Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003439.1 Hibiscus syriacus cultivar Beakdansim tig00007249_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: 57080
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1760 original size:7 final size:7
Alignment explanation
Indices: 1729--1772 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
1719 GAACGAAAAA
1729 AAAT-AT
1 AAATAAT
1735 AAA-AAT
1 AAATAAT
*
1741 AAATAGT
1 AAATAAT
1748 -AATAAT
1 AAATAAT
1754 AAATAAT
1 AAATAAT
1761 AAATAAT
1 AAATAAT
1768 AAATA
1 AAATA
1773 TATGTATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
6 13 0.39
7 20 0.61
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:1790 original size:2 final size:2
Alignment explanation
Indices: 1785--1816 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1775 TGTATTTGTG
1785 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
1817 ATAAAGTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3012 original size:4 final size:4
Alignment explanation
Indices: 2995--3051 Score: 62
Period size: 4 Copynumber: 14.0 Consensus size: 4
2985 AACAATAATA
* * *
2995 AAAT AAAC AAAT AAAT -AAT AAAT GAAAT AAAAT AAAT AAAT AGAT AGAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT
3044 AAAT AAAT
1 AAAT AAAT
3052 TAAAAACATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
3 3 0.07
4 35 0.76
5 8 0.17
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3034 original size:25 final size:25
Alignment explanation
Indices: 2995--3055 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
2985 AACAATAATA
*
2995 AAAT-AAACAAATAAATA-ATAAAT
1 AAATAAAATAAATAAATAGATAAAT
*
3018 GAAATAAAATAAATAAATAGATAGAT
1 -AAATAAAATAAATAAATAGATAAAT
*
3044 AAATAAATTAAA
1 AAATAAAATAAA
3056 AACATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.12
25 23 0.72
26 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (25 bp):
AAATAAAATAAATAAATAGATAAAT
Found at i:3035 original size:29 final size:29
Alignment explanation
Indices: 2991--3056 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
2981 AACAAACAAT
2991 AATAAAATAAACAAATAAATA-ATAAATGA
1 AATAAAATAAACAAATAAATAGATAAAT-A
* *
3020 AATAAAATAAATAAATAGATAGATAAATA
1 AATAAAATAAACAAATAAATAGATAAATA
3049 AATTAAAA
1 AA-TAAAA
3057 ACATTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (29 bp):
AATAAAATAAACAAATAAATAGATAAATA
Found at i:3045 original size:21 final size:20
Alignment explanation
Indices: 2988--3051 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
2978 TGAAACAAAC
*
2988 AATAATAAAAT-AAACAAATA
1 AATAAT-AAATGAAATAAATA
3008 AATAATAAATGAAATAAAATA
1 AATAATAAATGAAAT-AAATA
* *
3029 AATAAATAGAT-AGATAAATA
1 AAT-AATAAATGAAATAAATA
3049 AAT
1 AAT
3052 TAAAAACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.11
20 17 0.45
21 11 0.29
22 6 0.16
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (20 bp):
AATAATAAATGAAATAAATA
Found at i:3130 original size:38 final size:37
Alignment explanation
Indices: 3061--3396 Score: 435
Period size: 37 Copynumber: 8.9 Consensus size: 37
3051 TTAAAAACAT
* * *
3061 TTTTTAAAACTATACAATATAT-GTTTTAAAAAATAA
1 TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
*
3097 TTTTCAAAACCATATAATATATATTTTTAAAAAATAA
1 TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
*
3134 TTTTCAAAACTATATAATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
* *
3171 TTTTCAAAACTATATAATATATATATTTTTAAAACTAA
1 TTTTCAAAACTATATAATATATAT-TTTTAAAAAATAA
*
3209 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATAT-TTTTAAAAAATAA
3247 TTTTCAAAACTATATAATATATA-TTTTAAAAAACTAA
1 TTTTCAAAACTATATAATATATATTTTTAAAAAA-TAA
* **
3284 TTTTCAAAACTATATAATATATATGTTTTTCAAAAATGT
1 TTTTCAAAACTATATAATATATA--TTTTTAAAAAATAA
*
3323 TTTTTAAAACTATATATTATATATATATTTTTAAAAAA-AA
1 TTTTCAAAAC--TATA-TA-ATATATATTTTTAAAAAATAA
* *
3363 GTTTTCAAAACAATATAATATATATTTTCAAAAA
1 -TTTTCAAAACTATATAATATATATTTTTAAAAA
3397 CTATTTATTA
Statistics
Matches: 270, Mismatches: 19, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
36 28 0.10
37 114 0.42
38 74 0.27
39 13 0.05
40 9 0.03
41 23 0.09
42 2 0.01
43 7 0.03
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (37 bp):
TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
Found at i:3394 original size:23 final size:23
Alignment explanation
Indices: 3364--3419 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
3354 TAAAAAAAAG
3364 TTTTCAAAACAATATAATATATA
1 TTTTCAAAACAATATAATATATA
* * * *
3387 TTTTCAAAAACTATTTATTATTTA
1 TTTTC-AAAACAATATAATATATA
3411 TTTTCAAAA
1 TTTTCAAAA
3420 TATTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTTCAAAACAATATAATATATA
Found at i:9176 original size:34 final size:35
Alignment explanation
Indices: 9137--9220 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
9127 AGTATAATTT
*
9137 TAAATACAACAAACTTACAATAA-G-TATTAAATGA
1 TAAATA-AACAAAATTACAATAACGATATTAAATGA
*
9171 TAAATAAA-AAAATTACAATAACTGATATTAAATGG
1 TAAATAAACAAAATTACAATAAC-GATATTAAATGA
9206 T-AATAAACAAAATTA
1 TAAATAAACAAAATTA
9221 ACAAAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 12 0.27
33 2 0.05
34 13 0.30
35 17 0.39
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (35 bp):
TAAATAAACAAAATTACAATAACGATATTAAATGA
Found at i:10941 original size:23 final size:23
Alignment explanation
Indices: 10897--10960 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
10887 CAGCTCATAT
10897 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * * *
10920 AATTGCACCGTAGTTCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
