA-AGATTAAAATAAGTT
1 AAAA-ATA-ATT-AAATAAGTT
138355 AAAAATAATTAAATAAG
1 AAAAATAATTAAATAAG
138372 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.16
18 3 0.10
19 11 0.35
20 5 0.16
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAAATAATTAAATAAGTT
Found at i:139794 original size:3 final size:3
Alignment explanation
Indices: 139778--139833 Score: 87
Period size: 3 Copynumber: 18.3 Consensus size: 3
139768 GGCCTGAAAT
139778 ATA ATA A-A ATTA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
139824 ATA ATA ATA A
1 ATA ATA ATA A
139834 AACCAAATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 43 0.86
4 5 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:140733 original size:114 final size:113
Alignment explanation
Indices: 140249--140870 Score: 998
Period size: 113 Copynumber: 5.5 Consensus size: 113
140239 GTTGAACAAG
* * ** * *
140249 TTCTTC-TCCTTTTTCAGATGAGTTCTTCTTATTATGAACT-TTCTCTGGAAAAGTTGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC-CTGGCAATGTTGATCCATC
* * * * *
140312 GAGTGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAAT
65 GAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
*
140361 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCG
140426 AATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 AATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
* * *
140474 TTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCG
140539 AATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 AATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
* *
140587 TTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGACCTGGCAATATTGATCCATCG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCG
*
140652 AATGATGAATTCAAGTGAAAAGTTTGAACAAGTTCTTCTCATTATGAAC
66 AATGATGAATTCAAGCGAAAAG-TTGAACAAGTTCTTCTCATTATGAAC
*
140701 TTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCG
140766 AATGATGAATTCAAGCGAAAAGTTTGAACAAGTTCTTCTCATTATGAAC
66 AATGATGAATTCAAGCGAAAAG-TTGAACAAGTTCTTCTCATTATGAAC
* *
140815 TTCTTCTTTCCTT-TTCAGATGAGTTATTCTCATTATGAACTCGACCTGGAAATGTT
1 TTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGTT
140871 TTAAGAAAAA
Statistics
Matches: 482, Mismatches: 24, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
112 6 0.01
113 285 0.59
114 185 0.38
115 6 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCG
AATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:141058 original size:75 final size:77
Alignment explanation
Indices: 140879--141060 Score: 287
Period size: 75 Copynumber: 2.4 Consensus size: 77
140869 TTTTAAGAAA
* * * * *
140879 AAACATTATGCACTGTAGGGCTTACAGCTGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTATAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
140944 AGGCTTTTTTGG
66 AGGCTTTTTTGG
*
140956 AAACATCATGCACTGTAGGACTTATAGATGACCC-TAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTATAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
141020 AGGC-TTTTTGG
66 AGGCTTTTTTGG
*
141031 AAACATCATGTACTGTAGGACTTATAGATG
1 AAACATCATGCACTGTAGGACTTATAGATG
141061 TGAGAAATAG
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
75 36 0.37
76 32 0.33
77 30 0.31
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (77 bp):
AAACATCATGCACTGTAGGACTTATAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTTGG
Found at i:144575 original size:114 final size:114
Alignment explanation
Indices: 144375--144819 Score: 710
Period size: 114 Copynumber: 3.9 Consensus size: 114
144365 GATCATGCAG
* * * * *
144375 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
144440 ATACTTACAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
144489 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATGCTAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * * *
144554 ATACTTCTAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* * * *
144603 TTCCTCTTTCAAATCTAATGATTGGTTTTAGGGTTTATACCAAACCAGATCAGATAATTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
144668 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
144717 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
