Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001564.1 Hibiscus syriacus cultivar Beakdansim tig00003098_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: 94498
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2786 original size:19 final size:19
Alignment explanation
Indices: 2764--2805 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2754 AAATCGCAAC
2764 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
2783 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
2802 GCGA
1 GCGA
2806 TTCCCTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:2806 original size:19 final size:19
Alignment explanation
Indices: 2773--2924 Score: 86
Period size: 19 Copynumber: 8.8 Consensus size: 19
2763 CGCGAATTTA
2773 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
2792 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
2809 ----C-CTGTTGCGATTTTC
1 ATTTCGC-GTTGCGATTTTC
*
2824 ATTTCGCATTGCGA-----
1 ATTTCGCGTTGCGATTTTC
*
2838 AATTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
2857 ATTTCGCATTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
* *
2874 ---TCTCGTTACGATTTTC
1 ATTTCGCGTTGCGATTTTC
* ** *
2890 ATTTCGCATTGCGATAGTA
1 ATTTCGCGTTGCGATTTTC
2909 ATTTCCGCGTTGCGAT
1 ATTT-CGCGTTGCGAT
2925 AGACATTAAG
Statistics
Matches: 99, Mismatches: 15, Indels: 37
0.66 0.10 0.25
Matches are distributed among these distances:
12 1 0.01
13 8 0.08
14 20 0.20
15 3 0.03
16 3 0.03
17 6 0.06
19 47 0.47
20 11 0.11
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.42
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:2869 original size:65 final size:66
Alignment explanation
Indices: 2775--2903 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 66
2765 CGAATTTAAT
* *
2775 TTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCT-GTTGCGATTTTCATTTCGCATTGCGAA
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGCGAA
2839 A
66 A
*
2840 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATTTCGCATTGCGA
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGCGA
2904 TAGTAATTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 35 0.58
66 25 0.42
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (66 bp):
TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGCGAA
A
Found at i:2904 original size:33 final size:33
Alignment explanation
Indices: 2779--2904 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
2769 TTTAATTTCG
* *
2779 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
2812 -GTTGCGATTTTCATTTCGCATTGCGAAAT-TCG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
2844 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
2877 CGTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2905 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
32 27 0.33
33 56 0.67
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:5188 original size:12 final size:12
Alignment explanation
Indices: 5171--5205 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5161 TCTTCGGGGA
5171 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5183 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5195 C-TTTTCTTCTT
1 CTTTTTCTTCTT
5206 AGGATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5414 original size:24 final size:23
Alignment explanation
Indices: 5376--5429 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
5366 CTGAAACATC
*
5376 ATCAAATCCGAGTATTGACCAAT
1 ATCAAATCCGAGTATTGACCAAG
*
5399 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAA-TCCGAGTATTGACCAAG
5423 ATCAAAT
1 ATCAAAT
5430 TTCGAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
ATCAAATCCGAGTATTGACCAAG
Found at i:6225 original size:20 final size:21
Alignment explanation
Indices: 6200--6251 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6190 TTTTCCTAAT
*
6200 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
6220 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
6241 TCGCAATGCGA
1 TCGCAATGCGA
6252 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:6273 original size:20 final size:20
Alignment explanation
Indices: 6240--6320 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
6230 AATTTGGAAA
* *
6240 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
6260 ATCGCAACGAGATAAT-ACAAAAA
1 ATCGCAACGAGATACTGAC----T
*
6283 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
6303 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
6321 AAATCGAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
