Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001744.1 Hibiscus syriacus cultivar Beakdansim tig00003531_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: 87192
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3559 original size:6 final size:6
Alignment explanation
Indices: 3548--3574 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3538 GCTAATCCCT
3548 TCCTTC TCCTTC TCCTTC TCCTTC TCC
1 TCCTTC TCCTTC TCCTTC TCCTTC TCC
3575 ATGGCTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCTTC
Found at i:5357 original size:25 final size:25
Alignment explanation
Indices: 5323--5373 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5313 TTACACTGTG
5323 TAAAACTTTTTTAGGTTCTTTGGAT
1 TAAAACTTTTTTAGGTTCTTTGGAT
5348 TAAAACTTTTTTAGGTTCTTTGGAT
1 TAAAACTTTTTTAGGTTCTTTGGAT
5373 T
1 T
5374 GAGGGAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (25 bp):
TAAAACTTTTTTAGGTTCTTTGGAT
Found at i:5530 original size:2 final size:2
Alignment explanation
Indices: 5523--5547 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5513 CCTATCTATA
5523 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
5548 ATGAACGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17122 original size:21 final size:22
Alignment explanation
Indices: 17051--17117 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
17041 TTACTACAGA
* * * *
17051 GGGAATCGATACCCCACTTGAAG
1 GGGAACCGATTCCCC-CTTTAAT
17074 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTT-AAT
*
17097 GGGAACTGATTCCCTCCTTTA
1 GGGAACCGATTCCC-CCTTTA
17118 GGGAATCAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.08
23 29 0.78
24 5 0.14
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTTAAT
Found at i:25208 original size:6 final size:6
Alignment explanation
Indices: 25197--25221 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25187 TCACCAAGAG
25197 AATTGC AATTGC AATTGC AATTGC A
1 AATTGC AATTGC AATTGC AATTGC A
25222 TGCATGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
AATTGC
Found at i:32051 original size:22 final size:22
Alignment explanation
Indices: 32026--32071 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
32016 TAGACATTTT
32026 AATAAAAATATGA-AAAAAATTA
1 AATAAAAA-ATGACAAAAAATTA
* *
32048 AATAAATAATGACATAAAATTA
1 AATAAAAAATGACAAAAAATTA
32070 AA
1 AA
32072 ACAACAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (22 bp):
AATAAAAAATGACAAAAAATTA
Found at i:33823 original size:21 final size:21
Alignment explanation
Indices: 33794--33932 Score: 122
Period size: 20 Copynumber: 6.8 Consensus size: 21
33784 CGCGTTGCAT
33794 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
* * * ** *
33815 ATCGTGTTGCGAT-TTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
33835 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
* * ** *
33856 ATCGCGTTGCGAT-TTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
33876 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
* ** *
33897 TTCGCGTTGCGAT-TTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
33917 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
33933 CTACAGTTGT
Statistics
Matches: 88, Mismatches: 27, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
20 45 0.51
21 43 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTTGAAA
Found at i:33838 original size:41 final size:41
Alignment explanation
Indices: 33791--33932 Score: 266
Period size: 41 Copynumber: 3.5 Consensus size: 41
33781 ATTCGCGTTG
*
33791 CATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
33832 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
33873 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
33914 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
33933 CTACAGTTGT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:33949 original size:22 final size:22
Alignment explanation
Indices: 33921--33992 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
33911 TTCCATTTCG
33921 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
33943 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
33962 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
33984 CGTTGCGAT
1 CGTTGCGAT
33993 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:33966 original size:19 final size:19
Alignment explanation
Indices: 33942--34007 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
33932 TCTACAGTTG
33942 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
33961 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
33982 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
34002 TCGTTG
1 TCGTTG
34008 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:33966 original size:41 final size:41
Alignment explanation
Indices: 33820--34014 Score: 197
Period size: 41 Copynumber: 4.7 Consensus size: 41
33810 TGAAAATCGT
* * * *
33820 GTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-C
1 GTTGCGATTTTCCAATTC-CGTTGCGATAGTCT-ACAGTTGTC
* *
33861 GTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGA-AATTCG-C
1 GTTGCGATTTTCCAATTC-CGTTGCGATAGTCT-ACAGTT-GTC
*
33902 GTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTC
1 GTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTGTC
33944 GTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGTC
1 GTTGCGATTTTCC-AATTCCGTTGCGATAGTCTACAGTTGTC
