Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005199.1 Hibiscus syriacus cultivar Beakdansim tig00011747_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: 124700
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4560 original size:47 final size:43
Alignment explanation
Indices: 4469--4584 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 43
4459 GTAAGTATGC
*
4469 AAATAAGCTTAGAGCTTAT-GAATAATGGCAAGTATATTGATA
1 AAATAAGCTTAGAGCTTATGGAATAATAGCAAGTATATTGATA
* * *
4511 AAATAAGCTTATGAGCTTATGGAATTTAAATAGTAAGTATCTTGGTA
1 AAATAAGCTTA-GAGCTTATGGAA--T-AATAGCAAGTATATTGATA
*
4558 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTA-GAGCTTATGGAATAA
4585 ATGGTAAGGG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
42 11 0.17
43 8 0.13
44 5 0.08
45 1 0.02
46 1 0.02
47 37 0.59
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.32
Consensus pattern (43 bp):
AAATAAGCTTAGAGCTTATGGAATAATAGCAAGTATATTGATA
Found at i:5055 original size:3 final size:3
Alignment explanation
Indices: 5047--5077 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5037 GAATAGGGTT
5047 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
5078 ATTTCGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:5910 original size:13 final size:13
Alignment explanation
Indices: 5892--5922 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5882 TATGGTACAC
5892 ATTTTAAAAATAA
1 ATTTTAAAAATAA
*
5905 ATTTTATAAATAA
1 ATTTTAAAAATAA
5918 ATTTT
1 ATTTT
5923 CGATTTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTAAAAATAA
Found at i:8771 original size:32 final size:32
Alignment explanation
Indices: 8735--8822 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 32
8725 AGAGTGTACC
* * * **
8735 TTGGGGCCTAATAGCCTACCTAAGGGAATACA
1 TTGGGGCCTTAGAGCCTACCCAAGAAAATACA
*
8767 TTGGGGCCTTAGAGCCTACCCAAGAAAATACC
1 TTGGGGCCTTAGAGCCTACCCAAGAAAATACA
*
8799 TTGGGGCCTTAGAGCCTAACCAAG
1 TTGGGGCCTTAGAGCCTACCCAAG
8823 TGTCACCTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (32 bp):
TTGGGGCCTTAGAGCCTACCCAAGAAAATACA
Found at i:8772 original size:64 final size:64
Alignment explanation
Indices: 8688--8816 Score: 159
Period size: 64 Copynumber: 2.0 Consensus size: 64
8678 GTAGATGACA
* * * * *** *
8688 ACCTAAGGGATTACCTTGGGGCCTGAGAACGTACTCAAGAGTGTACCTTGGGGCCTAATAGCCT
1 ACCTAAGGGAATACATTGGGGCCTGAGAACCTACCCAAGAAAATACCTTGGGGCCTAAGAGCCT
* * *
8752 ACCTAAGGGAATACATTGGGGCCTTAGAGCCTACCCAAGAAAATACCTTGGGGCCTTAGAGCCT
1 ACCTAAGGGAATACATTGGGGCCTGAGAACCTACCCAAGAAAATACCTTGGGGCCTAAGAGCCT
8816 A
1 A
8817 ACCAAGTGTC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (64 bp):
ACCTAAGGGAATACATTGGGGCCTGAGAACCTACCCAAGAAAATACCTTGGGGCCTAAGAGCCT
Found at i:14541 original size:32 final size:31
Alignment explanation
Indices: 14501--14606 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 31
14491 AAGAAATTAT
**
14501 CCTACCCAAGAGTGTACCTTGGGGCCTAAGAG
1 CCTACCCAAG-GAATACCTTGGGGCCTAAGAG
* * * *
14533 CCTTCCCAAGGGAATACCTTGGGGCTTTAGAT
1 CCTACCCAA-GGAATACCTTGGGGCCTAAGAG
14565 CCTACCCAAGGAAATACCTTGGGGCCTCAA-AG
1 CCTACCCAAGG-AATACCTTGGGGCCT-AAGAG
14597 CCTACCCAAG
1 CCTACCCAAG
14607 TGTCACCTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
31 2 0.03
32 57 0.93
33 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (31 bp):
CCTACCCAAGGAATACCTTGGGGCCTAAGAG
Found at i:16419 original size:20 final size:20
Alignment explanation
Indices: 16394--16431 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16384 CACATGTTAA
16394 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
16414 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
16432 TCAAGGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:21442 original size:19 final size:19
Alignment explanation
Indices: 21418--21466 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
21408 AATGCAATTG
21418 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
21437 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
21456 GTGCATCGATG
1 GTGCATCGATG
21467 TATCCCCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (19 bp):
GTGCATCGATGCATAAGGA
Found at i:21566 original size:20 final size:22
Alignment explanation
Indices: 21521--21578 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
21511 GCATGGGTAG
21521 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
21545 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
21565 TGCATCGATGCACT
1 TGCATCGATGCACT
21579 TCAAGGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:22665 original size:2 final size:2
Alignment explanation
Indices: 22660--22769 Score: 220
Period size: 2 Copynumber: 55.0 Consensus size: 2
22650 AGAAAAAATG
22660 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
22702 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