10943 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
10961 TATAAGGTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:11435 original size:2 final size:2
Alignment explanation
Indices: 11428--11486 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
11418 TTCATCTTCC
11428 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
11470 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
11487 CATTTTTCCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14870 original size:28 final size:29
Alignment explanation
Indices: 14837--14908 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
14827 CAAAAAAAAT
*
14837 TATTAAATAAAATATTA-AAAAT-TTAAA
1 TATTAAATAAAATATAACAAAATATTAAA
14864 TAATTAAATAAAATACTAACAAAATATTAAA
1 T-ATTAAATAAAATA-TAACAAAATATTAAA
14895 TA-T-AATAAAATATA
1 TATTAAATAAAATATA
14909 TCTTAAAGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 22 0.55
29 3 0.08
30 6 0.15
31 6 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
TATTAAATAAAATATAACAAAATATTAAA
Found at i:14906 original size:17 final size:18
Alignment explanation
Indices: 14874--14907 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14864 TAATTAAATA
14874 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
14892 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
14908 ATCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:15168 original size:51 final size:51
Alignment explanation
Indices: 15106--15204 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 51
15096 ACCCATGCAC
* * * * *
15106 CGCGCCTTACCCAACGTGTCGCCATGTCAGCATAAGGCGCGGTGCATGGGT
1 CGCGCCTTACCCAACGTGGCGCCATATCAACATAAGACGCGATGCATGGGT
* * * *
15157 CGCGTCTTACCCCACTTGGCGCCATATCAACGTAAGACGCGATGCATG
1 CGCGCCTTACCCAACGTGGCGCCATATCAACATAAGACGCGATGCATG
15205 AGCCGCACCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.20, C:0.32, G:0.27, T:0.20
Consensus pattern (51 bp):
CGCGCCTTACCCAACGTGGCGCCATATCAACATAAGACGCGATGCATGGGT
Found at i:16631 original size:34 final size:34
Alignment explanation
Indices: 16593--16677 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
16583 TATGATTGAT
16593 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
16627 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
16661 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
16678 GCTGTGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:16731 original size:22 final size:22
Alignment explanation
Indices: 16699--16752 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
16689 GACTGGACGT
*
16699 GAGAAATCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTGCAAG
16721 GAGAAAGCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTGCAAG
16743 GAGAAAGCAC
1 GAGAAAGCAC
16753 AGAAATCACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.33, T:0.13
Consensus pattern (22 bp):
GAGAAAGCACGGGTTCTGCAAG
Found at i:16808 original size:23 final size:23
Alignment explanation
Indices: 16782--16825 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
16772 TCCTGCAGGG
16782 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
16805 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
16826 GCATGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:16832 original size:23 final size:22
Alignment explanation
Indices: 16779--16832 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
16769 GGGTCCTGCA
16779 GGGCTGCACGTCTGCATGTGGG
1 GGGCTGCACGTCTGCATGTGGG
*
16801 GGTCCTGCACGTCTGCATGTGGG
1 GG-GCTGCACGTCTGCATGTGGG
16824 GGGCATGCA
1 GGGC-TGCA
16833 ACTGTTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (22 bp):
GGGCTGCACGTCTGCATGTGGG
Found at i:17570 original size:172 final size:173
Alignment explanation
Indices: 17283--17641 Score: 578
Period size: 172 Copynumber: 2.1 Consensus size: 173
17273 TTGTAAAGTT
* * *
17283 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
*
17348 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
17411 GGATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
* * *
17455 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGGAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
* *
17520 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
17585 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
*
17628 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
17642 ATATTTGATG
Statistics
Matches: 172, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
172 111 0.65
173 60 0.35
174 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (173 bp):
TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:19389 original size:6 final size:6
Alignment explanation
Indices: 19378--19408 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
19368 CAAGAAGGAC
*
19378 TGGGAG TGGGAG TGGGAG TGGGAG TAGGAG T
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG T
19409 TCTTCTCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.61, T:0.19
Consensus pattern (6 bp):
TGGGAG
Found at i:19975 original size:37 final size:37
Alignment explanation
Indices: 19925--20747 Score: 425
Period size: 37 Copynumber: 22.1 Consensus size: 37
19915 CATTAAAATT
* *
19925 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATCATTAAATAATTAAAATTAAATCATTA
* *
19962 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATCATTAAATAATTAAA--ATTAAATCATTA
* ** * *
20001 AAGTAATTATTATTAAAGCATT-AAAGT-AATTATT-
1 AAGTAATTATCATTAAATAATTAAAATTAAATCATTA
* *
20035 -ATTAA--ATCATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATCATTAAATAATTAAA--ATTAAATCATTA
* *
20071 AAGTAATTATTATT--A-AA-T--CATTAAATCATTA
1 AAGTAATTATCATTAAATAATTAAAATTAAATCATTA
