Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005008.1 Hibiscus syriacus cultivar Beakdansim tig00011239_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: 79317
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2038 original size:24 final size:23
Alignment explanation
Indices: 1999--2070 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
1989 AGTAACGGAG
1999 ATATCAGAATCAAAATAGAATTC
1 ATATCAGAATCAAAATAGAATTC
*
2022 ATATCAGATATCAAAATAGAATAC
1 ATATCAGA-ATCAAAATAGAATTC
* * *
2046 ATACCAGAAATCAGAACAGAATTC
1 ATATCAG-AATCAAAATAGAATTC
2070 A
1 A
2071 GATAAGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 8 0.19
24 33 0.79
25 1 0.02
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (23 bp):
ATATCAGAATCAAAATAGAATTC
Found at i:2065 original size:12 final size:12
Alignment explanation
Indices: 2050--2087 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2040 GAATACATAC
2050 CAGAAATCAGAA
1 CAGAAATCAGAA
*
2062 CAGAATTCAGATA
1 CAGAAATCAGA-A
2075 -AGAAATCAGAA
1 CAGAAATCAGAA
2086 CA
1 CA
2088 AATTCAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:5892 original size:2 final size:2
Alignment explanation
Indices: 5885--5929 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
5875 TATTGTACAT
5885 TA TA TA TA TA TA TGA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5927 TA T
1 TA T
5930 CATCCCTTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6106 original size:29 final size:29
Alignment explanation
Indices: 6073--6133 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
6063 AGTCCATTAT
6073 TCTTTTACTCAACAATGTTT-AATCGTTCA
1 TCTTTTACTCAACAATGTTTAAAT-GTTCA
* *
6102 TCTTTTACTTAACAATTTTTAAATGTTCA
1 TCTTTTACTCAACAATGTTTAAATGTTCA
6131 TCT
1 TCT
6134 AACTGGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (29 bp):
TCTTTTACTCAACAATGTTTAAATGTTCA
Found at i:6599 original size:59 final size:59
Alignment explanation
Indices: 6465--6810 Score: 480
Period size: 59 Copynumber: 5.9 Consensus size: 59
6455 ATTCCCATAT
* * * *
6465 GGAAATTCATACACTTAGTATGAGTTTCTTATCTTTTTA-CACATAAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
* *
6523 GGAAATTCATACACTTAGTATGAATTTCTAAACATTTTAGCACATAAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
** *
6582 GGAAATTCATATGCTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
* * * **
6641 GGAAATTCATACACTTAGTATGAATTTCTTTATATTTTAGCAGACCTAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
* *
6700 -GAAATTTGATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCCATAC
1 GGAAA-TTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
* * * * *
6759 GGAAATTAATACACTTAGTCTGAATTTCATAACATTTTAGCTCACATAGTGC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
6811 AATTTGGTAA
Statistics
Matches: 256, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
58 39 0.15
59 213 0.83
60 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
Found at i:10994 original size:22 final size:22
Alignment explanation
Indices: 10969--11014 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
10959 AAGTTTACCG
10969 TTGACTGGTAAGACCGTTGACT
1 TTGACTGGTAAGACCGTTGACT
* *
10991 TTGACTGTTATGACCGTTGACT
1 TTGACTGGTAAGACCGTTGACT
11013 TT
1 TT
11015 AACCGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (22 bp):
TTGACTGGTAAGACCGTTGACT
Found at i:23488 original size:133 final size:132
Alignment explanation
Indices: 23246--23497 Score: 290
Period size: 133 Copynumber: 1.9 Consensus size: 132
23236 ACGTTGACCG
* * *
23246 TGACCAAAAAGTCAAATTTTCGAAAAGTCATATTTTATGTTTTTCGATGTCCTGAGTCCGAATCT
1 TGACCAAAAAGTCAAATTTTCGAAAAGACATATTTTATGTCTTTCGACGTCCTGAGTCCGAATCT
* * * ** *
23311 GAAGTCTGTTTTTCTAAATTCAAACCCGAAAGCCTCTTATTTGTCAATCAAACCCATTGACTGAC
66 GAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATTGTCAATCAAACCCATTGACTGAC
23376 TT
131 TT
* * * * * *
23378 TGACCAAAAAGTCAAAATTTTTGAAATGACATATTTTTTGTCTTTCGACGTCCTGATTCTG-ATT
1 TGACCAAAAAGTC-AAATTTTCGAAAAGACATATTTTATGTCTTTCGACGTCCTGAGTCCGAATC
* * * * * *
23442 TCGCAGTCCGTTTTGCCAAATTCGAAGCTGAAATCCTCCAAATTGTCAGTCAAACC
65 T-GAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATTGTCAATCAAACC
23498 AGAGAAATGC
Statistics
Matches: 97, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
132 16 0.16
133 81 0.84
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (132 bp):
TGACCAAAAAGTCAAATTTTCGAAAAGACATATTTTATGTCTTTCGACGTCCTGAGTCCGAATCT
GAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATTGTCAATCAAACCCATTGACTGAC
TT
Found at i:42035 original size:21 final size:20
Alignment explanation
Indices: 42008--42105 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
41998 AATCAGTGTC
42008 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
42029 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
42049 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
42069 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
42090 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
42106 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:42058 original size:41 final size:41
Alignment explanation
Indices: 41949--42105 Score: 117
Period size: 41 Copynumber: 3.9 Consensus size: 41
41939 AAATGACCAA
* * **
41949 CAAAATCGCAACGCGAA-ATAAAAAACGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
41988 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
42029 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
42070 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
42106 ACACATAAAT
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 16 0.19
41 53 0.62
42 4 0.05
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:42115 original size:20 final size:20
Alignment explanation
Indices: 42092--42262 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
42082 GCGAATATGA
