Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001282.1 Hibiscus syriacus cultivar Beakdansim tig00002516_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: 180784
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:281 original size:13 final size:13
Alignment explanation
Indices: 263--287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253 AACTGTTAAC
263 TAACTAATTGAAT
1 TAACTAATTGAAT
276 TAACTAATTGAA
1 TAACTAATTGAA
288 CTGTAATGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
TAACTAATTGAAT
Found at i:910 original size:19 final size:18
Alignment explanation
Indices: 851--961 Score: 107
Period size: 19 Copynumber: 5.8 Consensus size: 18
841 AGTAGGAAAA
* *
851 TCGCAATGCGATTACGTAT
1 TCGCATTGCGATTTC-TAT
*
870 TCGCATTGCGATTT-TCCT
1 TCGCATTGCGATTTCT-AT
888 TCGCATTGCGATTTCTACT
1 TCGCATTGCGATTTCTA-T
907 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTT-CT-AT
*
928 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTT-C-TAT
948 TCGCATTGCGATTT
1 TCGCATTGCGATTT
962 AGTAATCGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.01
18 15 0.19
19 25 0.32
20 22 0.28
21 15 0.19
22 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (18 bp):
TCGCATTGCGATTTCTAT
Found at i:910 original size:37 final size:38
Alignment explanation
Indices: 851--961 Score: 145
Period size: 37 Copynumber: 2.9 Consensus size: 38
841 AGTAGGAAAA
* *
851 TCGCAATGCGATTACGTATTCGCATTGCGATTTTCC-T
1 TCGCATTGCGATTTCGTATTCGCATTGCGATTTTCCAT
888 TCGCATTGCGATTTC-TACTTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCGTA-TTCGCATTGCGATTTTCC--AT
*
928 TCGCATTGCGATTTACGTAATCGCATTGCGATTT
1 TCGCATTGCGATTT-CGTATTCGCATTGCGATTT
962 AGTAATCGCA
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
36 2 0.03
37 31 0.48
40 15 0.23
41 15 0.23
42 2 0.03
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (38 bp):
TCGCATTGCGATTTCGTATTCGCATTGCGATTTTCCAT
Found at i:932 original size:21 final size:21
Alignment explanation
Indices: 769--961 Score: 127
Period size: 21 Copynumber: 9.7 Consensus size: 21
759 ATTCTGACTA
*
769 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCTAAT
* *
790 TCGCGTTGCGATTTTCCTAAA
1 TCGCATTGCGATTTTCCTAAT
* ** *
811 TCGCAATGCGA--TTAGTAAA
1 TCGCATTGCGATTTTCCTAAT
* ** **** *
830 TCGCAATGCGAAGTAGGAAAA
1 TCGCATTGCGATTTTCCTAAT
* * *
851 TCGCAATGCGA-TTACGT-AT
1 TCGCATTGCGATTTTCCTAAT
870 TCGCATTGCGATTTTCC---T
1 TCGCATTGCGATTTTCCTAAT
*
888 TCGCATTGCGA-TTT-CTACT
1 TCGCATTGCGATTTTCCTAAT
907 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
928 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
948 TCGCATTGCGATTT
1 TCGCATTGCGATTT
962 AGTAATCGCA
Statistics
Matches: 144, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.01
17 3 0.02
18 12 0.08
19 40 0.28
20 23 0.16
21 65 0.45
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:968 original size:19 final size:19
Alignment explanation
Indices: 809--971 Score: 93
Period size: 19 Copynumber: 8.4 Consensus size: 19
799 GATTTTCCTA
*
809 AATCGCAATGCGA-TTAGT
1 AATCGCATTGCGATTTAGT
* ** *
827 AAATCGCAATGCGAAGTAGGAA
1 -AATCGCATTGCGATTTA-G-T
*
849 AATCGCAATGCGA-TTACGT
1 AATCGCATTGCGATTTA-GT
*
868 ATTCGCATTGCGATTT--T
1 AATCGCATTGCGATTTAGT
** *
885 CCTTCGCATTGCGATTT-CT
1 -AATCGCATTGCGATTTAGT
* **
904 ACTTCGCATTGCGATTTTCCT
1 A-ATCGCATTGCGA-TTTAGT
925 AATTCGCATTGCGATTTACGT
1 AA-TCGCATTGCGATTTA-GT
946 AATCGCATTGCGATTTAGT
1 AATCGCATTGCGATTTAGT
965 AATCGCA
1 AATCGCA
972 ACGATTCTGA
Statistics
Matches: 121, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.01
18 15 0.12
19 46 0.38
20 28 0.23
21 31 0.26
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (19 bp):
AATCGCATTGCGATTTAGT
Found at i:977 original size:58 final size:57
Alignment explanation
Indices: 868--977 Score: 125
Period size: 58 Copynumber: 1.9 Consensus size: 57
858 GCGATTACGT
* * *
868 ATTCGCATTGCGATTTTCCTTCGCATTGCGATTTCTACTTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACCTTCGCATTGCGATTTCTACATCGCA-TACGATTTTCCTA
* *
926 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTAGTA-ATCGCA-ACGATT
1 ATTCGCATTGCGATTTACCT--TCGCATTGCGATTT-CTACATCGCATACGATT
978 CTGACTATCG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
58 23 0.52
60 19 0.43
61 2 0.05
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (57 bp):
ATTCGCATTGCGATTTACCTTCGCATTGCGATTTCTACATCGCATACGATTTTCCTA
Found at i:1831 original size:24 final size:24
Alignment explanation
Indices: 1804--1856 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1794 AGTATCGAAA
1804 TTGATCTTGGTCAATACCCGGACT
1 TTGATCTTGGTCAATACCCGGACT
* *
1828 TTGATCTTGGTCAATACGCGGATT
1 TTGATCTTGGTCAATACCCGGACT
1852 TTGAT
1 TTGAT
1857 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (24 bp):
TTGATCTTGGTCAATACCCGGACT
Found at i:4372 original size:19 final size:20
Alignment explanation
Indices: 4291--4373 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
4281 GGCATTCATT
*
4291 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
4311 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
4332 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
4352 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
4371 TGA
1 TGA
4374 AAATCACAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
