Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004038.1 Hibiscus syriacus cultivar Beakdansim tig00008820_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: 154161
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:789 original size:29 final size:29
Alignment explanation
Indices: 730--789 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
720 TTTATGTTCA
* * *
730 TTTTATTTTTATTCTATGTTTTTACTATT
1 TTTTATTTTTATTATATGTTTTAAATATT
*
759 TTTTATTTTTATTATTTGTTTTAAA-ATT
1 TTTTATTTTTATTATATGTTTTAAATATT
787 TTT
1 TTT
790 AATTAAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (29 bp):
TTTTATTTTTATTATATGTTTTAAATATT
Found at i:1488 original size:48 final size:50
Alignment explanation
Indices: 1420--1513 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 50
1410 TTGCATATAC
1420 TTTCCATTCAGACACATTTCAGAAC-TTTCATATTTCATGTTCATATTAT
1 TTTCCATTCAGACACATTTCAGAACTTTTCATATTTCATGTTCATATTAT
* * * *
1469 TTTCCTTTCAGTCAC-TTTCAGAACTTTTCTTATTTCATTTTCATA
1 TTTCCATTCAGACACATTTCAGAACTTTTCATATTTCATGTTCATA
1514 GAACAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 9 0.22
49 31 0.77
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.49
Consensus pattern (50 bp):
TTTCCATTCAGACACATTTCAGAACTTTTCATATTTCATGTTCATATTAT
Found at i:1926 original size:20 final size:20
Alignment explanation
Indices: 1897--1935 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1887 AGAGCTCATA
*
1897 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
1917 TAGGAGCATATAGATGCAT
1 TAGGAGCATATAGATGCAT
1936 GTGGTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:10436 original size:20 final size:20
Alignment explanation
Indices: 10407--10445 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10397 AGAGCTCATA
*
10407 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
10427 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
10446 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:12153 original size:20 final size:20
Alignment explanation
Indices: 12130--12168 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12120 AAATATGAAC
*
12130 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
12150 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
12169 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:13570 original size:3 final size:3
Alignment explanation
Indices: 13562--13644 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
13552 AATATATATT
* *
13562 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
13610 TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
13645 TGGATAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:14215 original size:113 final size:113
Alignment explanation
Indices: 13963--14408 Score: 750
Period size: 113 Copynumber: 4.0 Consensus size: 113
13953 AGAATTATGC
* * * *
13963 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
14028 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCCTCAAATGATGGATTCAGGT
*
14075 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
14140 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCCTCAAATGATGGATTCAGGT
14188 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
14253 TATGAACTTTCTCTGGAAAAGCTAATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCCTCAAATGATGGATTCAGGT
14301 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
14366 TATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGATAGATT
66 TATGAACTTTCTCTGGAAAAGATAATCCCTCAAATGATGGATT
14409 TGAATCTTTG
Statistics
Matches: 318, Mismatches: 15, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
112 68 0.21
113 250 0.79
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCCTCAAATGATGGATTCAGGT
Found at i:15340 original size:83 final size:83
Alignment explanation
Indices: 15202--15459 Score: 464
Period size: 83 Copynumber: 3.1 Consensus size: 83
15192 TTTACTATGA
* * *
15202 GCAAATTCATCTTCTAAACTCAATGATTG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
15266 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
15284 GCAAATTCATCTTCTAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
*
15349 TTCCAGAAGATGTTATTG
66 TTCCAGAAGATGCTATTG
*
15367 GCAAATTCATCTTCCAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
15432 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
15450 GCAAATTCAT
1 GCAAATTCAT
15460 TTGTTCTATT
Statistics
Matches: 169, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 27 0.16
83 142 0.84
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.29
Consensus pattern (83 bp):
GCAAATTCATCTTCTAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:16549 original size:10 final size:10
Alignment explanation
Indices: 16499--16550 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
16489 CTTGAACCCC
16499 CCTTTTTTTT
1 CCTTTTTTTT
16509 CTCTTTTTTTT
1 C-CTTTTTTTT
* *
16520 TCTTTTATTT
1 CCTTTTTTTT
**
16530 ATTTTTTTTT
1 CCTTTTTTTT
16540 CCTTTTTTTT
1 CCTTTTTTTT
16550 C
1 C
16551 AAGCATAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (10 bp):
CCTTTTTTTT
Found at i:27956 original size:20 final size:20
Alignment explanation
Indices: 27933--27971 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27923 AAATATGAAC
*
27933 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
27953 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
27972 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:29368 original size:3 final size:3
Alignment explanation
Indices: 29360--29457 Score: 160
Period size: 3 Copynumber: 32.7 Consensus size: 3
29350 TTAATATATT
*
29360 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
29408 TAG TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29456 TA
1 TA
29458 TGGATAAAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:36031 original size:2 final size:2
Alignment explanation
Indices: 36024--36067 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
36014 ATTTACCTTT
36024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36066 TA
1 TA
36068 CTATTCATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40243 original size:2 final size:2
Alignment explanation
Indices: 40232--40262 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40222 ATTATTATTA
40232 AT AT -T 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
40263 CCAGCCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:42729 original size:40 final size:40
Alignment explanation
Indices: 42685--42839 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
42675 TCAGTTTCCA
* ** *
42685 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
42725 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
42765 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
42805 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
42840 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:42747 original size:20 final size:20
Alignment explanation
Indices: 42685--42838 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
42675 TCAGTTTCCA
* ** *
42685 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
42705 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