42092 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
42112 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
42132 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
42152 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
42172 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
42192 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
42212 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
42232 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
42252 AAATCGCAACG
1 AAATCGCAACG
42263 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:42157 original size:60 final size:58
Alignment explanation
Indices: 42072--42281 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
42062 CGATTTTCCA
* ** * *
42072 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
42132 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
42192 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
42252 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
42282 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:42263 original size:20 final size:20
Alignment explanation
Indices: 42126--42281 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
42116 CGCAATGCGT
*
42126 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
42146 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
42166 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
42186 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
42206 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
42226 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
42246 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
42266 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
42282 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:42263 original size:40 final size:40
Alignment explanation
Indices: 42092--42281 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
42082 GCGAATATGA
* *
42092 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
42132 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
42172 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
42212 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
42252 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
42282 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:43003 original size:24 final size:24
Alignment explanation
Indices: 42964--43010 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42954 AAATTTGGTC
42964 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
42988 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
43011 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:43202 original size:12 final size:12
Alignment explanation
Indices: 43185--43209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43175 ATATAATCCT
43185 GAAGAAGAAAAA
1 GAAGAAGAAAAA
43197 GAAGAAGAAAAA
1 GAAGAAGAAAAA
43209 G
1 G
43210 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:45511 original size:19 final size:19
Alignment explanation
Indices: 45489--45757 Score: 300
Period size: 19 Copynumber: 15.4 Consensus size: 19
45479 CGGAAATTAC
*
45489 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45508 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
45522 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
45542 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
45556 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45575 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45594 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
45608 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45627 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45646 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
45660 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45679 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45698 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45717 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
45731 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45750 AATCGCAA
1 AATCGCAA
45758 CGAGAGAATC
Statistics
Matches: 215, Mismatches: 9, Indels: 52
0.78 0.03 0.19
Matches are distributed among these distances:
14 48 0.22
15 2 0.01
16 16 0.07
17 15 0.07
18 3 0.01
19 118 0.55
20 13 0.06
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:45576 original size:33 final size:33
Alignment explanation
Indices: 45489--45779 Score: 302
Period size: 33 Copynumber: 8.5 Consensus size: 33
45479 CGGAAATTAC
* * *
45489 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
45522 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* *
45556 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * * *
45588 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
* *
45627 AATCGCAATACGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
45660 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
*
45698 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
45731 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
45764 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
45780 TATAAACGCA
Statistics
Matches: 219, Mismatches: 21, Indels: 36
0.79 0.08 0.13
Matches are distributed among these distances:
31 7 0.03
32 7 0.03
33 113 0.52
34 31 0.14
35 4 0.02
36 4 0.02
37 1 0.00
38 38 0.17
39 7 0.03
40 7 0.03
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:45604 original size:52 final size:52
Alignment explanation
Indices: 45517--45779 Score: 410
Period size: 52 Copynumber: 5.0 Consensus size: 52
45507 AAATCCCAAC
45517 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
45570 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
45622 ATGAAAATCGCAATACGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
45674 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