22744 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
22770 GAAGATGAAT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 108 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23313 original size:23 final size:23
Alignment explanation
Indices: 23245--23313 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
23235 CAACCTTATA
*
23245 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
23268 CGGCACTACAGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
23291 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
23314 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:24287 original size:27 final size:28
Alignment explanation
Indices: 24229--24290 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
24219 AGGGCTTGGA
* * **
24229 GGTATTTTAGGTCATTTTACACTTTAGG
1 GGTATTTTAGGTCATTTTACAATTCAAC
24257 GGTATTTT-GGTCATTTTACAATTCAAC
1 GGTATTTTAGGTCATTTTACAATTCAAC
24284 GGTATTT
1 GGTATTT
24291 CAGTCTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (28 bp):
GGTATTTTAGGTCATTTTACAATTCAAC
Found at i:26739 original size:41 final size:41
Alignment explanation
Indices: 26694--26958 Score: 460
Period size: 41 Copynumber: 6.5 Consensus size: 41
26684 ATTCGCGTTG
26694 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
26735 CATTTCGCGTTGCGATAGTTGAAAATCGCATCGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
26776 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
26817 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
26858 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
26899 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
26940 CGTTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
26959 CTACAGTTGT
Statistics
Matches: 211, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 1 0.00
41 209 0.99
42 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:26992 original size:41 final size:40
Alignment explanation
Indices: 26694--26999 Score: 402
Period size: 41 Copynumber: 7.5 Consensus size: 40
26684 ATTCGCGTTG
26694 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
26735 CATTTCGCGTTGCGATAGTTGAAAATCGCATCGCGATTTTC
1 CATTTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
26776 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
26817 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
26858 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTC
1 CATTTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
26899 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * * *
26940 CGTTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
*
26982 CGAATT-CGTTGCGATAGT
1 C-ATTTCCGTTGCGATAGT
27000 CTTAAAAAAA
Statistics
Matches: 244, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
40 1 0.00
41 225 0.92
42 16 0.07
43 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (40 bp):
CATTTCCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:26992 original size:123 final size:122
Alignment explanation
Indices: 26694--26999 Score: 447
Period size: 123 Copynumber: 2.5 Consensus size: 122
26684 ATTCGCGTTG
26694 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC-CGTTGCGATAGTTGAAA
* *
26759 ATCGCATCGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
65 ATCGCATCGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTC
26817 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC-CGTTGCGATAGTTGAAA
* * *
26882 ATCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
65 ATCGCATCGCGATTTTCCATTTCGCGTTGCGATAGTCT-AAAATCGCGTTGCGATTTTC
* * * * *
26940 CGTTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCGAATT-CGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-ATTTCCGTTGCGATAGT
27000 CTTAAAAAAA
Statistics
Matches: 169, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
122 1 0.01
123 150 0.89
124 15 0.09
125 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (122 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCCGTTGCGATAGTTGAAAA
TCGCATCGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTC
Found at i:27575 original size:6 final size:6
Alignment explanation
Indices: 27555--27626 Score: 130
Period size: 6 Copynumber: 12.3 Consensus size: 6
27545 CGTCCGTCTC
27555 GTCG-G GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
27601 GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GT
27627 AATACGTGTC
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 9 0.14
6 57 0.86
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GTCGTG
Found at i:27753 original size:22 final size:22
Alignment explanation
Indices: 27726--27794 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
27716 AATTTGGAAA
27726 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
27748 ATCGCAACG--AA-T-TTG--G
1 ATCGCAACGACAACTGTAGACT