23 14 0.29
24 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:6552 original size:20 final size:19
Alignment explanation
Indices: 6527--6595 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
6517 ATTCATTTGA
6527 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGC-AAAATGG
** * *
6547 CTATCGCAATTCGAAATGA
1 CTATCGCAACGCAAAATGG
**
6566 AAATCGCAACGCGAAAATGG
1 CTATCGCAACGC-AAAATGG
6586 CTATCGCAAC
1 CTATCGCAAC
6596 TAAAATCGCA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
19 13 0.36
20 23 0.64
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (19 bp):
CTATCGCAACGCAAAATGG
Found at i:6623 original size:31 final size:32
Alignment explanation
Indices: 6565--6624 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
6555 ATTCGAAATG
***
6565 AAAATCGCAACGCGAAAATGGCTATCGCAACT
1 AAAATCGCAACGCGAAAATGAAAATCGCAACT
*
6597 AAAATCGCAATGCG-AAATGAAAATCGCA
1 AAAATCGCAACGCGAAAATGAAAATCGCA
6625 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.46
32 13 0.54
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.15
Consensus pattern (32 bp):
AAAATCGCAACGCGAAAATGAAAATCGCAACT
Found at i:6644 original size:14 final size:16
Alignment explanation
Indices: 6624--6697 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
6614 TGAAAATCGC
6624 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
6639 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
6656 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
6675 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
6691 -TTGCGAT
1 ATTGCGAT
6698 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:6661 original size:19 final size:19
Alignment explanation
Indices: 6620--6687 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
6610 GAAATGAAAA
6620 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
6636 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6653 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6672 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
6688 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:6713 original size:20 final size:20
Alignment explanation
Indices: 6690--6740 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
6680 CGATTTTCTC
6690 GTTGCGATAGTCAGTTTCGT
1 GTTGCGATAGTCAGTTTCGT
6710 GTTGCGATAGTCAGTTTCGT
1 GTTGCGATAGTCAGTTTCGT
6730 GTTGCGATAGT
1 GTTGCGATAGT
6741 TTTGCCTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.14, G:0.31, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTCGT
Found at i:8754 original size:20 final size:20
Alignment explanation
Indices: 8731--8779 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
8721 GAAACTTTAA
8731 ATCGCAACGC-GAAAATGACT
1 ATCGCAACGCAG-AAATGACT
*
8751 ATCGCAACGCAGAAATGGCT
1 ATCGCAACGCAGAAATGACT
8771 ATCGCAACG
1 ATCGCAACG
8780 ATAAAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCAGAAATGACT
Found at i:8786 original size:20 final size:19
Alignment explanation
Indices: 8731--8786 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
8721 GAAACTTTAA
*
8731 ATCGCAACGCGAAAATGACT
1 ATCGCAACG-AAAAATGACT
* *
8751 ATCGCAACGCAGAAATGGCT
1 ATCGCAACG-AAAAATGACT
8771 ATCGCAACGATAAAAT
1 ATCGCAACGA-AAAAT
8787 CGCAATGCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAACGAAAAATGACT
Found at i:8806 original size:19 final size:19
Alignment explanation
Indices: 8782--8861 Score: 109
Period size: 19 Copynumber: 4.5 Consensus size: 19
8772 TCGCAACGAT
8782 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
8801 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
8820 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
8834 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
8853 -AAATCGCAA
1 AAAATCGCAA
8862 CGACAAAATC
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 10 0.19
19 29 0.54
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:8831 original size:52 final size:53
Alignment explanation
Indices: 8729--8863 Score: 175
Period size: 52 Copynumber: 2.6 Consensus size: 53
8719 ACGAAACTTT
* ** *** *
8729 AAATCGCAACGCGAAAATGACTATCGCAACGCAGAAATGGCTATCGCAACGATA
1 AAATCGCAATGCG-AAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGACA
*
8783 AAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGACA
1 AAATCGCAATGCGAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGACA
8835 AAATCGCAATGCGAAATG-AAATCGCAACG
1 AAATCGCAATGCGAAATGAAAATCGCAACG
8864 ACAAAATCGC
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