* *
20102 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTAA
1 AAGTAATTATCATTAAATAATTAAA--ATTAAATCATT-A
* * **
20142 AATTAA--ATCAGTAAAGTAATTATTATTAAATCATTAA
1 AAGTAATTATCATTAAA-TAATTAAAATTAAATCATT-A
* **
20179 AATTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATTATCATTAAA-TAATTAAAATTAAATCATTA
**
20215 AAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAG-TAATTATCATTAAA-TAATTAAAATTAAATCATTA
* **
20252 AA-TCATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATT--ATCATTAAA-TAATTAAAATTAAATCATTA
*
20291 AAGTTAA--ATCATTAAATCATTAAAATTAAATCA-T-
1 AAG-TAATTATCATTAAATAATTAAAATTAAATCATTA
**
20325 ---TAA--ATCATTAAAGTAATTATTATTAAATCATTAA
1 AAGTAATTATCATTAAA-TAATTAAAATTAAATCATT-A
* **
20359 AATTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATTATCATTAAA-TAATTAAAATTAAATCATTA
**
20395 AAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTAA
1 AAG-TAATTATCATTAAA-TAATTAAAATTAAATCATT-A
* **
20433 AATTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATTATCATTAAA-TAATTAAAATTAAATCATTA
**
20469 AAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAG-TAATTATCATTAAA-TAATTAAAATTAAATCATTA
* * *
20506 AAGTTAAATAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAG-----TAATTATCATTAAATAATTAAAATTAAATCATTA
* * *
20548 AAGTGATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATCATTAAATAATTAAA--ATTAAATCATTA
**
20587 AAGTAATTATTATTAAATCATTAAAGTAATTATTATTAAATCATTAA
1 AAG----TA--ATT--ATCATTAAA-TAATTAAAATTAAATCATT-A
* **
20634 AATTAA--ATCATTAAAGTAATTATTATTAAATCATTAA
1 AAGTAATTATCATTAAA-TAATTAAAATTAAATCATT-A
* **
20671 AATTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATTATCATTAAA-TAATTAAAATTAAATCATTA
**
20707 AAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAG-TAATTATCATTAAA-TAATTAAAATTAAATCATTA
20744 AAGT
1 AAGT
20748 TAAATAATTA
Statistics
Matches: 681, Mismatches: 49, Indels: 113
0.81 0.06 0.13
Matches are distributed among these distances:
30 12 0.02
31 52 0.08
32 3 0.00
33 5 0.01
34 3 0.00
35 17 0.02
36 30 0.04
37 375 0.55
38 12 0.02
39 100 0.15
40 6 0.01
41 6 0.01
42 19 0.03
43 11 0.02
45 3 0.00
46 11 0.02
47 11 0.02
48 5 0.01
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (37 bp):
AAGTAATTATCATTAAATAATTAAAATTAAATCATTA
Found at i:20017 original size:23 final size:22
Alignment explanation
Indices: 19989--20780 Score: 269
Period size: 23 Copynumber: 33.3 Consensus size: 22
19979 TCATTAAATC
19989 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA-TAATTATT
*
20012 ATTAAAGCATTAAAGTAATTATT
1 ATTAAATCATTAAA-TAATTATT
* *
20035 ATTAAATCATTAAATCATTAAATC
1 ATTAAATCATTAAATAATT--ATT
20059 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA-TAATTATT
* *
20082 ATTAAATCATTAAATCATTA-A
1 ATTAAATCATTAAATAATTATT
* * * *
20103 AGT-AATTATT-ATTAA--ATC
1 ATTAAATCATTAAATAATTATT
* **
20121 ATTAAATCATTAAATCATTAAA
1 ATTAAATCATTAAATAATTATT
*
20143 ATTAAATCAGTAAAGTAATTATT
1 ATTAAATCATTAAA-TAATTATT
*
20166 ATTAAATCATTAAAATTAAATCATT
1 ATTAAATCATT-AAA-T-AATTATT
* * * *
20191 AAAGTAATTATTATTAAATCATTA-A
1 --ATTAA--ATCATTAAATAATTATT
20216 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAA-TAATTATT
* *
20240 ATTAAATCATTAAATCATTAAATC
1 ATTAAATCATTAAATAATT--ATT
* * *
20264 ATTAAAGTAATTATTATTAAATCATT
1 ATTAAA-TCATTA--AAT-AATTATT
* **
20290 AAAGTTAAATCATTAAATCATTAAA
1 --A-TTAAATCATTAAATAATTATT
* *
20315 ATTAAATCATTAAATCATTA-A
1 ATTAAATCATTAAATAATTATT
* * * **
20336 AGTAATTATTATTAAATCATTAAA
1 ATTAA--ATCATTAAATAATTATT
20360 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA-TAATTATT
*
20383 ATTAAATCATTAAAGTTAAATCATT
1 ATTAAATCATTAAA--T-AATTATT
* * * **
20408 AAAGTAATTATTATTAAATCATTAAA
1 --ATTAA--ATCATTAAATAATTATT
20434 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA-TAATTATT
*
20457 ATTAAATCATTAAAGTTAAATCATT
1 ATTAAATCATTAAA--T-AATTATT
* * * *
20482 AAAGTAATTATTATTAAATCATTA-A
1 --ATTAA--ATCATTAAATAATTATT
* * *
20507 AGTTAAATAATTATTATTAAATCATT
1 A-TTAAATCATTA--AAT-AATTATT
*
20533 AAAGTTAAATCATTAAAGTGATTATT
1 --A-TTAAATCATTAAA-TAATTATT
* *
20559 ATTAAATCATTAAATCATTAAATC
1 ATTAAATCATTAAATAATT--ATT
* * *
20583 ATTAAAGTAATTATTATTAAATCATT
1 ATTAAA-TCATTA--AAT-AATTATT
* * * **
20609 AAAGTAATTATTATTAAATCATTAAA
1 --ATTAA--ATCATTAAATAATTATT
20635 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA-TAATTATT
*
20658 ATTAAATCATTAAAATTAAATCATT
1 ATTAAATCATT-AAA-T-AATTATT
* * * *
20683 AAAGTAATTATTATTAAATCATTA-A
1 --ATTAA--ATCATTAAATAATTATT
20708 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAA-TAATTATT
*
20732 ATTAAATCATTAAAGTTAA--ATA
1 ATTAAATCATTAAA--TAATTATT
20754 ATTAAAT--TTAAATAATTATT
1 ATTAAATCATTAAATAATTATT
20774 ATTAAAT
1 ATTAAAT
20781 ATGTACTCGA
Statistics
Matches: 576, Mismatches: 118, Indels: 153
0.68 0.14 0.18
Matches are distributed among these distances:
17 1 0.00
18 5 0.01
19 9 0.02
20 23 0.04
21 7 0.01
22 105 0.18
23 187 0.32
24 72 0.12
25 44 0.08
26 27 0.05
27 27 0.05
28 32 0.06
29 36 0.06
30 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (22 bp):
ATTAAATCATTAAATAATTATT
Found at i:20596 original size:39 final size:39
Alignment explanation
Indices: 20494--20611 Score: 174
Period size: 39 Copynumber: 3.2 Consensus size: 39
20484 AGTAATTATT
*
20494 ATTAAATCATTAAA--GTTAAA-TAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
* *
20530 ATTAAA--GTTAAATCATTAAAGTGATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
20567 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
20606 ATTAAA
1 ATTAAA
20612 GTAATTATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