144782 ACACTTCCAGAAGATGCTATTGGGTCTTCTTAATTCTA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTA
144820 TTACGAGAAC
Statistics
Matches: 305, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 305 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:148885 original size:14 final size:14
Alignment explanation
Indices: 148868--148933 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
148858 GTAATTATGG
148868 AAATATGCAAATGT
1 AAATATGCAAATGT
**
148882 AAATA--CAAACAT
1 AAATATGCAAATGT
*
148894 AAAAATGCAAATGT
1 AAATATGCAAATGT
*
148908 AAATATGTAAATGT
1 AAATATGCAAATGT
148922 AACA-ATGCAAAT
1 AA-ATATGCAAAT
148934 TGTATAGTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
12 9 0.22
14 31 0.76
15 1 0.02
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (14 bp):
AAATATGCAAATGT
Found at i:148998 original size:7 final size:7
Alignment explanation
Indices: 148964--149005 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
148954 ATAAGAATAT
148964 AAATGCA
1 AAATGCA
* *
148971 CAATGAA
1 AAATGCA
148978 AAATGCA
1 AAATGCA
148985 AAGATGCA
1 AA-ATGCA
148993 AAATGC-
1 AAATGCA
148999 AAATGCA
1 AAATGCA
149006 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:151361 original size:3 final size:3
Alignment explanation
Indices: 151353--151391 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
151343 TTTATGACTA
* *
151353 AAT AAT AAT AAT AAT AAT AAT ACT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
151392 TAAGAGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:152743 original size:3 final size:3
Alignment explanation
Indices: 152723--152789 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
152713 ATTGGGCCTG
152723 TAA T-A TAA TAA -AA TTAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
152768 TAA TAA TAA TAA -AA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
152790 AAAACCAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 8 0.14
3 46 0.78
4 5 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:155416 original size:27 final size:28
Alignment explanation
Indices: 155354--155427 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
155344 GAATGATTTA
155354 AAAACTAGAAAATTTTGGGTCAGTTTTACT
1 AAAA-TAGAAAA-TTTGGGTCAGTTTTACT
*
155384 AAAATAGAAAATTTGGGTC-GTTTT-GT
1 AAAATAGAAAATTTGGGTCAGTTTTACT
*
155410 AAGAATAGAGAATTTGGG
1 AA-AATAGAAAATTTGGG
155428 ATTCCTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 3 0.07
27 19 0.46
28 8 0.20
29 7 0.17
30 4 0.10
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (28 bp):
AAAATAGAAAATTTGGGTCAGTTTTACT
Found at i:155458 original size:18 final size:18
Alignment explanation
Indices: 155435--155469 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
155425 GGGATTCCTA
*
155435 TATAATAATAATTTTAAT
1 TATAATAATAAGTTTAAT
155453 TATAATAATAAGTTTAA
1 TATAATAATAAGTTTAA
155470 GAATTCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TATAATAATAAGTTTAAT
Found at i:156091 original size:2 final size:2
Alignment explanation
Indices: 156084--156113 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
156074 GGTTTTAGGA
156084 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
156114 GACCATATTG
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:162759 original size:34 final size:34
Alignment explanation
Indices: 162720--162803 Score: 168
Period size: 34 Copynumber: 2.5 Consensus size: 34
162710 AAAAATGGAA
162720 GTGTTTGGAGTATTTCAAGTTAAGGCTATTTTTT
1 GTGTTTGGAGTATTTCAAGTTAAGGCTATTTTTT
162754 GTGTTTGGAGTATTTCAAGTTAAGGCTATTTTTT
1 GTGTTTGGAGTATTTCAAGTTAAGGCTATTTTTT
162788 GTGTTTGGAGTATTTC
1 GTGTTTGGAGTATTTC
162804 GTGTTAGTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (34 bp):
GTGTTTGGAGTATTTCAAGTTAAGGCTATTTTTT
Found at i:168491 original size:25 final size:25
Alignment explanation
Indices: 168457--168507 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
168447 AAACTATCAG
168457 TCCTGGTCTGTTTTAATACCTAAAC
1 TCCTGGTCTGTTTTAATACCTAAAC
168482 TCCTGGTCTGTTTTAATACCTAAAC
1 TCCTGGTCTGTTTTAATACCTAAAC
168507 T
1 T
168508 TTCAATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (25 bp):