27764 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
27786 ATCGCAACG
1 ATCGCAACG
27795 CGAAATGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
16 9 0.24
18 4 0.11
19 2 0.05
20 4 0.11
22 18 0.49
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:27761 original size:41 final size:40
Alignment explanation
Indices: 27720--27924 Score: 233
Period size: 41 Copynumber: 5.0 Consensus size: 40
27710 ACAACGAATT
*
27720 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA-CGAATT
1 TGGAAAATCGCAACG-CAACTGTAGACTATCGCAACCGAA-A
27761 TGG---ATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CAACTGTAGACTATCGCAAC-CGAAA
* *
27800 TGGAAAATCGCAACGCGATCT-TCA-ACTATCGCAACGCGAAG
1 TGGAAAATCGCAACGC-AACTGT-AGACTATCGCAAC-CGAAA
*
27841 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTAGACTATCGCAAC-CGAAA
* *
27882 TGGAAAATCGCAACGCGACTGTAGACTATCGCAATGCGAAA
1 TGGAAAATCGCAACGCAACTGTAGACTATCGCAA-CCGAAA
27923 TG
1 TG
27925 CAACACGAAT
Statistics
Matches: 147, Mismatches: 7, Indels: 20
0.84 0.04 0.11
Matches are distributed among these distances:
38 29 0.20
39 3 0.02
40 7 0.05
41 95 0.65
42 13 0.09
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (40 bp):
TGGAAAATCGCAACGCAACTGTAGACTATCGCAACCGAAA
Found at i:27811 original size:20 final size:20
Alignment explanation
Indices: 27786--27899 Score: 113
Period size: 20 Copynumber: 5.6 Consensus size: 20
27776 ACTGTAGACT
27786 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
27806 ATCGCAACGCGATCTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
27827 ATCGCAACGCGAAGTGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
27847 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
27868 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
27888 ATCGCAACGCGA
1 ATCGCAACGCGA
27900 CTGTAGACTA
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.04
20 40 0.54
21 28 0.38
22 3 0.04
ACGTcount: A:0.37, C:0.25, G:0.24, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:27873 original size:82 final size:83
Alignment explanation
Indices: 27720--27921 Score: 276
Period size: 82 Copynumber: 2.5 Consensus size: 83
27710 ACAACGAATT
* *
27720 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATTTGG---ATCGCAACGACAACTG
1 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAA-GTGGAAAATCGCAACGACAACTG
27780 TAGACTATCGCAACGCGAAA
64 TAGACTATCGCAACGCGAAA
*
27800 TGGAAAATCGCAACGCGATCT-TCA-ACTATCGCAACGCGAAGTGGAAAATCGCAACG-CGACTG
1 TGGAAAATCGCAACGCGA-CTGT-AGACTATCGCAACGCGAAGTGGAAAATCGCAACGACAACTG
27862 TAGACTATCGCAACGCGAAA
64 TAGACTATCGCAACGCGAAA
*
27882 TGGAAAATCGCAACGCGACTGTAGACTATCGCAATGCGAA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAA
27922 ATGCAACACG
Statistics
Matches: 109, Mismatches: 4, Indels: 16
0.84 0.03 0.12
Matches are distributed among these distances:
79 13 0.12
80 21 0.19
81 7 0.06
82 59 0.54
83 9 0.08
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (83 bp):
TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAGTGGAAAATCGCAACGACAACTGTA
GACTATCGCAACGCGAAA
Found at i:27981 original size:21 final size:20
Alignment explanation
Indices: 27957--28097 Score: 89
Period size: 21 Copynumber: 7.2 Consensus size: 20
27947 AGATCGCGTT
27957 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAA-TATCGCAAC
** ** *
27978 GCGAAATGGAAAATCGCAAC
1 GCGATTTTCAATATCGCAAC
* *
27998 GCGATTTTCAAATATCGAAAT
1 GCGATTTTC-AATATCGCAAC
28019 G-GA-----AA-ATCGCAAC
1 GCGATTTTCAATATCGCAAC
28032 GCGATTTTCAAATATCGCAAC
1 GCGATTTTC-AATATCGCAAC
** ** *
28053 GCGAAATGGAAAATCGCAAC
1 GCGATTTTCAATATCGCAAC
28073 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAA-TATCGCAAC
28094 GCGA
1 GCGA
28098 AATGCAACGC
Statistics
Matches: 86, Mismatches: 24, Indels: 20
0.66 0.18 0.15
Matches are distributed among these distances:
13 7 0.08
14 4 0.05
20 34 0.40
21 41 0.48
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
GCGATTTTCAATATCGCAAC
Found at i:28002 original size:41 final size:41
Alignment explanation
Indices: 27957--28101 Score: 223
Period size: 41 Copynumber: 3.7 Consensus size: 41
27947 AGATCGCGTT
27957 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
*
27998 GCGATTTTCAA--AT----A-TCGAAATGGAAAATCGCAAC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
*
28032 GCGATTTTCAAATATCGCAACGCGAAATGGAAAATCGCAAC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
28073 GCGATTTTCAACTATCGCAACGCGAAATG
1 GCGATTTTCAACTATCGCAACGCGAAATG
28102 CAACGCGAAT
Statistics
Matches: 94, Mismatches: 3, Indels: 14
0.85 0.03 0.13
Matches are distributed among these distances:
34 30 0.32
35 1 0.01
36 2 0.02
39 2 0.02
40 1 0.01
41 58 0.62
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
Found at i:28022 original size:34 final size:34
Alignment explanation