19 8 0.16
20 27 0.55
21 13 0.27
22 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:4421 original size:32 final size:33
Alignment explanation
Indices: 4357--4482 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
4347 GGAAATGACT
*
4357 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
4390 ATCGCAATGTGAAATGAAAAT-GCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
4422 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
4455 ATCACAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
4483 CGAATTTAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
32 30 0.35
33 56 0.65
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4431 original size:65 final size:66
Alignment explanation
Indices: 4357--4482 Score: 200
Period size: 65 Copynumber: 1.9 Consensus size: 66
4347 GGAAATGACT
* * *
4357 ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGTGAAATGAAAAT-GCAACGAGAG
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAAAGCGAAATGAAAATCGCAACGAGAG
4421 A
66 A
* *
4422 ATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCACAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAAAGCGAAATGAAAATCGCAACG
4483 CGAATTTAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
65 49 0.89
66 6 0.11
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAAAGCGAAATGAAAATCGCAACGAGAG
A
Found at i:4485 original size:19 final size:18
Alignment explanation
Indices: 4337--4486 Score: 65
Period size: 19 Copynumber: 8.7 Consensus size: 18
4327 CTTAATGTCT
**
4337 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
4357 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
4376 ATCACAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
4390 ATCGCAATGTGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
4409 AT-GCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
4422 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
4441 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
4455 ATCACAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
4474 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
4487 TTTAGTTTCG
Statistics
Matches: 96, Mismatches: 17, Indels: 35
0.65 0.11 0.24
Matches are distributed among these distances:
13 5 0.05
14 20 0.21
15 4 0.04
16 6 0.06
17 4 0.04
18 9 0.09
19 39 0.41
20 9 0.09
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:4524 original size:19 final size:19
Alignment explanation
Indices: 4482--4554 Score: 77
Period size: 19 Copynumber: 4.1 Consensus size: 19
4472 AAATCGCAAC
*
4482 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
4501 GCGATTTTAGTTTCGTGTT
1 GCGATTTTAGTTTCGCGTT
4520 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
4534 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
4553 GC
1 GC
4555 AATTCTCTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 31 0.69
ACGTcount: A:0.11, C:0.16, G:0.26, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:4539 original size:33 final size:33
Alignment explanation
Indices: 4497--4586 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
4487 TTTAGTTTCG
* * * *
4497 CGTTGCGATTTT-AGTTTCGTGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCGTTGCAATTCTCT
4530 CGTTGCGATTTTCATTTCGCGTTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCAATTCTCT
*
4563 CGTTGCGA-TTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCGTTGC
4587 GATAGTCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
32 15 0.29
33 35 0.69
34 1 0.02
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCAATTCTCT
Found at i:4729 original size:13 final size:14
Alignment explanation
Indices: 4696--4731 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4686 CATCAATTAA
4696 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4710 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4724 -CAAATCAA
1 ACAAATCAA
4732 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6158 original size:42 final size:42
Alignment explanation
Indices: 6082--6204 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
6072 GTGAATCGGG
* ** *
6082 CTCTTGAATGGTGGGA-GGGACCTCTTC-AACAATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGACAGGGGC
*
6124 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
* * * * * *
6166 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGG
6205 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 61 0.91
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
Found at i:6670 original size:33 final size:33
Alignment explanation
Indices: 6624--6697 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
6614 AAAAATGACT
*
6624 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACACGAAATGAAAATCGCAACGAGAGA
6657 ATCGCAACACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACACGAAATGAAAATCGCAACGAGAGA
6690 ATCCGCAA
1 AT-CGCAA
6698 TGCGGAATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 34 0.87
34 5 0.13
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
ATCGCAACACGAAATGAAAATCGCAACGAGAGA
Found at i:6680 original size:19 final size:19
Alignment explanation
Indices: 6624--6683 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
6614 AAAAATGACT
*
6624 ATCGCAACGCGAAATGAAA
1 ATCGCAACACGAAATGAAA
*
