Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003478.1 Hibiscus syriacus cultivar Beakdansim tig00007352_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: 67543
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3196 original size:14 final size:14
Alignment explanation
Indices: 3177--3205 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3167 GCATAAGTTG
3177 TATTATTATTATAT
1 TATTATTATTATAT
3191 TATTATTATTATAT
1 TATTATTATTATAT
3205 T
1 T
3206 TATTTTCAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATAT
Found at i:3761 original size:21 final size:20
Alignment explanation
Indices: 3676--3832 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
3666 AAATGACCAA
**
3676 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
***
3695 -AAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3714 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3734 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3755 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3776 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3796 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
3817 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3833 ACACATAAAT
Statistics
Matches: 102, Mismatches: 29, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
18 15 0.15
19 1 0.01
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3894 original size:20 final size:20
Alignment explanation
Indices: 3800--4190 Score: 441
Period size: 20 Copynumber: 19.4 Consensus size: 20
3790 GATTTTCAAT
* ** *
3800 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3820 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3840 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3860 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
3880 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
3900 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3920 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
3940 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
3961 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3981 AATCGCAACGTGTATGCGTTA
1 AATCGCAACGCGTATCCG-TA
4002 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4022 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
4042 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4062 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
4082 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4102 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
4122 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
4142 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
4162 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
4182 AATCACAAC
1 AATCGCAAC
4191 ACTGAAATTT
Statistics
Matches: 317, Mismatches: 42, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.01
20 276 0.87
21 36 0.11
22 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:4900 original size:24 final size:24
Alignment explanation
Indices: 4861--4907 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4851 AAATTTGGTC
4861 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
4885 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
4908 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:7394 original size:19 final size:19
Alignment explanation
Indices: 7372--7626 Score: 316
Period size: 19 Copynumber: 14.4 Consensus size: 19
7362 CGGAAAATAC
*
7372 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
7391 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
7405 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
7425 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
7439 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
7458 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
7472 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
7491 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
7510 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
7529 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
7548 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
7567 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
7581 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
7600 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
7619 AATCGCAA
1 AATCGCAA
7627 CGAGATAATC
Statistics
Matches: 207, Mismatches: 8, Indels: 42
0.81 0.03 0.16
Matches are distributed among these distances:
14 40 0.19
15 2 0.01
16 11 0.05
17 10 0.05
18 3 0.01
19 128 0.62
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:7444 original size:14 final size:14
Alignment explanation
Indices: 7422--7479 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
7412 ATGCGGAAAT
7422 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
7436 GAGAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
7454 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
7469 GATAATCGCAA