51 10 0.14
52 35 0.49
53 15 0.21
54 12 0.17
ACGTcount: A:0.44, C:0.21, G:0.20, T:0.14
Consensus pattern (53 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGACA
Found at i:8862 original size:32 final size:33
Alignment explanation
Indices: 8801--8882 Score: 148
Period size: 32 Copynumber: 2.5 Consensus size: 33
8791 ATGCGAAATG
8801 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
8834 AAAATCGCAATGCGAAATG-AAATCGCAACGAC
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
*
8866 AAAATCGCAACGCGAAA
1 AAAATCGCAATGCGAAA
8883 CACAAATCGC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.60
33 19 0.40
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGAC
Found at i:8930 original size:14 final size:14
Alignment explanation
Indices: 8911--8968 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
8901 TTTCATTTCG
8911 CATTGCGATTTTAT
1 CATTGCGATTTTAT
8925 CATTGCGATTTTCATTT
1 CATTGCGATTTT-A--T
*
8942 GCATTGCGATTTTGT
1 -CATTGCGATTTTAT
*
8957 CGTTGCGATTTT
1 CATTGCGATTTT
8969 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
15 2 0.05
17 1 0.03
18 12 0.32
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (14 bp):
CATTGCGATTTTAT
Found at i:8951 original size:32 final size:33
Alignment explanation
Indices: 8892--8984 Score: 152
Period size: 32 Copynumber: 2.8 Consensus size: 33
8882 ACACAAATCG
*
8892 CATTGCGACTTTCATTTCGCATTGCGATTTTAT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTAT
*
8925 CATTGCGATTTTCATTT-GCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTAT
*
8957 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
8985 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.54
33 26 0.46
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTAT
Found at i:8991 original size:19 final size:20
Alignment explanation
Indices: 8969--9012 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
8959 TTGCGATTTT
8969 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
8988 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
9008 CATTT
1 CATTT
9013 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:9020 original size:20 final size:20
Alignment explanation
Indices: 8978--9023 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
8968 TCATTTCGCA
*
8978 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
8998 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
9018 TTGCGA
1 TTGCGA
9024 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:9528 original size:18 final size:18
Alignment explanation
Indices: 9502--9546 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
9492 GTCGATCAGA
**
9502 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGACGAGG
*
9520 TGATAGCTCTGGACGAGG
1 TGATGGCTCTGGACGAGG
9538 TGATGGCTC
1 TGATGGCTC
9547 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:11193 original size:20 final size:21
Alignment explanation
Indices: 11168--11215 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
11158 TCTGAGAGAT
11168 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
11188 GGAGATGGGACGGATTTCGTC
1 GGAGATGAGACGGATTTCGCC
*
11209 AGAGATG
1 GGAGATG
11216 GGTGAGATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.21
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:11201 original size:21 final size:21
Alignment explanation
Indices: 11175--11217 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
11165 GATGGAGATA
*
11175 GACGGATTTCGCCGGAGATGG
1 GACGGATTTCGCCAGAGATGG
*
11196 GACGGATTTCGTCAGAGATGG
1 GACGGATTTCGCCAGAGATGG
11217 G
1 G
11218 TGAGATAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (21 bp):
GACGGATTTCGCCAGAGATGG
Found at i:11488 original size:20 final size:20
Alignment explanation
Indices: 11385--11518 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
11375 CGCTTTGAAA
*
11385 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
11406 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
11426 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
11446 ATCTCGTTGCGATTTGT-ATT
1 ATCGCATTGCGA-TAGTCAGT
*
11466 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
11486 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
11506 ATCGCATTGCGAT
1 ATCGCATTGCGAT
11519 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
19 5 0.05
20 78 0.81
21 13 0.14
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:11490 original size:60 final size:60
Alignment explanation
Indices: 11385--11520 Score: 191