6643 ATCGC-A-ACG--A-GAGA
1 ATCGCAACACGAAATGAAA
6657 ATCGCAACACGAAATGAAA
1 ATCGCAACACGAAATGAAA
6676 ATCGCAAC
1 ATCGCAAC
6684 GAGAGAATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 3 0.09
17 2 0.06
18 2 0.06
19 16 0.48
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (19 bp):
ATCGCAACACGAAATGAAA
Found at i:6737 original size:20 final size:19
Alignment explanation
Indices: 6708--6776 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 19
6698 TGCGGAATGA
6708 TTGCGATTTTTGATTTCGCG
1 TTGCGATTTTTG-TTTCGCG
*
6728 TTGCGTTTTTTGGTTTCGCG
1 TTGCGATTTTT-GTTTCGCG
*
6748 TTGCGATTTTCGTTTCGCG
1 TTGCGATTTTTGTTTCGCG
6767 TTGCGATTTT
1 TTGCGATTTT
6777 CATTCTCTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.40
20 26 0.58
21 1 0.02
ACGTcount: A:0.06, C:0.16, G:0.26, T:0.52
Consensus pattern (19 bp):
TTGCGATTTTTGTTTCGCG
Found at i:6762 original size:19 final size:19
Alignment explanation
Indices: 6708--6802 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 19
6698 TGCGGAATGA
*
6708 TTGCGATTTTTGATTTCGCG
1 TTGCGATTTTCG-TTTCGCG
* *
6728 TTGCGTTTTTTGGTTTCGCG
1 TTGCG-ATTTTCGTTTCGCG
6748 TTGCGATTTTCGTTTCGCG
1 TTGCGATTTTCGTTTCGCG
* * *
6767 TTGCGATTTTCATTCTCTCA
1 TTGCGATTTTCGTT-TCGCG
*
6787 TTGCGATTTTCATTTC
1 TTGCGATTTTCGTTTC
6803 AACCAAAAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
19 27 0.41
20 34 0.52
21 5 0.08
ACGTcount: A:0.08, C:0.19, G:0.21, T:0.52
Consensus pattern (19 bp):
TTGCGATTTTCGTTTCGCG
Found at i:6791 original size:39 final size:39
Alignment explanation
Indices: 6707--6802 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 39
6697 ATGCGGAATG
* * **
6707 ATTGCGATTTTTGATTTCGCGTTGCGTTTTTTGGTTTCGC
1 ATTGCGATTTTCG-TTTCGCGTTGCGTATTTTCATTTCGC
* *
6747 GTTGCGATTTTCGTTTCGCGTTGCG-ATTTTCATTCTCTC
1 ATTGCGATTTTCGTTTCGCGTTGCGTATTTTCATT-TCGC
*
6786 ATTGCGATTTTCATTTC
1 ATTGCGATTTTCGTTTC
6803 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 6 0.13
39 30 0.64
40 11 0.23
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (39 bp):
ATTGCGATTTTCGTTTCGCGTTGCGTATTTTCATTTCGC
Found at i:6990 original size:94 final size:94
Alignment explanation
Indices: 6884--7342 Score: 687
Period size: 94 Copynumber: 5.0 Consensus size: 94
6874 ATGGATTGCA
* * * *
6884 TTAC-TTCAACCAAATGACAAAACAAAGAAAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
6948 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
6977 TTACTTTCAACCAAAGGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
7042 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
7071 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
7136 TTAGCAGAATTGGTAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
7165 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
7230 TT------A--GGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
7251 TTAC-TTCAACCAAAAGACAACA-AAAGATAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
7310 TTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
7339 TTAC
1 TTAC
7343 CTCGTTGCGT
Statistics
Matches: 343, Mismatches: 14, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
80 11 0.03
84 26 0.08
85 17 0.05
86 21 0.06
88 23 0.07
93 4 0.01
94 241 0.70
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:9007 original size:19 final size:19
Alignment explanation
Indices: 8943--9079 Score: 202
Period size: 19 Copynumber: 7.1 Consensus size: 19
8933 TCTTTTGGTT
*
8943 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
8962 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
8982 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
9002 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
9021 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
9040 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
9059 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
9078 GA
1 GA
9080 TTTTGGTTTC
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 75 0.69
20 31 0.29
21 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:9123 original size:33 final size:33
Alignment explanation
Indices: 9075--9163 Score: 119
Period size: 33 Copynumber: 2.8 Consensus size: 33
9065 AAAATCGCAA
**
9075 TGCGATTTTGGTTTCGCGTTGCGATTATATCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATATCGT
* *
9108 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATATCGT
*
9141 TGCGA-TTTCATTTCTCGTT-CGAT
1 TGCGATTTTCATTTCGCGTTGCGAT
9164 AGTCATTTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 4 0.08
32 13 0.25
33 34 0.67
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATATCGT
Found at i:9129 original size:19 final size:19
Alignment explanation
Indices: 9105--9205 Score: 63
Period size: 18 Copynumber: 5.6 Consensus size: 19
9095 GCGATTATAT
9105 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
9124 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
9138 CGTTGCGA-TTTCATTTCT
1 CGTTGCGATTTTCATTTCG
** *
9156 CGTT-CGATAGTCATTTTG
1 CGTTGCGATTTTCATTTCG
* * *
9174 TGTTGCGATTTTCGTTTTCA
1 CGTTGCGATTTTC-ATTTCG
*
9194 TGTTGCGATTTT
1 CGTTGCGATTTT
9206 AAGTTTAGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
17 6 0.09
18 16 0.25
19 14 0.22
20 15 0.23
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.50