34 5 0.07
36 11 0.15
37 21 0.29
39 35 0.49
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (39 bp):
ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
Found at i:20759 original size:37 final size:37
Alignment explanation
Indices: 20129--20611 Score: 719
Period size: 37 Copynumber: 13.4 Consensus size: 37
20119 TCATTAAATC
*
20129 ATTAAATCATTAAAATTAAATCAGTAAAGTAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
20166 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
*
20203 ATTAAATCATTAAAGTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
20240 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA--ATTAAATCATTAAAGTAATTATT
* * **
20279 ATTAAATCATTAAAGTTAAATCATTAAA-TCATTAAA
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
20315 ATTAAATC------ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
20346 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
*
20383 ATTAAATCATTAAAGTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
20420 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
*
20457 ATTAAATCATTAAAGTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
*
20494 ATTAAATC------ATTAAA--GTTAAA-TAATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
* *
20522 ATTAAATCATTAAAGTTAAATCATTAAAGTGATTATT
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
20559 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA--ATTAAATCATTAAAGTAATTATT
20598 ATTAAATCATTAAA
1 ATTAAATCATTAAA
20612 GTAATTATTA
Statistics
Matches: 405, Mismatches: 21, Indels: 38
0.87 0.05 0.08
Matches are distributed among these distances:
28 16 0.04
29 5 0.01
30 13 0.03
31 18 0.04
34 5 0.01
36 18 0.04
37 259 0.64
39 71 0.18
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (37 bp):
ATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
Found at i:20760 original size:8 final size:8
Alignment explanation
Indices: 19908--20745 Score: 469
Period size: 8 Copynumber: 111.8 Consensus size: 8
19898 AGTAATTATT
19908 ATTAAATC
1 ATTAAATC
19916 ATTAAA--
1 ATTAAATC
* *
19922 ATTAAGTA
1 ATTAAATC
*
19930 ATT--ATT
1 ATTAAATC
*
19936 ATTAAATT
1 ATTAAATC
19944 ATTAAA--
1 ATTAAATC
19950 ATTAAATC
1 ATTAAATC
*
19958 ATTAAAGTA
1 ATTAAA-TC
*
19967 ATT--ATT
1 ATTAAATC
19973 ATTAAATC
1 ATTAAATC
19981 ATTAAATC
1 ATTAAATC
19989 ATTAAATC
1 ATTAAATC
*
19997 ATTAAAGTA
1 ATTAAA-TC
*
20006 ATT--ATT
1 ATTAAATC
*
20012 ATTAAAGC
1 ATTAAATC
*
20020 ATTAAAGTA
1 ATTAAA-TC
*
20029 ATT--ATT
1 ATTAAATC
20035 ATTAAATC
1 ATTAAATC
20043 ATTAAATC
1 ATTAAATC
20051 ATTAAATC
1 ATTAAATC
20059 ATTAAATC
1 ATTAAATC
*
20067 ATTAAAGTA
1 ATTAAA-TC
*
20076 ATT--ATT
1 ATTAAATC
20082 ATTAAATC
1 ATTAAATC
20090 ATTAAATC
1 ATTAAATC
*
20098 ATTAAAGTA
1 ATTAAA-TC
*
20107 ATT--ATT
1 ATTAAATC
20113 ATTAAATC
1 ATTAAATC
20121 ATTAAATC
1 ATTAAATC
20129 ATTAAATC
1 ATTAAATC
20137 ATTAAA--
1 ATTAAATC
20143 ATTAAATC
1 ATTAAATC
* *
20151 AGTAAAGTA
1 ATTAAA-TC
*
20160 ATT--ATT
1 ATTAAATC
20166 ATTAAATC
1 ATTAAATC
20174 ATTAAA--
1 ATTAAATC
20180 ATTAAATC
1 ATTAAATC
*
20188 ATTAAAGTA
1 ATTAAA-TC
*
20197 ATT--ATT
1 ATTAAATC
20203 ATTAAATC
1 ATTAAATC
20211 ATTAAA--
1 ATTAAATC
*
20217 GTTAAATC
1 ATTAAATC
*
20225 ATTAAAGTA
1 ATTAAA-TC
*
20234 ATT--ATT
1 ATTAAATC
20240 ATTAAATC
1 ATTAAATC
20248 ATTAAATC
1 ATTAAATC
20256 ATTAAATC
1 ATTAAATC
*
20264 ATTAAAGTA
1 ATTAAA-TC
*
20273 ATT--ATT
1 ATTAAATC
20279 ATTAAATC
1 ATTAAATC
20287 ATTAAA--
1 ATTAAATC
*
20293 GTTAAATC
1 ATTAAATC
20301 ATTAAATC
1 ATTAAATC
20309 ATTAAA--
1 ATTAAATC
20315 ATTAAATC
1 ATTAAATC
20323 ATTAAATC
1 ATTAAATC
*
20331 ATTAAAGTA
1 ATTAAA-TC
*
20340 ATT--ATT
1 ATTAAATC
20346 ATTAAATC
1 ATTAAATC
20354 ATTAAA--
1 ATTAAATC
20360 ATTAAATC
1 ATTAAATC
*
20368 ATTAAAGTA
1 ATTAAA-TC
*
20377 ATT--ATT
1 ATTAAATC
20383 ATTAAATC
1 ATTAAATC
20391 ATTAAA--
1 ATTAAATC
*
20397 GTTAAATC
1 ATTAAATC
*
20405 ATTAAAGTA
1 ATTAAA-TC
*
20414 ATT--ATT
1 ATTAAATC
20420 ATTAAATC
1 ATTAAATC
20428 ATTAAA--
1 ATTAAATC
20434 ATTAAATC
1 ATTAAATC
*
20442 ATTAAAGTA
1 ATTAAA-TC
*
20451 ATT--ATT
1 ATTAAATC
20457 ATTAAATC
1 ATTAAATC
20465 ATTAAA--
1 ATTAAATC
*
20471 GTTAAATC
1 ATTAAATC
*
20479 ATTAAAGTA
1 ATTAAA-TC
*
20488 ATT--ATT
1 ATTAAATC
20494 ATTAAATC
1 ATTAAATC
20502 ATTAAA--
1 ATTAAATC
* *
20508 GTTAAATA
1 ATTAAATC
*
20516 ATT--ATT
1 ATTAAATC
20522 ATTAAATC
1 ATTAAATC
20530 ATTAAA--
1 ATTAAATC
*
20536 GTTAAATC
1 ATTAAATC
*
20544 ATTAAAGTG
1 ATTAAA-TC
*
20553 ATT--ATT
1 ATTAAATC
20559 ATTAAATC
1 ATTAAATC
20567 ATTAAATC
1 ATTAAATC
20575 ATTAAATC
1 ATTAAATC
*
20583 ATTAAAGTA
1 ATTAAA-TC
*
20592 ATT--ATT
1 ATTAAATC
20598 ATTAAATC
1 ATTAAATC
*
20606 ATTAAAGTA
1 ATTAAA-TC
*
20615 ATT--ATT
1 ATTAAATC
20621 ATTAAATC
1 ATTAAATC
20629 ATTAAA--
1 ATTAAATC
20635 ATTAAATC
1 ATTAAATC
*
20643 ATTAAAGTA
1 ATTAAA-TC
*
20652 ATT--ATT
1 ATTAAATC
20658 ATTAAATC
1 ATTAAATC
20666 ATTAAA--
1 ATTAAATC
20672 ATTAAATC
1 ATTAAATC
*
20680 ATTAAAGTA
1 ATTAAA-TC
*
20689 ATT--ATT
1 ATTAAATC
20695 ATTAAATC
1 ATTAAATC
20703 ATTAAA--
1 ATTAAATC
*
20709 GTTAAATC
1 ATTAAATC
*
20717 ATTAAAGTA
1 ATTAAA-TC
*
20726 ATT--ATT
1 ATTAAATC
20732 ATTAAATC
1 ATTAAATC
20740 ATTAAA
1 ATTAAA
20746 GTTAAATAAT
Statistics
Matches: 651, Mismatches: 83, Indels: 192
0.70 0.09 0.21
Matches are distributed among these distances:
6 177 0.27
7 20 0.03
8 376 0.58
9 78 0.12
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (8 bp):
ATTAAATC
Found at i:20778 original size:14 final size:13
Alignment explanation
Indices: 20301--20781 Score: 131
Period size: 14 Copynumber: 37.6 Consensus size: 13