42725 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
42745 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
42765 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
42785 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
42805 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
42826 AAATCGCAACGCG
1 AAATCGCAACGCG
42839 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:42749 original size:60 final size:59
Alignment explanation
Indices: 42624--42755 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 59
42614 AAATGACCAA
* * * * *
42624 CAAAATCGCAACGCGAAATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
1 CAAAATCGCAACGCGAAATAAAAATCGCAACGCGATACACAAAATCGCAAAGCAGTATC
* *
42683 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAACGC-GTATC
1 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATACACA-AAATCGCAAAGCAGTATC
*
42742 CGTAAATCGCAACG
1 C-AAAATCGCAACG
42756 TGTATCCGTA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
59 25 0.40
60 37 0.60
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (59 bp):
CAAAATCGCAACGCGAAATAAAAATCGCAACGCGATACACAAAATCGCAAAGCAGTATC
Found at i:43260 original size:33 final size:33
Alignment explanation
Indices: 43221--43291 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
43211 TTCACTTAGA
*
43221 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
43254 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
43287 TTTCA
1 TTTCA
43292 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:43434 original size:19 final size:19
Alignment explanation
Indices: 43382--43490 Score: 129
Period size: 19 Copynumber: 5.9 Consensus size: 19
43372 CGCAACGAGA
*
43382 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
***
43401 GAGAATGACTGTCGCAACGC
1 GA-AATGAAAATCGCAACGC
43421 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
43440 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
43457 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
43473 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
43491 AGAGAATCGC
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 44 0.59
20 15 0.20
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:43467 original size:14 final size:14
Alignment explanation
Indices: 43448--43504 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
43438 GCGAAATGAA
43448 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
43462 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
43481 AATCGCAACGAGAG
1 AATCGCAACGAGAG
43495 AATCGCAACG
1 AATCGCAACG
43505 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:43471 original size:33 final size:33
Alignment explanation
Indices: 43429--43520 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
43419 GCGAAATGAA
43429 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
43462 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
43495 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
43521 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.24, G:0.22, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:43490 original size:52 final size:55
Alignment explanation
Indices: 43382--43490 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 55
43372 CGCAACGAGA
43382 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAA-GAC--TCGCAACGCGAAATGAAAATCGCAACGC
43440 GAAATGAAAATCGCAACGAGAG-A-A-TCGCAACGCGAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACGAGAGAAGACTCGCAACGCGAAATGAAAATCGCAACG
43491 AGAGAATCGC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
52 27 0.53
55 1 0.02
57 1 0.02
58 22 0.43
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (55 bp):
GAAATGAAAATCGCAACGAGAGAAGACTCGCAACGCGAAATGAAAATCGCAACGC
Found at i:43518 original size:52 final size:52
Alignment explanation
Indices: 43412--43520 Score: 132
Period size: 52 Copynumber: 2.1 Consensus size: 52
43402 AGAATGACTG
* * * *
43412 TCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAAAGCGAAACCAGAGAA
* *
43464 TCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACCA-A-AA
1 TCGCAACGCGAAATGAAAATCGCAACGAGA-AAT-GAAAAGCGAAACCAGAGAA
43516 TCGCA
1 TCGCA
43521 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
52 36 0.73
53 4 0.08
54 9 0.18
ACGTcount: A:0.45, C:0.24, G:0.22, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAAAGCGAAACCAGAGAA
Found at i:43538 original size:19 final size:19
Alignment explanation
Indices: 43516--43566 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
43506 GAAACCAAAA
*
43516 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43535 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43554 TCGCGTTGCGATT
1 TCGCGTTGCGATT
43567 CTCTCGTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:44227 original size:20 final size:20
Alignment explanation
Indices: 44179--44268 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
44169 TGACGTCGAT
* *
44179 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATACGC
44199 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
44219 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
44239 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
44259 GTTGCGATTT
1 GTTGCGATTT
44269 TGGAAAATCG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 59 0.98
21 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:44285 original size:21 final size:21
Alignment explanation
Indices: 44255--44337 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
44245 ATTTTCATAT
*
44255 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
44276 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
44297 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
44318 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
44338 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:44328 original size:42 final size:43
Alignment explanation
Indices: 44235--44333 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
44225 ATTTATGTGT
* *
44235 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
44276 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
44318 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
44334 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:47189 original size:149 final size:150
Alignment explanation
Indices: 46983--47290 Score: 449
Period size: 149 Copynumber: 2.1 Consensus size: 150
46973 CGCTATTTAT
* * * * *
46983 TATGTTAAACTACCTACTAGTTTGTTTGAAGGTTATTAATAATGTAAATGGTAAAATAAAATAGG
1 TATGTTAAACTACCTACTAGTTTGTTTAAAAGTTACTAATAATGTAAATGATAAAATAAAACAGG
* *
47048 T-TATATCTATTACGTTAAAATACCTACAAGCTTGTTTAAAGGTTACTAATAATGTAAACGGTAA
66 TGT-TATCTATTACGTTAAAATACCTACAAGCTTGTTTAAAGGTTAATAATAATGTAAACGATAA
47112 AATAAAATAGACACTACCTAA
130 AATAAAATAGACACTACCTAA
*
47133 TATGTTAAACTACCTAC-GGTTTGTTTAAAAGTTACTAATAATGTAAATGATAAAATAAAACAGG
1 TATGTTAAACTACCTACTAGTTTGTTTAAAAGTTACTAATAATGTAAATGATAAAATAAAACAGG
* * * * *
47197 TGTTATCTATTACGTTAAACTAGCTACTAGTTTGTTTAAAGGTTAATAATAATGTAAATGATAAA
66 TGTTATCTATTACGTTAAAATACCTACAAGCTTGTTTAAAGGTTAATAATAATGTAAACGATAAA
** *
47262 ATAAAATAGACGTTACCTAT
131 ATAAAATAGACACTACCTAA
47282 TATGTTAAA
1 TATGTTAAA
47291 TAGGCGCTAC