Period size: 60 Copynumber: 2.2 Consensus size: 60
11375 CGCTTTGAAA
* * *
11385 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATT-TGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
11446 ATCTCGTTGCGATTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
11506 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
11521 TCCCAATTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 53 0.82
61 12 0.18
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (60 bp):
ATCGCATTGCGATTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:12011 original size:21 final size:21
Alignment explanation
Indices: 11938--12012 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
11928 CAGTTTCCAG
* *
11938 ATTCGCAACGCGATTTTGACT-
1 ATTCGCAATGCGATTTT-CCTA
* *
11959 A-TCGCATTGCGATTTTCCAA
1 ATTCGCAATGCGATTTTCCTA
* **
11979 ATTCACGTTGCGATTTTCCTA
1 ATTCGCAATGCGATTTTCCTA
12000 ATTCGCAATGCGA
1 ATTCGCAATGCGA
12013 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.02
20 14 0.33
21 27 0.64
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCCTA
Found at i:12044 original size:20 final size:20
Alignment explanation
Indices: 12021--12087 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
12011 GAATACGTAA
* *
12021 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
12041 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
* *
12061 ATCGTAATGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
12081 ATCGCAA
1 ATCGCAA
12088 TACTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:12956 original size:24 final size:23
Alignment explanation
Indices: 12924--12975 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
12914 AGTATTCGAA
*
12924 ATTTGATCTTGGTCAATACCCGG
1 ATTTTATCTTGGTCAATACCCGG
*
12947 ACTTTTATCTTGGTCAATACTCGG
1 A-TTTTATCTTGGTCAATACCCGG
12971 ATTTT
1 ATTTT
12976 GATGATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (23 bp):
ATTTTATCTTGGTCAATACCCGG
Found at i:15428 original size:20 final size:20
Alignment explanation
Indices: 15392--15497 Score: 133
Period size: 20 Copynumber: 5.3 Consensus size: 20
15382 CGCGGAAATT
15392 GCAACGC-GAATATGACTATC
1 GCAACGCGGAA-ATGACTATC
* * *
15412 GTAACACAGAAATGACTATC
1 GCAACGCGGAAATGACTATC
*
15432 GCAACGCGGAATTGACTATC
1 GCAACGCGGAAATGACTATC
* *
15452 GCAACTCGGGAATGACTATC
1 GCAACGCGGAAATGACTATC
*
15472 GCAACGCGGGAATGACTATC
1 GCAACGCGGAAATGACTATC
15492 GCAACG
1 GCAACG
15498 AGAGAATCGC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
20 72 0.96
21 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.18
Consensus pattern (20 bp):
GCAACGCGGAAATGACTATC
Found at i:15504 original size:20 final size:20
Alignment explanation
Indices: 15370--15504 Score: 126
Period size: 20 Copynumber: 7.0 Consensus size: 20
15360 GACATTCATT
15370 TGACTATCGCAACGCG-GAA
1 TGACTATCGCAACGCGAGAA
15389 --A-T-T-GCAACGCGA-ATA
1 TGACTATCGCAACGCGAGA-A
* *
15404 TGACTATCGTAACAC-AGAAA
1 TGACTATCGCAACGCGAG-AA
15424 TGACTATCGCAACGCG-GAA
1 TGACTATCGCAACGCGAGAA
* *
15443 TTGACTATCGCAACTCGGGAA
1 -TGACTATCGCAACGCGAGAA
*
15464 TGACTATCGCAACGCGGGAA
1 TGACTATCGCAACGCGAGAA
*
15484 TGACTATCGCAACGAGAGAA
1 TGACTATCGCAACGCGAGAA
15504 T
1 T
15505 CGCAATGCGA
Statistics
Matches: 96, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.09
15 2 0.02
16 1 0.01
17 2 0.02
18 1 0.01
19 4 0.04
20 73 0.76
21 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGAGAA
Found at i:15528 original size:33 final size:34
Alignment explanation
Indices: 15489--15563 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
15479 GGGAATGACT
*
15489 ATCGCAACGAGAGAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
* *
15522 ATCGCAACGAGAAAATCGCAATGTGAAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
15556 ATCGCAAC
1 ATCGCAAC
15564 ACGAATTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 23 0.61
34 15 0.39
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
Found at i:15674 original size:34 final size:33
Alignment explanation
Indices: 15579--15674 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
15569 TTTAGTTTCG
*
15579 CGTTGCGATTTTCATTTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
** *
15613 CGTTTTGATTTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
**
15646 CGTTGCGATAGTCATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
15675 AGTCTGTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 30 0.58
34 22 0.42
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:15798 original size:14 final size:14