*
33985 GTTGCGATTTTCCAAATT-CGTTGTGATAGT
1 GTTGCGATTTTCC-AATTCCGTTGCGATAGT
34015 TAAAAAAAAG
Statistics
Matches: 145, Mismatches: 4, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
40 3 0.02
41 121 0.83
42 18 0.12
43 3 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (41 bp):
GTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTTGTC
Found at i:33966 original size:82 final size:81
Alignment explanation
Indices: 33798--33998 Score: 248
Period size: 82 Copynumber: 2.4 Consensus size: 81
33788 TTGCATTTCG
* *
33798 CGTTGCGATAGTTGAAAATCGTGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGT
1 CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGT
*
33863 TGCGATTTTCCATTTC
66 TGCGATTTTCCAATTC
* * *
33879 GCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTTGT
1 -CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-
33943 CGTTGCGATTTTCCAAATT-
63 CGTTGCGATTTTCC-AATTC
*
33962 CGTTGCGATAGTCT-ACAGTT-GTCGTTGCGATTTTCCA
1 CGTTGCGATAGT-TGA-AATTCG-CGTTGCGATTTTCCA
33999 AATTCGTTGT
Statistics
Matches: 106, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
82 69 0.65
83 34 0.32
84 3 0.03
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (81 bp):
CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGT
TGCGATTTTCCAATTC
Found at i:34007 original size:123 final size:121
Alignment explanation
Indices: 33791--34015 Score: 269
Period size: 123 Copynumber: 1.8 Consensus size: 121
33781 ATTCGCGTTG
*
33791 CATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAA
*
33856 ATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
65 ATCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
* * *
33914 CATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTGCGATAGTCT-
1 CATTTCGCGTTGCGATAGT-TGAAAATCGT-GTTGCGATTTTCC-AATTCCGTTGCGATAGT-TG
* * * *
33976 ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTGTGATAGTT
62 AAAATCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGTT
34016 AAAAAAAAGA
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
123 52 0.60
124 29 0.33
125 6 0.07
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (121 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGTGTTGCGATTTTCCAATTCCGTTGCGATAGTTGAAAA
TCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
Found at i:34595 original size:6 final size:6
Alignment explanation
Indices: 34574--34634 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
34564 TCTCGTCTCG
34574 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
34620 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
34635 AATATGTGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.18
6 45 0.82
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:34744 original size:20 final size:20
Alignment explanation
Indices: 34719--34756 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34709 TCAACGAATT
* *
34719 TGGAAAATCGCAACGCGAAA
1 TGGAAAACCACAACGCGAAA
34739 TGGAAAACCACAACGCGA
1 TGGAAAACCACAACGCGA
34757 TTTTCAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.24, G:0.24, T:0.08
Consensus pattern (20 bp):
TGGAAAACCACAACGCGAAA
Found at i:34785 original size:21 final size:21
Alignment explanation
Indices: 34724--34785 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
34714 GAATTTGGAA
*
34724 AATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAAATGCAAC
* * ** *
34744 AACCACAACGCGATTTTCAAC
1 AATCGCAACGCGAAATGCAAC
*
34765 TATCGCAACGCGAAATGCAAC
1 AATCGCAACGCGAAATGCAAC
34786 GCGAATTTGC
Statistics
Matches: 29, Mismatches: 12, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.15
Consensus pattern (21 bp):
AATCGCAACGCGAAATGCAAC
Found at i:34837 original size:20 final size:20
Alignment explanation
Indices: 34814--34919 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
34804 AGATCGTGTT
*
34814 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
34834 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
*
34854 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
34875 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
34895 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
34916 GCGA
1 GCGA
34920 AATGCAACGT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 28 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:34866 original size:41 final size:41
Alignment explanation
Indices: 34821--34923 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
34811 GTTGCGATTT
*
34821 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
34862 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
34903 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
34924 CAACGTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:34927 original size:21 final size:21
Alignment explanation
Indices: 34821--34927 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
34811 GTTGCGATTT
34821 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
34842 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
34862 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
34883 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
34903 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
34924 CAAC
1 CAAC
34928 GTGAATTTGC
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:37527 original size:32 final size:31
Alignment explanation
