Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007839.1 Hibiscus syriacus cultivar Beakdansim tig00110190_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: 137618
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:443 original size:18 final size:18
Alignment explanation
Indices: 404--534 Score: 80
Period size: 18 Copynumber: 7.6 Consensus size: 18
394 TAGTTTACTT
* *
404 TCGCAACACGAAACTTAAA
1 TCGCAACGCGAAAC-AAAA
*
423 TCGCAACGCGAACCAAAA
1 TCGCAACGCGAAACAAAA
**
441 TCGCAACGCGAAATGAAA
1 TCGCAACGCGAAACAAAA
*
459 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAACAAAA
* *
473 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
492 TCGCAA--CG-AA-AGAA
1 TCGCAACGCGAAACAAAA
**
506 TCGCAACGCGAAATGAAA
1 TCGCAACGCGAAACAAAA
*
524 TCGCAATGCGA
1 TCGCAACGCGA
535 TTTTGGTTTC
Statistics
Matches: 88, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
14 18 0.20
16 8 0.09
17 4 0.05
18 37 0.42
19 21 0.24
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.11
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:476 original size:14 final size:14
Alignment explanation
Indices: 457--513 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
447 CGCGAAATGA
*
457 AATCGCAACGACAG
1 AATCGCAACGAAAG
471 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
488 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
504 AATCGCAACG
1 AATCGCAACG
514 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:498 original size:33 final size:32
Alignment explanation
Indices: 439--529 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 32
429 CGCGAACCAA
*
439 AATCGCAACGCGAAATGAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAATCGCAACGAAAG
*
471 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATG-AAATCGCAACGAAAG
504 AATCGCAACGCGAAATGAAATCGCAA
1 AATCGCAACGCGAAATGAAATCGCAA
530 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 25 0.45
33 30 0.55
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (32 bp):
AATCGCAACGCGAAATGAAATCGCAACGAAAG
Found at i:552 original size:19 final size:19
Alignment explanation
Indices: 530--658 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
520 GAAATCGCAA
530 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
549 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
563 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
582 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
596 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
615 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
634 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
654 TGCGA
1 TGCGA
659 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:572 original size:33 final size:33
Alignment explanation
Indices: 530--621 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
520 GAAATCGCAA
530 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
563 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
596 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
622 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1006 original size:90 final size:93
Alignment explanation
Indices: 702--1076 Score: 708
Period size: 90 Copynumber: 4.1 Consensus size: 93
692 TTGAATGGAT
702 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAAT--AC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
765 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
793 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
857 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
885 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTC-CAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
948 AGTTTAGCAGAATTGGCAGC-ACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
975 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1040 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1068 AAATTTACT
1 AAATTTACT
1077 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
90 103 0.37
91 47 0.17
92 77 0.28
93 51 0.18
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1010 original size:183 final size:183
Alignment explanation
Indices: 702--1076 Score: 702
Period size: 183 Copynumber: 2.0 Consensus size: 183
692 TTGAATGGAT