TCCTGGTCTGTTTTAATACCTAAAC
Found at i:169024 original size:16 final size:16
Alignment explanation
Indices: 169005--169043 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
168995 TTGCGCCAAG
* *
169005 ATAAAATAAAGTAAAA
1 ATAAAACAAAATAAAA
169021 ATAAAACAAAATAAAA
1 ATAAAACAAAATAAAA
169037 ATGAAAA
1 AT-AAAA
169044 GTGATGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (16 bp):
ATAAAACAAAATAAAA
Found at i:169493 original size:30 final size:30
Alignment explanation
Indices: 169357--169579 Score: 148
Period size: 30 Copynumber: 7.5 Consensus size: 30
169347 AGAAATTTTC
** * *
169357 AGGACTAAAATAACAAAAATAGAAACTTAA
1 AGGACTAAAATAGTAAATATAGAAAGTTAA
* ** *
169387 ATGACTAAAATAACAAAAATAGAAAGTTAA
1 AGGACTAAAATAGTAAATATAGAAAGTTAA
* *
169417 AGGACTAAAATAG-AAAAAAAGAAAGTTAA
1 AGGACTAAAATAGTAAATATAGAAAGTTAA
** * *
169446 AGGGTTGAACT-GTAAATATAGAAAGTTAA
1 AGGACTAAAATAGTAAATATAGAAAGTTAA
* * * * *
169475 AGGACCACAATAGTAAATACAAAAATTTAA
1 AGGACTAAAATAGTAAATATAGAAAGTTAA
* * *
169505 ATGACTAAAATAGTAAAAATA-AACATTTAA
1 AGGACTAAAATAGTAAATATAGAA-AGTTAA
* * * * * *
169535 GGGTCT-AAATAGAAAAAATAGAAACTTAG
1 AGGACTAAAATAGTAAATATAGAAAGTTAA
*
169564 AGGACTAAAACAGTAA
1 AGGACTAAAATAGTAA
169580 TTACAAATAA
Statistics
Matches: 153, Mismatches: 35, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
28 1 0.01
29 64 0.42
30 88 0.58
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (30 bp):
AGGACTAAAATAGTAAATATAGAAAGTTAA
Found at i:171219 original size:3 final size:3
Alignment explanation
Indices: 171205--171253 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
171195 TCAAAATACT
171205 TAA TAA -AA TAA TAA TAA TAA TAA -ATA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
171248 TTAA TA
1 -TAA TA
171254 TTTTAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 5 0.12
3 32 0.78
4 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:171233 original size:18 final size:18
Alignment explanation
Indices: 171205--171253 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
171195 TCAAAATACT
171205 TAATAAA-ATAATAATAA
1 TAATAAATATAATAATAA
171222 TAATAAATATAATAATAA
1 TAATAAATATAATAATAA
171240 TAATATAAT-TAATA
1 TAATA-AATATAATA
171254 TTTTAATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.23
18 20 0.67
19 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAAATATAATAATAA
Found at i:171722 original size:134 final size:131
Alignment explanation
Indices: 171435--171801 Score: 477
Period size: 134 Copynumber: 2.7 Consensus size: 131
171425 ATGAAGAGTT
* * * *
171435 CTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACT-GC
1 CTGGTTATCTAGGGGTGACA-GACTCCTACGTGATGAGGAGATCTGGTC--AGGATGACA-TAGC
* ** *
171499 TCATACGTGATGAAGAGCTCTTGGCCATCTTTAGGAAGGGTGATAACTCGATTCCTGTGTGCTGA
62 TCATACGTGATGAAGAG-TTTTGGCCATCTTTAGGAAGGGTGATAACTCGATTCCTACGTGATGA
*
171564 GGACAG
126 GGACAA
*
171570 TTGGTTATCTAGGGGTGACATGACTCCTACGTGATGAGGAGATCTGGTCAATGGATGACATAGCT
1 CTGGTTATCTAGGGGTGACA-GACTCCTACGTGATGAGGAGATCTGGTC-A-GGATGACATAGCT
*
171635 CATACGTGATAAAGAGTTTTGGCCATCTTTAGGAAGGGTGATAACTC-ATTTCCTACGTGATGAG
63 CATACGTGATGAAGAGTTTTGGCCATCTTTAGGAAGGGTGATAACTCGA-TTCCTACGTGATGAG
171699 GACAA
127 GACAA
* * * *
171704 CTGGTTATCTAGGGGTGACACAGCTCATACGTGATGAGGTGATCTGGTCAGGAAATGACACAGCT
1 CTGGTTATCTAGGGGTGACAGA-CTCCTACGTGATGAGGAGATCTGGTCAGG--ATGACATAGCT
171769 CATACGTGATGAAGAGTTTTGGCCATCTTTAGG
63 CATACGTGATGAAGAGTTTTGGCCATCTTTAGG
171802 GATAATGGTT
Statistics
Matches: 207, Mismatches: 19, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
132 2 0.01
133 3 0.01
134 132 0.64
135 70 0.34
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (131 bp):
CTGGTTATCTAGGGGTGACAGACTCCTACGTGATGAGGAGATCTGGTCAGGATGACATAGCTCAT
ACGTGATGAAGAGTTTTGGCCATCTTTAGGAAGGGTGATAACTCGATTCCTACGTGATGAGGACA
A
Found at i:171751 original size:43 final size:40
Alignment explanation
Indices: 171688--171780 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 40
171678 ACTCATTTCC
**
171688 TACGTGATGAGGACAACTGGTTATCTAGG-GGTGACACAGCTCA
1 TACGTGATGAGGACAACTGG---TC-AGGAAATGACACAGCTCA
** *
171731 TACGTGATGAGGTGATCTGGTCAGGAAATGACACAGCTCA