Indices: 37490--37580 Score: 112
Period size: 32 Copynumber: 2.9 Consensus size: 31
37480 GAAGGACCTA
*
37490 TCCATATGTTCCGAAGAACATAGGTAACACTG
1 TCCATATGTTCCGAAG-ACATAGGTAACACTC
*
37522 TCCATATGTCCCGAAGGACATAGGTAA-ACTC
1 TCCATATGTTCCGAA-GACATAGGTAACACTC
**
37553 TCCATATGTCTCAAAAGACATAGGTAAC
1 TCCATATGT-TCCGAAGACATAGGTAAC
37581 CCTCGACTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
31 23 0.45
32 27 0.53
33 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (31 bp):
TCCATATGTTCCGAAGACATAGGTAACACTC
Found at i:37560 original size:31 final size:32
Alignment explanation
Indices: 37490--37580 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 32
37480 GAAGGACCTA
* * *
37490 TCCATATGTTCCGAAGAACATAGGTAACACTG
1 TCCATATGTCCCGAAGGACATAGGTAACACTC
37522 TCCATATGTCCCGAAGGACATAGGTAA-ACTC
1 TCCATATGTCCCGAAGGACATAGGTAACACTC
* * *
37553 TCCATATGTCTCAAAAGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
37581 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 27 0.52
32 25 0.48
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (32 bp):
TCCATATGTCCCGAAGGACATAGGTAACACTC
Found at i:37712 original size:21 final size:21
Alignment explanation
Indices: 37653--37712 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
37643 TTTTATCTTT
*
37653 TCACATATTCATATAAACATA
1 TCACATATTCATATAAGCATA
* * *
37674 TGACATATTCATAGAAGCCTA
1 TCACATATTCATATAAGCATA
37695 TCACATATTCATATAAGC
1 TCACATATTCATATAAGC
37713 TCATAGCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (21 bp):
TCACATATTCATATAAGCATA
Found at i:38554 original size:19 final size:19
Alignment explanation
Indices: 38530--38580 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
38520 TCTTAACGTG
38530 TGTATCGATACACTACCTA
1 TGTATCGATACACTACCTA
38549 TGTATCGATACACTACCTA
1 TGTATCGATACACTACCTA
*
38568 TATATCGATACAC
1 TGTATCGATACAC
38581 AAATTACATT
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:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (19 bp):
TGTATCGATACACTACCTA
Found at i:41028 original size:65 final size:65
Alignment explanation
Indices: 40868--41028 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
40858 TTGTTTAAGG
* * * **
40868 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
40931 A
65 A
*
40932 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
40996 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
41029 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:41543 original size:18 final size:18
Alignment explanation
Indices: 41520--41554 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41510 CTAGGAGATT
41520 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
41538 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
41555 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:42619 original size:149 final size:149
Alignment explanation
Indices: 42446--42760 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
42436 GAGTCGAGGG
* **
42446 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
42511 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
42575 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
*
42595 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
42660 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
42725 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
42744 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
42761 TGCAATTATA
Statistics
Matches: 159, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
150 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:42761 original size:23 final size:23
Alignment explanation
Indices: 42728--42772 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
42718 ATTATTATAT
*
42728 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
42751 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
42773 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:46061 original size:65 final size:65
Alignment explanation
Indices: 45901--46061 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 65
45891 TTGTTTAAGG
* * * ** **
45901 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATATTATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
45964 A
65 A
*
45965 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
46029 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
46062 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.71
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:46574 original size:18 final size:18
Alignment explanation
Indices: 46551--46585 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46541 CTAGGAGATT
46551 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
46569 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
46586 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:47669 original size:17 final size:17
Alignment explanation
Indices: 47649--47682 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
47639 TCGGGATATA
*
47649 TATATATTCTGTGGAAC
1 TATATATTCTATGGAAC
47666 TATATATTCTATGGAAC
1 TATATATTCTATGGAAC
47683 ATGTGTGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (17 bp):
TATATATTCTATGGAAC
Found at i:47785 original size:166 final size:167
Alignment explanation
Indices: 47499--47808 Score: 536
Period size: 166 Copynumber: 1.9 Consensus size: 167