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:9761 original size:21 final size:20
Alignment explanation
Indices: 9737--9826 Score: 117
Period size: 20 Copynumber: 4.4 Consensus size: 20
9727 GTCGCTATGT
*
9737 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCG-ATTACGA
*
9758 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGA
* *
9778 AAATCGCAAAGCGAATTAGGA
1 AAATCGCAATGCG-ATTACGA
*
9799 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGA
9819 AAATCGCA
1 AAATCGCA
9827 TTCTACTTCG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
20 30 0.50
21 30 0.50
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (20 bp):
AAATCGCAATGCGATTACGA
Found at i:9781 original size:20 final size:21
Alignment explanation
Indices: 9735--9826 Score: 125
Period size: 21 Copynumber: 4.5 Consensus size: 21
9725 ATGTCGCTAT
*
9735 GTAAATCGCAATGCGAATTAG
1 GTAAATCGCAATGCGAATTAC
*
9756 GAAAATCGCAATGCG-ATTAC
1 GTAAATCGCAATGCGAATTAC
* *
9776 GTAAATCGCAAAGCGAATTAG
1 GTAAATCGCAATGCGAATTAC
*
9797 GAAAATCGCAATGCG-ATTAC
1 GTAAATCGCAATGCGAATTAC
9817 GTAAATCGCA
1 GTAAATCGCA
9827 TTCTACTTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
20 30 0.49
21 31 0.51
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (21 bp):
GTAAATCGCAATGCGAATTAC
Found at i:9792 original size:41 final size:41
Alignment explanation
Indices: 9735--9826 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
9725 ATGTCGCTAT
*
9735 GTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTAC
1 GTAAATCGCAAAGCGAATTAGGAAAATCGCAATGCGATTAC
9776 GTAAATCGCAAAGCGAATTAGGAAAATCGCAATGCGATTAC
1 GTAAATCGCAAAGCGAATTAGGAAAATCGCAATGCGATTAC
9817 GTAAATCGCA
1 GTAAATCGCA
9827 TTCTACTTCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (41 bp):
GTAAATCGCAAAGCGAATTAGGAAAATCGCAATGCGATTAC
Found at i:13212 original size:30 final size:30
Alignment explanation
Indices: 13176--13245 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
13166 ATCTTGTGGT
*
13176 AAAAACTGTATCGAATGACAT-TACATGAGC
1 AAAAACTGCATCGAATGACATATA-ATGAGC
*
13206 AAAAACTGCATCGAATGATATATAATGAGC
1 AAAAACTGCATCGAATGACATATAATGAGC
13236 AAAAACTGCA
1 AAAAACTGCA
13246 CATCTCAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (30 bp):
AAAAACTGCATCGAATGACATATAATGAGC
Found at i:19974 original size:33 final size:33
Alignment explanation
Indices: 19937--20001 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
19927 AATTCTTCCA
*
19937 AAAAGAACGACCACGTCACTTGATCTTTAGATG
1 AAAAGAACGACCACCTCACTTGATCTTTAGATG
*
19970 AAAAGAACGGCCACCTCACTTGATCTTTAGAT
1 AAAAGAACGACCACCTCACTTGATCTTTAGAT
20002 ACTCTCATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (33 bp):
AAAAGAACGACCACCTCACTTGATCTTTAGATG
Found at i:24046 original size:41 final size:41
Alignment explanation
Indices: 23983--24292 Score: 300
Period size: 41 Copynumber: 7.5 Consensus size: 41
23973 ACGAGAGTGG
* * * *
23983 CGTTTATATAAAAATGGCACTAAAGTACGAGTCTATAGCGA
1 CGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGA
* * * *
24024 AGTTTGTATAAAAACGCCACTAAAGTACGAGACTATAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGA
* * * *
24065 CGTTTGTATAAAAACGCCACCAAAGTATGAGTCTTTAGAGT
1 CGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGA
* * *
24106 CGTTTGTACAAAAATGCCACTAAAGTATGAGTCTTTAGC-A
1 CGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGA
* * * *
24146 GCGTTTGTATAAAAAACGCAACTAAAGTACGAGTCTATAACGT
1 -CGTTTGTAT-AAAAACGCCACTAAAGTACGAGTCTTTAGCGA
* ** * * *
24189 CGTTTTTATAAAAATACCACTAAAGTAC-ATTCTTTAGTGG
1 CGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGA
* * * *
24229 CATTTGTATAAAAACTCCACTAAAGTACGAGTATTTAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGA
* *
24270 CGTTTGTTCTAAAAACACCACTA
1 CGTTTG-TATAAAAACGCCACTA
24293 TAAACCCATC
Statistics
Matches: 220, Mismatches: 44, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
40 31 0.14
41 142 0.65
42 47 0.21
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (41 bp):
CGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGA
Found at i:24098 original size:82 final size:82
Alignment explanation
Indices: 23981--24292 Score: 338
Period size: 82 Copynumber: 3.8 Consensus size: 82
23971 GCACGAGAGT
* * * ** *
23981 GGCGTTTATATAAAAATGGCACTAAAGTACGAGTCTATAGCGAAGTTTGTATAAAAACGCCACTA
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGTCGTTTGTATAAAAACACCACTA
* *
24046 AAGTACGAGACTATAGC
66 AAGTACGAGTCTTTAGC
* * * * * **
24063 GGCGTTTGTATAAAAACGCCACCAAAGTATGAGTCTTTAGAGTCGTTTGTACAAAAATGCCACTA
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGTCGTTTGTATAAAAACACCACTA
*
24128 AAGTATGAGTCTTTAGC
66 AAGTACGAGTCTTTAGC
* * * * *
24145 AGCGTTTGTATAAAAAACGCAACTAAAGTACGAGTCTATAACGTCGTTTTTATAAAAATACCACT
1 GGCGTTTGTAT-AAAAACGCCACTAAAGTACGAGTCTATAGCGTCGTTTGTATAAAAACACCACT
* *
24210 AAAGTAC-ATTCTTTAGT
65 AAAGTACGAGTCTTTAGC
* * * * * *
24227 GGCATTTGTATAAAAACTCCACTAAAGTACGAGTATTTAGCGGCGTTTGTTCTAAAAACACCACT
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGTCGTTTG-TATAAAAACACCACT
24292 A
65 A
24293 TAAACCCATC
Statistics
Matches: 190, Mismatches: 38, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
81 31 0.16
82 109 0.57
83 50 0.26
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (82 bp):
GGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGTCGTTTGTATAAAAACACCACTA
AAGTACGAGTCTTTAGC
Found at i:24138 original size:123 final size:122
Alignment explanation
Indices: 23981--24292 Score: 358
Period size: 123 Copynumber: 2.5 Consensus size: 122
23971 GCACGAGAGT
* * * *
23981 GGCGTTTATATAAAAATGGCACTAAAGTACGAGTCTATAGCGAAGTTTGTATAAAAACGCCACTA
1 GGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAACGCCACTA
* * *
24046 AAGTACGAGACTATAGCGGCGTTTGTATAAAAACGCCACCAAAGTATGAGTCTTTAGA
66 AAGTACGAGACTATAACGGCGTTTGTATAAAAACACCACCAAAGTA-CAGTCTTTAGA
* * * *
24104 GTCGTTTGTACAAAAATGCCACTAAAGTATGAGTCTTTAGC-AGCGTTTGTATAAAAAACGCAAC
1 GGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGA-CGTTTGTAT-AAAAACGCCAC
* * * * * * *
24168 TAAAGTACGAGTCTATAACGTCGTTTTTATAAAAATACCACTAAAGTACATTCTTTAGT
64 TAAAGTACGAGACTATAACGGCGTTTGTATAAAAACACCACCAAAGTACAGTCTTTAGA
* * * * *
24227 GGCATTTGTATAAAAACT-CCACTAAAGTACGAGTATTTAGCGGCGTTTGTTCTAAAAACACCAC
1 GGCGTTTGTATAAAAA-TGCCACTAAAGTACGAGTCTTTAGCGACGTTTG-TATAAAAACGCCAC
24291 TA
64 TA
24293 TAAACCCATC
Statistics
Matches: 157, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
122 1 0.01
123 102 0.65
124 54 0.34
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (122 bp):
GGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAACGCCACTA
AAGTACGAGACTATAACGGCGTTTGTATAAAAACACCACCAAAGTACAGTCTTTAGA
Found at i:25435 original size:2 final size:2
Alignment explanation
Indices: 25426--25460 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
25416 TTCTAGGGTT
25426 TA TA -A 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
25461 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25465 original size:2 final size:2
Alignment explanation
Indices: 25460--25497 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25450 ATATATATAT
25460 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25498 GGGAAGGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25595 original size:22 final size:22
Alignment explanation
Indices: 25567--25613 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
25557 CACGCGCAGC
25567 AGCTAATATAATGATATACATA
1 AGCTAATATAATGATATACATA
25589 AGCTAATATAATGATATACATA
1 AGCTAATATAATGATATACATA
25611 AGC
1 AGC
25614 ATCACGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (22 bp):
AGCTAATATAATGATATACATA
Found at i:26006 original size:7 final size:7
Alignment explanation
Indices: 25994--26133 Score: 100
Period size: 7 Copynumber: 19.9 Consensus size: 7
25984 AATTGTGTGA
25994 TAGGGTT
1 TAGGGTT
26001 TAGGGTT
1 TAGGGTT
26008 TAGGGTT
1 TAGGGTT
26015 TAGGGTT
1 TAGGGTT
**
26022 TAGTATT
1 TAGGGTT
26029 TAGGGTT
1 TAGGGTT
26036 TAGGGTT
1 TAGGGTT
*
26043 TAGAGTT
1 TAGGGTT
**
26050 TAGTATT
1 TAGGGTT
26057 TAGGGTT
1 TAGGGTT
**
26064 TAAGATTT
1 T-AGGGTT
*
26072 TATGGTT
1 TAGGGTT
**
26079 TAGCATT
1 TAGGGTT
**
26086 TAGGGCC
1 TAGGGTT
**
26093 TAAAGTT
1 TAGGGTT
*
26100 TAGAGTT
1 TAGGGTT
*
26107 TATGGTT
1 TAGGGTT
**
26114 TATAGTT
1 TAGGGTT
*
26121 TAGGTTT
1 TAGGGTT
26128 TAGGGT
1 TAGGGT
26134 CTAAGTTATG
Statistics
Matches: 99, Mismatches: 33, Indels: 2
0.74 0.25 0.01
Matches are distributed among these distances:
7 94 0.95
8 5 0.05
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (7 bp):
TAGGGTT
Found at i:26039 original size:28 final size:28
Alignment explanation
Indices: 25999--26090 Score: 130
Period size: 28 Copynumber: 3.2 Consensus size: 28
25989 TGTGATAGGG
25999 TTTAGGGTTTAGGGTTTAGGGTTTAGTA
1 TTTAGGGTTTAGGGTTTAGGGTTTAGTA
*
26027 TTTAGGGTTTAGGGTTTAGAGTTTAGTA
1 TTTAGGGTTTAGGGTTTAGGGTTTAGTA
** * *
26055 TTTAGGGTTTAAGATTTTATGGTTTAGCA
1 TTTAGGGTTT-AGGGTTTAGGGTTTAGTA
26084 TTTAGGG
1 TTTAGGG
26091 CCTAAAGTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 37 0.65
29 20 0.35
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.47
Consensus pattern (28 bp):
TTTAGGGTTTAGGGTTTAGGGTTTAGTA
Found at i:26683 original size:59 final size:59
Alignment explanation
Indices: 26552--26683 Score: 128
Period size: 59 Copynumber: 2.2 Consensus size: 59
26542 AAATGAATAG
* ** *
26552 TTGAGTGACA-ATTTTTTAACTTTTAATAGTCGATGACTCAACAAAACGTCGCCCTATAA
1 TTGAGTGA-ATATTTTATAACTTTTAATAGTCGATGACTCAACAAAACAACACCCTATAA
* * * *
26611 TAAGAG-GACTATTTTATAATTTTTAATAGTCAAGA-GACTCAACAAAA-AACATCCTATAA
1 T-TGAGTGAATATTTTATAACTTTTAATAGTC--GATGACTCAACAAAACAACACCCTATAA
26670 TTGAGTGAATATTT
1 TTGAGTGAATATTT
26684 ATGTACTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
58 3 0.05
59 38 0.66
60 15 0.26
61 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (59 bp):
TTGAGTGAATATTTTATAACTTTTAATAGTCGATGACTCAACAAAACAACACCCTATAA
Found at i:27456 original size:16 final size:17
Alignment explanation
Indices: 27435--27466 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27425 TTACTATTCA
27435 CGTGAATAGT-GAATTT
1 CGTGAATAGTGGAATTT
27451 CGTGAATAGTGGAATT
1 CGTGAATAGTGGAATT
27467 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGGAATTT
Found at i:35092 original size:31 final size:31
Alignment explanation
Indices: 35045--35103 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
35035 ATTTTGAACT
* *
35045 TTTTCGAGTTCGAGTCGAGTTTCAATAATATA
1 TTTTCGAGTTCAAGTCGAGCTT-AATAATATA
35077 TTTT-GAGTTCAAGTCGAGCTTAATAAT
1 TTTTCGAGTTCAAGTCGAGCTTAATAAT