1 GAAAATCGCAA
7480 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:7459 original size:33 final size:34
Alignment explanation
Indices: 7372--7626 Score: 304
Period size: 33 Copynumber: 7.2 Consensus size: 34
7362 CGGAAAATAC
* *
7372 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
7405 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
*
7439 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
7472 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
7510 AATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
7548 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
7580 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
7619 AATCGCAA
1 AATCGCAA
7627 CGAGATAATC
Statistics
Matches: 201, Mismatches: 7, Indels: 23
0.87 0.03 0.10
Matches are distributed among these distances:
32 2 0.01
33 85 0.42
34 30 0.15
35 5 0.02
36 2 0.01
37 2 0.01
38 73 0.36
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:7525 original size:13 final size:13
Alignment explanation
Indices: 7472--7567 Score: 51
Period size: 13 Copynumber: 7.6 Consensus size: 13
7462 GCAACGAGAT
*
7472 AATCGCAATGCGA
1 AATCGAAATGCGA
*
7485 AAT-GAAAAT-CGC
1 AATCG-AAATGCGA
*
7497 AATGCGAAATG-AA
1 AAT-CGAAATGCGA
*
7510 AATCGCAATGCGA
1 AATCGAAATGCGA
* *
7523 AATGGAAAT-CGC
1 AATCGAAATGCGA
*
7535 AATGCGAAATG-AA
1 AAT-CGAAATGCGA
*
7548 AATCGCAATGCGA
1 AATCGAAATGCGA
7561 AAT-GAAA
1 AATCGAAA
7568 ATCGCAACGA
Statistics
Matches: 60, Mismatches: 15, Indels: 17
0.65 0.16 0.18
Matches are distributed among these distances:
12 26 0.43
13 33 0.55
14 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (13 bp):
AATCGAAATGCGA
Found at i:7664 original size:52 final size:52
Alignment explanation
Indices: 7439--7648 Score: 348
Period size: 52 Copynumber: 3.9 Consensus size: 52
7429 GCAACGAGAG
*
7439 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATGAA
7491 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT---AATCGCAATGCGAAATGAA
*
7548 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATGAA
*
7600 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAAT
7649 TATAAACGCA
Statistics
Matches: 149, Mismatches: 4, Indels: 10
0.91 0.02 0.06
Matches are distributed among these distances:
52 93 0.62
54 5 0.03
55 5 0.03
57 46 0.31
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATGAA
Found at i:7745 original size:19 final size:19
Alignment explanation
Indices: 7655--7737 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
7645 AAATTATAAA
7655 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
7674 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
7694 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
7710 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
7727 CGCATTGCGAT
1 CGCATTGCGAT
7738 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:7860 original size:13 final size:14
Alignment explanation
Indices: 7844--7879 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
7834 CATCAATTAC
7844 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
7857 ACAAATCATCTTTT
1 ACAAATCAACTTTT
7871 ACAAATCAA
1 ACAAATCAA
7880 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:9847 original size:14 final size:14
Alignment explanation
Indices: 9828--9884 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
9818 GCGAAATGAA
*
9828 AATCGCAACGACAG
1 AATCGCAACGAAAG
9842 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
9859 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
9875 AATCGCAACG
1 AATCGCAACG
9885 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:9855 original size:33 final size:33
Alignment explanation
Indices: 9809--9901 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
9799 GCGAAACCAA
*
9809 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
9842 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
9875 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
9902 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:9866 original size:19 final size:19
Alignment explanation
Indices: 9772--9906 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
9762 TAGTTTACTT
* *
9772 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
9792 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
9811 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
9830 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
9844 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
9863 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
9877 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
9896 TCGCAATGCGA
1 TCGCAACGCGA
9907 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:9924 original size:19 final size:19
Alignment explanation
Indices: 9902--10028 Score: 121
Period size: 19 Copynumber: 7.2 Consensus size: 19
9892 AAAATCGCAA
9902 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