47489 CTTCGGGATA
* **
47499 TATATATATCTTTGGAACATGTGTGAAGTCTGGTGAGACACATATATGATCCCTAGCATATGTAT
1 TATATATATCTATGGAACATGTGTGAAGTCTGGAAAGACACATATATGATCCCTAGCATATGTAT
47564 ATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAATTCT
66 ATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAATTCT
47629 ACGCGGTCA-TTCGGGATATATATATATTCTGTGGAAC
131 ACGCGG-CACTTCGGGATATATATATATTCTGTGGAAC
*
47666 TATATAT-TCTATGGAACATGTGTGAAGTCTTGAAAGACACATACT-TGATCCCTAGCATATGTA
1 TATATATATCTATGGAACATGTGTGAAGTCTGGAAAGACACATA-TATGATCCCTAGCATATGTA
*
47729 TATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAATTC
65 TATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAATTC
47794 TACGCGGCACTTCGG
130 TACGCGGCACTTCGG
47809 TGCAATTATA
Statistics
Matches: 136, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
165 2 0.01
166 126 0.93
167 8 0.06
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (167 bp):
TATATATATCTATGGAACATGTGTGAAGTCTGGAAAGACACATATATGATCCCTAGCATATGTAT
ATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAATTCT
ACGCGGCACTTCGGGATATATATATATTCTGTGGAAC
Found at i:47809 original size:23 final size:23
Alignment explanation
Indices: 47776--47820 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
47766 ATTATTATAT
*
47776 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
47799 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
47821 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:54418 original size:45 final size:45
Alignment explanation
Indices: 54354--54506 Score: 252
Period size: 45 Copynumber: 3.4 Consensus size: 45
54344 GGATGTTACA
* *
54354 AAGTATACTGGTAAAATAAGCTTACGAGATTATGGAATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGT
* *
54399 AAGTATATTGTTAAAATAAGCTTACGAGCTTATGGAATAAATGTT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGT
*
54444 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGT
*
54489 AAGTATAATGGTAAAATA
1 AAGTATATTGGTAAAATA
54507 TTATATATGT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 100 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (45 bp):
AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGT
Found at i:56024 original size:2 final size:2
Alignment explanation
Indices: 56017--56056 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
56007 TGCACCTTTC
*
56017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56057 CCACACATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:56368 original size:29 final size:30
Alignment explanation
Indices: 56326--56391 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
56316 CCCGAAGGAC
56326 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* *
56355 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
*
56385 CTGTCCA
1 CTATCCA
56392 TATGTTCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCCCGGTAA
Found at i:56422 original size:31 final size:30
Alignment explanation
Indices: 56380--56477 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
56370 AAAGATCCTC
*
56380 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
56410 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
56441 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
56473 GGTAA
1 GGTAA
56478 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:57275 original size:21 final size:21
Alignment explanation
Indices: 57245--57289 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57235 ATTCTGTCGT
* *
57245 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
57266 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
57287 TTG
1 TTG
57290 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:60820 original size:2 final size:2
Alignment explanation
Indices: 60807--60876 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
60797 TGCACCTTTC
*
60807 AT AT AG 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
*
60849 AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60877 CCACACATAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61186 original size:29 final size:30
Alignment explanation
Indices: 61144--61209 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
61134 CCCGAAGGAC
61144 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* *
61173 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
*
61203 CTGTCCA
1 CTATCCA
61210 TATGTTCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCCCGGTAA
Found at i:61242 original size:31 final size:31
Alignment explanation
Indices: 61201--61297 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
61191 GATCCTCGGT
*
61201 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * * *
61232 TATTGTCCATATGTCTCGAAAG-ACATAGGTAA
1 AACTGTCCATATGT-TCCATAGAACATAGGT-A
*
61264 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
61295 AAC
1 AAC
61298 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
31 28 0.53
32 25 0.47
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:62091 original size:21 final size:21
Alignment explanation
Indices: 62061--62105 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62051 ATTCTTTCGT
* *
62061 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
62082 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
62103 TTG
1 TTG
62106 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:63014 original size:14 final size:14