Indices: 27979--28089 Score: 150
Period size: 34 Copynumber: 3.1 Consensus size: 34
27969 TATCGCAACG
27979 CGAAATGGAAAATCGCAACGCGATTTTCAAATAT
1 CGAAATGGAAAATCGCAACGCGATTTTCAAATAT
28013 CGAAATGGAAAATCGCAACGCGATTTTCAAATAT
1 CGAAATGGAAAATCGCAACGCGATTTTCAAATAT
*
28047 CGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
1 -------CGAAATGGAAAATCGCAACGCGATTTTCAAATAT
28088 CG
1 CG
28090 CAACGCGAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 14
0.82 0.01 0.17
Matches are distributed among these distances:
34 36 0.52
41 33 0.48
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (34 bp):
CGAAATGGAAAATCGCAACGCGATTTTCAAATAT
Found at i:28089 original size:177 final size:180
Alignment explanation
Indices: 27783--28130 Score: 510
Period size: 177 Copynumber: 1.9 Consensus size: 180
27773 ACAACTGTAG
*
27783 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTTCAACTATCGCAACGCGAAGTGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTTCAAATATCG-AA--C-AAGTGGAAAA
*
27848 TCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCG
62 TCGCAACGCGACTGTAGAATATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCG
*
27913 CAATGCGAAATGCAACACGAATTTGCGATTA-TGGAGATCGCGTTGCGATTTTCA
127 CAACGCGAAATGCAACACGAATTTGCGA-TAGTGGAGATCGCGTTGCGATTTTCA
*
27967 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAAATATCG-A-AA-TGGAAAATCGC
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTTCAAATATCGAACAAGTGGAAAATCGC
* * * *
28029 AACGCGATTTTCA-AATATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCA
66 AACGCGACTGT-AGAATATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-AGACTATCGCA
*
28092 ACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
129 ACGCGAAATGCAACACGAATTTGCGATAGTGGAGATCGC
28131 AATGCGAATT
Statistics
Matches: 152, Mismatches: 9, Indels: 13
0.87 0.05 0.07
Matches are distributed among these distances:
176 2 0.01
177 99 0.65
178 4 0.03
182 1 0.01
184 46 0.30
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (180 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTTCAAATATCGAACAAGTGGAAAATCGC
AACGCGACTGTAGAATATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAAC
GCGAAATGCAACACGAATTTGCGATAGTGGAGATCGCGTTGCGATTTTCA
Found at i:33581 original size:21 final size:21
Alignment explanation
Indices: 33557--33598 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33547 AAAAATTTAA
*
33557 AAAATGGATAAAATTTATATT
1 AAAATGGATAAAATATATATT
**
33578 AAAATGTTTAAAATATATATT
1 AAAATGGATAAAATATATATT
33599 CCTTGAAGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAATGGATAAAATATATATT
Found at i:39612 original size:21 final size:21
Alignment explanation
Indices: 39583--39623 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39573 ATCGGGTCGG
*
39583 GTTTGGGTCGGGTGGAATCTT
1 GTTTGGGTCGGGTCGAATCTT
*
39604 GTTTTGGTCGGGTCGAATCT
1 GTTTGGGTCGGGTCGAATCT
39624 CAGGCGGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.12, G:0.39, T:0.39
Consensus pattern (21 bp):
GTTTGGGTCGGGTCGAATCTT
Found at i:42285 original size:29 final size:29
Alignment explanation
Indices: 42250--42331 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
42240 AAACTAAATT
*
42250 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTACTTACATCATTTAAGTAAA
*
42279 GATGTCATTACTTACATCATTTAAGTAAT
1 GATGTCATTACTTACATCATTTAAGTAAA
*
42308 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTACTTACATC-ATTTA
42332 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTACTTACATCATTTAAGTAAA
Found at i:47041 original size:29 final size:29
Alignment explanation
Indices: 47006--47087 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
46996 AAACTAAATT
* *
47006 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
47035 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
47064 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
47088 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:53627 original size:2 final size:2
Alignment explanation
Indices: 53620--53649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53610 ATTCTCCTCA
53620 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
53650 GTTAACGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69510 original size:17 final size:17
Alignment explanation
Indices: 69488--69532 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
69478 ACGGTCGACT
*
69488 GTTGACCATTGACCTGC
1 GTTGACCATTGACCGGC
69505 GTTGACCATTGACCGGC
1 GTTGACCATTGACCGGC
69522 GTTGACCATTG
1 GTTGACCATTG
69533 TTGACCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (17 bp):
GTTGACCATTGACCGGC
Found at i:72118 original size:24 final size:24
Alignment explanation
Indices: 71986--72104 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
71976 ATCGATTTGA
71986 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