702 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAG
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAG
767 TTTAGCAGAATTGGCAGCAACCGAACAAATTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
66 TTTAGCAGAATTGGCAGCAACCGAACAAATTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
832 TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
885 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTC-CAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAAT--AC
948 AGTTTAGCAGAATTGGCAGC-ACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
64 AGTTTAGCAGAATTGGCAGCAACCGAACAAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAA
1012 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
128 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1068 AAATTTACT
1 AAATTTACT
1077 AAGCAATCTA
Statistics
Matches: 189, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
181 14 0.07
182 16 0.08
183 159 0.84
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (183 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2802 original size:19 final size:18
Alignment explanation
Indices: 2778--2875 Score: 86
Period size: 19 Copynumber: 5.7 Consensus size: 18
2768 CGCAACGGAG
2778 AATCGCAACGCGAGATGA
1 AATCGCAACGCGAGATGA
2796 CAATCGCAA--CGAGA-G-
1 -AATCGCAACGCGAGATGA
*
2811 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
2830 AATCGCAA--CGAGA-G-
1 AATCGCAACGCGAGATGA
*
2844 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
*
2863 AATCGCAATGCGA
1 AATCGCAACGCGA
2876 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
14 16 0.25
16 10 0.15
17 11 0.17
19 28 0.43
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AATCGCAACGCGAGATGA
Found at i:2816 original size:14 final size:14
Alignment explanation
Indices: 2765--2853 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
2755 TTGAAATGAA
2765 AATCGCAACG-GAG
1 AATCGCAACGAGAG
2778 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
2795 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
2811 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2830 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2844 AATCGCAACG
1 AATCGCAACG
2854 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 21
0.73 0.02 0.24
Matches are distributed among these distances:
13 8 0.13
14 20 0.32
15 3 0.05
16 5 0.08
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2817 original size:33 final size:33
Alignment explanation
Indices: 2757--2870 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
2747 TCTTTTGGTT
2757 GAAATGAAAATCGCAACG-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
2789 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2822 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2855 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2871 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 16 0.21
33 61 0.79
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2906 original size:14 final size:14
Alignment explanation
Indices: 2887--2941 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2877 TTTGGTTTCG
2887 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2901 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
2920 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2934 CGTTGCGA
1 CGTTGCGA
2942 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3103 original size:33 final size:33
Alignment explanation
Indices: 3061--3131 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3051 AATACTAACT
*
3061 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3094 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3127 TGAAA
1 TGAAA
3132 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3535 original size:20 final size:20
Alignment explanation
Indices: 3510--3702 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
3500 CTTTAAATAT
3510 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3530 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3552 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3571 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3591 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3611 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3631 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3651 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3671 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3691 CGCGTTGCGATT