45729 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
45778 AT
1 AT
45780 TATAAACGCA
Statistics
Matches: 196, Mismatches: 6, Indels: 19
0.89 0.03 0.09
Matches are distributed among these distances:
47 10 0.05
48 1 0.01
49 5 0.03
50 2 0.01
52 144 0.73
53 16 0.08
54 3 0.02
55 5 0.03
56 1 0.01
57 9 0.05
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:45641 original size:71 final size:69
Alignment explanation
Indices: 45489--45779 Score: 288
Period size: 71 Copynumber: 4.2 Consensus size: 69
45479 CGGAAATTAC
* *
45489 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAAAATCGCAA--
1 AATCGCAATGCGAAATGAAAATCGCAACGA--AAGAATCGCAA-GC-G-AATGAAAATCGCAATG
*
45550 CG--A-GAG
61 CGAAATGAA
*
45556 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAAGCGAATGAAAATCGCAATG
45618 CGAAATGAA
61 CGAAATGAA
* *
45627 AATCGCAATACGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA-GCG-AATGAAAATCGCAATGCGA
45692 AATGAA
64 AATGAA
45698 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA--CG-
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA-GCG-AATGAAAATCGCAATGCGA
*
45760 -A-GAG
64 AATGAA
45764 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
45780 TATAAACGCA
Statistics
Matches: 197, Mismatches: 10, Indels: 35
0.81 0.04 0.14
Matches are distributed among these distances:
66 36 0.18
67 27 0.14
68 7 0.04
69 8 0.04
70 4 0.02
71 107 0.54
72 8 0.04
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (69 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAGCGAATGAAAATCGCAATGCGAAA
TGAA
Found at i:45895 original size:19 final size:19
Alignment explanation
Indices: 45786--45887 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
45776 AAATTATAAA
*
45786 CGCATTGTGATTTTCATTT
1 CGCATTGCGATTTTCATTT
45805 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
45825 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
45841 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
45858 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
45877 CGCATTGCGAT
1 CGCATTGCGAT
45888 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.49
20 18 0.24
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:46013 original size:14 final size:14
Alignment explanation
Indices: 45994--46030 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
45984 CATCAATTAC
45994 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
46008 ACAAATCATCTTTT
1 ACAAATCAACTTTT
46022 ACAAATCAA
1 ACAAATCAA
46031 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:48030 original size:14 final size:14
Alignment explanation
Indices: 48011--48067 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
48001 GCGAAATGAA
*
48011 AATCGCAACGACAG
1 AATCGCAACGAAAG
48025 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
48042 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
48058 AATCGCAACG
1 AATCGCAACG
48068 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:48038 original size:33 final size:33
Alignment explanation
Indices: 47992--48084 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
47982 GCGAAACCAA
*
47992 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
48025 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
48058 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
48085 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:48049 original size:19 final size:19
Alignment explanation
Indices: 47955--48089 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
47945 TAGTTTACTT
* *
47955 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
47975 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
47994 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
48013 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
48027 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
48046 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
48060 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
48079 TCGCAATGCGA
1 TCGCAACGCGA
48090 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:48107 original size:19 final size:19
Alignment explanation
Indices: 48085--48197 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
48075 AAAATCGCAA
48085 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
48104 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
48118 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
48137 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
48151 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
48170 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
48189 TGCGATTTT
1 TGCGATTTT
48198 AACTTTCGTG
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 48 0.62
ACGTcount: A:0.07, C:0.18, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:48127 original size:33 final size:33
Alignment explanation
Indices: 48085--48176 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
48075 AAAATCGCAA
48085 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
48118 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
48151 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
48177 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:48210 original size:20 final size:18
Alignment explanation
Indices: 48115--48213 Score: 80
Period size: 19 Copynumber: 5.4 Consensus size: 18
48105 GCGATCTTGT
*
48115 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
* *
48134 CGTTGCGA--TTCTGT--
1 CGTTGCGATTTTATTTCG
48148 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTT-ATTTCG
*
48167 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
48186 CGTTGCGATTTTAACTTTCG
1 CGTTGCGATTTT-A-TTTCG
*
48206 TGTTGCGA
1 CGTTGCGA
48214 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 8 0.12
16 4 0.06
17 4 0.06
19 37 0.57
20 12 0.18
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTATTTCG
Found at i:48377 original size:93 final size:93
Alignment explanation
Indices: 48261--48729 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
48251 ATGGATTGCA
*
48261 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
48325 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
48353 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
48418 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
48446 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
48511 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
48539 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
48604 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
48632 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
48697 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
48725 TTACT
1 TTACT
48730 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 370 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:50455 original size:14 final size:14
Alignment explanation
Indices: 50436--50525 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
50426 TTGAAATGAA
50436 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
50450 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
50469 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
50483 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
50502 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
50516 AATCACAACG
1 AATCGCAACG
50526 CGAAATAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:50473 original size:33 final size:33
Alignment explanation
Indices: 50428--50542 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
50418 TCTTTTGGTT
50428 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
50461 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
50494 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
50527 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
50543 TGCGATTTGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.48, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:50474 original size:19 final size:19
Alignment explanation
Indices: 50450--50547 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
50440 GCAACGAGAG
*
50450 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
50469 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
50483 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
50502 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* *
50516 AATCACAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
50535 AATCGCAATGCGA
1 AATCGCAACGCGA
50548 TTTGGTTTCC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.49
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:50577 original size:14 final size:14
Alignment explanation
Indices: 50558--50614 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
50548 TTTGGTTTCC
50558 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
50572 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
50591 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
50605 CGTTGCGATT
1 CGTTGCGATT
50615 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:50596 original size:19 final size:19
Alignment explanation
Indices: 50572--50660 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
50562 GCGATTCTCT
50572 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
50591 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
50605 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
50624 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
50644 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
50661 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:50652 original size:39 final size:33
Alignment explanation
Indices: 50553--50660 Score: 144
Period size: 33 Copynumber: 3.1 Consensus size: 33
50543 TGCGATTTGG
*
50553 TTTCCCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
50586 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
50619 TTTCGCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTT--G-C-G--ATTCTCTCGTTGCGATTTTCA
50658 TTT
1 TTT
50661 ATCTCGTTGC
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
33 40 0.61
35 1 0.02
36 1 0.02
37 1 0.02
39 23 0.35
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.44
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:50794 original size:33 final size:33
Alignment explanation
Indices: 50752--50822 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
50742 AATACTAACT
50752 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
50785 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
50818 TGAAA
1 TGAAA
50823 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:51230 original size:20 final size:20
Alignment explanation
Indices: 51205--51398 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
51195 CTTTAAATAT
51205 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
51225 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
51247 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
51266 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
51286 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
51306 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
51326 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
51346 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
51366 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
51386 CGCGTTGCGATTT
1 CGCGTTGCGATTT
51399 TTGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:51370 original size:60 final size:60
Alignment explanation
Indices: 51207--51378 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
51197 TTAAATATCG
* ** *
51207 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* *** * *
51268 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