20291 AAGTTAAATC
*
20301 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
20315 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
20329 TCATTAAAGTAATTATT
1 --ATTAAA-TAATTA-A
*
20346 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
20360 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
20373 AGT-AATTATT--
1 ATTAAATAATTAA
*
20383 ATTAAATCATTAA
1 ATTAAATAATTAA
*
20396 AGTTAAATCATTAA
1 A-TTAAATAATTAA
* *
20410 AGT-AATTATT--
1 ATTAAATAATTAA
*
20420 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
20434 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
20447 AGT-AATTATT--
1 ATTAAATAATTAA
*
20457 ATTAAATCATTAA
1 ATTAAATAATTAA
*
20470 AGTTAAATCATTAA
1 A-TTAAATAATTAA
* *
20484 AGT-AATTATT--
1 ATTAAATAATTAA
*
20494 ATTAAATCATTAA
1 ATTAAATAATTAA
*
20507 AGTTAAATAATTATT
1 A-TTAAATAATTA-A
*
20522 ATTAAATCATTAA
1 ATTAAATAATTAA
*
20535 AGTTAAATCATTAA
1 A-TTAAATAATTAA
* * *
20549 AGT-GATTATT--
1 ATTAAATAATTAA
*
20559 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
20573 TCATTAAATCATTAA
1 --ATTAAATAATTAA
* *
20588 AGT-AATTATT--
1 ATTAAATAATTAA
*
20598 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
20611 AGT-AATTATT--
1 ATTAAATAATTAA
*
20621 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
20635 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
20648 AGT-AATTATT--
1 ATTAAATAATTAA
*
20658 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
20672 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
20685 AGT-AATTATT--
1 ATTAAATAATTAA
*
20695 ATTAAATCATTAA
1 ATTAAATAATTAA
*
20708 AGTTAAATCATTAA
1 A-TTAAATAATTAA
* *
20722 AGT-AATTATT--
1 ATTAAATAATTAA
*
20732 ATTAAATCATTAA
1 ATTAAATAATTAA
20745 AGTTAAATAATTAA
1 A-TTAAATAATTAA
*
20759 ATTTAAATAATTATT
1 A-TTAAATAATTA-A
20774 ATTAAATA
1 ATTAAATA
20782 TGTACTCGAG
Statistics
Matches: 365, Mismatches: 53, Indels: 98
0.71 0.10 0.19
Matches are distributed among these distances:
10 20 0.05
11 59 0.16
12 59 0.16
13 30 0.08
14 164 0.45
15 11 0.03
16 18 0.05
17 4 0.01
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (13 bp):
ATTAAATAATTAA
Found at i:24208 original size:18 final size:18
Alignment explanation
Indices: 24185--24233 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
24175 GCATACAACA
24185 AATCTCACGCTTCAGACG
1 AATCTCACGCTTCAGACG
24203 AATCTCACGCTTCAGACG
1 AATCTCACGCTTCAGACG
24221 AATCTCACGCTTC
1 AATCTCACGCTTC
24234 GACCACAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (18 bp):
AATCTCACGCTTCAGACG
Found at i:28251 original size:16 final size:16
Alignment explanation
Indices: 28230--28264 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28220 TCGAGAGCAG
28230 TCGATTTTTCAACTTA
1 TCGATTTTTCAACTTA
28246 TCGATTTTTCAACTTA
1 TCGATTTTTCAACTTA
28262 TCG
1 TCG
28265 TAACGAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (16 bp):
TCGATTTTTCAACTTA
Found at i:29989 original size:15 final size:15
Alignment explanation
Indices: 29969--30032 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 15
29959 AACTTTGAAA
*
29969 AAACATTTTTCAAAG
1 AAACATTTATCAAAG
29984 AAACATTTATCAAACTTTG
1 AAACATTTATCAAA----G
30003 AAAACCATTT-TCAAAG
1 -AAA-CATTTATCAAAG
30019 AAACATTTATCAAA
1 AAACATTTATCAAA
30033 CTTTGAAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
14 5 0.12
15 21 0.51
16 1 0.02
19 1 0.02
20 8 0.20
21 5 0.12
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (15 bp):
AAACATTTATCAAAG
Found at i:30014 original size:35 final size:35
Alignment explanation
Indices: 29948--30053 Score: 169
Period size: 35 Copynumber: 3.0 Consensus size: 35
29938 AACATCTACC
* *
29948 AAAC-TTTACCAAACTTTGAAAAAACATTTTTCAAAG
1 AAACATTTATCAAACTTTG-AAAACCA-TTTTCAAAG
29984 AAACATTTATCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTATCAAACTTTGAAAACCATTTTCAAAG
30019 AAACATTTATCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTATCAAACTTTGAAAACCATTTTCAAAG
30054 TTGGTTGTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 44 0.66
36 10 0.15
37 13 0.19
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (35 bp):
AAACATTTATCAAACTTTGAAAACCATTTTCAAAG
Found at i:30016 original size:20 final size:21
Alignment explanation
Indices: 29987--30052 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
29977 TTCAAAGAAA
29987 CATTTATCAAACTTTGAAAAC
1 CATTTATCAAACTTTGAAAAC
30008 CATTT-TCAAA----G-AAA-
1 CATTTATCAAACTTTGAAAAC
30022 CATTTATCAAACTTTGAAAAC
1 CATTTATCAAACTTTGAAAAC
30043 CATTT-TCAAA
1 CATTTATCAAA
30053 GTTGGTTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
14 5 0.13
15 8 0.21
16 1 0.03
19 1 0.03
20 13 0.34
21 10 0.26
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTATCAAACTTTGAAAAC
Found at i:34624 original size:21 final size:21
Alignment explanation
Indices: 34600--34660 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
34590 TTCAAAGAAA
34600 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
34621 CATTT-TCAAA----GAAAA-
1 CATTTACCAAACTTTGAAAAC
34636 -ATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
34656 CATTT
1 CATTT
34661 TCAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 4 0.13
15 4 0.13
16 5 0.16
19 5 0.16
20 4 0.13
21 9 0.29
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:34627 original size:35 final size:35
Alignment explanation
Indices: 34560--34666 Score: 162
Period size: 35 Copynumber: 3.0 Consensus size: 35
34550 AACATCTACC
*
34560 AAAC-TTTACCAAACTTTGAAAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTG--AAAACCA-TTTTCAAAG
34597 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