1 CGCGTTGCGATT
3703 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3697 original size:60 final size:60
Alignment explanation
Indices: 3510--3702 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
3500 CTTTAAATAT
**
3510 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3571 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3631 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3691 CGCGTTGCGATT
1 CGCGTTGCGATT
3703 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3783 original size:20 final size:20
Alignment explanation
Indices: 3758--3809 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3748 AAGAATCGCG
*
3758 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3778 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3798 TTGCGATTCTGG
1 TTGCGATTCTGG
3810 GGATCGCGTT
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:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:6107 original size:18 final size:17
Alignment explanation
Indices: 6086--6141 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
6076 TTAAACTCTG
6086 ATTTCCTTTTTCTCTCTC
1 ATTTCCTTTTTCTCTC-C
6104 ATTTACTCTCTTTT-TC-CC
1 ATTT-C-CT-TTTTCTCTCC
*
6122 CTTTCCTTTTTCTCTCC
1 ATTTCCTTTTTCTCTCC
6139 ATT
1 ATT
6142 CTCCATAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 5 0.16
18 8 0.26
19 2 0.06
20 4 0.13
21 4 0.13
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTCCTTTTTCTCTCC
Found at i:19628 original size:18 final size:18
Alignment explanation
Indices: 19567--19636 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
19557 TTGTATATTA
*
19567 AAAAATTAATAAATTAGT
1 AAAAATTAATAAATTAAT
* * * *
19585 GATAATT-ATTAATCAAT
1 AAAAATTAATAAATTAAT
**
19602 AATTTATTAATAAATTAAT
1 AA-AAATTAATAAATTAAT
19621 AAAAATTAATAAATTA
1 AAAAATTAATAAATTA
19637 GGAAATTAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
17 8 0.21
18 21 0.54
19 10 0.26
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAAATTAATAAATTAAT
Found at i:19630 original size:26 final size:26
Alignment explanation
Indices: 19601--19658 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
19591 TATTAATCAA
* *
19601 TAATTTATTAATAAATTAATAAAAAT
1 TAATTAATTAAGAAATTAATAAAAAT
* * **
19627 TAATAAATTAGGAAATTAATAATTAT
1 TAATTAATTAAGAAATTAATAAAAAT
19653 TAATTA
1 TAATTA
19659 GACTTTTTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
TAATTAATTAAGAAATTAATAAAAAT
Found at i:20213 original size:20 final size:20
Alignment explanation
Indices: 20169--20262 Score: 93
Period size: 20 Copynumber: 4.6 Consensus size: 20
20159 ACTTCGACTA
* *
20169 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACATAT
*
20190 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
20210 TCGCATTGCGA-TAATCGA-AGT
1 TCGCATTGCGATTTA-C-ATA-T
*
20231 TCGCTTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
20251 TCGCATTGCGAT
1 TCGCATTGCGAT
20263 AGTCGAAGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.03
20 32 0.53
21 24 0.40
22 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:20221 original size:41 final size:41
Alignment explanation
Indices: 20169--20278 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 41
20159 ACTTCGACTA
**
20169 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACATAT
1 TCGCATTGCGATAATCCAAATTCGCGTTGCGATTTACATAT
* * *
20210 TCGCATTGCGATAATCGAAGTTCGCTTTGCGATTTACATAT
1 TCGCATTGCGATAATCCAAATTCGCGTTGCGATTTACATAT
* * *
20251 TCGCATTGCGATAGTCGAAGTTCGCGTT
1 TCGCATTGCGATAATCCAAATTCGCGTT
20279 ACCCAAAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (41 bp):
TCGCATTGCGATAATCCAAATTCGCGTTGCGATTTACATAT
Found at i:21139 original size:21 final size:21
Alignment explanation
Indices: 21110--21242 Score: 96
Period size: 21 Copynumber: 6.5 Consensus size: 21
21100 GCGATTTTGG
21110 GCAACGCGAACTTCGACTATC
1 GCAACGCGAACTTCGACTATC
* *
21131 GCAATGCGAA-TAT-GTA-AATC
1 GCAACGCGAACT-TCG-ACTATC
* *
21151 GCAACACGAACTTCAACTATC
1 GCAACGCGAACTTCGACTATC
* * **
21172 GCAA--CGAATTTGGAAAATC
1 GCAACGCGAACTTCGACTATC
* *
21191 GCAACACGAACTCCGACTATC