Statistics
Matches: 141, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
149 123 0.87
150 18 0.13
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (150 bp):
TATGTTAAACTACCTACTAGTTTGTTTAAAAGTTACTAATAATGTAAATGATAAAATAAAACAGG
TGTTATCTATTACGTTAAAATACCTACAAGCTTGTTTAAAGGTTAATAATAATGTAAACGATAAA
ATAAAATAGACACTACCTAA
Found at i:47282 original size:75 final size:75
Alignment explanation
Indices: 46980--47290 Score: 385
Period size: 75 Copynumber: 4.2 Consensus size: 75
46970 ATGCGCTATT
* * *
46980 TATTATGTTAAACTACCTACTAGTTTGTTTGAAGGTTATTAATAATGTAAATGGTAAAATAAAAT
1 TATTATGTTAAACTACCTACTAGTTTGTTTAAAGGTTACTAATAATGTAAATGATAAAATAAAAT
*
47045 AG--GTTATATC
66 AGACG-T-TACC
* * * * * *
47055 TATTACGTTAAAATACCTACAAGCTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAATAAAAT
1 TATTATGTTAAACTACCTACTAGTTTGTTTAAAGGTTACTAATAATGTAAATGATAAAATAAAAT
**
47120 AGACACTACC
66 AGACGTTACC
* * * *
47130 TAATATGTTAAACTACCTAC-GGTTTGTTTAAAAGTTACTAATAATGTAAATGATAAAATAAAAC
1 TATTATGTTAAACTACCTACTAGTTTGTTTAAAGGTTACTAATAATGTAAATGATAAAATAAAAT
** *
47194 AGGTGTTATC
66 AGACGTTACC
* * *
47204 TATTACGTTAAACTAGCTACTAGTTTGTTTAAAGGTTAATAATAATGTAAATGATAAAATAAAAT
1 TATTATGTTAAACTACCTACTAGTTTGTTTAAAGGTTACTAATAATGTAAATGATAAAATAAAAT
47269 AGACGTTACC
66 AGACGTTACC
47279 TATTATGTTAAA
1 TATTATGTTAAA
47291 TAGGCGCTAC
Statistics
Matches: 198, Mismatches: 35, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
74 60 0.30
75 138 0.70
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (75 bp):
TATTATGTTAAACTACCTACTAGTTTGTTTAAAGGTTACTAATAATGTAAATGATAAAATAAAAT
AGACGTTACC
Found at i:47291 original size:23 final size:23
Alignment explanation
Indices: 47265--47336 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
47255 TGATAAAATA
* *
47265 AAATAGACGTTACCTATTATGTT
1 AAATAGACGCTACCTATTACGTT
*
47288 AAATAGGCGCTACCTATTACGTT
1 AAATAGACGCTACCTATTACGTT
* * * *
47311 AAATAAACACTATCTATTAAGTT
1 AAATAGACGCTACCTATTACGTT
47334 AAA
1 AAA
47337 CTAGCTATTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (23 bp):
AAATAGACGCTACCTATTACGTT
Found at i:47352 original size:121 final size:121
Alignment explanation
Indices: 47200--47457 Score: 392
Period size: 121 Copynumber: 2.1 Consensus size: 121
47190 AAACAGGTGT
*
47200 TATCTATTACGTTAAACTAGCTACTAGTTTGTTTAAAGGTTAATAATAATGTAAATGATAAAATA
1 TATCTATTACGTTAAACTAGCTACTAGTTTGTTTAAAGGTTAATAATAATGTAAACGATAAAATA
* * *
47265 AAATAGACGTTACCTATTATGTTAAATAGGCGCTACCTATTACGTTAAATAAACAC
66 AAATAGACGCTACCTATTATGTGAAATAGGCGCTACCTATTACATTAAATAAACAC
* * *
47321 TATCTATTAAGTTAAACTAGCTA-TTGATTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAAT
1 TATCTATTACGTTAAACTAGCTACTAG-TTTGTTTAAAGGTTAATAATAATGTAAACGATAAAAT
* * * *
47385 AAAATAGGCGCTACCTATTATGTGAAATAGGCGCTACTTATTACATTAAATAAGCGC
65 AAAATAGACGCTACCTATTATGTGAAATAGGCGCTACCTATTACATTAAATAAACAC
*
47442 TACCTATTACGTTAAA
1 TATCTATTACGTTAAA
47458 TAAGTGCTAC
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
120 2 0.02
121 121 0.98
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (121 bp):
TATCTATTACGTTAAACTAGCTACTAGTTTGTTTAAAGGTTAATAATAATGTAAACGATAAAATA
AAATAGACGCTACCTATTATGTGAAATAGGCGCTACCTATTACATTAAATAAACAC
Found at i:47412 original size:23 final size:23
Alignment explanation
Indices: 47386--47480 Score: 127
Period size: 23 Copynumber: 4.1 Consensus size: 23
47376 CGGTAAAATA
* * *
47386 AAATAGGCGCTACCTATTATGTG
1 AAATAAGCGCTACCTATTACGTT
* * *
47409 AAATAGGCGCTACTTATTACATT
1 AAATAAGCGCTACCTATTACGTT
47432 AAATAAGCGCTACCTATTACGTT
1 AAATAAGCGCTACCTATTACGTT
*
47455 AAATAAGTGCTACCTATTACGTT
1 AAATAAGCGCTACCTATTACGTT
47478 AAA
1 AAA
47481 CTAGCTACCG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTACGTT
Found at i:47527 original size:144 final size:144
Alignment explanation
Indices: 47286--47601 Score: 470
Period size: 144 Copynumber: 2.2 Consensus size: 144
47276 ACCTATTATG
* * **
47286 TTAAATAGGCGCTACCTATTACGTTAAATAAACACTATCTATTAAGTTAAACTAGCTATTGATTT
1 TTAAATAAGCGCTACCTATTACGTTAAATAAACACTACCTATTAAGTTAAACTAGCTACCGATTT
* * *
47351 GTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTATGTGAAATAGG
66 GTTTAAAGGTTAATAATAATGTAAACGATAAAATAAAATAAGCGCTACCTACTATGTGAAATAGG
47416 CGCTACTTATTACA
131 CGCTACTTATTACA
*** *
47430 TTAAATAAGCGCTACCTATTACGTTAAATAAGTGCTACCTATTACGTTAAACTAGCTACCGATTT
1 TTAAATAAGCGCTACCTATTACGTTAAATAAACACTACCTATTAAGTTAAACTAGCTACCGATTT
* * *
47495 GTTTAAAGGTTAATAATAATGTAAACGATAAAATAAAATAAGTGTTACCTACTATGTTAAATAGG
66 GTTTAAAGGTTAATAATAATGTAAACGATAAAATAAAATAAGCGCTACCTACTATGTGAAATAGG
* * *
47560 CGTTATTTATTACG
131 CGCTACTTATTACA
*
47574 TTAAATAAGTGCTACCTATTACGTTAAA
1 TTAAATAAGCGCTACCTATTACGTTAAA
47602 CTAGCTACTT
Statistics
Matches: 154, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
144 154 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (144 bp):
TTAAATAAGCGCTACCTATTACGTTAAATAAACACTACCTATTAAGTTAAACTAGCTACCGATTT
GTTTAAAGGTTAATAATAATGTAAACGATAAAATAAAATAAGCGCTACCTACTATGTGAAATAGG
CGCTACTTATTACA
Found at i:47534 original size:121 final size:121
Alignment explanation
Indices: 47409--47650 Score: 333
Period size: 121 Copynumber: 2.0 Consensus size: 121
47399 CTATTATGTG
* * *
47409 AAATAGGCGCTACTTATTACATTAAATAAGCGCTACCTATTACGTTAAATAAGTGCTACCTATTA
1 AAATAAGCGCTACCTACTACATTAAATAAGCGCTACCTATTACGTTAAATAAGTGCTACCTATTA
47474 CGTTAAACTAGCTAC-CGATTTGTTTAAAGGTTAATAATAATGTAAACGATAAAATA
66 CGTTAAACTAGCTACTCG-TTTGTTTAAAGGTTAATAATAATGTAAACGATAAAATA
* * ** * * **
47530 AAATAAGTGTTACCTACTATGTTAAATAGGCGTTATTTATTACGTTAAATAAGTGCTACCTATTA
1 AAATAAGCGCTACCTACTACATTAAATAAGCGCTACCTATTACGTTAAATAAGTGCTACCTATTA
* * * *
47595 CGTTAAACTAGCTACTTGTTTGTTTAAAGGTTAATAGTAATGTAAATGGTAAAATA
66 CGTTAAACTAGCTACTCGTTTGTTTAAAGGTTAATAATAATGTAAACGATAAAATA
47651 TACACTACTT
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
121 104 0.99
122 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (121 bp):
AAATAAGCGCTACCTACTACATTAAATAAGCGCTACCTATTACGTTAAATAAGTGCTACCTATTA
CGTTAAACTAGCTACTCGTTTGTTTAAAGGTTAATAATAATGTAAACGATAAAATA
Found at i:47557 original size:23 final size:23
Alignment explanation
Indices: 47530--47601 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
47520 CGATAAAATA
* *
47530 AAATAAGTGTTACCTACTATGTT
1 AAATAAGTGTTACCTATTACGTT
* * **
47553 AAATAGGCGTTATTTATTACGTT
1 AAATAAGTGTTACCTATTACGTT
*
47576 AAATAAGTGCTACCTATTACGTT
1 AAATAAGTGTTACCTATTACGTT
47599 AAA
1 AAA
47602 CTAGCTACTT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (23 bp):
AAATAAGTGTTACCTATTACGTT
Found at i:53855 original size:3 final size:3
Alignment explanation
Indices: 53842--53903 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
53832 CGGGTCTTTT
** **
53842 TTA TATA TTA TTA TTA TCG TTA TT- TTAA TTA TTA TTA TTA GCA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
53888 TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TT
53904 TACATATTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.81
4 5 0.11
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:55132 original size:19 final size:19
Alignment explanation
Indices: 55086--55132 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