1 TACGTGATGAGGACAACTGGTCAGGAAATGACACAGCTCA
171771 TACGTGATGA
1 TACGTGATGA
171781 AGAGTTTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 3 0.07
40 24 0.55
43 17 0.39
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (40 bp):
TACGTGATGAGGACAACTGGTCAGGAAATGACACAGCTCA
Found at i:171951 original size:30 final size:28
Alignment explanation
Indices: 171902--172005 Score: 104
Period size: 28 Copynumber: 3.6 Consensus size: 28
171892 GAGATACCAA
*
171902 ATTTTGTTTCCAAAGAAACAGACTCAAAG
1 ATTTT-TTTCAAAAGAAACAGACTCAAAG
* *
171931 ATGATTTTGTT-AAGAGAAACAGACTTAAAG
1 AT--TTTT-TTCAAAAGAAACAGACTCAAAG
171961 ATTTTTTTCAAAATG-AACAGACTCAAAG
1 ATTTTTTTCAAAA-GAAACAGACTCAAAG
* *
171989 ATTTGTTTCAAGAGAAA
1 ATTTTTTTCAAAAGAAA
172006 TTGTTTCAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
27 3 0.05
28 32 0.52
29 3 0.05
30 19 0.31
31 5 0.08
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (28 bp):
ATTTTTTTCAAAAGAAACAGACTCAAAG
Found at i:177500 original size:16 final size:16
Alignment explanation
Indices: 177481--177519 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
177471 TTGCGCCGAG
* *
177481 ATAAAATAAAGTAAAA
1 ATAAAACAAAATAAAA
177497 ATAAAACAAAATAAAA
1 ATAAAACAAAATAAAA
177513 ATTAAAA
1 A-TAAAA
177520 GCGATGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
ATAAAACAAAATAAAA
Found at i:177883 original size:30 final size:30
Alignment explanation
Indices: 177828--177914 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 30
177818 TTTTTAGGAC
* ** *
177828 TAAAACAACAAAAACTTAAACTTAAACGAA
1 TAAAATAACAAAAACAGAAAGTTAAACGAA
* *
177858 TAAAATAACAAAAACAGAAAGTTAAAGGAC
1 TAAAATAACAAAAACAGAAAGTTAAACGAA
* * *
177888 TAAAATAGAAAAAAATAGAAAGGTAAA
1 TAAAATA-ACAAAAACAGAAAGTTAAA
177915 GGATTGAGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 31 0.66
31 16 0.34
ACGTcount: A:0.66, C:0.09, G:0.10, T:0.15
Consensus pattern (30 bp):
TAAAATAACAAAAACAGAAAGTTAAACGAA
Found at i:177963 original size:30 final size:30
Alignment explanation
Indices: 177849--178040 Score: 140
Period size: 30 Copynumber: 6.5 Consensus size: 30
177839 AAACTTAAAC
* * *
177849 TTAAACGAATAAAATA-ACAAAAACAGAAAG
1 TTAAAGGACTAAAATAGA-AAAAATAGAAAG
177879 TTAAAGGACTAAAATAGAAAAAAATAGAAAG
1 TTAAAGGACTAAAATAG-AAAAAATAGAAAG
* ** * * * *
177910 GTAAAGGA-TTGAGTTGTAAATATAGAAAG
1 TTAAAGGACTAAAATAGAAAAAATAGAAAG
* * *
177939 TTAAAGGACTACAATAGAAAATATAGAAAT
1 TTAAAGGACTAAAATAGAAAAAATAGAAAG
* * * *
177969 TTAAAGGATTAAAATAGTAAAAATAGACAT
1 TTAAAGGACTAAAATAGAAAAAATAGAAAG
* * * *
177999 TTAAGGGTCT-AAATAGCAAAAA-AGAAAC
1 TTAAAGGACTAAAATAGAAAAAATAGAAAG
*
178027 TTACAGGACTAAAA
1 TTAAAGGACTAAAA
178041 CAGTAATTAC
Statistics
Matches: 127, Mismatches: 31, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
28 11 0.09
29 32 0.25
30 65 0.51
31 18 0.14
32 1 0.01
ACGTcount: A:0.57, C:0.06, G:0.16, T:0.21
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGAAAAAATAGAAAG
Found at i:177989 original size:60 final size:59
Alignment explanation
Indices: 177845--178046 Score: 174
Period size: 60 Copynumber: 3.4 Consensus size: 59
177835 ACAAAAACTT
* * ** *
177845 AAACTTAAACGAATAAAATAACAAAAACAGAAAGTTAAAGGACTAAAATAGAAAAAAATAG
1 AAACTTAAAGGATTAAAATAGTAAAAATAGAAAGTTAAAGGACT-AAATAG-AAAAAATAG
** * * * * *
177906 AAAGGTAAAGGATT-GAGTTGTAAATATAGAAAGTTAAAGGACTACAATAGAAAATATAG
1 AAACTTAAAGGATTAAAATAGTAAAAATAGAAAGTTAAAGGACTA-AATAGAAAAAATAG
* * * * * *
177965 AAATTTAAAGGATTAAAATAGTAAAAATAGACATTTAAGGGTCTAAATAGCAAAAA-AG
1 AAACTTAAAGGATTAAAATAGTAAAAATAGAAAGTTAAAGGACTAAATAGAAAAAATAG
* * *
178023 AAACTTACAGGACTAAAACAGTAA
1 AAACTTAAAGGATTAAAATAGTAA
178047 TTACAAATAA
Statistics
Matches: 111, Mismatches: 28, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
58 22 0.20
59 30 0.27
60 49 0.44
61 10 0.09
ACGTcount: A:0.57, C:0.07, G:0.16, T:0.20
Consensus pattern (59 bp):
AAACTTAAAGGATTAAAATAGTAAAAATAGAAAGTTAAAGGACTAAATAGAAAAAATAG
Found at i:179667 original size:3 final size:3
Alignment explanation
Indices: 179652--179709 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
179642 TCAAAATACT
*