1 GCAACGCGAACTTCGACTATC
* *
21212 GCAATGCGAACTTGGACTATC
1 GCAACGCGAACTTCGACTATC
*
21233 GCAATGCGAA
1 GCAACGCGAA
21243 TATGTAAATC
Statistics
Matches: 85, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
19 14 0.16
20 15 0.18
21 56 0.66
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
GCAACGCGAACTTCGACTATC
Found at i:21201 original size:40 final size:40
Alignment explanation
Indices: 21110--21221 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
21100 GCGATTTTGG
* *
21110 GCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATC
1 GCAACACGAACTTCGACTATCGCAA-GCGAATATGAAAATC
* *
21151 GCAACACGAACTTCAACTATCGCAA-CGAATTTGGAAAATC
1 GCAACACGAACTTCGACTATCGCAAGCGAATAT-GAAAATC
*
21191 GCAACACGAACTCCGACTATCGCAATGCGAA
1 GCAACACGAACTTCGACTATCGCAA-GCGAA
21222 CTTGGACTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
39 6 0.10
40 29 0.47
41 23 0.37
42 4 0.06
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.19
Consensus pattern (40 bp):
GCAACACGAACTTCGACTATCGCAAGCGAATATGAAAATC
Found at i:21296 original size:21 final size:21
Alignment explanation
Indices: 21267--21317 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
21257 CAGGAATTTG
*
21267 GAAAATCGCAATGCGATAGTC
1 GAAATTCGCAATGCGATAGTC
* **
21288 GAAGTTCGCGTTGCGATAGTC
1 GAAATTCGCAATGCGATAGTC
21309 GAAATTCGC
1 GAAATTCGC
21318 GTTGCGAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (21 bp):
GAAATTCGCAATGCGATAGTC
Found at i:21333 original size:21 final size:21
Alignment explanation
Indices: 21278--21324 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21268 AAAATCGCAA
*
21278 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAATTCGCGT
21299 TGCGATAGTCGAAATTCGCGT
1 TGCGATAGTCGAAATTCGCGT
21320 TGCGA
1 TGCGA
21325 ATCTAGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAATTCGCGT
Found at i:37440 original size:60 final size:61
Alignment explanation
Indices: 37372--37492 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
37362 AATGCTGCGC
37372 CCCATGCTTGCTTC-TTGGACCACCTTTAATTTGTATTACCATTCCCTTACCGTTACAAAA
1 CCCATGCTTGCTTCTTTGGACCACCTTTAATTTGTATTACCATTCCCTTACCGTTACAAAA
37432 CCCATGCTTGCTTCTTTGGACCACCTTTAATTTGTATTACCATTCCCTTACCGTTACAAAA
1 CCCATGCTTGCTTCTTTGGACCACCTTTAATTTGTATTACCATTCCCTTACCGTTACAAAA
37493 ATATATTATT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 14 0.23
61 46 0.77
ACGTcount: A:0.23, C:0.30, G:0.10, T:0.37
Consensus pattern (61 bp):
CCCATGCTTGCTTCTTTGGACCACCTTTAATTTGTATTACCATTCCCTTACCGTTACAAAA
Found at i:39246 original size:19 final size:20
Alignment explanation
Indices: 39222--39261 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39212 TACATTTCTT
39222 TCAACTCTT-GCCGGCATGA
1 TCAACTCTTCGCCGGCATGA
* *
39241 TCAACTTTTCGTCGGCATGA
1 TCAACTCTTCGCCGGCATGA
39261 T
1 T
39262 TAATGGCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (20 bp):
TCAACTCTTCGCCGGCATGA
Found at i:40699 original size:48 final size:52
Alignment explanation
Indices: 40602--40723 Score: 148
Period size: 48 Copynumber: 2.4 Consensus size: 52
40592 TCTTTTCAAC
*
40602 TTATGAAATTATATTTTATACTAAGATACCCTCTCCTTTTTTTTCATATTAA
1 TTATGAAATTATATTTTATACTAAGATACCCTCTCCTTTTTTATCATATTAA
40654 TTATG-AATT-TA-TTTATA-TAAGATACCCTCTCCTTTTTTCAT-ATATTATA
1 TTATGAAATTATATTTTATACTAAGATACCCTCTCCTTTTTT-ATCATATTA-A
*
40703 TATAT-ATATTATACTTTTATA
1 T-TATGAAATTATA-TTTTATA
40724 ATATTCTATT
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
48 27 0.44
49 9 0.15
50 8 0.13
51 6 0.10
52 5 0.08
53 6 0.10
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (52 bp):
TTATGAAATTATATTTTATACTAAGATACCCTCTCCTTTTTTATCATATTAA
Found at i:45429 original size:2 final size:2
Alignment explanation
Indices: 45417--45453 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
45407 TTAGGTTATC
*
45417 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45454 TTTCATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:48922 original size:22 final size:19
Alignment explanation
Indices: 48882--48918 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
48872 TTTATTTTAT
48882 TCGTAAAAAATAAATATAA
1 TCGTAAAAAATAAATATAA
48901 TCGTAAAAAAT-AATATAA
1 TCGTAAAAAATAAATATAA
48919 ATAAGGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