55076 CATTAATTTG
*
55086 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
55106 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
55126 TATATTT
1 TATATTT
55133 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:59589 original size:11 final size:11
Alignment explanation
Indices: 59561--59601 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
59551 AAGAGCAAAG
59561 AGAAAAATCAA
1 AGAAAAATCAA
59572 AGCAAAAATCAA
1 AG-AAAAATCAA
* *
59584 AGAAAAAGCGA
1 AGAAAAATCAA
59595 AGAAAAA
1 AGAAAAA
59602 AGAGGATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.71, C:0.10, G:0.15, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:60765 original size:4 final size:4
Alignment explanation
Indices: 60756--60819 Score: 114
Period size: 4 Copynumber: 16.5 Consensus size: 4
60746 CGAGAAAAGT
60756 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
60804 ATAC --AC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC AT
60820 GATACATAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
4 56 0.97
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:61387 original size:30 final size:30
Alignment explanation
Indices: 61351--61590 Score: 102
Period size: 30 Copynumber: 7.3 Consensus size: 30
61341 AAAACAAAAT
61351 GAAACAAAAATCTTTGAGTTTGTTTCTTTG
1 GAAACAAAAATCTTTGAGTTTGTTTCTTTG
* * * ** *
61381 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTT
1 GAAACAAAA------ATCT-TTGAGTTTGTTTCTTTG
*
61418 GAAACAAAAATCTTTGAGTCTGTTTCTTTG
1 GAAACAAAAATCTTTGAGTTTGTTTCTTTG
* * * ** *
61448 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTT
1 GAAACAAAA------ATCT-TTGAGTTTGTTTCTTTG
*
61485 GAAACAAAAATCTTTGAGTCTGTTTCTTTG
1 GAAACAAAAATCTTTGAGTTTGTTTCTTTG
* * * ** *
61515 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTT
1 GAAACAAAA------ATCT-TTGAGTTTGTTTCTTTG
*
61552 GAAACAAAAATCTTTGAGTCTGTTTCTTTG
1 GAAACAAAAATCTTTGAGTTTGTTTCTTTG
61582 GAAACAAAA
1 GAAACAAAA
61591 TTTTGTCTCT
Statistics
Matches: 148, Mismatches: 41, Indels: 42
0.64 0.18 0.18
Matches are distributed among these distances:
30 69 0.47
31 9 0.06
36 9 0.06
37 61 0.41
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (30 bp):
GAAACAAAAATCTTTGAGTTTGTTTCTTTG
Found at i:61424 original size:67 final size:67
Alignment explanation
Indices: 61350--61645 Score: 574
Period size: 67 Copynumber: 4.4 Consensus size: 67
61340 TAAAACAAAA
*
61350 TGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
1 TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
61415 TT
66 TT
61417 TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
1 TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
61482 TT
66 TT
61484 TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
1 TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
61549 TT
66 TT
61551 TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
1 TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
61616 TT
66 TT
*
61618 TGAAACAAAAATCTTTGAATCTGTTTCT
1 TGAAACAAAAATCTTTGAGTCTGTTTCT
61646 CTTAAAATGA
Statistics
Matches: 227, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 227 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (67 bp):
TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCT
TT
Found at i:62689 original size:28 final size:28
Alignment explanation
Indices: 62618--62699 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
62608 TAAAAATATC
* * *
62618 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
** *
62646 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
62674 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
62700 CATAACTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:62786 original size:40 final size:40
Alignment explanation
Indices: 62728--62918 Score: 143
Period size: 40 Copynumber: 4.5 Consensus size: 40
62718 CCAGCCGTCC
* * * *
62728 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTTT
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
* ** * *
62768 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCCAG---ACCAGATC-TCT
* * * * *
62811 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--CAGA---CCAGATCTCT
62857 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCT
62897 TCATCACGTATGAGCCGTGTCA
1 TCATCACGTATGAGCCGTGTCA
62919 CCCTAGATAA
Statistics
Matches: 118, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
40 54 0.46
42 1 0.01
43 29 0.25
44 1 0.01
46 30 0.25
47 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
Found at i:63034 original size:133 final size:129
Alignment explanation
Indices: 62745--63039 Score: 418
Period size: 133 Copynumber: 2.3 Consensus size: 129
62735 GTAGGAACCG
**
62745 TGTCA-TCCCCAGACCAGATCTTTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGT
1 TGTCATTCCCCA-ACCAGATCTCCTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGT
*
62809 CCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
65 CCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCA
* * * *
62874 TGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACCCTAGATAACCAGTCGTC
1 TGTCATTCCCCAACCAGATCTCCTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTC
*
62938 CTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGTCAGAACTCTTCATCACGTATGA
66 CTCATCACGTAGGAACCGTGTTATCA-CCTT--T--AGATGGCCAGAACTCTTCATCACGTATGA
63003 GCCA
126 GCCA
63007 TGTCA-TCCACCAACCAG-TCGTCCTCATCACGTA
1 TGTCATTCC-CCAACCAGATC-TCCTCATCACGTA
63040 GGAACCGAGT
Statistics
Matches: 150, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
128 44 0.29
129 40 0.27
130 5 0.03
131 1 0.01
132 5 0.03
133 55 0.37
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (129 bp):
TGTCATTCCCCAACCAGATCTCCTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTC
CTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCA
Found at i:63052 original size:91 final size:92
Alignment explanation
Indices: 62884--63094 Score: 273
Period size: 91 Copynumber: 2.3 Consensus size: 92
62874 TGTCATTCCC
* * *
62884 CGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAACCAGTCGTCCTCATCACGTA
1 CGACCAGAACTCTTCATCACGTATGAGCCATGTCACCCTAGACAACCAGTCGTCCTCATCACGTA
* **
62949 GGAACCGTGTTATCACCCTTCCTAAAGA
66 GGAACCGAGTTATCACCCACCCT-AAGA
* ** * *
62977 TGGTCAGAACTCTTCATCACGTATGAGCCATGTCATCC-A-CCAACCAGTCGTCCTCATCACGTA
1 CGACCAGAACTCTTCATCACGTATGAGCCATGTCACCCTAGACAACCAGTCGTCCTCATCACGTA
* *
63040 GGAACCGAGTTATCATCCACCCTTAGA
66 GGAACCGAGTTATCACCCACCCTAAGA
*
63067 CGACCAGACCTCTTCATCACGTATGAGC
1 CGACCAGAACTCTTCATCACGTATGAGC
63095 AGTGTCGTCC
Statistics
Matches: 101, Mismatches: 17, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
90 27 0.27
91 41 0.41
92 1 0.01
93 32 0.32
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (92 bp):
CGACCAGAACTCTTCATCACGTATGAGCCATGTCACCCTAGACAACCAGTCGTCCTCATCACGTA
GGAACCGAGTTATCACCCACCCTAAGA
Found at i:63263 original size:3 final size:3
Alignment explanation
Indices: 63250--63311 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
63240 CGGGTCTTTT
** **
63250 TTA TATA TTA TTA TTA TCG TTA TT- TTAA TTA TTA TTA TTA GCA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