72010 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
72034 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
72058 ATTCTGATCTAATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
72082 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
72105 AATTATGTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 84 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:72246 original size:35 final size:34
Alignment explanation
Indices: 72188--72253 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
72178 GAATACCTGG
* * *
72188 AGGCTCCTCGGCTTTGTGCTCAAGGCCTTACTTGC
1 AGGCTACTCAGCTGTGTGCTCAAGG-CTTACTTGC
*
72223 AGGCTACTCAGCTGTGTGTTCAAGGCTTACT
1 AGGCTACTCAGCTGTGTGCTCAAGGCTTACT
72254 GGATGTGACG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 6 0.22
35 21 0.78
ACGTcount: A:0.15, C:0.27, G:0.26, T:0.32
Consensus pattern (34 bp):
AGGCTACTCAGCTGTGTGCTCAAGGCTTACTTGC
Found at i:72322 original size:2 final size:2
Alignment explanation
Indices: 72315--72343 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
72305 TGAATGGGGG
72315 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 T
72344 GTTTTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76959 original size:24 final size:24
Alignment explanation
Indices: 76831--76945 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
76821 ATTTGAATTA
* *
76831 TGATCTGATACTTGACATTGATTC
1 TGATATGATACTTGACATGGATTC
*
76855 TGATTTGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
* *
76879 TGATCTGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTC
*
76903 TGATATGATACTTGACATGGATTT
1 TGATATGATACTTGACATGGATTC
76927 TGATATGATACTTGACATG
1 TGATATGATACTTGACATG
76946 AATTATGTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:77074 original size:35 final size:35
Alignment explanation
Indices: 77028--77096 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
77018 GAATACCTGG
*
77028 AGGCTCCTCGGCTTTGTGCTCAGGGCCTTACTTGC
1 AGGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTGC
77063 AGGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTG
1 AGGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTG
77097 ACGTGACGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.09, C:0.30, G:0.30, T:0.30
Consensus pattern (35 bp):
AGGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTGC
Found at i:80267 original size:302 final size:302
Alignment explanation
Indices: 79721--80328 Score: 1189
Period size: 302 Copynumber: 2.0 Consensus size: 302
79711 GTAACGCATG
79721 GGGAAGGATTAGCACCCCCATAAGCGCCCAAAAATTGGTACCTAGTTAATTACCTTATATTTAAA
1 GGGAAGGATTAGCACCCCCATAAGCGCCCAAAAATTGGTACCTAGTTAATTACCTTATATTTAAA
79786 ATTGGAAACTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAGGATGCAGAGTTTGAAAAG
66 ATTGGAAACTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAGGATGCAGAGTTTGAAAAG
79851 GGTATTCGTTTATTGAGACCGATAGCATTCGCCCCCGAGCGTAAATGCGGGAGATCAGCTATTTT
131 GGTATTCGTTTATTGAGACCGATAGCATTCGCCCCCGAGCGTAAATGCGGGAGATCAGCTATTTT
*
79916 GTCTAATAACCGAGTATTGCCTCATTTTTAGAAAACATGAAGTGGTTTTGAAAAGGATGTCTACT
196 GTCTAATAACCGAGCATTGCCTCATTTTTAGAAAACATGAAGTGGTTTTGAAAAGGATGTCTACT
*
79981 TATTTGGGGAATTATCAGTAGTCACCCCCTGAGCATGATCGC
261 TATTTGGGGAATTATCAGTAGTCACCCCCTGAGCATGATCAC
80023 GGGAAGGATTAGCACCCCCATAAGCGCCCAAAAATTGGTACCTAGTTAATTACCTTATATTTAAA
1 GGGAAGGATTAGCACCCCCATAAGCGCCCAAAAATTGGTACCTAGTTAATTACCTTATATTTAAA
80088 ATTGGAAACTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAGGATGCAGAGTTTGAAAAG
66 ATTGGAAACTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAGGATGCAGAGTTTGAAAAG
80153 GGTATTCGTTTATTGAGACCGATAGCATTCGCCCCCGAGCGTAAATGCGGGAGATCAGCTATTTT
131 GGTATTCGTTTATTGAGACCGATAGCATTCGCCCCCGAGCGTAAATGCGGGAGATCAGCTATTTT
*
80218 GTCTAATAACCGAGCATTGCCTCATTTTTAGAAAACATGATGTGGTTTTGAAAAGGATGTCTACT
196 GTCTAATAACCGAGCATTGCCTCATTTTTAGAAAACATGAAGTGGTTTTGAAAAGGATGTCTACT
80283 TATTTGGGGAATTATCAGTAGTCACCCCCTGAGCATGATCAC
261 TATTTGGGGAATTATCAGTAGTCACCCCCTGAGCATGATCAC
80325 GGGA
1 GGGA
80329 GATATACTAT
Statistics
Matches: 303, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
302 303 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (302 bp):
GGGAAGGATTAGCACCCCCATAAGCGCCCAAAAATTGGTACCTAGTTAATTACCTTATATTTAAA
ATTGGAAACTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAGGATGCAGAGTTTGAAAAG
GGTATTCGTTTATTGAGACCGATAGCATTCGCCCCCGAGCGTAAATGCGGGAGATCAGCTATTTT
GTCTAATAACCGAGCATTGCCTCATTTTTAGAAAACATGAAGTGGTTTTGAAAAGGATGTCTACT
TATTTGGGGAATTATCAGTAGTCACCCCCTGAGCATGATCAC
Found at i:82124 original size:48 final size:48
Alignment explanation
Indices: 82067--82430 Score: 444
Period size: 48 Copynumber: 7.8 Consensus size: 48
82057 GAATCAGGGT
*
82067 AGACTTGTTCCACTTACTCTGAAGGGAATATTAAATCTTGGAAAAGAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