TCGTAAAAAATAAATATAA
Found at i:50430 original size:251 final size:252
Alignment explanation
Indices: 49937--50442 Score: 923
Period size: 251 Copynumber: 2.0 Consensus size: 252
49927 TGCATAATCG
49937 AATAGGTACACGAAATGTTACAAGGATGCACAACAGGTTCACATGTAATTGAGCAATGTCTAGCC
1 AATAGGTACACGAAATGTTACAAGGATGCACAACAGGTTCACATGTAATTGAGCAATGTCTAGCC
50002 TGAAGCGTGAGGTTCTCCATATAATCCTTATCGCAATAAATATGATGTGTGACCATGGTTTTCAG
66 TGAAGCGTGAGGTTCTCCATATAATCCTTATCGC-A-AAATATGATGTGTGACCATGGTTTTCAG
50067 AACCGGACCGGTTAGTGAACCGTCATGCTACCGGTAAAACATATTAAATAATAAATAATATATAA
129 AACCGGACCGGTTAGTGAACCGTCATGCTACCGGTAAAACATATTAAATAATAAATAATATATAA
50132 CTATAATTAAAAAATAAATTTGGGGTTAAAAATCATAACAAAATTATATAACTATAATT
194 CTATAATTAAAAAATAAATTTGGGGTTAAAAATCATAACAAAATTATATAACTATAATT
50191 AATAGGTACACGAAATGTTACAAGGATGCACAACAGGTTCACATGTAATTGAGCAATGTCTACGC
1 AATAGGTACACGAAATGTTACAAGGATGCACAACAGGTTCACATGTAATTGAGCAATGTCTA-GC
50256 CTGAAGCGTGAGGTTCTCCATATAATCC-TATCGC-AAATAT-ATGTGTGACCATGGTTTTCAGA
65 CTGAAGCGTGAGGTTCTCCATATAATCCTTATCGCAAAATATGATGTGTGACCATGGTTTTCAGA
50318 ACCGGACCGGTTAGTGAACCGGTCATGCTACCGGT-AAACATATTAAATAATAAAT-ATAATTAT
130 ACCGGACCGGTTAGTGAACC-GTCATGCTACCGGTAAAACATATTAAATAATAAATAAT-A-TAT
50381 AACTATAATTAAAAAATAAATTTGGGGTTAAAAATCATAACAAAATTATATAACTATAATT
192 AACTATAATTAAAAAATAAATTTGGGGTTAAAAATCATAACAAAATTATATAACTATAATT
50442 A
1 A
50443 TATAACTATT
Statistics
Matches: 248, Mismatches: 0, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
249 2 0.01
250 63 0.25
251 85 0.34
254 68 0.27
255 30 0.12
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (252 bp):
AATAGGTACACGAAATGTTACAAGGATGCACAACAGGTTCACATGTAATTGAGCAATGTCTAGCC
TGAAGCGTGAGGTTCTCCATATAATCCTTATCGCAAAATATGATGTGTGACCATGGTTTTCAGAA
CCGGACCGGTTAGTGAACCGTCATGCTACCGGTAAAACATATTAAATAATAAATAATATATAACT
ATAATTAAAAAATAAATTTGGGGTTAAAAATCATAACAAAATTATATAACTATAATT
Found at i:50443 original size:14 final size:14
Alignment explanation
Indices: 50424--50451 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50414 ATCATAACAA
50424 AATTATATAACTAT
1 AATTATATAACTAT
50438 AATTATATAACTAT
1 AATTATATAACTAT
50452 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:51430 original size:35 final size:35
Alignment explanation
Indices: 51384--51457 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
51374 AGACCCATTA
51384 ATCACATCGAGATGTCAT-ATAAAAAGGTTTATAGG
1 ATCACATCGAGATGTCATAAT-AAAAGGTTTATAGG
51419 ATCACATCGAGATGTCATAATAAAAGGTTTATAGG
1 ATCACATCGAGATGTCATAATAAAAGGTTTATAGG
51454 ATCA
1 ATCA
51458 ATGCCAACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 36 0.95
36 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (35 bp):
ATCACATCGAGATGTCATAATAAAAGGTTTATAGG
Found at i:52665 original size:2 final size:2
Alignment explanation
Indices: 52658--52705 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
52648 AGATTACTAG
52658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52698 AT AT AT AT
1 AT AT AT AT
52706 CGGATATTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54605 original size:196 final size:197
Alignment explanation
Indices: 54270--54720 Score: 494
Period size: 196 Copynumber: 2.3 Consensus size: 197
54260 ACCTCTAAGC
* * * * * * *
54270 TTAGAATATCTCGAATGTAACGATATTTGGCTAAACATAAAGAAAAGTTGCAATATTAGGTCTCT
1 TTAGAATGTCTCGAATGTGACGATATTAGGCTCAACTTAAAGAAAAGTTGCAATACTAGGCCTCT
* *
54335 AAACTTATAAATTACGAAAAATCTACTATTTACAACATGAAAATAACACTCTAACATGCCTATGA
66 AAACTTATAAATTACGAAAAATCTACTATTTACAACACGAAAATAACACTCAAACATGCCTATGA
* * *
54400 AGCCATTTTGCCTT-TTGATGAACAAAAGCATTCTTCCTAATCATTTTCAGGGCC-TTTTTTACC
131 AGCCATTTTGCCTTATTGATGAACAAAAGCATACTTCCGAATCATTTTCA-GGCCAATTTTTACC
54463 CAT-
195 C-TG
* * * *
54466 TTAGAATGTCTCGAATGTGGCGATATTAGGTTCAACTTAAAGAAAATTTGTAATACTAGGCCTCT
1 TTAGAATGTCTCGAATGTGACGATATTAGGCTCAACTTAAAGAAAAGTTGCAATACTAGGCCTCT
** * * * * * * *
54531 ATGCTTATAAATTACGAAAAATTTGCTATTTACAACCCGATAATAAGAGTCAAACATGGCTATGA
66 AAACTTATAAATTACGAAAAATCTACTATTTACAACACGAAAATAACACTCAAACATGCCTATGA
* * * * *
54596 AGTCATTTTGTCTTACACTTGATGAACAAAATCATACTTTCGATTCATTTTCAGGCCAATTTTTA
131 AGCCATTTTGCCTT--A-TTGATGAACAAAAGCATACTTCCGAATCATTTTCAGGCCAATTTTTA
*
54661 TCCTGG
193 CCCT-G
* * * * * *