Alignment explanation
Indices: 15781--15817 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
15771 ATCAATTAAA
15781 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
15795 ACAAATCATCTTTT
1 ACAAATCAACATTT
15809 ACAAATCAA
1 ACAAATCAA
15818 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:17305 original size:42 final size:42
Alignment explanation
Indices: 17207--17308 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
17197 TTGGGAGGGA
* * *
17207 CCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGGGAGGAG
1 CCTCTTGAACGATGACAGTGGCCTCTTGAACGATAGGAGGAG
* ** *
17249 ACTCTTGAGGGATGATA-TGGGCCTCTTGAACGATAGG-GGAGG
1 CCTCTTGAACGATGACAGT-GGCCTCTTGAACGATAGGAGGA-G
17291 CCTCTTGAACGATGACAG
1 CCTCTTGAACGATGACAG
17309 GTGAGTCGGG
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
41 4 0.09
42 42 0.91
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGTGGCCTCTTGAACGATAGGAGGAG
Found at i:17810 original size:20 final size:20
Alignment explanation
Indices: 17787--17835 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
17777 GAAACTTAAA
17787 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
17807 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
17827 ATCGCAACG
1 ATCGCAACG
17836 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:17905 original size:20 final size:20
Alignment explanation
Indices: 17880--17926 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
17870 GATTCTTTCG
17880 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
17900 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
17920 TTGCGAT
1 TTGCGAT
17927 TTTGTTGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:17951 original size:53 final size:53
Alignment explanation
Indices: 17842--17959 Score: 141
Period size: 53 Copynumber: 2.2 Consensus size: 53
17832 AACGAGAGAA
* **
17842 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
* ** *
17895 TCGCATTGCGATAGTCATTTTCGCATTGCGATT-TTGTTGTTGCGATTTTC-ATT
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGATTCTT-TCGTTGCGATAGTCAAAT
17948 TCGCATTGCGAT
1 TCGCATTGCGAT
17960 TCTCTCGTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 30 0.54
54 26 0.46
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (53 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
Found at i:17955 original size:33 final size:34
Alignment explanation
Indices: 17900--17993 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
17890 CAAATTCGCA
* * *
17900 TTGCGATAGTCATTTTCGCATTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
**
17934 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
*
17967 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
17994 AGTCATTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.55
34 23 0.45
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:17956 original size:87 final size:87
Alignment explanation
Indices: 17848--18013 Score: 296
Period size: 87 Copynumber: 1.9 Consensus size: 87
17838 AGAATCGCAA
*
17848 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
17913 TTTCGCATTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
** *
17935 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
18000 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
18014 AGTAAACTAT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:17990 original size:20 final size:20
Alignment explanation
Indices: 17965--18016 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
17955 GCGATTCTCT
17965 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
17985 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
18005 CATTGCGATAGT
1 CGTTGCGATAGT
18017 AAACTATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:19939 original size:20 final size:20
Alignment explanation
Indices: 19881--19950 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
19871 GAAACTTTAA
* **
19881 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
19901 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
19921 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
19941 ATCGCAACGC
1 ATCGCAACGC
19951 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:19989 original size:33 final size:33
Alignment explanation
Indices: 19880--19993 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
19870 TGAAACTTTA
* *
19880 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-ACA-G
* **
19918 ACTATCGCAACGCGAATTTGACTATCGCAACG-CAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGAC-AG