Alignment explanation
Indices: 62997--63037 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
62987 GATTGGGTTA
*
62997 AACATAAATGAACG
1 AACATAAACGAACG
*
63011 AACATAACCGAACG
1 AACATAAACGAACG
63025 AACATAAACGAAC
1 AACATAAACGAAC
63038 ATAACCAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:63058 original size:24 final size:24
Alignment explanation
Indices: 63006--63058 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
62996 AAACATAAAT
* *
63006 GAACGAACATAACCGAACGAACAT
1 GAACGAACATAACCAAACGAACAC
* **
63030 AAACGAACATAACCAAACGTTCAC
1 GAACGAACATAACCAAACGAACAC
63054 GAACG
1 GAACG
63059 TAAATGAACG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.26, G:0.15, T:0.09
Consensus pattern (24 bp):
GAACGAACATAACCAAACGAACAC
Found at i:64210 original size:38 final size:36
Alignment explanation
Indices: 64118--64221 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
64108 CTTAATATTC
* *
64118 AATAAG-AAAATATCCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATAAAACCTTT
*
64153 AATAAGAAAAATACTCAAATTTCTTATAAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATAAAACCTTT
64189 AATAAGAAAAAAATACCCAAATTTCTTATAAAA
1 AATAAG--AAAAATACCCAAATTTCTTATAAAA
64222 TCTAAATTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 6 0.10
36 32 0.52
38 24 0.39
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.31
Consensus pattern (36 bp):
AATAAGAAAAATACCCAAATTTCTTATAAAACCTTT
Found at i:69205 original size:21 final size:20
Alignment explanation
Indices: 69181--69221 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
69171 TTAGTCCCTC
*
69181 GTTTTTTTTAAATATTATAAA
1 GTTTATTTTAAA-ATTATAAA
*
69202 GTTTATTTTATAATTATAAA
1 GTTTATTTTAAAATTATAAA
69222 TAACTAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
GTTTATTTTAAAATTATAAA
Found at i:74558 original size:32 final size:32
Alignment explanation
Indices: 74517--74578 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
74507 GCATAATCTA
* *
74517 CCTCTGTGTATGCTTCCAAAGTCGAGTTCCTC
1 CCTCCGTGTATGCTTCCAAAGTCAAGTTCCTC
*
74549 CCTCCGTGTATGCTTCCAGAGTCAAGTTCC
1 CCTCCGTGTATGCTTCCAAAGTCAAGTTCC
74579 CCTCTCTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.32
Consensus pattern (32 bp):
CCTCCGTGTATGCTTCCAAAGTCAAGTTCCTC
Found at i:80511 original size:14 final size:14
Alignment explanation
Indices: 80488--80523 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
80478 ATAGCCGATA
*
80488 AATAGAACATATAT
1 AATAGTACATATAT
80502 AATAGTACATATAT
1 AATAGTACATATAT
80516 AATAGTAC
1 AATAGTAC
80524 TTATTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (14 bp):
AATAGTACATATAT
Found at i:83086 original size:21 final size:21
Alignment explanation
Indices: 83056--83201 Score: 115
Period size: 21 Copynumber: 7.0 Consensus size: 21
83046 GATTTACATA
*
83056 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
83077 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
83100 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
83119 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
83142 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
83161 TTCGCGTTGCAATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
83184 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
83202 AATCGCAATG
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
19 24 0.24
21 49 0.49
23 26 0.26
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:83109 original size:42 final size:42
Alignment explanation
Indices: 83062--83201 Score: 244
Period size: 42 Copynumber: 3.3 Consensus size: 42
83052 CATATTCGCA
*
83062 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
83104 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
83146 TTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
83188 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
83202 AATCGCAATG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 94 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:83317 original size:5 final size:6
Alignment explanation
Indices: 83285--83324 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
83275 AGACAGTATT
83285 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG A-CACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
83325 GACGGACGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 1 0.03
5 11 0.33
6 21 0.64
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:84016 original size:21 final size:21
Alignment explanation
Indices: 83949--84022 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
83939 TTTGGAATAA
* * *
83949 ATCGCAACGCAAACTTCGACT
1 ATCGCAATGCGAACTTAGACT
*
83970 ATCGCAATGCGAA--TATGTA-A
1 ATCGCAATGCGAACTTA-G-ACT
83990 ATCGCAATGCGAACTTAGACT
1 ATCGCAATGCGAACTTAGACT
*
84011 ATCGCATTGCGA
1 ATCGCAATGCGA
84023 TTTACATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 1 0.02
20 15 0.36
21 24 0.57
22 2 0.05
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTAGACT
Found at i:84084 original size:21 final size:21
Alignment explanation
Indices: 84031--84076 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
84021 GATTTACATA
84031 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
84052 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
84073 TTCG
1 TTCG
84077 TGTTGCGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Done.