179652 TAA TAA -AA AAA TAA TAA -ATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
179696 TAA T-A TAA TTAA TA
1 TAA TAA TAA -TAA TA
179710 TTTTGTAGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
2 5 0.10
3 40 0.82
4 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:180683 original size:19 final size:18
Alignment explanation
Indices: 180642--180683 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
180632 AACAAAAATA
180642 TATATAATATAAATAAAG
1 TATATAATATAAATAAAG
*
180660 AATATAAT-TATAATAAAAG
1 TATATAATATA-AAT-AAAG
180679 TATAT
1 TATAT
180684 TTTATATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 10 0.50
19 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
TATATAATATAAATAAAG
Found at i:182282 original size:15 final size:15
Alignment explanation
Indices: 182262--182292 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
182252 GATTAAAAGC
182262 TTTGTAATGGAAGTT
1 TTTGTAATGGAAGTT
182277 TTTGTAATGGAAGTT
1 TTTGTAATGGAAGTT
182292 T
1 T
182293 GTATGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (15 bp):
TTTGTAATGGAAGTT
Found at i:183616 original size:18 final size:19
Alignment explanation
Indices: 183576--183616 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
183566 AGAATATTTA
183576 AACATTCATAATGGTCTGC
1 AACATTCATAATGGTCTGC
183595 -ACATCTCA-AATGGTCT-C
1 AACAT-TCATAATGGTCTGC
183612 AACAT
1 AACAT
183617 ATTTCAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.05
18 16 0.80
19 3 0.15
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (19 bp):
AACATTCATAATGGTCTGC
Found at i:183623 original size:10 final size:10
Alignment explanation
Indices: 183610--183635 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
183600 TCAAATGGTC
183610 TCAACATATT
1 TCAACATATT
183620 TCAACATATT
1 TCAACATATT
183630 TCAACA
1 TCAACA
183636 ACATATCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (10 bp):
TCAACATATT
Found at i:185492 original size:15 final size:15
Alignment explanation
Indices: 185465--185642 Score: 90
Period size: 15 Copynumber: 11.9 Consensus size: 15
185455 TTGTCTTTCT
185465 CATTGTCTC-TTTCAA
1 CATTGTC-CATTTCAA
* *
185480 CATTATCCATTTCTA
1 CATTGTCCATTTCAA
* **
185495 CACT-AACACTTTCAA
1 CATTGTCCA-TTTCAA
*
185510 CATTGTCCCTTTCAA
1 CATTGTCCATTTCAA
* ** *
185525 CACTACCCATTTCAG
1 CATTGTCCATTTCAA
* *
185540 CATTGTCCCTTTCTA
1 CATTGTCCATTTCAA
* *
185555 CACTGTCCATTTCAG
1 CATTGTCCATTTCAA
* *
185570 CATTGTCCCTTTCTA
1 CATTGTCCATTTCAA
* * *
185585 CACTGCCCATTTCAG
1 CATTGTCCATTTCAA
* *
185600 CATTGTCCCTTTCTA
1 CATTGTCCATTTCAA
* ** *
185615 CACTACCCATTTCAG
1 CATTGTCCATTTCAA
*
185630 CATTATCCATTTC
1 CATTGTCCATTTC
185643 TACACCAGCA
Statistics
Matches: 113, Mismatches: 47, Indels: 6
0.68 0.28 0.04
Matches are distributed among these distances:
14 3 0.03
15 109 0.96
16 1 0.01
ACGTcount: A:0.22, C:0.34, G:0.06, T:0.38
Consensus pattern (15 bp):
CATTGTCCATTTCAA
Found at i:185507 original size:30 final size:30
Alignment explanation
Indices: 185473--185838 Score: 267
Period size: 30 Copynumber: 12.2 Consensus size: 30
185463 CTCATTGTCT
*
185473 CTTTCAACATTATCCATTTCTACACTAACA
1 CTTTCAGCATTATCCATTTCTACACTAACA
* * * * *
185503 CTTTCAACATTGTCCCTTTCAACACT-ACC
1 CTTTCAGCATTATCCATTTCTACACTAACA
* * **
185532 CATTTCAGCATTGTCCCTTTCTACACTGTC-
1 C-TTTCAGCATTATCCATTTCTACACTAACA
* * * *
185562 CATTTCAGCATTGTCCCTTTCTACACT-GCC
1 C-TTTCAGCATTATCCATTTCTACACTAACA
* * *
185592 CATTTCAGCATTGTCCCTTTCTACACT-ACC
1 C-TTTCAGCATTATCCATTTCTACACTAACA
* *
185622 CATTTCAGCATTATCCATTTCTACACCAGCA
1 C-TTTCAGCATTATCCATTTCTACACTAACA
* * *
185653 CTTTCAGCACTATCCATTTCTACACCACCA
1 CTTTCAGCATTATCCATTTCTACACTAACA
* * * *
185683 CTTTCAGCATTGTCCCTTTCAACACT-ACC
1 CTTTCAGCATTATCCATTTCTACACTAACA
* * *
185712 CATTTCAGTATTGTCCATTTCTACACT-ACC
1 C-TTTCAGCATTATCCATTTCTACACTAACA
* * * * * * *
185742 CATTTTAGTAGTATCTATTTCTGCACCACCA
1 C-TTTCAGCATTATCCATTTCTACACTAACA
* *
185773 CTTTCAGCATTATCCATTTCTACACCACCA
1 CTTTCAGCATTATCCATTTCTACACTAACA
* * *
185803 CTTTCAGCATTATCCACTTCTACACCACCA
1 CTTTCAGCATTATCCATTTCTACACTAACA
185833 CTTTCA
1 CTTTCA
185839 TAACATCCAC
Statistics