19954 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
19987 AATCGCA
1 AATCGCA
19994 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
33 21 0.33
34 14 0.22
36 2 0.03
37 1 0.02
38 4 0.06
39 3 0.05
40 18 0.29
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:20381 original size:22 final size:22
Alignment explanation
Indices: 20318--20383 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
20308 TGACCGTGAA
*
20318 TGATTTCG-CTGGAGATGGAGAC
1 TGATTTCGTC-GGAGATGGGGAC
*
20340 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
20362 TGATTTCGTCGGAGACGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
20384 GGATGTCGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 38 0.97
23 1 0.03
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:20602 original size:20 final size:20
Alignment explanation
Indices: 20579--20717 Score: 269
Period size: 20 Copynumber: 7.0 Consensus size: 20
20569 CAATAATCAG
20579 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
20599 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
20619 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
20639 TTTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
20659 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
20679 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
20699 ATTCGCATTGCGATTTACG
1 ATTCGCATTGCGATTTACG
20718 AAAATCGCAA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 117 1.00
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:21187 original size:35 final size:33
Alignment explanation
Indices: 21148--21215 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
21138 TGAAAAATAT
* *
21148 TTATATTTTCTTTAAAAAATTTAAATTCATAAAAA
1 TTATATTTT-TTTAAAAAATTGAAAAT-ATAAAAA
*
21183 TTATATTTTTTTACAAAATTGAAAATATAAAAA
1 TTATATTTTTTTAAAAAATTGAAAATATAAAAA
21216 GTTTGATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 7 0.23
34 14 0.47
35 9 0.30
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (33 bp):
TTATATTTTTTTAAAAAATTGAAAATATAAAAA
Found at i:26065 original size:6 final size:6
Alignment explanation
Indices: 26054--26091 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
26044 TATAGATGAC
26054 CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG CA
1 CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG CA
26092 TGCATTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.47, T:0.16
Consensus pattern (6 bp):
CAGTGG
Found at i:28440 original size:31 final size:31
Alignment explanation
Indices: 28405--28464 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
28395 GATGGAGTGT
* *
28405 TCATTTTGTTATAAATTGATAATGTTAGTAG
1 TCATTTTATTATAAATCGATAATGTTAGTAG
*
28436 TCATTTTATTATAAATCGATATTGTTAGT
1 TCATTTTATTATAAATCGATAATGTTAGT
28465 GACCTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (31 bp):
TCATTTTATTATAAATCGATAATGTTAGTAG
Found at i:28475 original size:31 final size:31
Alignment explanation
Indices: 28406--28477 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
28396 ATGGAGTGTT
* * *
28406 CATTTTGTTATAAATTGATAATGTTAGTAGT
1 CATTTTATTATAAATCGATAATGTTAGTAGA
*
28437 CATTTTATTATAAATCGATATTGTTAGT-GA
1 CATTTTATTATAAATCGATAATGTTAGTAGA
*
28467 CCTATTTATTA
1 CAT-TTTATTA
28478 ATTTTGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (31 bp):
CATTTTATTATAAATCGATAATGTTAGTAGA
Found at i:31392 original size:15 final size:13
Alignment explanation
Indices: 31360--31384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31350 CTAATTTTTA
31360 AAAAACAGAAAAT
1 AAAAACAGAAAAT
31373 AAAAACAGAAAA
1 AAAAACAGAAAA
31385 AATAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAACAGAAAAT
Found at i:32369 original size:36 final size:36
Alignment explanation
Indices: 32322--32397 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
32312 AATAAGAAAT
32322 TTTG-TTGATTTGATTCATTTGGCCATTGTAATGGA
1 TTTGATTGATTTGATTCATTTGGCCATTGTAATGGA
32357 TTTGATTGATTTGATTCATTTGGCCATTGTAATGGA
1 TTTGATTGATTTGATTCATTTGGCCATTGTAATGGA
32393 TTTGA
1 TTTGA
32398 GATGGTAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 4 0.10
36 36 0.90
ACGTcount: A:0.21, C:0.08, G:0.22, T:0.49
Consensus pattern (36 bp):
TTTGATTGATTTGATTCATTTGGCCATTGTAATGGA
Found at i:41139 original size:18 final size:18
Alignment explanation
Indices: 41111--41153 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
41101 TCTTCTTATT
*
41111 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