35104 TTTTAGCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 15 0.60
32 4 0.16
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (31 bp):
TTTTCGAGTTCAAGTCGAGCTTAATAATATA
Found at i:39150 original size:21 final size:21
Alignment explanation
Indices: 39120--39169 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
39110 AAAGCAATTT
39120 TACG-AAAAAATCATTTTTAA
1 TACGAAAAAAATCATTTTTAA
39140 TACGAAAAAAATCATTTTTAA
1 TACGAAAAAAATCATTTTTAA
*
39161 GAC-AAAAAA
1 TACGAAAAAA
39170 TTGGTATGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.28
Consensus pattern (21 bp):
TACGAAAAAAATCATTTTTAA
Found at i:42485 original size:138 final size:138
Alignment explanation
Indices: 42228--42486 Score: 306
Period size: 138 Copynumber: 1.9 Consensus size: 138
42218 GGGTCAATCT
* * * *
42228 AGATAATTTAAAGACAACGCGGTTCCTTCGTGTTGAGGAAGTCTGGCTATCTGATGATGACACTG
1 AGATAATTTAAAGACAACACAGTTCCTTCGTGTTGAGGAAGTCTGACTATCTGAGGATGACACTG
* * * * * *
42293 CTCCTTTGTGTTGAGGAGATCTGGTCGTTAGATGACTTGTTCCTTTGTGTTGAGGACATCTAGTC
66 CTCCTTTGTGTTAAGGAGATCTGGTCGTGAGACGACCTATTCCTTTGTGGTGAGGACATCTAGTC
42358 GTATTTGA
131 GTATTTGA
** * * * * * *
42366 AGATAATTTGGAGACAACACAGTTCTTTCGTTTTGAGGAAGTTTGATTGTTTGAGGATGACACTG
1 AGATAATTTAAAGACAACACAGTTCCTTCGTGTTGAGGAAGTCTGACTATCTGAGGATGACACTG
* *
42431 CTCCTTTGTGTTAAGGAGATCTGGTCG-GGGACGACACTATT-CTTTCTTGGTGAGGA
66 CTCCTTTGTGTTAAGGAGATCTGGTCGTGAGACGAC-CTATTCCTTT-GTGGTGAGGA
42487 TGTCTAGCTG
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
137 9 0.09
138 90 0.91
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.35
Consensus pattern (138 bp):
AGATAATTTAAAGACAACACAGTTCCTTCGTGTTGAGGAAGTCTGACTATCTGAGGATGACACTG
CTCCTTTGTGTTAAGGAGATCTGGTCGTGAGACGACCTATTCCTTTGTGGTGAGGACATCTAGTC
GTATTTGA
Found at i:43075 original size:71 final size:74
Alignment explanation
Indices: 42942--43156 Score: 226
Period size: 73 Copynumber: 2.9 Consensus size: 74
42932 AACATTTCAA
* * * * *
42942 AATTTGTGTTTCAAGGGAAAATTGTCTCAAGCGAGATGAAA-TTTATTTTTAAGA-AGAACAATC
1 AATTT-TGTTTCAA-GAAAAATTGTCTCAAACAAGATGAAACTTT-GTTTCAAGAGA-AACAATC
*
43005 TCAAATGTTG-TC
62 TCAAATGTAGATC
* *
43017 AA-TTT-TTTGAAGAAAAATTGTCTCAAACAAGATGAAACTGTGTTTCAAGAGAAACAATCTCAA
1 AATTTTGTTTCAAGAAAAATTGTCTCAAACAAGATGAAACTTTGTTTCAAGAGAAACAATCTCAA
*
43080 GTG-AGATC
66 ATGTAGATC
* ** **
43088 AATTTTGTTTCAAGAAAAACTGTCTCAAACAAGACAAAACTTTGTTTGTAGAGAAACAATCTCAA
1 AATTTTGTTTCAAGAAAAATTGTCTCAAACAAGATGAAACTTTGTTTCAAGAGAAACAATCTCAA
43153 ATGT
66 ATGT
43157 GACATACAAT
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
70 1 0.01
71 47 0.40
72 11 0.09
73 54 0.46
74 2 0.02
75 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (74 bp):
AATTTTGTTTCAAGAAAAATTGTCTCAAACAAGATGAAACTTTGTTTCAAGAGAAACAATCTCAA
ATGTAGATC
Found at i:43079 original size:37 final size:36
Alignment explanation
Indices: 43037--43153 Score: 108
Period size: 37 Copynumber: 3.2 Consensus size: 36
43027 AGAAAAATTG
*
43037 TCTCAAACAAGATGAAACTGTGTTTCAAGAGAAACAA
1 TCTCAAACAAGAT-AAACTTTGTTTCAAGAGAAACAA
*** * * * **
43074 TCTCAAGTGAGATCAATTTTGTTTCAAGAAAAACTG
1 TCTCAAACAAGATAAACTTTGTTTCAAGAGAAACAA
* **
43110 TCTCAAACAAGACAAAACTTTGTTTGTAGAGAAACAA
1 TCTCAAACAAGA-TAAACTTTGTTTCAAGAGAAACAA
43147 TCTCAAA
1 TCTCAAA
43154 TGTGACATAC
Statistics
Matches: 59, Mismatches: 20, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
36 26 0.44
37 33 0.56
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (36 bp):
TCTCAAACAAGATAAACTTTGTTTCAAGAGAAACAA
Found at i:44713 original size:44 final size:44
Alignment explanation
Indices: 44650--44774 Score: 214
Period size: 44 Copynumber: 2.8 Consensus size: 44
44640 GTATTCCTGT
*
44650 ATGATATGGGCCTTCAAAAATACCTCAACACTTATCAGTTCTGG
1 ATGATATGGGCCTTCAAAAATGCCTCAACACTTATCAGTTCTGG
*
44694 ATGATATGGGCCTTCAAAAATGCCTCAACACTTATCAGTTCTTG
1 ATGATATGGGCCTTCAAAAATGCCTCAACACTTATCAGTTCTGG
* *
44738 ATGATATGGGCCTTCAAAAATGTCACAACACTTATCA
1 ATGATATGGGCCTTCAAAAATGCCTCAACACTTATCA
44775 TTTATTTGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 77 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (44 bp):
ATGATATGGGCCTTCAAAAATGCCTCAACACTTATCAGTTCTGG
Found at i:50867 original size:3 final size:3
Alignment explanation
Indices: 50855--50890 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
50845 TAAAATTTAG
50855 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
50891 TCGGACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:50979 original size:45 final size:46
Alignment explanation
Indices: 50914--51041 Score: 141
Period size: 50 Copynumber: 2.7 Consensus size: 46
50904 GTTGTCTATA
50914 AGTGTAAGTATGTGTTAAGTGTTATATTTTTTTATTCACTTATACC
1 AGTGTAAGTATGTGTTAAGTGTTATATTTTTTTATTCACTTATACC
* * * **
50960 AGTGT-AGTATGAGTTAAGTGTTACACTTGTTTATTTTATTCATTTATATT
1 AGTGTAAGTATGTGTTAAGTGTT--A--TATTT-TTTTATTCACTTATACC
* *
51010 GGTGTAAGTATGTGTTAAGTATTATATTTTTT
1 AGTGTAAGTATGTGTTAAGTGTTATATTTTTT
51042 GTAGTATGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
45 16 0.24
46 8 0.12
47 5 0.07
49 5 0.07
50 18 0.27
51 15 0.22
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (46 bp):
AGTGTAAGTATGTGTTAAGTGTTATATTTTTTTATTCACTTATACC
Found at i:53477 original size:19 final size:19
Alignment explanation