* * * *
82115 AAACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAAAA-AG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
* * * *
82162 AGACATGTTCCACTTACTCTGAAGAGAATATCAGATC-T-G----G-C
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
*
82203 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
* * * * *
82251 AGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAGAATAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
* * *
82299 AGACTTGTTCCACTCACTCTGAAGGGAATATCAAATCTTTG-AGA-AG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
* *
82345 AGACTTGTTCCACTTACTCTGAAGGGAATACCAAATCTT-AAAGAAGAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAA-AAGAG
* *
82393 AGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCT
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
82431 GAGAAGTTGA
Statistics
Matches: 273, Mismatches: 32, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
41 34 0.12
42 1 0.00
43 1 0.00
45 1 0.00
46 41 0.15
47 38 0.14
48 157 0.58
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (48 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
Found at i:82390 original size:142 final size:136
Alignment explanation
Indices: 82067--82430 Score: 541
Period size: 136 Copynumber: 2.6 Consensus size: 136
82057 GAATCAGGGT
* *
82067 AGACTTGTTCCACTTACTCTGAAGGGAATATTAAATCTTGGAA-AAGAGAAACCTGTTCCGCTTA
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTT-GAAGAAGAGAGACCTGTTCCGCTTA
* *
82131 CTCTGAAGGGAATATCAGATCTTGGAAAAAGAGACATGTTCCACTTACTCTGAAGAGAATATCAG
65 CTCTGAAGGGAATATCAGATCTTGGAAAAAGAGACATGTTCCACTCACTCTGAAGAGAATATCAA
82196 ATCTGGC
130 ATCTGGC
* *
82203 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACATGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCGCTTAC
* * *
82268 TCTGAAGGGAATATCAGATCTTGGAGAATAGAGACTTGTTCCACTCACTCTGAAGGGAATATCAA
66 TCTGAAGGGAATATCAGATCTTGGA-AAAAGAGACATGTTCCACTCACTCTGAAGAGAATATCAA
*
82333 ATCTTTGAGAAG
130 ATC--TG-G--C
* * *
82345 AGACTTGTTCCACTTACTCTGAAGGGAATACCAAATCTTAAAGAAGAGAGACCTGTTCCACTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCGCTTAC
82410 TCTGAAGGGAATATCAGATCT
66 TCTGAAGGGAATATCAGATCT
82431 GAGAAGTTGA
Statistics
Matches: 206, Mismatches: 15, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
135 2 0.01
136 83 0.40
137 37 0.18
139 2 0.01
140 1 0.00
142 81 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (136 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCGCTTAC
TCTGAAGGGAATATCAGATCTTGGAAAAAGAGACATGTTCCACTCACTCTGAAGAGAATATCAAA
TCTGGC
Found at i:82513 original size:112 final size:113
Alignment explanation
Indices: 82345--82563 Score: 368
Period size: 112 Copynumber: 1.9 Consensus size: 113
82335 CTTTGAGAAG
*
82345 AGACTTGTTCCACTTACTCTGAAGGGAATACCAAATCTTAAAGAAGAGAGACCTGTTCCACTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATACCAAATCTTAAAGAAGAGAGACCTGTTCCAATTAC
82410 TCTGAAGGGAATATCAGATCT-GAGAAGTTGATCCATTGAATCAAAGC
66 TCTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAATCAAAGC
* ** *
82457 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGATAGACCTGTTCCAATTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATACCAAATCTTAAAGAAGAGAGACCTGTTCCAATTAC
* *
82522 TCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAAT
66 TCTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAAT
82564 TGGGATCAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
112 81 0.82
113 18 0.18
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (113 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATACCAAATCTTAAAGAAGAGAGACCTGTTCCAATTAC
TCTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAATCAAAGC
Found at i:83690 original size:18 final size:19
Alignment explanation
Indices: 83641--83691 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 19
83631 ATCCTTTTAT
*
83641 TTTTTTTATTTTTTT--TC
1 TTTTTTCATTTTTTTAGTC
83658 TTTTTTCA-TTTTTTAGTC
1 TTTTTTCATTTTTTTAGTC
83676 -TTTTTCATTTTTTTAG
1 TTTTTTCATTTTTTTAG
83692 GCGAAATACT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.20
17 14 0.47
18 10 0.33
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTTCATTTTTTTAGTC
Found at i:90390 original size:24 final size:24
Alignment explanation
Indices: 90350--90395 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
90340 TTTGTTCCCA
*
90350 TTCTTTTTTAATCTCCTTATCCTG
1 TTCTTTTTTAATCTCCTCATCCTG
*
90374 TTCTTTTTT-GTCTTCCTCATCC
1 TTCTTTTTTAATC-TCCTCATCC
90396 AGATCAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.09, C:0.28, G:0.04, T:0.59
Consensus pattern (24 bp):
TTCTTTTTTAATCTCCTCATCCTG
Found at i:95811 original size:21 final size:21
Alignment explanation
Indices: 95773--95817 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
95763 TATTTATTTG
*
95773 TGGTATTTCATGTGGGGGAAA