54667 TTAGTATGTCTCAAATGTGTCGATACTAGGCTCAAATTAAAGACAAGTTGCAAT
1 TTAGAATGTCTCGAATGTGACGATATTAGGCTCAACTTAAAGAAAAGTTGCAAT
54721 TCTTCACATT
Statistics
Matches: 208, Mismatches: 40, Indels: 9
0.81 0.16 0.04
Matches are distributed among these distances:
196 120 0.58
199 5 0.02
200 38 0.18
201 45 0.22
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (197 bp):
TTAGAATGTCTCGAATGTGACGATATTAGGCTCAACTTAAAGAAAAGTTGCAATACTAGGCCTCT
AAACTTATAAATTACGAAAAATCTACTATTTACAACACGAAAATAACACTCAAACATGCCTATGA
AGCCATTTTGCCTTATTGATGAACAAAAGCATACTTCCGAATCATTTTCAGGCCAATTTTTACCC
TG
Found at i:54940 original size:2 final size:2
Alignment explanation
Indices: 54933--54957 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54923 AAAATTGCCT
54933 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
54958 CGTTAAACTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59366 original size:26 final size:24
Alignment explanation
Indices: 59324--59378 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
59314 TATATATATA
59324 ATTA-ATATAAGAAAATATAAAAAT
1 ATTATATATAAGAAAATAT-AAAAT
* *
59348 ATATATATATAATATAATATAAAAT
1 AT-TATATATAAGAAAATATAAAAT
59373 ATTATA
1 ATTATA
59379 CCTTGCCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 9 0.33
26 12 0.44
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATTATATATAAGAAAATATAAAAT
Found at i:62677 original size:6 final size:6
Alignment explanation
Indices: 62634--62693 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
62624 GAGTGACAGT
*
62634 GAGAGG GAG-GA G-GAGG GAG-GG GAG-GG GAGAGTG GAGAGG GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAG-G GAGAGG GAGAGG
* *
62679 GAGAGC CAGAGG GAG
1 GAGAGG GAGAGG GAG
62694 GGGGTCGGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 1 0.02
5 14 0.32
6 23 0.52
7 6 0.14
ACGTcount: A:0.30, C:0.03, G:0.65, T:0.02
Consensus pattern (6 bp):
GAGAGG
Found at i:64727 original size:22 final size:23
Alignment explanation
Indices: 64692--64738 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
64682 ATTCAATTTT
**
64692 TATATTCTATAAATTGTATAATA
1 TATATTCTATAAATAATATAATA
*
64715 TATATTTTA-AAATAATATAATA
1 TATATTCTATAAATAATATAATA
64737 TA
1 TA
64739 ATAAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATTCTATAAATAATATAATA
Found at i:65373 original size:11 final size:11
Alignment explanation
Indices: 65357--65483 Score: 65
Period size: 11 Copynumber: 10.6 Consensus size: 11
65347 AAAAATTAAG
65357 AGCTCGATTCA
1 AGCTCGATTCA
*
65368 AGCTCGAGACTCA
1 AGCTC--GATTCA
* **
65381 AGCTAGATTTTG
1 AGCTCGA-TTCA
*
65393 AGCTCGATTGAAA
1 AGCTCGATT--CA
* *
65406 AACTCGATGCA
1 AGCTCGATTCA
*
65417 AGCTCGATTGAGA
1 AGCTCGATT--CA
*
65430 AGCTCGATTAAAA
1 AGCTCGATT--CA
*
65443 AGCTCGATTTTA
1 AGCTCGA-TTCA
*
65455 AGCTCGTTTCA
1 AGCTCGATTCA
65466 AGCTCGATTCA
1 AGCTCGATTCA
65477 AGCTCGA
1 AGCTCGA
65484 AAACGGGTTA
Statistics
Matches: 88, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
11 37 0.42
12 14 0.16
13 35 0.40
14 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:66212 original size:3 final size:3
Alignment explanation
Indices: 66198--66228 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
66188 TTCCCCTTGC
*
66198 TCT TCT TAT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
66229 TACTTGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:66888 original size:14 final size:15
Alignment explanation
Indices: 66869--66898 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
66859 CATAATCGGA
66869 TTTAGGGTTT-AGGT
1 TTTAGGGTTTAAGGT
66883 TTTAGGGTTTAAGGT
1 TTTAGGGTTTAAGGT
66898 T
1 T
66899 CATTACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (15 bp):
TTTAGGGTTTAAGGT
Found at i:67196 original size:15 final size:14
Alignment explanation
Indices: 67170--67199 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
67160 TTTATTCATC
67170 AATAATGTATTTTT
1 AATAATGTATTTTT
*
67184 AATAATGTAATTTT
1 AATAATGTATTTTT
67198 AA
1 AA
67200 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:73048 original size:19 final size:18
Alignment explanation
Indices: 72987--73062 Score: 54
Period size: 19 Copynumber: 4.3 Consensus size: 18
72977 TTTATGTTAG
*
72987 TATTTTTTTTAAATAGTTA
1 TATTTTTATTAAATA-TTA
73006 T-TATTTT-TT--ATATTAA