9921 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
9935 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
9954 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
9968 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
9987 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
10006 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
10026 TGC
1 TGC
10029 AAAAGTAAAC
Statistics
Matches: 88, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.55
20 11 0.12
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:9944 original size:33 final size:33
Alignment explanation
Indices: 9902--9993 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
9892 AAAATCGCAA
9902 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
9935 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
9968 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
9994 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:10365 original size:92 final size:92
Alignment explanation
Indices: 10074--10727 Score: 1258
Period size: 92 Copynumber: 7.1 Consensus size: 92
10064 TTGAATGGAT
10074 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
10139 AGTTTAGCAGAATTGGCAGCAACCGAAC
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
10167 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATA-TTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
10231 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
10258 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
10323 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
10350 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
10415 AGTTTAGCAGAATTGGCAGCAACCGAAC
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
10443 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
10508 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
10535 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
10600 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
10627 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
*
10691 AGTTTAGCAGAATTGGCAGCAACCGAAT
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
10719 AAATTTACT
1 AAATTTACT
10728 AAGCAATCTA
Statistics
Matches: 557, Mismatches: 1, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
91 106 0.19
92 320 0.57
93 131 0.24
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (92 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:10699 original size:184 final size:184
Alignment explanation
Indices: 10074--10727 Score: 1258
Period size: 185 Copynumber: 3.5 Consensus size: 184
10064 TTGAATGGAT
10074 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
10139 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
10204 TATA-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
10258 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
10323 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
10388 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 A-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
10443 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
10508 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
10573 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
10627 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
*
10691 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
10728 AAGCAATCTA
Statistics
Matches: 466, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
183 107 0.23
184 178 0.38
185 181 0.39
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (184 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:12451 original size:14 final size:14
Alignment explanation
Indices: 12432--12521 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
12422 TTGAAATGAA
12432 AATCGCAACGAGAG
1 AATCGCAACGAGAG
12446 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
12463 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
12479 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
12498 AATCGCAACGAGAG
1 AATCGCAACGAGAG
12512 AATCGCAACG
1 AATCGCAACG
12522 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:12469 original size:33 final size:33
Alignment explanation
Indices: 12424--12538 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
12414 TCTTTTGGTT
12424 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
12457 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
12490 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
12523 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
12539 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:12470 original size:19 final size:18
Alignment explanation
Indices: 12431--12543 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
12421 GTTGAAATGA
12431 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
12446 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
12463 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