41130 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
41148 -TTATTT
1 TTTATTT
41154 TAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:41315 original size:22 final size:22
Alignment explanation
Indices: 41287--41337 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
41277 TATTTCCATT
41287 ATTTATTGATTGAGAATAAGGA
1 ATTTATTGATTGAGAATAAGGA
41309 ATTTATTGATTGAGAATAAGGA
1 ATTTATTGATTGAGAATAAGGA
41331 ATTTATT
1 ATTTATT
41338 TTGACACCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (22 bp):
ATTTATTGATTGAGAATAAGGA
Found at i:41321 original size:26 final size:24
Alignment explanation
Indices: 41284--41341 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
41274 ATGTATTTCC
41284 ATTATTTATTGATTGAGAATAAGGA
1 ATTA-TTATTGATTGAGAATAAGGA
41309 A-T-TTATTGATTGAGAATAAGGA
1 ATTATTATTGATTGAGAATAAGGA
41331 ATTTATT-TTGA
1 A-TTATTATTGA
41342 CACCGAAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 21 0.70
24 6 0.20
25 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (24 bp):
ATTATTATTGATTGAGAATAAGGA
Found at i:46358 original size:11 final size:11
Alignment explanation
Indices: 46344--46376 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
46334 TTTAAAAACA
46344 ATTATTTTTTT
1 ATTATTTTTTT
*
46355 ATTATTTTATT
1 ATTATTTTTTT
46366 ATTATTTTTTT
1 ATTATTTTTTT
46377 GCTTATCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTATTTTTTT
Found at i:47143 original size:18 final size:18
Alignment explanation
Indices: 47115--47157 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
47105 TCTTCTTATT
*
47115 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
47134 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
47152 -TTATTT
1 TTTATTT
47158 TAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:57434 original size:23 final size:22
Alignment explanation
Indices: 57385--57467 Score: 89
Period size: 21 Copynumber: 3.8 Consensus size: 22
57375 AGAACCCGTG
* *
57385 GGGGGTATCGATTCCC-TCAAT
1 GGGGGAATCGATTCCCTTCAAA
*
57406 GAGGGAATCGATTCCCATTCAAA
1 GGGGGAATCGATTCCC-TTCAAA
*
57429 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGATT-CCCTTCAAA
*
57451 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
57468 CTGTACTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
21 18 0.35
22 13 0.25
23 18 0.35
24 3 0.06
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCTTCAAA
Found at i:57455 original size:22 final size:23
Alignment explanation
Indices: 57385--57466 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
57375 AGAACCCGTG
* *
57385 GGGGGTATCGATTCCC--TCAAT
1 GGGGGAATCGATTCCCATTCAAA
*
57406 GAGGGAATCGATTCCCATTCAAA
1 GGGGGAATCGATTCCCATTCAAA
* *
57429 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGATTCCCATTCAAA
*
57451 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
57467 TCTGTACTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 14 0.27
22 16 0.31
23 21 0.41
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (23 bp):
GGGGGAATCGATTCCCATTCAAA
Found at i:62664 original size:24 final size:24
Alignment explanation
Indices: 62637--62682 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
62627 TCAGTGACGG
62637 AGTTACTATGGTAAAAAGTGACAA
1 AGTTACTATGGTAAAAAGTGACAA
62661 AGTTACTATGGTAAAAAGTGAC
1 AGTTACTATGGTAAAAAGTGAC
62683 TCCTAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (24 bp):
AGTTACTATGGTAAAAAGTGACAA
Found at i:81820 original size:22 final size:21
Alignment explanation
Indices: 81794--81884 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 21
81784 TTGGTGCAGA
* *
81794 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCC-TGAAG
* *
81816 GGGAACTGATTCCCTCTTTGAAG
1 GGGAACCGATTCCC-C-CTGAAG
*
81839 GGGAACCGATTTCCCCCTGTAG
1 GGGAACCGA-TTCCCCCTGAAG
*
81861 GGGAACCGATTTCCCCCTGTAG
1 GGGAACCGA-TTCCCCCTGAAG
81883 GG
1 GG
81885 TAATTGATAC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
22 39 0.66
23 15 0.25
24 5 0.08
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.23
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTGAAG
Found at i:88409 original size:17 final size:16
Alignment explanation
Indices: 88379--88412 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
88369 ATGATGTTGA
88379 TCGGTGATGGCTCGGC
1 TCGGTGATGGCTCGGC
*
88395 TCGGTTGATGTCTCGGC
1 TCGG-TGATGGCTCGGC
88412 T
1 T
88413 TGGCCATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.06, C:0.24, G:0.38, T:0.32
Consensus pattern (16 bp):
TCGGTGATGGCTCGGC
Done.