Matches: 290, Mismatches: 40, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
29 6 0.02
30 279 0.96
31 5 0.02
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.36
Consensus pattern (30 bp):
CTTTCAGCATTATCCATTTCTACACTAACA
Found at i:185584 original size:90 final size:89
Alignment explanation
Indices: 185473--185827 Score: 374
Period size: 90 Copynumber: 4.0 Consensus size: 89
185463 CTCATTGTCT
* *
185473 CTTTCAACATTATCCATTTCTACACTAACACTTTCAACATTGTCCCTTTCAACACTACCCATTTC
1 CTTTCAGCATTATCCATTTCTACACTAACACTTTCAGCATTGTCCCTTTCAACACTACCCATTTC
*
185538 AGCATTGTCCCTTTCTACACTGTC-
66 AGCATTGTCCATTTCTACACTG-CA
* * * * *
185562 CATTTCAGCATTGTCCCTTTCTACACT-GCCCATTTCAGCATTGTCCCTTTCTACACTACCCATT
1 C-TTTCAGCATTATCCATTTCTACACTAACAC-TTTCAGCATTGTCCCTTTCAACACTACCCATT
* *
185626 TCAGCATTATCCATTTCTACACCAGCA
64 TCAGCATTGTCCATTTCTACA-CTGCA
* * *
185653 CTTTCAGCACTATCCATTTCTACACCACCACTTTCAGCATTGTCCCTTTCAACACTACCCATTTC
1 CTTTCAGCATTATCCATTTCTACACTAACACTTTCAGCATTGTCCCTTTCAACACTACCCATTTC
* * *
185718 AGTATTGTCCATTTCTACACTACC
66 AGCATTGTCCATTTCTACACTGCA
* * * * * * * * * * *
185742 CATTTTAGTAGTATCTATTTCTGCACCACCACTTTCAGCATTATCCATTTCTACACCA-CCACTT
1 C-TTTCAGCATTATCCATTTCTACACTAACACTTTCAGCATTGTCCCTTTCAACACTACCCA-TT
* *
185806 TCAGCATTATCCACTTCTACAC
64 TCAGCATTGTCCATTTCTACAC
185828 CACCACTTTC
Statistics
Matches: 225, Mismatches: 34, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
89 9 0.04
90 211 0.94
91 5 0.02
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (89 bp):
CTTTCAGCATTATCCATTTCTACACTAACACTTTCAGCATTGTCCCTTTCAACACTACCCATTTC
AGCATTGTCCATTTCTACACTGCA
Found at i:185821 original size:16 final size:16
Alignment explanation
Indices: 185770--185821 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
185760 TTCTGCACCA
185770 CCACTTTCAGCATTAT
1 CCACTTTCAGCATTAT
**
185786 CCA-TTTCTA-CACCA-
1 CCACTTTC-AGCATTAT
185800 CCACTTTCAGCATTAT
1 CCACTTTCAGCATTAT
185816 CCACTT
1 CCACTT
185822 CTACACCACC
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.25, C:0.37, G:0.04, T:0.35
Consensus pattern (16 bp):
CCACTTTCAGCATTAT
Found at i:185829 original size:60 final size:60
Alignment explanation
Indices: 185473--185838 Score: 352
Period size: 60 Copynumber: 6.1 Consensus size: 60
185463 CTCATTGTCT
* * * * * *
185473 CTTTCAACATTATCCATTTCTACACTAACACTTTCAACATTGTCCCTTTCAACACTACC-
1 CTTTCAGCATTATCCATTTCTACACTACCACTTTCAGCATTATCCCTTTCTACACCACCA
* * * *
185532 CATTTCAGCATTGTCCCTTTCTACACTGTCCA-TTTCAGCATTGTCCCTTTCTACACTGC-CCA
1 C-TTTCAGCATTATCCATTTCTACACT-ACCACTTTCAGCATTATCCCTTTCTACAC--CACCA
* * * *
185594 -TTTCAGCATTGTCCCTTTCTACACTACC-CATTTCAGCATTATCCATTTCTACACCAGCA
1 CTTTCAGCATTATCCATTTCTACACTACCAC-TTTCAGCATTATCCCTTTCTACACCACCA
* * * * *
185653 CTTTCAGCACTATCCATTTCTACACCACCACTTTCAGCATTGTCCCTTTCAACACTACC-
1 CTTTCAGCATTATCCATTTCTACACTACCACTTTCAGCATTATCCCTTTCTACACCACCA
* * * * * ** *
185712 CATTTCAGTATTGTCCATTTCTACACTACC-CATTTTAGTAGTATCTATTTCTGCACCACCA
1 C-TTTCAGCATTATCCATTTCTACACTACCAC-TTTCAGCATTATCCCTTTCTACACCACCA
*
185773 CTTTCAGCATTATCCATTTCTACACCACCACTTTCAGCATTATCCAC-TTCTACACCACCA
1 CTTTCAGCATTATCCATTTCTACACTACCACTTTCAGCATTATCC-CTTTCTACACCACCA
185833 CTTTCA
1 CTTTCA
185839 TAACATCCAC
Statistics
Matches: 249, Mismatches: 43, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
58 1 0.00
59 7 0.03
60 234 0.94
61 7 0.03
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.36
Consensus pattern (60 bp):
CTTTCAGCATTATCCATTTCTACACTACCACTTTCAGCATTATCCCTTTCTACACCACCA
Found at i:187612 original size:45 final size:45
Alignment explanation
Indices: 187548--187638 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
187538 CAAAAAGGGG
187548 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
1 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
*
187593 TACTTATTTCTATGTTTCCATTTTCAATTGTTTTTGTAATTTGCT
1 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
187638 T
1 T
187639 GTACATGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.59
Consensus pattern (45 bp):
TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
Found at i:200213 original size:13 final size:13