63296 TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TT
63312 TACATATTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.81
4 5 0.11
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:64535 original size:19 final size:19
Alignment explanation
Indices: 64489--64535 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
64479 CATTAATTTG
*
64489 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
64509 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
64529 TATATTT
1 TATATTT
64536 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:67339 original size:2 final size:2
Alignment explanation
Indices: 67332--67362 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
67322 TGCCTTAAAT
67332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67363 TTCTCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71882 original size:29 final size:29
Alignment explanation
Indices: 71849--71931 Score: 148
Period size: 29 Copynumber: 2.9 Consensus size: 29
71839 GGAACATATG
71849 CTATTGAATCTAAACTAGCGTCAATAATA
1 CTATTGAATCTAAACTAGCGTCAATAATA
71878 CTATTGAATCTAAACTAGCGTCAATAATA
1 CTATTGAATCTAAACTAGCGTCAATAATA
* *
71907 CTATTGAATTTAAACTAGAGTCAAT
1 CTATTGAATCTAAACTAGCGTCAAT
71932 CATAATACAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (29 bp):
CTATTGAATCTAAACTAGCGTCAATAATA
Found at i:73063 original size:141 final size:140
Alignment explanation
Indices: 72841--73218 Score: 442
Period size: 141 Copynumber: 2.7 Consensus size: 140
72831 ACTTTTGCAA
* * * * *
72841 GACCTTCTTTGGCGATCCTCATTATCATCATCATCAGAATTATGCCGTGAATGACGATGCTGATC
1 GACCTTCTTCGGCGATCCTCATTA-CATCATCATCCGAATCATGCCGTGAACGACGATGATGATC
** * * *
72906 CCTATTTCTACGCCTATCATTTTCAGATTCCGGCAATCTACCATCACTTATATTCTCTCCTTCCG
65 CCTATTTCTATACCTATCATTTTCAGATTCCAGCAACCAACCATCACTTATATTCTCTCCTT-CG
*
72971 -TACTTCTGTGG
129 ATACTTCTGCGG
* * * *
72982 GACCTTCTACGGCGATCCTCATTACCATCATCATCCGAATCATGCCGCGAACGACAATGGTGATC
1 GACCTTCTTCGGCGATCCTCATTA-CATCATCATCCGAATCATGCCGTGAACGACGATGATGATC
* **
73047 CCTATTTCTATACCTATCATTTTCAGATTCTAGCTCCCAACCATCACTTATATTCTCTCCTTCGA
65 CCTATTTCTATACCTATCATTTTCAGATTCCAGCAACCAACCATCACTTATATTCTCTCCTTCGA
*
73112 TTCTTCTGCGG
130 TACTTCTGCGG
** * * *
73123 GACCTTCTTCTTCGATCCTC-GT-CATCA-CTATCCGAATCATGCCGTGAGCGACGGCT-ATGAT
1 GACCTTCTTCGGCGATCCTCATTACATCATC-ATCCGAATCATGCCGTGAACGAC-GATGATGAT
* *
73184 CCCTATTTCTATATCGATCATTTTCAGATTCCAGC
64 CCCTATTTCTATACCTATCATTTTCAGATTCCAGC
73219 CGTCTATCAC
Statistics
Matches: 203, Mismatches: 31, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
137 1 0.00
138 62 0.31
139 1 0.00
140 3 0.01
141 136 0.67
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34
Consensus pattern (140 bp):
GACCTTCTTCGGCGATCCTCATTACATCATCATCCGAATCATGCCGTGAACGACGATGATGATCC
CTATTTCTATACCTATCATTTTCAGATTCCAGCAACCAACCATCACTTATATTCTCTCCTTCGAT
ACTTCTGCGG
Found at i:74759 original size:31 final size:31
Alignment explanation
Indices: 74685--74751 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
74675 CAGTTACATT
*
74685 GGGGACCATATTGCAAACATACTAAATGTTA
1 GGGGACCATATTGCAAACAGACTAAATGTTA
* *
74716 GGGGACCATATTGCAAACGGATTAAATGTTA
1 GGGGACCATATTGCAAACAGACTAAATGTTA
74747 GGGGA
1 GGGGA
74752 TTGTATTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTA
Found at i:78706 original size:35 final size:35
Alignment explanation
Indices: 78632--78699 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
78622 TTAATGTTCA
78632 AAATTCCAAAACACTTCAATTACATTATAAACCTC
1 AAATTCCAAAACACTTCAATTACATTATAAACCTC
* * * *
78667 AAATTCCAAAATACTTTAATTATATTCTAAACC
1 AAATTCCAAAACACTTCAATTACATTATAAACC
78700 CTAAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTATAAACCTC
Found at i:80915 original size:14 final size:14
Alignment explanation
Indices: 80896--80922 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
80886 TTTCTTTGTT
80896 TATATATCTATATC
1 TATATATCTATATC
80910 TATATATCTATAT
1 TATATATCTATAT
80923 ACATGTTAGG
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:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATATCTATATC
Found at i:83019 original size:48 final size:48
Alignment explanation
Indices: 82961--83055 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
82951 ATAGTTACAT
*
82961 ACTACCTTAGTTTAGAAAGCTTTGGATGACTCCTAGAATAATTCCTTC
1 ACTACCTTAGTTTAGAAAACTTTGGATGACTCCTAGAATAATTCCTTC
83009 ACTACCTTAGTTTAGAAAACTTTGGATGACTCCTAGAATAATTCCTT
1 ACTACCTTAGTTTAGAAAACTTTGGATGACTCCTAGAATAATTCCTT
83056 ATGTGCAGTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (48 bp):
ACTACCTTAGTTTAGAAAACTTTGGATGACTCCTAGAATAATTCCTTC
Found at i:86766 original size:14 final size:14
Alignment explanation
Indices: 86747--86778 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
86737 AGCTATAGTA
86747 TATTATCATAAATT
1 TATTATCATAAATT
*
86761 TATTATCATAACTT
1 TATTATCATAAATT
86775 TATT
1 TATT
86779 TCAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:86812 original size:4 final size:4
Alignment explanation
Indices: 86803--86828 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
86793 AACCGAGAAT
86803 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
86829 ATCATAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:86979 original size:26 final size:29
Alignment explanation
Indices: 86936--86991 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
86926 ATATAAATTT
* *
86936 TATAAATTTAAATTTAATA-AA-AATATA
1 TATAAATTGAAATATAATACAATAATATA
86963 TATAAATTGAAA-ATAATACAATAATATA
1 TATAAATTGAAATATAATACAATAATATA
86991 T
1 T
86992 TTTCTATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 13 0.52
28 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
TATAAATTGAAATATAATACAATAATATA
Found at i:92804 original size:37 final size:37
Alignment explanation
Indices: 92728--92804 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
92718 TTTTTATATT
*
92728 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
92765 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
92802 TTT
1 TTT
92805 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:94812 original size:5 final size:5
Alignment explanation
Indices: 94774--94802 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
94764 ATTTCACACT
94774 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
94803 CTTATCTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:98780 original size:15 final size:15
Alignment explanation
Indices: 98760--98791 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
98750 TGATAGAAAA
98760 AAAATCATAAAGTTT
1 AAAATCATAAAGTTT
98775 AAAATCATAAAGTTT
1 AAAATCATAAAGTTT
98790 AA
1 AA
98792 TGCAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (15 bp):
AAAATCATAAAGTTT
Found at i:100472 original size:32 final size:32
Alignment explanation
Indices: 100434--100499 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
100424 AATCAAAGCC
100434 TTAGTTTATTTATAGCTAAAGAAAATTGGGGT
1 TTAGTTTATTTATAGCTAAAGAAAATTGGGGT
100466 TTAGTTTATTTATAGCTAAAGAAAATTGGGGT
1 TTAGTTTATTTATAGCTAAAGAAAATTGGGGT
100498 TT
1 TT
100500 TTCATCCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.42
Consensus pattern (32 bp):
TTAGTTTATTTATAGCTAAAGAAAATTGGGGT