Indices: 53453--53503 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
53443 AAAAATATTC
53453 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
53472 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
53491 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
53504 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:53481 original size:66 final size:65
Alignment explanation
Indices: 53353--53505 Score: 209
Period size: 66 Copynumber: 2.4 Consensus size: 65
53343 TGCACCAAGT
* ***
53353 ATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTGTGCATCG
1 ATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGAGTGCATCG
* **
53417 ATGCATCAAATGCATTCGATGTTTTGAAAAATATTCAGAGTGCATCGATGCATGGAGAGTGCATC
1 ATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATGGAGAGTGCATC
53482 G
65 G
* *
53483 GTGCATGGAATGCATTCGATGTT
1 ATGCATGAAATGCATTCGATGTT
53506 CAATTAATTC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 20 0.26
65 13 0.17
66 44 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
ATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGAGTGCATCG
Found at i:62005 original size:64 final size:64
Alignment explanation
Indices: 61952--62114 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
61942 CGGTGCACCA
*
61952 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
62016 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
62081 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
62115 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:62086 original size:19 final size:19
Alignment explanation
Indices: 62062--62112 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
62052 GAAAATATTC
62062 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
62081 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
62100 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
62113 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:62154 original size:65 final size:65
Alignment explanation
Indices: 61956--62163 Score: 207
Period size: 65 Copynumber: 3.2 Consensus size: 65
61946 GCACCAAGTG
* * ** *
61956 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
62019 G-
64 GA
* * *
62020 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
62083 A
65 A
* *
62084 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
62146 CTGA
62 CTGA
62150 TGCATCGGTGCATG
1 TGCATCGGTGCATG
62164 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.06
64 51 0.41
65 60 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:62683 original size:15 final size:16
Alignment explanation
Indices: 62658--62687 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
62648 TATTTCATTA
62658 ATTTCAAAATTTTAAT
1 ATTTCAAAATTTTAAT
62674 ATTT-AAAATTTTAA
1 ATTTCAAAATTTTAA
62688 ATTAGATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTCAAAATTTTAAT
Found at i:65165 original size:3 final size:3
Alignment explanation
Indices: 65157--65243 Score: 52
Period size: 3 Copynumber: 28.3 Consensus size: 3
65147 TGATTGCTTT
* *
65157 GAA GAA GAA GAA AAA GAAA GAA GGAA GAA GAA GAA -ATA -AA AAA GAA
1 GAA GAA GAA GAA GAA G-AA GAA -GAA GAA GAA GAA GA-A GAA GAA GAA
* * * * **
65203 GGAA GAA GAA GAA AAA GCA TAA GAG GTG GAA GAA GAA GAA G
1 -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
65244 TTGCCGCGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
2 2 0.03
3 55 0.83
4 9 0.14
ACGTcount: A:0.64, C:0.01, G:0.31, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:65205 original size:24 final size:23
Alignment explanation
Indices: 65157--65218 Score: 106
Period size: 24 Copynumber: 2.7 Consensus size: 23
65147 TGATTGCTTT
*
65157 GAAGAAGAAGAAAAAGAAAGAAG
1 GAAGAAGAAGAAAAAAAAAGAAG
65180 GAAGAAGAAGAAATAAAAAAGAAG
1 GAAGAAGAAGAAA-AAAAAAGAAG
65204 GAAGAAGAAGAAAAA
1 GAAGAAGAAGAAAAA
65219 GCATAAGAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
23 15 0.41
24 22 0.59
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (23 bp):
GAAGAAGAAGAAAAAAAAAGAAG
Found at i:65233 original size:27 final size:24
Alignment explanation
Indices: 65157--65242 Score: 104
Period size: 24 Copynumber: 3.5 Consensus size: 24
65147 TGATTGCTTT
65157 GAAGAAGAAGAAAAAGAAAGA-AG
1 GAAGAAGAAGAAAAAGAAAGAGAG
*
65180 GAAGAAGAAGAAATAAAAAAGA-AG
1 GAAGAAGAAGAAA-AAGAAAGAGAG
*
65204 GAAGAAGAAGAAAAAGCATAAGAGGTG
1 GAAGAAGAAGAAAAAG-A-AAGA-GAG
65231 GAAGAAGAAGAA
1 GAAGAAGAAGAA
65243 GTTGCCGCGT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.27
24 23 0.42
25 4 0.07
27 13 0.24
ACGTcount: A:0.65, C:0.01, G:0.30, T:0.03
Consensus pattern (24 bp):
GAAGAAGAAGAAAAAGAAAGAGAG
Found at i:71116 original size:54 final size:54
Alignment explanation
Indices: 71034--71153 Score: 179
Period size: 54 Copynumber: 2.2 Consensus size: 54
71024 AAATGACTAG
*
71034 GGGTATCGGTACCCGTTAGGCATTCTGTTTTTCTCAG-AGCCAAAATTGACATAA
1 GGGTATCGGTACCCATTAGGCATTCTGTTTTTCTC-GCAGCCAAAATTGACATAA
* * * *
71088 GGGTATCGGTATCCATTGGGCATTCTGTTTTTCTCGCAGCCAAAATTGGCATAG
1 GGGTATCGGTACCCATTAGGCATTCTGTTTTTCTCGCAGCCAAAATTGACATAA
71142 GGGTATCGGTAC
1 GGGTATCGGTAC
71154 ACCCTATGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.02
54 58 0.98
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (54 bp):