1 TGGTATTTAATGTGGGGGAAA
*
95794 TGGTATTTAAT-TGAGGGGTAA
1 TGGTATTTAATGTG-GGGGAAA
95815 TGG
1 TGG
95818 AGAATGGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.24, C:0.02, G:0.38, T:0.36
Consensus pattern (21 bp):
TGGTATTTAATGTGGGGGAAA
Found at i:100745 original size:16 final size:17
Alignment explanation
Indices: 100724--100755 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
100714 TGAAACTTCT
100724 TTTTTTCA-CTTTTTTC
1 TTTTTTCAGCTTTTTTC
100740 TTTTTTCAGCTTTTTT
1 TTTTTTCAGCTTTTTT
100756 TATATTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTTCAGCTTTTTTC
Found at i:104286 original size:20 final size:20
Alignment explanation
Indices: 104261--104310 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
104251 ACAACCAACA
104261 AATTCGCAACACAGAATTAG
1 AATTCGCAACACAGAATTAG
104281 AATTCGCAACACAGAATTAG
1 AATTCGCAACACAGAATTAG
*
104301 AATTTGCAAC
1 AATTCGCAAC
104311 TCGAACATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (20 bp):
AATTCGCAACACAGAATTAG
Found at i:105116 original size:78 final size:78
Alignment explanation
Indices: 105022--105189 Score: 282
Period size: 78 Copynumber: 2.2 Consensus size: 78
105012 GAAATTGAAG
* *
105022 AATTCGAGTTACGAAATCCGAATTCGTGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTT
1 AATTCGCGTTACGAAATCCGAATTCGAGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTT
* *
105087 TACCTATATTGGT
66 TACCTATATCGGA
*
105100 AATTCGCGTTGCGAAATCCGAATTCGAGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTT
1 AATTCGCGTTACGAAATCCGAATTCGAGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTT
105165 TACCTATATCGGA
66 TACCTATATCGGA
*
105178 AAGTCGCGTTAC
1 AATTCGCGTTAC
105190 AAAAATTTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (78 bp):
AATTCGCGTTACGAAATCCGAATTCGAGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTT
TACCTATATCGGA
Found at i:105236 original size:20 final size:20
Alignment explanation
Indices: 105208--105281 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
105198 TCATGTTCGA
* *
105208 GTTGTGAATTCTAATTTTGT
1 GTTGCGAATTCTAAATTTGT
**
105228 GTTGCGAATTCTAAATTTAC
1 GTTGCGAATTCTAAATTTGT
* *
105248 GTTGCGAAATT-GAAATTCGT
1 GTTGCG-AATTCTAAATTTGT
105268 GTTGCGAATT-TAAA
1 GTTGCGAATTCTAAA
105282 ATCGCATTGC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 7 0.16
20 33 0.75
21 4 0.09
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTCTAAATTTGT
Found at i:105283 original size:20 final size:20
Alignment explanation
Indices: 105226--105297 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
105216 TTCTAATTTT
*
105226 GTGTTGCGAATTCTAAATTTAC
1 GTGTTGCGAATT-TAAAATT-C
* *
105248 --GTTGCGAAATTGAAATTC
1 GTGTTGCGAATTTAAAATTC
105266 GTGTTGCGAATTTAAAA-TC
1 GTGTTGCGAATTTAAAATTC
**
105285 GCATTGCGAATTT
1 GTGTTGCGAATTT
105298 GTTGGTTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
18 1 0.02
19 18 0.44
20 22 0.54
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
GTGTTGCGAATTTAAAATTC
Found at i:106090 original size:21 final size:23
Alignment explanation
Indices: 106056--106099 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
106046 ATATTTTTAA
* *
106056 AAACGTGAATAAAT-TAA-GTTT
1 AAACGTAAAAAAATGTAATGTTT
106077 AAACGTAAAAAAATGTAATGTTT
1 AAACGTAAAAAAATGTAATGTTT
106100 TAAAAGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (23 bp):
AAACGTAAAAAAATGTAATGTTT
Found at i:106514 original size:12 final size:12
Alignment explanation
Indices: 106492--106579 Score: 52
Period size: 11 Copynumber: 8.1 Consensus size: 12
106482 TACGATTAAG
106492 AAAATATATTATT
1 AAAA-ATATTATT
106505 AAAAATATTATT
1 AAAAATATTATT
106517 ----ATATT-TT
1 AAAAATATTATT
* *
106524 AATAATTTTA-T
1 AAAAATATTATT
106535 AAAAAT-TTATT
1 AAAAATATTATT
*
106546 TAAAATATTATT
1 AAAAATATTATT
* *
106558 --ATAT-TTATC
1 AAAAATATTATT
106567 AAAAATATTATT
1 AAAAATATTATT
106579 A
1 A
106580 TTGGGCGTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 21
0.67 0.08 0.24
Matches are distributed among these distances:
7 2 0.03
8 5 0.09
9 4 0.07
10 6 0.10
11 19 0.33
12 18 0.31
13 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (12 bp):
AAAAATATTATT
Found at i:106534 original size:19 final size:20
Alignment explanation
Indices: 106496--106580 Score: 82
Period size: 21 Copynumber: 4.2 Consensus size: 20
106486 ATTAAGAAAA
106496 TATATTATTAAAAATATTAT
1 TATATTATTAAAAATATTAT
* *
106516 TATATT-TTAATAATTTTAT
1 TATATTATTAAAAATATTAT
* * *
106535 AAAAATTTATTTAAAATATTAT
1 -TATA-TTATTAAAAATATTAT
*
106557 TATATTTATCAAAAATATTAT
1 TATA-TTATTAAAAATATTAT
106578 TAT
1 TAT
106581 TGGGCGTTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
19 11 0.22
20 8 0.16
21 22 0.43
22 10 0.20
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (20 bp):
TATATTATTAAAAATATTAT