12479 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
12496 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
12512 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
12529 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
12544 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:12574 original size:14 final size:14
Alignment explanation
Indices: 12555--12609 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
12545 TTTGGTTTCG
12555 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
12569 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
12588 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
12602 CGTTGCGA
1 CGTTGCGA
12610 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:12587 original size:33 final size:33
Alignment explanation
Indices: 12539--12609 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
12529 AAAATCGCAA
**
12539 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
12572 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
12605 TGCGA
1 TGCGA
12610 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:12617 original size:33 final size:33
Alignment explanation
Indices: 12550--12631 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
12540 GCGATTTTGG
***
12550 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
12583 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
12616 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
12632 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:12636 original size:20 final size:20
Alignment explanation
Indices: 12562--12650 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
12552 TCGCGTTGCG
12562 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
12582 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
12595 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
12615 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
12635 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
12651 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:12772 original size:33 final size:33
Alignment explanation
Indices: 12730--12800 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
12720 AATACTAACT
12730 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
***
12763 TGAAAATCGCAACGAGAGAATCTTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
12796 TGAAA
1 TGAAA
12801 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:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:13034 original size:22 final size:22
Alignment explanation
Indices: 12982--13036 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
12972 TGGTTGTGAG
**
12982 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
13004 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
13026 GGATTTCTTCG
1 GGATTTCTTCG
13037 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:13207 original size:20 final size:20
Alignment explanation
Indices: 13182--13374 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
13172 CTTTAAATAT
13182 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
13202 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
13224 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
13243 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
13263 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
13283 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
13303 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
13323 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
13343 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
13363 CGCGTTGCGATT
1 CGCGTTGCGATT
13375 ATTGAAAATC
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:13369 original size:60 final size:60
Alignment explanation
Indices: 13182--13374 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
13172 CTTTAAATAT
**
13182 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
13243 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
13303 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
13363 CGCGTTGCGATT
1 CGCGTTGCGATT
13375 ATTGAAAATC
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:15169 original size:19 final size:17
Alignment explanation
Indices: 15145--15179 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
15135 AAAAACATGA
15145 ATTAAATATGTATAAAAAG
1 ATTAAA-AT-TATAAAAAG
15164 ATTAAAATTATAAAAA
1 ATTAAAATTATAAAAA
15180 ATATGACGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
ATTAAAATTATAAAAAG
Found at i:15912 original size:21 final size:20
Alignment explanation
Indices: 15849--15916 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
15839 GAACTCTAAT
15849 TTCGCAACACAGTTTCCAAA
1 TTCGCAACACAGTTTCCAAA
* *
15869 TTCGCAACGCGAATTTCACAAA
1 TTCGCAACAC-AGTTTC-CAAA
* *
15891 TTCGCAACTCAGTTTCGGAAA
1 TTCGCAACACAGTTTC-CAAA
15912 TTCGC
1 TTCGC
15917 GTTGCGATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 9 0.22
21 18 0.45
22 13 0.32