*
34632 AAAAATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
34667 TTGGTTGCCA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
35 43 0.64
36 6 0.09
37 4 0.06
38 14 0.21
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.29
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:37347 original size:59 final size:59
Alignment explanation
Indices: 37255--37373 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
37245 AAGAGTTTGG
37255 TGTTGATTTTACAGAGACATTTGCACCTGTGGCCAGATTTGATACCATCAGATTGTTGA
1 TGTTGATTTTACAGAGACATTTGCACCTGTGGCCAGATTTGATACCATCAGATTGTTGA
37314 TGTTGATTTTACAGAGACATTTGCACCTGTGGCCAGATTTGATACCATCAGATTGTTGA
1 TGTTGATTTTACAGAGACATTTGCACCTGTGGCCAGATTTGATACCATCAGATTGTTGA
37373 T
1 T
37374 TGCTTTGGCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (59 bp):
TGTTGATTTTACAGAGACATTTGCACCTGTGGCCAGATTTGATACCATCAGATTGTTGA
Found at i:38547 original size:3 final size:3
Alignment explanation
Indices: 38539--38588 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
38529 TGCCCAACAT
38539 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
38587 AA
1 AA
38589 TCAAACATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39041 original size:20 final size:20
Alignment explanation
Indices: 39018--39056 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39008 AGTCCTAATT
39018 TAATTAGGAT-AATTAGTTTA
1 TAATTA-GATAAATTAGTTTA
*
39038 TAATTATATAAATTAGTTT
1 TAATTAGATAAATTAGTTT
39057 TGATTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
TAATTAGATAAATTAGTTTA
Found at i:41970 original size:35 final size:35
Alignment explanation
Indices: 41917--42011 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
41907 TTATATGTCA
* *
41917 GATTTCAGTTTCTATCAGTTTTAGTTTAGATGACG
1 GATTTCGGTTTCTCTCAGTTTTAGTTTAGATGACG
* *
41952 GGTTTCGGTTTCTCTCAGTTTTAGTTTAGATGTCG
1 GATTTCGGTTTCTCTCAGTTTTAGTTTAGATGACG
*
41987 GATTTTGGTTTCTCTCAGTTTTAGT
1 GATTTCGGTTTCTCTCAGTTTTAGT
42012 CTTTCTTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.16, C:0.13, G:0.22, T:0.49
Consensus pattern (35 bp):
GATTTCGGTTTCTCTCAGTTTTAGTTTAGATGACG
Found at i:47006 original size:21 final size:20
Alignment explanation
Indices: 46982--47114 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 20
46972 CAGTTCCCAG
46982 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
* *
47002 GAATCGCAATGTGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
47023 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTAT-GAA
*
47045 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
47065 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
47085 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
47105 TATCGCAACG
1 AATCGCAACG
47115 AGTATCCGTA
Statistics
Matches: 85, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.54
21 33 0.39
22 3 0.04
23 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:47070 original size:20 final size:20
Alignment explanation
Indices: 47045--47336 Score: 227
Period size: 20 Copynumber: 14.5 Consensus size: 20
47035 GATTTTCCAT
* *
47045 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
47065 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
47085 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
47104 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
47126 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
47146 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
47167 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* *
47187 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
47207 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
* * *
47227 AATCGCAATGAGAATACATA
1 AATCGCAACGCGAATACGTA
** *
47247 AATCGCAATACGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
* *
47267 AATCGTAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
47287 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
47307 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
47327 AATCGCAACG
1 AATCGCAACG
47337 AGATTCTGAC
Statistics
Matches: 224, Mismatches: 36, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 177 0.79
21 39 0.17
22 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:47670 original size:14 final size:14
Alignment explanation
Indices: 47651--47735 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 14
47641 TTTCATTTCG
47651 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
47665 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
47684 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
47698 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
47717 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
47731 CGTTG
1 CGTTG
47736 AGATAGTCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
14 25 0.44
16 6 0.11
17 6 0.11
19 20 0.35
ACGTcount: A:0.08, C:0.25, G:0.22, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:47680 original size:33 final size:33
Alignment explanation
Indices: 47638--47788 Score: 212
Period size: 33 Copynumber: 4.4 Consensus size: 33
47628 TGTTTGGATA
47638 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
47671 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
*
47704 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGA
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
**
47737 GATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCGTTGC
1 GATTTTCATTT-CGCGTTGCG------ATTCTCTCGTTGC
47777 GATTTTCATTTC
1 GATTTTCATTTC
47789 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
33 74 0.70
34 9 0.09
39 1 0.01
40 21 0.20