51328 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
51379 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:51392 original size:60 final size:60
Alignment explanation
Indices: 51204--51519 Score: 230
Period size: 60 Copynumber: 5.2 Consensus size: 60
51194 GCTTTAAATA
* ** * *
51204 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * *** * * *
51265 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *
51325 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
** * * * * * *
51385 TCGCGTTGCGATTTTTGAAAATCGCAATGCGAATT-TG-ACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGGATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
51447 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
51506 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
51520 TGTTGGTCAT
Statistics
Matches: 206, Mismatches: 40, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
59 14 0.07
60 93 0.45
61 80 0.39
62 17 0.08
63 1 0.00
64 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:51409 original size:21 final size:20
Alignment explanation
Indices: 51365--51521 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
51355 ATTTATGTGT
* * *
51365 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTGAAAA
51385 TCGCGTTGCGATTTTTGAAAA
1 TCGCGTTGCGA-TTTTGAAAA
** * **
51406 TCGCAATGCGAATTTGACTA
1 TCGCGTTGCGATTTTGAAAA
* *
51426 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTGAA-AA
*
51447 TCGCGTTGCGATTTTGGAAA
1 TCGCGTTGCGATTTTGAAAA
** * ***
51467 -CTGATTTGCGATTCTGGGGA
1 TC-GCGTTGCGATTTTGAAAA
* **
51487 TCGCGTTGCGATTTT-TATT
1 TCGCGTTGCGATTTTGAAAA
51506 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
51522 TTGGTCATTT
Statistics
Matches: 104, Mismatches: 28, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTGAAAA
Found at i:51457 original size:41 final size:41
Alignment explanation
Indices: 51365--51462 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
51355 ATTTATGTGT
* * *
51365 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTTGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTTCAAAA
** *
51406 TCGCAATGCGAATTTGACTA-TCGCATTGCGA-TTTTCAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTTCAA-AA
51447 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
51463 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 6 0.13
41 38 0.83
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTTCAAAA
Found at i:66727 original size:17 final size:17
Alignment explanation
Indices: 66705--66745 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
66695 TCTTTATTTC
66705 CTTCTTCCTCA-TCTATT
1 CTTCTTCCTCATTCT-TT
*
66722 CTTCTTTCTCATTCTTT
1 CTTCTTCCTCATTCTTT
66739 CTTCTTC
1 CTTCTTC
66746 TTCTCTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (17 bp):
CTTCTTCCTCATTCTTT
Found at i:68051 original size:45 final size:45
Alignment explanation
Indices: 68002--68101 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 45
67992 TATACTTTGA
* *
68002 TCAGTGCTAATGCACTTCCA-TATCAGTGCTAA-AACACTTTAGTAT
1 TCAGTGCTAAGGCACTT-CAGTACCAGTGCTAAGAA-ACTTTAGTAT
* * *
68047 TCAGTGCCAAGGCACTTTAGTACCAGTGCTAAGGAACTTTAGTAT
1 TCAGTGCTAAGGCACTTCAGTACCAGTGCTAAGAAACTTTAGTAT
68092 T-AGTGCTAAG
1 TCAGTGCTAAG
68102 AAACTTTAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
44 9 0.19
45 37 0.79
46 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (45 bp):
TCAGTGCTAAGGCACTTCAGTACCAGTGCTAAGAAACTTTAGTAT
Found at i:68080 original size:22 final size:22
Alignment explanation
Indices: 68001--68101 Score: 105
Period size: 22 Copynumber: 4.5 Consensus size: 22
67991 ATATACTTTG
* *
68001 ATCAGTGCTAATGCACTTCCA-T
1 ATCAGTGCTAAGGCACTT-TAGT
**
68023 ATCAGTGCTAAAACACTTTAGT
1 ATCAGTGCTAAGGCACTTTAGT
*
68045 ATTCAGTGCCAAGGCACTTTAGT
1 A-TCAGTGCTAAGGCACTTTAGT
* *
68068 ACCAGTGCTAAGGAACTTTAGT
1 ATCAGTGCTAAGGCACTTTAGT
*
68090 ATTAGTGCTAAG
1 ATCAGTGCTAAG
68102 AAACTTTAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.02
22 46 0.70
23 19 0.29
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (22 bp):
ATCAGTGCTAAGGCACTTTAGT
Found at i:72632 original size:3 final size:3
Alignment explanation
Indices: 72624--72698 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
72614 TTACCCATTT
* * * *
72624 TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
72672 CTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA
72699 AAAAATAATA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:72646 original size:15 final size:15
Alignment explanation
Indices: 72626--72696 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
72616 ACCCATTTTT
*
72626 ATTATTATTACTATA
1 ATTATTATTATTATA
72641 ATTATTATTATTATA
1 ATTATTATTATTATA
72656 ATTATTATTATTATA
1 ATTATTATTATTATA
*
72671 ACTATTA-TA-TAT-
1 ATTATTATTATTATA
72683 ATTATTATTATTAT
1 ATTATTATTATTAT
72697 TAAAAAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
12 6 0.12
13 5 0.10
14 5 0.10
15 35 0.69
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:73217 original size:21 final size:21
Alignment explanation
Indices: 73193--73238 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
73183 GACAACCAGC
* *
73193 AACAAAACAACAACCAGCAAA
1 AACAAAAAAAAAACCAGCAAA
73214 AACAAAAAAAAAACCAGCAAA
1 AACAAAAAAAAAACCAGCAAA
73235 AACA
1 AACA
73239 GAGAACGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.72, C:0.24, G:0.04, T:0.00
Consensus pattern (21 bp):
AACAAAAAAAAAACCAGCAAA
Found at i:74478 original size:24 final size:24
Alignment explanation
Indices: 74423--74483 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
74413 CCTTTTCTGA
*
74423 TATTTC-TAAATAAATAAATATTT
1 TATTTCATAAATATATAAATATTT
74446 TATTT-ATAAATATATAAATTATTT
1 TATTTCATAAATATATAAA-TATTT
*
74470 T-TTTCATAATTATA
1 TATTTCATAAATATA
74484 ATTTTGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTCATAAATATATAAATATTT
Done.