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACACAGTTTCCAAA
Found at i:16014 original size:77 final size:77
Alignment explanation
Indices: 15930--16090 Score: 252
Period size: 77 Copynumber: 2.1 Consensus size: 77
15920 GCGATAGTTG
* * * *
15930 TGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACA
1 TGTTTACCTATATCGGTAATTAACATTACGAATTTGAAAATCGCATTGCGATAGTACTATTTACA
*
15995 CTGA-GATAGTAC
66 -TGACCATAGTAC
16007 TGTTTACCTATATCGGTAATTAACATTACGAATTTGAAAATCGCATTGCGATAGTACTATTTACA
1 TGTTTACCTATATCGGTAATTAACATTACGAATTTGAAAATCGCATTGCGATAGTACTATTTACA
*
16072 TTACCATAGTAC
66 TGACCATAGTAC
16084 TGTTTAC
1 TGTTTAC
16091 ATTGCGATAG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
76 2 0.03
77 75 0.97
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (77 bp):
TGTTTACCTATATCGGTAATTAACATTACGAATTTGAAAATCGCATTGCGATAGTACTATTTACA
TGACCATAGTAC
Found at i:16080 original size:20 final size:20
Alignment explanation
Indices: 16050--16138 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
16040 TTGAAAATCG
*
16050 CATTGCGATAGTACTATTTA
1 CATTGCGATAGTACTGTTTA
* *
16070 CATTACCATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
* *
16090 CATTGCGATAGAATTGTTTA
1 CATTGCGATAGTACTGTTTA
16110 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
16130 CATTGCGAT
1 CATTGCGAT
16139 TTTCAAATTC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:17647 original size:60 final size:59
Alignment explanation
Indices: 17578--17694 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 59
17568 CTTCATTGGG
*
17578 AAATGGTCCTTAAACTTATAAAAATTCCAATTTCATCC-TAAATCTATGAATCTCATTCT
1 AAATGGTCCTTAAACTTATAAAAATTCCAATTCCATCCTTAAA-CTATGAATCTCATTCT
* * * *
17637 AAATGAGTCCTTAAACTTTTGAACATTCCAATTCCATCCTTAAACTATGACTCTCATT
1 AAATG-GTCCTTAAACTTATAAAAATTCCAATTCCATCCTTAAACTATGAATCTCATT
17695 GTAGATTGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 5 0.10
60 42 0.82
61 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (59 bp):
AAATGGTCCTTAAACTTATAAAAATTCCAATTCCATCCTTAAACTATGAATCTCATTCT
Found at i:17735 original size:60 final size:60
Alignment explanation
Indices: 17578--17735 Score: 155
Period size: 60 Copynumber: 2.6 Consensus size: 60
17568 CTTCATTGGG
* * * *
17578 AAATG-GTCCTTAAACTTATAAAAATTCCAATTTCATCCTAAATCTATGAATCTCATTCT
1 AAATGAGTCCTCAAACTTTTGAACATTCCAATTTCATCCTAAATCTATGAATCTCATTCT
* * * *
17637 AAATGAGTCCTTAAACTTTTGAACATTCCAATTCCATCCTTAAA-CTATGACTCTCATTGT
1 AAATGAGTCCTCAAACTTTTGAACATTCCAATTTCATCC-TAAATCTATGAATCTCATTCT
* *
17697 AGATTG-GTCAC-CAAACTTTTGAATC-TTCTAATTTCATCC
1 A-AATGAGTC-CTCAAACTTTTGAA-CATTCCAATTTCATCC
17736 CCATGTTCAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
59 5 0.06
60 70 0.83
61 9 0.11
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (60 bp):
AAATGAGTCCTCAAACTTTTGAACATTCCAATTTCATCCTAAATCTATGAATCTCATTCT
Found at i:19774 original size:21 final size:21
Alignment explanation
Indices: 19748--19791 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19738 CGTCAACTCC
19748 TATATAAAAAGGGTTAGTTTA
1 TATATAAAAAGGGTTAGTTTA
19769 TATATAAAAAGGGTTAGTTTA
1 TATATAAAAAGGGTTAGTTTA
19790 TA
1 TA
19792 ATTAACCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (21 bp):
TATATAAAAAGGGTTAGTTTA
Found at i:24540 original size:124 final size:121
Alignment explanation
Indices: 24294--24602 Score: 352
Period size: 124 Copynumber: 2.5 Consensus size: 121
24284 TAACGTTGAG
* * * **
24294 TTTTGAAAATAATTAAAATTTTAGGTACTAAAATGGACCAAAATTGACCGTTTAGGTACTAAATC
1 TTTT-AAAA-AATTAAAAGTTAAGGTACTAAAATGGACCAAAACTGATAGTTTAGGTACTAAATC
* * * **
24359 TGTTAAGTTTTTAATGACGAGATACTAAAATGAAACAAAAACTAAACATCATTTATGA
64 TGATAAGTTTTTAATGACGAAATACTAAAATAAAACAAAAACTAAACATCAGATATGA
* *
24417 TTTTGAAAAAATTTGAAAGTTAAAGGTACTAAAATGGACAAAAACTGATAGTTTAGGTACTAAA-
1 TTTT-AAAAAA-TTAAAAGTT-AAGGTACTAAAATGGACCAAAACTGATAGTTTAGGTACTAAAT
** * *
24481 CGTGATAAGTTTTTAATGACGAAATACTAAAATAAAATGAAAATTAAA-AGTTAGATATGA
63 C-TGATAAGTTTTTAATGACGAAATACTAAAATAAAACAAAAACTAAACA-TCAGATATGA
* * * * *
24541 TTTTAAAAAATTAAAAGTTTAGGTATTTAAATAGACCAAAACTGATAGTTTATGTACTAAAT
1 TTTTAAAAAATTAAAAGTTAAGGTACTAAAATGGACCAAAACTGATAGTTTAGGTACTAAAT
24603 ATATAATTTA
Statistics
Matches: 158, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
121 36 0.23
122 10 0.06
123 24 0.15
124 88 0.56
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (121 bp):
TTTTAAAAAATTAAAAGTTAAGGTACTAAAATGGACCAAAACTGATAGTTTAGGTACTAAATCTG
ATAAGTTTTTAATGACGAAATACTAAAATAAAACAAAAACTAAACATCAGATATGA
Found at i:26148 original size:15 final size:14
Alignment explanation
Indices: 26122--26158 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
26112 ATATATTAAT
26122 TAAAAT-TTTAAAA
1 TAAAATATTTAAAA
26135 GTAAAATATTTAAAA
1 -TAAAATATTTAAAA
26150 TAAAATATT
1 TAAAATATT
26159 ATTTTTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TAAAATATTTAAAA
Found at i:26174 original size:10 final size:10
Alignment explanation