Alignment explanation
Indices: 200195--200312 Score: 74
Period size: 12 Copynumber: 9.3 Consensus size: 13
200185 CTTGAAGAAG
200195 AAAAAAAA-GAG-
1 AAAAAAAATGAGA
200206 AAAAAAAATGATG-
1 AAAAAAAATGA-GA
200219 AAAAAAAATGATGA
1 AAAAAAAATGA-GA
200233 AAAAAAAATGATG-
1 AAAAAAAATGA-GA
* *
200246 -GAAAAAACG-GA
1 AAAAAAAATGAGA
200257 AAAAAAAA-GAGA
1 AAAAAAAATGAGA
*
200269 AGAAGAAAATG-GA
1 A-AAAAAAATGAGA
*
200282 AGAAAAAATGA-A
1 AAAAAAAATGAGA
*
200294 AAATGAAAAAAGAGA
1 AAA--AAAAATGAGA
200309 AAAA
1 AAAA
200313 TGAAAAAAGA
Statistics
Matches: 87, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
10 1 0.01
11 9 0.10
12 28 0.32
13 24 0.28
14 21 0.24
15 4 0.05
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.08
Consensus pattern (13 bp):
AAAAAAAATGAGA
Found at i:200223 original size:14 final size:13
Alignment explanation
Indices: 200194--200252 Score: 86
Period size: 14 Copynumber: 4.5 Consensus size: 13
200184 GCTTGAAGAA
200194 GAAAAAAAA-GA-
1 GAAAAAAAATGAT
200205 GAAAAAAAATGAT
1 GAAAAAAAATGAT
200218 GAAAAAAAATGAT
1 GAAAAAAAATGAT
200231 GAAAAAAAAATGAT
1 G-AAAAAAAATGAT
200245 GGAAAAAA
1 -GAAAAAA
200253 CGGAAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.20
12 2 0.05
13 14 0.32
14 18 0.41
15 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (13 bp):
GAAAAAAAATGAT
Found at i:200236 original size:27 final size:24
Alignment explanation
Indices: 200194--200312 Score: 91
Period size: 27 Copynumber: 4.7 Consensus size: 24
200184 GCTTGAAGAA
200194 GAAAAAAAAGAGAAAAAAAATGAT
1 GAAAAAAAAGAGAAAAAAAATGAT
200218 GAAAAAAAATGATGAAAAAAAAATGAT
1 GAAAAAAAA-GA-G-AAAAAAAATGAT
* * *
200245 GGAAAAAACG-GAAAAAAAAAGA-
1 GAAAAAAAAGAGAAAAAAAATGAT
*
200267 GAAGAAGAAAATG-GAAGAAAAAATGAA
1 GAA-AA-AAAA-GAGAA-AAAAAATGAT
*
200294 AAATGAAAAAAGAGAAAAA
1 GAA--AAAAAAGAGAAAAA
200313 TGAAAAAAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
22 2 0.03
23 12 0.15
24 13 0.17
25 6 0.08
26 14 0.18
27 28 0.36
28 3 0.04
ACGTcount: A:0.72, C:0.01, G:0.19, T:0.08
Consensus pattern (24 bp):
GAAAAAAAAGAGAAAAAAAATGAT
Found at i:200296 original size:8 final size:8
Alignment explanation
Indices: 200283--200320 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
200273 GAAAATGGAA
200283 GAAAAAAT
1 GAAAAAAT
200291 G-AAAAAT
1 GAAAAAAT
200298 GAAAAAA-
1 GAAAAAAT
200305 GAGAAAAAT
1 GA-AAAAAT
200314 GAAAAAA
1 GAAAAAA
200321 GAGAGAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 9 0.33
8 16 0.59
9 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:200303 original size:16 final size:16
Alignment explanation
Indices: 200291--200333 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
200281 AAGAAAAAAT
200291 GAAAAATGAAAAAAGA
1 GAAAAATGAAAAAAGA
200307 GAAAAATGAAAAAAGA
1 GAAAAATGAAAAAAGA
*
200323 GAGAAAT-AAAA
1 GAAAAATGAAAA
200334 GGAGGGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (16 bp):
GAAAAATGAAAAAAGA
Found at i:201521 original size:51 final size:51
Alignment explanation
Indices: 201460--201706 Score: 476
Period size: 51 Copynumber: 4.8 Consensus size: 51
201450 TGAAGCAAAT
*
201460 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
*
201511 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
201562 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
201613 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
201664 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
201707 ATACTCTCTG
Statistics
Matches: 195, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 195 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (51 bp):
AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
Found at i:201712 original size:20 final size:20
Alignment explanation
Indices: 201687--201726 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
201677 ATTGAGTCCT
201687 ATACTCTCTGAAGGAATAGG
1 ATACTCTCTGAAGGAATAGG
201707 ATACTCTCTGAAGGAATAGG
1 ATACTCTCTGAAGGAATAGG
201727 GAGCGGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (20 bp):
ATACTCTCTGAAGGAATAGG
Found at i:201720 original size:71 final size:71
Alignment explanation