Found at i:102418 original size:16 final size:16
Alignment explanation
Indices: 102397--102463 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
102387 GTTTATGTCG
102397 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
102413 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
102429 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
102445 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
102459 TTTAT
1 TTTAT
102464 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 41 0.84
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:102430 original size:32 final size:32
Alignment explanation
Indices: 102394--102455 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
102384 AATGTTTATG
102394 TCGTTTATGTTCGTGTTCATTTATGTTCGTGT
1 TCGTTTATGTTCGTGTTCATTTATGTTCGTGT
102426 TCGTTTATGTTCGTGTTCATTTATGTTCGT
1 TCGTTTATGTTCGTGTTCATTTATGTTCGT
102456 TTATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (32 bp):
TCGTTTATGTTCGTGTTCATTTATGTTCGTGT
Found at i:115193 original size:2 final size:2
Alignment explanation
Indices: 115186--115212 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
115176 CAATTGAGTT
115186 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
115213 TCAGCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:122637 original size:23 final size:23
Alignment explanation
Indices: 122605--122663 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
122595 AAATATAAAA
*
122605 TATAATAAAA-AAATATTATTTAT
1 TATAAAAAAATAAATATTA-TTAT
*
122628 TATAAAAAAATTAATATTATTAT
1 TATAAAAAAATAAATATTATTAT
* *
122651 TTTAAAAATATAA
1 TATAAAAAAATAA
122664 GAATAATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATAAAAAAATAAATATTATTAT
Found at i:122647 original size:20 final size:20
Alignment explanation
Indices: 122609--122650 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
122599 ATAAAATATA
*
122609 ATAAAAAAATATTATTTATT
1 ATAAAAAAATAATATTTATT
122629 ATAAAAAAATTAATA-TTATT
1 ATAAAAAAA-TAATATTTATT
122649 AT
1 AT
122651 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAAAAATAATATTTATT
Found at i:123045 original size:23 final size:23
Alignment explanation
Indices: 123003--123058 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
122993 ATTATTATAT
123003 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
123027 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
123050 TAATATTTT
1 T-ATATTTT
123059 TATTAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:126251 original size:158 final size:153
Alignment explanation
Indices: 125952--126258 Score: 436
Period size: 158 Copynumber: 1.9 Consensus size: 153
125942 TCTTTTGTTT
* * *
125952 GTCCACCTTCAGAATCCAATTGCTTCTTCTCCTTCTTAGATTCATCCGACTCACTTTCTTCAGTT
1 GTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCCGACTCACTCTCTTCAGTT
* *
126017 TCTGGTATGTTGCCAGTACCACCATCTTTAGCCCCACTGGCATCCTTGGGTAAATTCTCACCACT
66 TCTGGTAAGTTGCCAGTACCACCATCTTTAGCCCCACTAGCATCCTTGGGTAAATTCTCACCAC-
*
126082 GTTGTTGTTGTTGTTTGTCACTTTGTCC
130 ----TTATTGTTGTTTGTCACTTTGTCC
* *
126110 GTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCTGACTTACTCTCTTCAGTT
1 GTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCCGACTCACTCTCTTCAGTT
126175 TCTGGTGTGTTTAAGTTGCCAGTACCACCATCTTTAGCCCCACTAGCATCCTTGGGTAAATTCTC
66 TC---TG-G--TAAGTTGCCAGTACCACCATCTTTAGCCCCACTAGCATCCTTGGGTAAATTCTC
126240 ACCAC-TATTGTTGTTTGTC
125 ACCACTTATTGTTGTTTGTC
126259 CGTCCAACTT
Statistics
Matches: 135, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
158 75 0.56
161 2 0.01
162 1 0.01
164 57 0.42
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.39
Consensus pattern (153 bp):
GTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCCGACTCACTCTCTTCAGTT
TCTGGTAAGTTGCCAGTACCACCATCTTTAGCCCCACTAGCATCCTTGGGTAAATTCTCACCACT
TATTGTTGTTTGTCACTTTGTCC
Found at i:128078 original size:6 final size:6
Alignment explanation
Indices: 128067--129178 Score: 2189
Period size: 6 Copynumber: 186.2 Consensus size: 6
128057 ACCACCTCTC
128067 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128115 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128163 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128211 ACAAAT AC-AAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128258 AC-AA- ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128304 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128352 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128400 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128448 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT AC-AAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128495 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128543 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128591 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128639 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128687 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128735 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128783 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128831 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128879 ACAAAT ACAAAT ACAAAT AC-AAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128926 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
128974 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
129022 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
129070 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
129118 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
129166 ACAAAT ACAAAT A
1 ACAAAT ACAAAT A
129179 TCTCATATAA
Statistics
Matches: 1101, Mismatches: 0, Indels: 10
0.99 0.00 0.01
Matches are distributed among these distances:
4 2 0.00
5 19 0.02
6 1080 0.98
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ACAAAT
Found at i:130927 original size:19 final size:19
Alignment explanation
Indices: 130903--130939 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
130893 ATGACCAACA
*
130903 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
130922 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
130940 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:131030 original size:21 final size:20
Alignment explanation
Indices: 130965--131051 Score: 66
Period size: 21 Copynumber: 4.2 Consensus size: 20
130955 GTTTCTAGAT
* **
130965 TCGCAATGCGATTTTGACTA
1 TCGCATTGCGATTTTGAAAA
* *
130985 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTT-GAAAA
*
131006 TCGCGTTGCGATTTTAGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * * *
131027 TCGCAATGCGAATATGTAAA
1 TCGCATTGCGATTTTGAAAA
131047 TCGCA
1 TCGCA
131052 ACGCGATAAT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 23 0.44
21 29 0.56
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:131093 original size:20 final size:20
Alignment explanation
Indices: 131068--131112 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
131058 TAATACAAAA
*
131068 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
*
131088 ATCGCAACGCGATTTTGACT
1 ATCGCAACGCGATTCTGACT
131108 ATCGC
1 ATCGC