1 TAT-TTTTATTAAATATT-A
*
73022 TATATTTATGTAAATATTA
1 TATTTTTAT-TAAATATTA
*
73041 TATTTTTATTAAA-ATAA
1 TATTTTTATTAAATATTA
73058 TATTT
1 TATTT
73063 ATATAATAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
15 2 0.04
16 8 0.17
17 10 0.21
18 8 0.17
19 14 0.30
20 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTTTTATTAAATATTA
Found at i:73060 original size:17 final size:19
Alignment explanation
Indices: 73019--73062 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
73009 TTTTTTATAT
*
73019 TAATATATTTATGTAAATA
1 TAATATTTTTATGTAAATA
*
73038 TTATATTTTTAT-TAAA-A
1 TAATATTTTTATGTAAATA
73055 TAATATTT
1 TAATATTT
73063 ATATAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TAATATTTTTATGTAAATA
Found at i:73248 original size:17 final size:17
Alignment explanation
Indices: 73226--73279 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
73216 AATGTTAATA
73226 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
73243 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
73260 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
73277 TTT
1 TTT
73280 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:74887 original size:21 final size:21
Alignment explanation
Indices: 74861--74954 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
74851 TATGCCATCT
* *
74861 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
74882 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
74903 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
74924 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
74945 CCGCAGGGTT
1 CCGCAGGGTT
74955 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:75536 original size:33 final size:34
Alignment explanation
Indices: 75477--75573 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
75467 AAATGTTTTT
* *
75477 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
75511 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
75544 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
75574 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:75580 original size:34 final size:32
Alignment explanation
Indices: 75475--75580 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
75465 ATAAATGTTT
*
75475 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
75509 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
75541 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
75576 TTAAA
1 TTAAA
75581 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:76283 original size:128 final size:128
Alignment explanation
Indices: 75974--77752 Score: 3199
Period size: 128 Copynumber: 13.9 Consensus size: 128
75964 TTACCTGATT
*
75974 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
76039 TGATGAAATAATGGAAGGCGC-CCCCTGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
76101 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
76166 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
76229 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATATGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
76294 TAACGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
76357 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
76422 TGACG-AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
76484 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
76549 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
76612 TACTGATATATCTAGTGTCCCCGAGGGAGATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
76677 TGACGAAATAATGGAAGGCGCGTCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
76740 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
76805 TAACGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
76868 TACTGATATATCTAGTGTCCCCGAGGGACACGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
76933 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
76996 TACTGATATATCTAGTGTCCCCGAGGGACACGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
77061 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
77124 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
77189 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
77252 TACTGATATATCTAGTGTCCCCGAGGGAGATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