Indices: 201636--201777 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
201626 ATTGAGTCCT
201636 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
201701 AATAGG
66 AATAGG
201707 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
201772 AATAGG
66 AATAGG
201778 GAGCGGACAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.25
Consensus pattern (71 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
AATAGG
Found at i:201768 original size:51 final size:51
Alignment explanation
Indices: 201707--201879 Score: 337
Period size: 51 Copynumber: 3.4 Consensus size: 51
201697 AAGGAATAGG
201707 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCT
201758 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCT
*
201809 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCT
201860 ATACTCTCTGAAGGAATAGG
1 ATACTCTCTGAAGGAATAGG
201880 ATACTCTCTG
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 121 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (51 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCT
Found at i:201802 original size:122 final size:122
Alignment explanation
Indices: 201585--201828 Score: 488
Period size: 122 Copynumber: 2.0 Consensus size: 122
201575 ATTGAGTCCT
201585 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
201650 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
66 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
201707 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
201772 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
66 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
201829 GAGCGGACAA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (122 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
Found at i:201823 original size:173 final size:173
Alignment explanation
Indices: 201534--202013 Score: 816
Period size: 173 Copynumber: 2.8 Consensus size: 173
201524 ATTGAGTCCT
*
201534 ATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
201599 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
66 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
*
201664 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
131 AAGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
201707 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
201772 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
66 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
201837 AAGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
131 AAGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
* * *
201880 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTTCTATACTCCCTGAACG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
** ** * * *
201945 AATAGGGAGCGGACTCGTTTATTGAAGATTTTTTGAGTTCTATACTCTCTGAAGGAAGAGAGAGC
66 AATAGGGAGCGGACAAGTTCGTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGC
202010 GGAC
127 GGAC
202014 CCGTTTTATT
Statistics
Matches: 291, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
173 257 0.88
177 34 0.12
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (173 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
AAGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGG
Found at i:201884 original size:122 final size:123
Alignment explanation
Indices: 201758--202001 Score: 391
Period size: 122 Copynumber: 2.0 Consensus size: 123
201748 ATTGAGTCCT
* *
201758 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAACG
201823 AATAGGGAGCGGACAAGTTCATTGAAGA-TTGAGTCCTATACTCTCTGAAGGAATAGG
66 AATAGGGAGCGGACAAGTTCATTGAAGATTTGAGTCCTATACTCTCTGAAGGAATAGG
*
201880 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTTCTATACTCCCTGAACG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAACG
** * *
201945 AATAGGGAGCGGACTCGTTTATTGAAGATTTTTTGAGTTCTATACTCTCTGAAGGAA
66 AATAGGGAGCGGACAAGTTCATTGAAGA---TTTGAGTCCTATACTCTCTGAAGGAA
202002 GAGAGAGCGG
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
122 87 0.78
126 24 0.22
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (123 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAACG
AATAGGGAGCGGACAAGTTCATTGAAGATTTGAGTCCTATACTCTCTGAAGGAATAGG
Done.