131113 TATACTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:131968 original size:24 final size:24
Alignment explanation
Indices: 131941--131990 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
131931 TCGAAATTTA
*
131941 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGGCAATACCCGGACTTTG
* *
131965 ATCTTGGGCAATACTCGGATTTTG
1 ATCTTGGGCAATACCCGGACTTTG
131989 AT
1 AT
131991 GATGTTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (24 bp):
ATCTTGGGCAATACCCGGACTTTG
Found at i:132209 original size:14 final size:14
Alignment explanation
Indices: 132180--132216 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
132170 AGAAAAAGAA
132180 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
132195 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
132209 GAAGAAAA
1 GAAGAAAA
132217 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:134463 original size:20 final size:20
Alignment explanation
Indices: 134438--134534 Score: 140
Period size: 20 Copynumber: 4.8 Consensus size: 20
134428 TTACACATTC
* *
134438 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGTGA
134458 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGTGA
*
134478 ATTTGACTATCGTAACGTGA
1 ATTTGACTATCGCAACGTGA
* * *
134498 ATTTGATTATCACAACGGGA
1 ATTTGACTATCGCAACGTGA
134518 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
134535 AGAAAATCGC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (20 bp):
ATTTGACTATCGCAACGTGA
Found at i:134628 original size:20 final size:20
Alignment explanation
Indices: 134577--134628 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
134567 CGCGAATTGA
*
134577 CTTTCGCGTTGCGATTTTGG
1 CTTTAGCGTTGCGATTTTGG
** *
134597 CTTTCTCATTGCGATTTTGAG
1 CTTTAGCGTTGCGATTTTG-G
134618 -TTTAGCGTTGC
1 CTTTAGCGTTGC
134629 AAAAGTGTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (20 bp):
CTTTAGCGTTGCGATTTTGG
Found at i:134794 original size:67 final size:68
Alignment explanation
Indices: 134682--134859 Score: 191
Period size: 71 Copynumber: 2.6 Consensus size: 68
134672 TATTGAAATC
** * ** * *
134682 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAAGAA-TTA-TTTACACATCA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAA-AAAAAATAAGAATTTATTTTACACATCA
134745 ATTA
65 ATTA
* * *
134749 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAATAATAATTCTTATTTTCCTCAT
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAA-AATAAGAA-T-TTATTTTACACAT
134814 CAATTA
63 CAATTA
*
134820 AACAAATCAACTTTTA-AGAATCAATTAAACAATCAAAAAA
1 AACAAATCAACTTTTACA-AATCAATTAAACAAACAAAAAA
134860 GTGTACCCCA
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
66 2 0.02
67 38 0.40
70 4 0.04
71 50 0.53
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (68 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAAAATAAGAATTTATTTTACACATCAA
TTA
Found at i:136195 original size:21 final size:21
Alignment explanation
Indices: 136171--136271 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
136161 GGGAGGGACT
*
136171 TCTTCAACGATGACAGGGGCC
1 TCTTGAACGATGACAGGGGCC
* ** *
136192 TCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGATGACAGGGGCC
** * *
136213 TCTTGAGGGATGATATGGGCC
1 TCTTGAACGATGACAGGGGCC
* *
136234 TCTTGAACGAT-AGGAGAGGCC
1 TCTTGAACGATGA-CAGGGGCC
136255 TCTTGAACGATGACAGG
1 TCTTGAACGATGACAGG
136272 TGAGTCGGGC
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 57 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
TCTTGAACGATGACAGGGGCC
Found at i:136208 original size:42 final size:41
Alignment explanation
Indices: 136149--136271 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 41
136139 TTGAATCGGG
** *
136149 CTCTTGAATAGTGGGAGGGACTTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGAC-TCTTGAACGATGACAGGGGC
** * *
136191 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATATGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTGAACGATGACAGGGGC
* * *
136233 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAG-GGACTCTTGAACGATGACAGG
136272 TGAGTCGGGC
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 1 0.02
42 59 0.91
43 5 0.08
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTGAACGATGACAGGGGC
Found at i:136780 original size:20 final size:20
Alignment explanation
Indices: 136757--136805 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
136747 GAAACTTAAA
136757 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
136777 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
136797 ATCGCAACA
1 ATCGCAACA
136806 AGATAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:136878 original size:20 final size:20
Alignment explanation
Indices: 136849--136886 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
136839 CGAAACTAAA
*
136849 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
136869 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
136887 CGTTACGATT
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:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:136926 original size:20 final size:19
Alignment explanation
Indices: 136897--136934 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
136887 CGTTACGATT
136897 ATCCCGTTGCGATAGTCAA
1 ATCCCGTTGCGATAGTCAA
136916 ATCCGCGTTGCGATAGTCA
1 ATCC-CGTTGCGATAGTCA
136935 TTTTTACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (19 bp):
ATCCCGTTGCGATAGTCAA
Found at i:138890 original size:20 final size:20
Alignment explanation
Indices: 138867--138971 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
138857 TCTGAAACTT
* *
138867 AAAATTGCAACTCGAAAATG
1 AAAATCGCAACACGAAAATG
138887 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * * **
138907 ACTATCGTAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
138927 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
* * *
138946 AAAATCGTAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
138965 AAAATCG
1 AAAATCG
138972 TATTGTGATT
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
19 21 0.30
20 48 0.70
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:138957 original size:19 final size:19
Alignment explanation
Indices: 138882--138973 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 19
138872 TGCAACTCGA
* *
138882 AAATGAAAATCGCAACACG
1 AAATGAAAATCGTAACGCG
**
138901 AAAATGACTATCGTAACGCG
1 -AAATGAAAATCGTAACGCG
* ** *
138921 AATTTGACTATCGCAACGCG
1 AA-ATGAAAATCGTAACGCG
138941 AAATGAAAATCGTAACGCG
1 AAATGAAAATCGTAACGCG
138960 AAACT-AAAATCGTA
1 AAA-TGAAAATCGTA
138974 TTGTGATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 27 0.45
20 33 0.55
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (19 bp):
AAATGAAAATCGTAACGCG
Found at i:139389 original size:22 final size:22
Alignment explanation
Indices: 139362--139412 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
139352 GATGGAGATA
139362 GATGGATTTCACCGGAGATGGG
1 GATGGATTTCACCGGAGATGGG
***
139384 GATGGATTTTGTCGGAGATGGG
1 GATGGATTTCACCGGAGATGGG
*
139406 GACGGAT
1 GATGGAT
139413 GTCGTCATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.10, G:0.43, T:0.25
Consensus pattern (22 bp):
GATGGATTTCACCGGAGATGGG
Found at i:139587 original size:20 final size:20