Indices: 26159--26194 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
26149 ATAAAATATT
*
26159 ATTTTTCATA
1 ATTTTTAATA
26169 ATTTTTAATA
1 ATTTTTAATA
26179 ATTTTTTAATA
1 A-TTTTTAATA
26190 ATTTT
1 ATTTT
26195 AAAGGTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:26184 original size:11 final size:11
Alignment explanation
Indices: 26160--26194 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
26150 TAAAATATTA
*
26160 TTTTTCATAA-
1 TTTTTAATAAT
26170 TTTTTAATAAT
1 TTTTTAATAAT
26181 TTTTTAATAAT
1 TTTTTAATAAT
26192 TTT
1 TTT
26195 AAAGGTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:31464 original size:10 final size:10
Alignment explanation
Indices: 31449--31509 Score: 95
Period size: 10 Copynumber: 6.1 Consensus size: 10
31439 TTGCAGTGAC
31449 TAAATTAAAA
1 TAAATTAAAA
*
31459 TAAATTGAAA
1 TAAATTAAAA
*
31469 TAAATTGAAA
1 TAAATTAAAA
31479 TAAATTAAAA
1 TAAATTAAAA
31489 TAAATTAAAA
1 TAAATTAAAA
*
31499 TAAATTGAAA
1 TAAATTAAAA
31509 T
1 T
31510 TAAACATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:31483 original size:30 final size:30
Alignment explanation
Indices: 31449--31509 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
31439 TTGCAGTGAC
*
31449 TAAATTAAAATAAATTGAAATAAATTGAAA
1 TAAATTAAAATAAATTAAAATAAATTGAAA
31479 TAAATTAAAATAAATTAAAATAAATTGAAA
1 TAAATTAAAATAAATTAAAATAAATTGAAA
31509 T
1 T
31510 TAAACATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (30 bp):
TAAATTAAAATAAATTAAAATAAATTGAAA
Found at i:40571 original size:2 final size:2
Alignment explanation
Indices: 40564--40606 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
40554 TAGGTTTGAT
40564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40606 T
1 T
40607 TCACTAACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42912 original size:2 final size:2
Alignment explanation
Indices: 42905--42952 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
42895 CAAAGAGATG
42905 AT AT AT 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
42947 AT AT AT
1 AT AT AT
42953 GACCTCTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44024 original size:2 final size:2
Alignment explanation
Indices: 44017--44044 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44007 GCGCATTTGG
44017 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
44045 GGCCTTTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44872 original size:22 final size:23
Alignment explanation
Indices: 44827--44872 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
44817 ATTTCACCTC
* * *
44827 TAATATATTATTTTTTTCAATTA
1 TAATATATTAATTATTTAAATTA
44850 TAATAT-TTAATTATTTAAATTA
1 TAATATATTAATTATTTAAATTA
44872 T
1 T
44873 GTTAATTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATATATTAATTATTTAAATTA
Found at i:48073 original size:60 final size:60
Alignment explanation
Indices: 48009--48159 Score: 232
Period size: 60 Copynumber: 2.5 Consensus size: 60
47999 AGTCTAATGA
* *
48009 CCATTTTGTAACTTTTAATAGTCGAGGGACTCAATAAAGCAACACTTTATAGTTC-AAGGG
1 CCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAG-TCGAAGGG
* *
48069 CCATTTTGTAACTTTTAATAGTCAAGGGACTCGACAAAGCAACACTCTATAGTCGAAGGG
1 CCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAGTCGAAGGG
* *
48129 CCATTTTGTAACTTTTAATGGTCGAGAGACT
1 CCATTTTGTAACTTTTAATAGTCGAGGGACT
48160 TGATAAAGTA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
59 2 0.02
60 81 0.98
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (60 bp):
CCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAGTCGAAGGG
Found at i:48180 original size:60 final size:57
Alignment explanation
Indices: 48009--48193 Score: 217
Period size: 60 Copynumber: 3.1 Consensus size: 57
47999 AGTCTAATGA
*
48009 CCATTTTGTAACTTTTAATAGTCGAGGGACTCAATAAAGCAACACTTTATAGTTCAAGGG
1 CCATTTTGTAACTTTTAATAGTCGAGGGACTCGATAAAGCAAC-C-TTATAG-TCAAGGG
* *
48069 CCATTTTGTAACTTTTAATAGTCAAGGGACTCGACAAAGCAACACTCTATAGTCGAAGGG
1 CCATTTTGTAACTTTTAATAGTCGAGGGACTCGATAAAGCAAC-CT-TATAGTC-AAGGG
* * * * * *
48129 CCATTTTGTAACTTTTAATGGTCGAGAGACTTGATAAAGTAGTACCTTATAGTCATGGA
1 CCATTTTGTAACTTTTAATAGTCGAGGGACTCGATAAAGCA--ACCTTATAGTCAAGGG
48188 CCATTT
1 CCATTT
48194 GTATGCTTAA
Statistics
Matches: 110, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
59 12 0.11
60 94 0.85
61 2 0.02
62 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (57 bp):
CCATTTTGTAACTTTTAATAGTCGAGGGACTCGATAAAGCAACCTTATAGTCAAGGG
Found at i:48742 original size:31 final size:31
Alignment explanation
Indices: 48682--48753 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
48672 ACGCATTTCG
* **
48682 TACTTAAACTATTCATTTTGGTCTGTTTTAA
1 TACTTAAACTATTCATTTTGGCCCATTTTAA
*
48713 TACTTAAACTATT-AGTTTTGGCCCATTTTAG
1 TACTTAAACTATTCA-TTTTGGCCCATTTTAA
*
48744 TACCTAAACT
1 TACTTAAACT
48754 TAAAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.46
Consensus pattern (31 bp):
TACTTAAACTATTCATTTTGGCCCATTTTAA
Done.