77317 TGACGAAATAATGGAAGGCGCGTCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
77380 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
77445 TAACGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
77508 TACTGATATATCTAGTGTCCCCGAGGGACACGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
77573 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
77636 TACTGATATATCTAGTGTCCCCGAGGGACACGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
77701 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
77753 ACTCCGATTA
Statistics
Matches: 1587, Mismatches: 57, Indels: 15
0.96 0.03 0.01
Matches are distributed among these distances:
127 212 0.13
128 1372 0.86
129 3 0.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:88626 original size:13 final size:13
Alignment explanation
Indices: 88608--88636 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
88598 TGCAGCACAT
88608 TATTTTGATCATG
1 TATTTTGATCATG
88621 TATTTTGATCATG
1 TATTTTGATCATG
88634 TAT
1 TAT
88637 GCTACCACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (13 bp):
TATTTTGATCATG
Found at i:95976 original size:100 final size:93
Alignment explanation
Indices: 95775--96142 Score: 505
Period size: 88 Copynumber: 4.0 Consensus size: 93
95765 TAGTGTCCCA
* * *
95775 AAACTCGGAATAGAAAACCTGC--A---AATTGTTACATATTGATTTTGATTATATTGCCTACAA
1 AAACTCGGAATAGAAAACCTGCAAATTGAATTGTTACATTTTGATTGTGATTAGATTGCCTACAA
95835 ATAAACTAAACTGAATAGAAAATCCGAG
66 ATAAACTAAACTGAATAGAAAATCCGAG
95863 AAACTCGGAATAGAAAACCTGCAAATTGTTACATTTTGAGTTACATTTTGATTGTGATTAGATTG
1 AAACTCGGAATAGAAAACCTGCAAATTG--A-A--TT--GTTACATTTTGATTGTGATTAGATTG
95928 CCTACAAATAAACTAAACTGAATAGAAAATCCGAG
59 CCTACAAATAAACTAAACTGAATAGAAAATCCGAG
*
95963 AAACTCGGTATAGAAAACCTGCAAATTG--TTG---CATTTTGATTGTGATTAGATTGCCTACAA
1 AAACTCGGAATAGAAAACCTGCAAATTGAATTGTTACATTTTGATTGTGATTAGATTGCCTACAA
96023 ATAAACTAAACTGAATAGAAAATCCGAG
66 ATAAACTAAACTGAATAGAAAATCCGAG
* *
96051 AAACTTGGAATAGAAAACTTGC--A---AATTGTTACATTTTGATTGTGATTAGATTGCCTACAA
1 AAACTCGGAATAGAAAACCTGCAAATTGAATTGTTACATTTTGATTGTGATTAGATTGCCTACAA
*
96111 ATAAACTATACTGAATAGAAAATCCGAG
66 ATAAACTAAACTGAATAGAAAATCCGAG
96139 AAAC
1 AAAC
96143 CACTTTGGAC
Statistics
Matches: 255, Mismatches: 8, Indels: 34
0.86 0.03 0.11
Matches are distributed among these distances:
85 3 0.01
86 1 0.00
88 158 0.62
90 1 0.00
91 1 0.00
93 2 0.01
95 1 0.00
96 1 0.00
98 2 0.01
100 85 0.33
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.29
Consensus pattern (93 bp):
AAACTCGGAATAGAAAACCTGCAAATTGAATTGTTACATTTTGATTGTGATTAGATTGCCTACAA
ATAAACTAAACTGAATAGAAAATCCGAG
Found at i:98675 original size:18 final size:18
Alignment explanation
Indices: 98654--98688 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
98644 TTAGGGATGA
98654 TTGATTTCTCAGGGAAGG
1 TTGATTTCTCAGGGAAGG
*
98672 TTGATTTCTCGGGGAAG
1 TTGATTTCTCAGGGAAG
98689 ATTAAGGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.34, T:0.34
Consensus pattern (18 bp):
TTGATTTCTCAGGGAAGG
Found at i:117978 original size:33 final size:33
Alignment explanation
Indices: 117936--118001 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
117926 CATTTATCCA
117936 GATAAGAAATAACTTAACAATTTCTCTGGGTTG
1 GATAAGAAATAACTTAACAATTTCTCTGGGTTG
117969 GATAAGAAATAACTTAACAATTTCTCTGGGTTG
1 GATAAGAAATAACTTAACAATTTCTCTGGGTTG
118002 CGTTTGATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (33 bp):
GATAAGAAATAACTTAACAATTTCTCTGGGTTG
Found at i:125734 original size:18 final size:18
Alignment explanation
Indices: 125711--125751 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
125701 TCATTTCCAA
125711 AGTTTTAGCAAGGAGACT
1 AGTTTTAGCAAGGAGACT
125729 AGTTTTAGCAAGGAGACT
1 AGTTTTAGCAAGGAGACT
125747 AGTTT
1 AGTTT
125752 CAGTGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (18 bp):
AGTTTTAGCAAGGAGACT
Found at i:129381 original size:16 final size:16
Alignment explanation
Indices: 129360--129391 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
129350 AAAAATCCAG
129360 AGTGTTGTCCTGCTGT
1 AGTGTTGTCCTGCTGT
129376 AGTGTTGTCCTGCTGT
1 AGTGTTGTCCTGCTGT
129392 TCTGCTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.31, T:0.44
Consensus pattern (16 bp):
AGTGTTGTCCTGCTGT
Done.