Alignment explanation
Indices: 139564--139713 Score: 79
Period size: 20 Copynumber: 7.3 Consensus size: 20
139554 GAAAATCACA
139564 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
** ** *
139584 TTGCGATTTTTTGTATTATCGTG
1 TTGCGATAGTCAG-A--ATCGCG
*
139607 TTGTGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* **
139627 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--TAGTCAGAATCGCG
*
139648 TTGCGATAGTCAGAATCGCT
1 TTGCGATAGTCAGAATCGCG
* * * * *
139668 TTGTGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCG
* *
139688 TTGCGATAGTCAAAATCGCA
1 TTGCGATAGTCAGAATCGCG
139708 TTGCGA
1 TTGCGA
139714 ATCTGGAAAC
Statistics
Matches: 94, Mismatches: 28, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
19 4 0.04
20 58 0.62
21 15 0.16
22 4 0.04
23 13 0.14
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:139656 original size:41 final size:41
Alignment explanation
Indices: 139564--139713 Score: 178
Period size: 41 Copynumber: 3.6 Consensus size: 41
139554 GAAAATCACA
*
139564 TTGCGATAGTCAGAATCGCGTTGCGATTTTTTGTATTATCGTG
1 TTGCGATAGTCAGAATCGCGTTGCGA--TTTTGTATTATCGCG
*
139607 TTGTGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGCG
* * ** *
139648 TTGCGATAGTCAGAATCGCTTTGTGA-TTTACA-TATTCGCA
1 TTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTA-TCGCG
* *
139688 TTGCGATAGTCAAAATCGCATTGCGA
1 TTGCGATAGTCAGAATCGCGTTGCGA
139714 ATCTGGAAAC
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
39 2 0.02
40 31 0.33
41 37 0.39
43 25 0.26
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (41 bp):
TTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGCG
Found at i:140806 original size:50 final size:50
Alignment explanation
Indices: 140712--140806 Score: 111
Period size: 50 Copynumber: 1.9 Consensus size: 50
140702 CTTTTGTAGC
* * *
140712 AAGGCGCGCCCCTGCAGCGCGCTTTACGCTGATTTGGTGCCACGTTGGGT
1 AAGGCGCGCCCCTGCAGCGCGCTTTACACTGAGTTGGTGACACGTTGGGT
* * * *
140762 AAGGTGCGCTCCTGTAGCGCGCTTTATACTGAGTTGGAT-ACACGT
1 AAGGCGCGCCCCTGCAGCGCGCTTTACACTGAGTTGG-TGACACGT
140807 GCATAAAGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
50 36 0.97
51 1 0.03
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (50 bp):
AAGGCGCGCCCCTGCAGCGCGCTTTACACTGAGTTGGTGACACGTTGGGT
Found at i:143074 original size:35 final size:34
Alignment explanation
Indices: 143035--143123 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 34
143025 AATGGTAATA
* *
143035 AACAAAATTAACCAAAATACATTAACAAA-AAGTCC
1 AACAAAATTAA-CAAAATAAATTAA-AAATAAATCC
*
143070 AACAAATTTAACAAAATAAATTAAAAATAAATCC
1 AACAAAATTAACAAAATAAATTAAAAATAAATCC
* **
143104 AACCAAATTAATGAAATAAA
1 AACAAAATTAACAAAATAAA
143124 GTAAGTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 3 0.07
34 33 0.72
35 10 0.22
ACGTcount: A:0.63, C:0.15, G:0.02, T:0.20
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTAAAAATAAATCC
Found at i:145412 original size:16 final size:16
Alignment explanation
Indices: 145379--145429 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
145369 TTATATCTGC
*
145379 AATAAAA-ATTAATTA
1 AATAAAATATTAAATA
*
145394 AATAAAATATTAAAAA
1 AATAAAATATTAAATA
*
145410 AATTAAATACTTAAATA
1 AATAAAATA-TTAAATA
145427 AAT
1 AAT
145430 TACAAACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 7 0.23
16 14 0.47
17 9 0.30
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAAATATTAAATA
Found at i:145423 original size:17 final size:16
Alignment explanation
Indices: 145393--145431 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
145383 AAAATTAATT
*
145393 AAATAAAATATTAAAA
1 AAATTAAATATTAAAA
*
145409 AAATTAAATACTTAAAT
1 AAATTAAATA-TTAAAA
145426 AAATTA
1 AAATTA
145432 CAAACAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAATATTAAAA
Found at i:147213 original size:226 final size:227
Alignment explanation
Indices: 146819--147368 Score: 782
Period size: 226 Copynumber: 2.4 Consensus size: 227
146809 ATATTGACTT
* * * * * * *
146819 TAACATAACAGATTAATTACTGTAAATATTATCAAACATAATAACATATTAAGTAGCCCTTATGT
1 TAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
* ** * *
146884 AACGTAACTGA-TAGCGCCTTTTTAAAACTGAT-ACGGCCTTAGAAATCTGACGATAATAAAATA
66 AACGTAA-TAAGTAGCGCCTTTTTAAAGTTGATGACGGCATTAGAAATCTGACGATAACAAAATA
* * *
146947 GGTCAATTACTTTATTTGTTATCAGTATTATAAACATATTAGGTAACGCCTAAAATGTTACCAAA
130 AGTCAATTACTTAATTTGTTATCAGTATTATAAACATATTAGGTAACACCTAAAATGTTACCAAA
* *
147012 GTTTAAGCTGATGGAGCCTTAGAAATCCAACAA
195 GTTAAAGCTGATAGAGCCTTAGAAATCCAACAA
147045 TAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
1 TAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
* *
147110 AACGTAATAAGTAGCGTCTTTTTAAAGTTGATGA-GGCATTAGAAATCTGACTATAACAAAATAA
66 AACGTAATAAGTAGCGCCTTTTTAAAGTTGATGACGGCATTAGAAATCTGACGATAACAAAATAA
* * * * * *
147174 GTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTGACACTTAAAATGTTACTAAAG
131 GTCAATTACTTAATTTGTTATCAGTATTATAAACATATTAGGTAACACCTAAAATGTTACCAAAG
* * *
147239 TTAAAGCTGATAGAGTCTTAGAAATCCGACGA
196 TTAAAGCTGATAGAGCCTTAGAAATCCAACAA
* *
147271 TAACATAATCGGTTAATTACTAGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
1 TAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
* *
147336 AACGTAATAGGTAGCACCTTTTTAAAGTTGATG
66 AACGTAATAAGTAGCGCCTTTTTAAAGTTGATG
147369 GTGTAACACC
Statistics
Matches: 289, Mismatches: 33, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
225 2 0.01
226 286 0.99
227 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (227 bp):
TAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
AACGTAATAAGTAGCGCCTTTTTAAAGTTGATGACGGCATTAGAAATCTGACGATAACAAAATAA
GTCAATTACTTAATTTGTTATCAGTATTATAAACATATTAGGTAACACCTAAAATGTTACCAAAG
TTAAAGCTGATAGAGCCTTAGAAATCCAACAA
Found at i:148139 original size:23 final size:23
Alignment explanation
Indices: 148105--148173 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
148095 CACCACAGCT
* *
148105 CGTATAAATGCACCGGAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
148128 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
148151 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
148174 TATAAGATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:148936 original size:2 final size:2
Alignment explanation
Indices: 148929--148970 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
148919 ACTTATAAAC
148929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
148971 GACTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152587 original size:16 final size:16
Alignment explanation
Indices: 152566--152603 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
152556 CAATGTATGA
152566 GATATGTATGTTTTGG
1 GATATGTATGTTTTGG
152582 GATATGTATGTTTTGG
1 GATATGTATGTTTTGG
152598 GATATG
1 GATATG
152604 AATTATATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
GATATGTATGTTTTGG
Found at i:153696 original size:2 final size:2
Alignment explanation
Indices: 153689--153719 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
153679 TAAGTATGGA
153689 AT 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 AT A
153720 CGTATCGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.