Found at i:107353 original size:2 final size:2
Alignment explanation
Indices: 107346--107377 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
107336 TATGTATGCA
107346 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
107378 TGTTTCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108215 original size:3 final size:3
Alignment explanation
Indices: 108197--108231 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
108187 ACTAAGATTG
* *
108197 CTT CCT CTT GTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
108232 CTCTCGTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:113787 original size:24 final size:24
Alignment explanation
Indices: 113760--113850 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
113750 CATAATTCAA
*
113760 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
113784 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
113808 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
113831 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
113851 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:113830 original size:47 final size:48
Alignment explanation
Indices: 113760--113850 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
113750 CATAATTCAA
* * *
113760 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
113808 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
113851 TCAAATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:116184 original size:13 final size:13
Alignment explanation
Indices: 116166--116221 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
116156 ACGGTCAACA
116166 GGTCAACGGGTCG
1 GGTCAACGGGTCG
**
116179 GGTCAACTAGTCG
1 GGTCAACGGGTCG
*
116192 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
116205 GGTAAACGGGTCG
1 GGTCAACGGGTCG
116218 GGTC
1 GGTC
116222 GGGTCGGGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:118257 original size:35 final size:35
Alignment explanation
Indices: 118184--118258 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
118174 CGTCACGTCT
* **
118184 AGTAAGGCCCTGAGCACACAGCCGATGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
118219 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
118254 AGTAA
1 AGTAA
118259 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:118362 original size:24 final size:24
Alignment explanation
Indices: 118335--118416 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
118325 CATAATTCAA
*
118335 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
118359 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
118383 GTCAA-TACCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
*
118406 GTCAGGTATCA
1 GTCAAGTATCA
118417 TAACATAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.41
24 29 0.59
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:118398 original size:23 final size:24
Alignment explanation
Indices: 118347--118409 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 24
118337 CAAGTATCAT
* *
118347 ATCAGAATCCAGGTCATGTATCAG
1 ATCAGAATCCAGGTCATATACCAG
*
118371 ATCAGAATCCATGTCA-ATACCAG
1 ATCAGAATCCAGGTCATATACCAG
118394 ATCAGAATCCAGGTCA
1 ATCAGAATCCAGGTCA
118410 GGTATCATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAGAATCCAGGTCATATACCAG
Found at i:118410 original size:12 final size:12
Alignment explanation
Indices: 118348--118410 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
118338 AAGTATCATA
118348 TCAGAATCCAGG
1 TCAGAATCCAGG
* *
118360 TCATGTAT-CAGA
1 TCA-GAATCCAGG
*
118372 TCAGAATCCATG
1 TCAGAATCCAGG
*
118384 TC--AATACCAGA
1 TCAGAAT-CCAGG
118395 TCAGAATCCAGG
1 TCAGAATCCAGG
118407 TCAG
1 TCAG
118411 GTATCATAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
10 3 0.08
11 8 0.21
12 21 0.55
13 6 0.16
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (12 bp):
TCAGAATCCAGG
Found at i:120722 original size:13 final size:13
Alignment explanation
Indices: 120702--120737 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
120692 ATCAACGGGT
*
120702 CGGGTCGGGTTAA
1 CGGGTCGGGTAAA
*
120715 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
120728 CGGGTCGGGT
1 CGGGTCGGGT
120738 CGGGTTATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.47, T:0.22
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:123999 original size:46 final size:46
Alignment explanation
Indices: 123932--124023 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
123922 TTGAGTTTGG
123932 CTGGAAGGTGAAAAAACTCTGACCCTACTCTATCCGAGGATAATAA
1 CTGGAAGGTGAAAAAACTCTGACCCTACTCTATCCGAGGATAATAA
123978 CTGGAAGGTGAAAAAACTCTGACCCTACTCTATCCGAGGATAATAA
1 CTGGAAGGTGAAAAAACTCTGACCCTACTCTATCCGAGGATAATAA
124024 TGTAATTTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (46 bp):
CTGGAAGGTGAAAAAACTCTGACCCTACTCTATCCGAGGATAATAA
Done.