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
Found at i:47765 original size:20 final size:19
Alignment explanation
Indices: 47638--47788 Score: 116
Period size: 20 Copynumber: 8.6 Consensus size: 19
47628 TGTTTGGATA
47638 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
47657 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
47671 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
47690 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
47704 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
* *
47723 GA--TTC---TCTCGTTGA
1 GATTTTCATTTCGCGTTGC
**
47737 GATAGTCATTTCCGCGTTGC
1 GATTTTCATTT-CGCGTTGC
*
47757 GATTTTCATTCTCTCGTTGC
1 GATTTTCATT-TCGCGTTGC
47777 GATTTTCATTTC
1 GATTTTCATTTC
47789 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 12, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
14 29 0.28
16 8 0.08
17 9 0.09
19 25 0.24
20 31 0.30
21 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:49820 original size:21 final size:21
Alignment explanation
Indices: 49796--49862 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
49786 TCATTCCTCG
49796 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
49817 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
49838 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
49859 AGAG
1 AGAG
49863 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:49820 original size:42 final size:42
Alignment explanation
Indices: 49744--49862 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
49734 GAATCGTCTG
* * * *
49744 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
49786 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
49828 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
49863 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:51229 original size:14 final size:14
Alignment explanation
Indices: 51210--51245 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
51200 ATTGTTTAAT
51210 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
51224 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
51238 TGATTTGT
1 TGATTTGT
51246 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:51455 original size:19 final size:19
Alignment explanation
Indices: 51347--51448 Score: 177
Period size: 19 Copynumber: 5.4 Consensus size: 19
51337 AAAACAGACT
*
51347 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
51366 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
51385 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
51404 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
51423 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
51442 ATCGCAA
1 ATCGCAA
51449 CACGAAACTA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 79 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:51481 original size:19 final size:19
Alignment explanation
Indices: 51459--51617 Score: 167
Period size: 19 Copynumber: 8.8 Consensus size: 19
51449 CACGAAACTA
*
51459 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
* *
51478 ATTTTTGTATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
51496 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
51512 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
51529 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
51545 ATTTCGCATTGCGATTTTT
1 ATTTCGCATTGCGATTTTC
*
51564 ATTTCGCATTTCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
51583 ATTTCGCATTGCGACTTTC
1 ATTTCGCATTGCGATTTTC
51602 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
51618 CTCTCGTTGA
Statistics
Matches: 115, Mismatches: 14, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
14 12 0.10
16 13 0.11
17 10 0.09
18 4 0.03
19 66 0.57
20 10 0.09
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:51528 original size:33 final size:33
Alignment explanation
Indices: 51465--51596 Score: 156
Period size: 33 Copynumber: 3.8 Consensus size: 33
51455 ACTAATTTCG
* *
51465 CGTTGCGATTTTCATTTTTGTATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
51499 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* *
51532 CGTTGCGATTTTCATTTCGCATTGCGATTTTTATTT
1 CGTTGCGATTTTCATTTCGCATTGCGA--TTCA-CT
*
51568 CGCATTTCGATTTTCATTTCGCATTGCGA
1 CG--TTGCGATTTTCATTTCGCATTGCGA
51597 CTTTCATTTC
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 43 0.50
34 14 0.16
35 2 0.02
36 3 0.03
38 24 0.28
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:51647 original size:20 final size:20
Alignment explanation
Indices: 51622--51676 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
51612 GCGATTCTCT
* *
51622 CGTTGATATAGTCATTTCCG
1 CGTTGAGATAGTCAATTCCG
51642 CGTTGAGATAGTCAATTCCG
1 CGTTGAGATAGTCAATTCCG
* *
51662 CATTGCGATAGTCAA
1 CGTTGAGATAGTCAA
51677 ATGAATGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGAGATAGTCAATTCCG
Found at i:53312 original size:24 final size:24
Alignment explanation
Indices: 53278--53331 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
53268 CTGAAAAATC
53278 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
53302 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
53326 ATCAAA
1 ATCAAA
53332 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:53345 original size:24 final size:24
Alignment explanation
Indices: 53278--53345 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
53268 CTGAAAAATC
* * *
53278 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
53302 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
53326 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
53346 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:54220 original size:20 final size:20
Alignment explanation
Indices: 54197--54425 Score: 223
Period size: 20 Copynumber: 11.4 Consensus size: 20
54187 ATCTCGTTGT
54197 GATTTACAG-ATTCGCATTGC
1 GATTTAC-GTATTCGCATTGC
54217 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
*
54237 GATTTACGTATTCGCATTGT
1 GATTTACGTATTCGCATTGC
*
54257 GATTTACGTATTCGCATTAC
1 GATTTACGTATTCGCATTGC
* * **
54277 GATTTACGGATACATATTGC
1 GATTTACGTATTCGCATTGC
*
54297 GATTTACAG-ATAT-GCGTTGC
1 GATTTAC-GTAT-TCGCATTGC
* *
54317 GATTTACGTATTCTCTTTGC
1 GATTTACGTATTCGCATTGC
* * *
54337 GATTTACGGATACGCGTTGC
1 GATTTACGTATTCGCATTGC
* *
54357 GATTTACGTATTCTCTTTGC
1 GATTTACGTATTCGCATTGC
* * *
54377 GATTTACGGATACGCGTTGC
1 GATTTACGTATTCGCATTGC
*
54397 GATTTTACGTATT-GTCGTTGC
1 GA-TTTACGTATTCG-CATTGC
54418 GATTTACG
1 GATTTACG
54426 GATACACGTT
Statistics
Matches: 174, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.02
20 154 0.89
21 17 0.10
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
GATTTACGTATTCGCATTGC
Found at i:54418 original size:41 final size:40
Alignment explanation
Indices: 54191--54461 Score: 276
Period size: 40 Copynumber: 6.7 Consensus size: 40
54181 GTCAGAATCT
* * * * *
54191 CGTTGTGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACGGATACG
* * * * * *
54231 CATTGCGATTTACGTATTCGCATTGTGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
* * * * * * *
54271 CATTACGATTTACGGATACAT-ATTGCGATTTACAGATATG
1 CGTTGCGATTTACGTATTC-TCGTTGCGATTTACGGATACG
*
54311 CGTTGCGATTTACGTATTCTCTTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
*
54351 CGTTGCGATTTACGTATTCTCTTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
* *
54391 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACA
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACG
* *
54432 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGA-TTTACGTATTCTCGTTGCGAT
54462 AGTCAGAATC
Statistics
Matches: 202, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 2 0.01
40 144 0.71
41 56 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:54435 original size:20 final size:20
Alignment explanation
Indices: 54189--54461 Score: 199
Period size: 20 Copynumber: 13.6 Consensus size: 20
54179 TAGTCAGAAT
* * *
54189 CTCGTTGTGATTTACAGATT
1 CTCGTTGCGATTTACGGATA
* * * *
54209 CGCATTGCGATTTACGTATT
1 CTCGTTGCGATTTACGGATA
* * * *
54229 CGCATTGCGATTTACGTATT
1 CTCGTTGCGATTTACGGATA
* * * * *
54249 CGCATTGTGATTTACGTATT
1 CTCGTTGCGATTTACGGATA
* * *
54269 CGCATTACGATTTACGGATA
1 CTCGTTGCGATTTACGGATA
* *
54289 CAT-ATTGCGATTTACAGATA
1 C-TCGTTGCGATTTACGGATA
* *
54309 -TGCGTTGCGATTTACGTATT
1 CT-CGTTGCGATTTACGGATA
*
54329 CTCTTTGCGATTTACGGATA
1 CTCGTTGCGATTTACGGATA
* * *
54349 CGCGTTGCGATTTACGTATT
1 CTCGTTGCGATTTACGGATA
*
54369 CTCTTTGCGATTTACGGATA
1 CTCGTTGCGATTTACGGATA
* * *
54389 CGCGTTGCGATTTTACGTATT
1 CTCGTTGCGA-TTTACGGATA
*
54410 GTCGTTGCGATTTACGGATA
1 CTCGTTGCGATTTACGGATA
*
54430 CACGTTGCGATTTTACGGATA
1 CTCGTTGCGA-TTTACGGATA
54451 CTCGTTGCGAT
1 CTCGTTGCGAT
54462 AGTCAGAATC
Statistics
Matches: 208, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
18 1 0.00
20 171 0.82
21 36 0.17
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
CTCGTTGCGATTTACGGATA
Found at i:54477 original size:41 final size:41
Alignment explanation
Indices: 54279--54483 Score: 161
Period size: 40 Copynumber: 5.0 Consensus size: 41
54269 CGCATTACGA
* * *
54279 TTTACGGATACAT-ATTGCGATTTAC-AGATATGCGTTGCGA-
1 TTTACGGATAC-TCGTTGCGATTCACGA-ATACGCGTTGCGAT
* * * * *
54319 TTTACGTATTCTCTTTGCGATTTACGGATACGCGTTGCGA-
1 TTTACGGATACTCGTTGCGATTCACGAATACGCGTTGCGAT
* * * * *
54359 TTTACGTATTCTCTTTGCGATTTACGGATACGCGTTGCGAT
1 TTTACGGATACTCGTTGCGATTCACGAATACGCGTTGCGAT
* ** * * *
54400 TTTACGTATTGTCGTTGCGATTTACGGATACACGTTGCGAT
1 TTTACGGATACTCGTTGCGATTCACGAATACGCGTTGCGAT
54441 TTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCGTTGCGAT
1 TTTACGGATACTCGTTGCGAT--TCACGAATACGCGTTGCGAT
54482 TT
1 TT
54484 ATATGTTCGC
Statistics
Matches: 146, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 72 0.49
41 68 0.47
42 3 0.02
43 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
TTTACGGATACTCGTTGCGATTCACGAATACGCGTTGCGAT
Found at i:54493 original size:20 final size:20
Alignment explanation
Indices: 54470--54518 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
54460 ATAGTCAGAA
*
54470 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
*
54490 TCGCGTTACGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
54510 TCGCGTTGC
1 TCGCGTTGC
54519 AATTATGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:56112 original size:20 final size:20
Alignment explanation
Indices: 56087--56132 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
56077 TGTAAATCGT
*
56087 AACACATAAGTCAAATTCGC
1 AACACAGAAGTCAAATTCGC
56107 AACACAGAAGTCAAATTCGC
1 AACACAGAAGTCAAATTCGC
56127 AACACA
1 AACACA
56133 ATTCGAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.26, G:0.11, T:0.15
Consensus pattern (20 bp):
AACACAGAAGTCAAATTCGC
Found at i:56724 original size:19 final size:19
Alignment explanation
Indices: 56675--56728 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
56665 GCAACGTAAC
* *
56675 GCGATTTTAGTTTCGCGTT
1 GCGATTTCATTTTCGCGTT
*
56694 GCGGTTTTTCATTTTCGCGTT
1 GC-G-ATTTCATTTTCGCGTT
56715 GCGATTTCATTTTC
1 GCGATTTCATTTTC
56729 AGAAACTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 12 0.41
20 2 0.07
21 15 0.52
ACGTcount: A:0.09, C:0.19, G:0.22, T:0.50
Consensus pattern (19 bp):
GCGATTTCATTTTCGCGTT
Done.