GGGTATCGGTACCCATTAGGCATTCTGTTTTTCTCGCAGCCAAAATTGACATAA
Found at i:71823 original size:21 final size:22
Alignment explanation
Indices: 71789--71830 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
71779 AAATATCATT
71789 CAAACCAAAATAAACATCCAAG
1 CAAACCAAAATAAACATCCAAG
*
71811 CAAA-CAAATTAAACATCCAA
1 CAAACCAAAATAAACATCCAA
71831 ATTCCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.60, C:0.26, G:0.02, T:0.12
Consensus pattern (22 bp):
CAAACCAAAATAAACATCCAAG
Found at i:73326 original size:13 final size:13
Alignment explanation
Indices: 73308--73341 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
73298 AATGGGAAAT
*
73308 TTTGAAAACTATG
1 TTTGAAAACAATG
73321 TTTGAAAACAATG
1 TTTGAAAACAATG
73334 TTTGAAAA
1 TTTGAAAA
73342 TCAGTATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:73882 original size:21 final size:22
Alignment explanation
Indices: 73828--73887 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
73818 GTACCCTTAT
73828 AGGGGTATCGATACACATTCAA
1 AGGGGTATCGATACACATTCAA
* * *
73850 AGAGGTTATCGATACACGTT-GA
1 AG-GGGTATCGATACACATTCAA
73872 AGGGGTATCGATACAC
1 AGGGGTATCGATACAC
73888 TCTGCACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 13 0.39
22 5 0.15
23 15 0.45
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (22 bp):
AGGGGTATCGATACACATTCAA
Found at i:76271 original size:85 final size:85
Alignment explanation
Indices: 76182--76370 Score: 283
Period size: 85 Copynumber: 2.2 Consensus size: 85
76172 TTATGATGTT
*
76182 CATTGAGTGTCATTGAATCCCCCATCATAAAT-TAAG-ATGACACACATTTGTGTGTCATAAATT
1 CATTGAGTGTCATTGAAGCCCCCATCATAAATCT--GCATGACACACATTTGTGTGTCATAAATT
76245 TATGACACACATGTATGACTTA
64 TATGACACACATGTATGACTTA
* * * *
76267 CATTGAGCGTCATTAAAGCCCCCATCATAAATCTGCTTGACATACATTTGTGTGTCATAAATTTA
1 CATTGAGTGTCATTGAAGCCCCCATCATAAATCTGCATGACACACATTTGTGTGTCATAAATTTA
*
76332 TGACACGCATGTATGACTTA
66 TGACACACATGTATGACTTA
*
76352 CATTGCGTGTCATTGAAGC
1 CATTGAGTGTCATTGAAGC
76371 ACATGTCATT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 1 0.01
85 91 0.98
86 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (85 bp):
CATTGAGTGTCATTGAAGCCCCCATCATAAATCTGCATGACACACATTTGTGTGTCATAAATTTA
TGACACACATGTATGACTTA
Found at i:76405 original size:85 final size:84
Alignment explanation
Indices: 76204--76407 Score: 221
Period size: 85 Copynumber: 2.4 Consensus size: 84
76194 TTGAATCCCC
* *
76204 CATCATAAATTAAGATGACACACATTTGTGTGTCATAAATTTATGACACACATGTATGACTTACA
1 CATCATAAA-AAAGACGACACACATTTGTGTGTCATAAATTTATGACACACATGTATGACTTACA
* *
76269 TTGAGCGTCATTAAAGCCCC
65 TTGAGCGTCATTAAAGCACA
*** * *
76289 CATCATAAATCTG-CTTGACATACATTTGTGTGTCATAAATTTATGACACGCATGTATGACTTAC
1 CATCATAAAAAAGAC--GACACACATTTGTGTGTCATAAATTTATGACACACATGTATGACTTAC
* * *
76353 ATTGCGTGTCATTGAAGCACA
64 ATTGAGCGTCATTAAAGCACA
** * *
76374 TGTCATTAAAAAAGACGACACACGTTCGTGTGTC
1 CATCA-TAAAAAAGACGACACACATTTGTGTGTC
76408 GTGATTGTAT
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
84 2 0.02
85 89 0.92
86 5 0.05
87 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (84 bp):
CATCATAAAAAAGACGACACACATTTGTGTGTCATAAATTTATGACACACATGTATGACTTACAT
TGAGCGTCATTAAAGCACA
Found at i:78610 original size:39 final size:39
Alignment explanation
Indices: 78523--78637 Score: 132
Period size: 39 Copynumber: 3.0 Consensus size: 39
78513 CGCGTCCTCC
* *
78523 TCCTTTGCGGTGTTCCCTCCTCC--TCTTCT-TTC-TTTT
1 TCCTTTGCGGTG-TCCCTTCTCCTTTCTACTCTTCATTTT
78559 TACCTCTT-CGGTGTCCCTTCTCCTTTCTACTCTTCATTTT
1 T-CCT-TTGCGGTGTCCCTTCTCCTTTCTACTCTTCATTTT
**
78599 TCCTTTGCGGTGTCCCTTCTCCTTTCCCCTCTTCATTTT
1 TCCTTTGCGGTGTCCCTTCTCCTTTCTACTCTTCATTTT
78638 CAACAAGTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
36 10 0.15
37 8 0.12
38 9 0.13
39 36 0.53
40 5 0.07
ACGTcount: A:0.03, C:0.37, G:0.10, T:0.50
Consensus pattern (39 bp):
TCCTTTGCGGTGTCCCTTCTCCTTTCTACTCTTCATTTT
Found at i:79935 original size:2 final size:2
Alignment explanation
Indices: 79928--79999 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
79918 TTTCTAAAAC
79928 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
79970 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
80000 ATACAGACTG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:81393 original size:15 final size:15
Alignment explanation
Indices: 81369--81415 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
81359 ATTTTCCTTA
81369 TTTGACGTTTTCTTC
1 TTTGACGTTTTCTTC
*
81384 TTTGATGTTTTCTTC
1 TTTGACGTTTTCTTC
*
81399 TTAT-ACGTTGTCTTC
1 TT-TGACGTTTTCTTC
81414 TT
1 TT
81416 ACCCCATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.62
Consensus pattern (15 bp):
TTTGACGTTTTCTTC
Found at i:83981 original size:20 final size:20
Alignment explanation
Indices: 83956--83995 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
83946 ATAAAATTCC
83956 CTTAACTTATTATTATATTT
1 CTTAACTTATTATTATATTT
83976 CTTAACTTATTATTATATTT
1 CTTAACTTATTATTATATTT
83996 TTATCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (20 bp):
CTTAACTTATTATTATATTT
Found at i:88528 original size:74 final size:75
Alignment explanation
Indices: 88432--88615 Score: 244
Period size: 74 Copynumber: 2.4 Consensus size: 75
88422 AAATGACTAG
* * * *
88432 GGGTATCGGTACCTCAAAGGGGGTATCGGTACCCATTAGGCATTATGTTTTTCTCGGAGC-CAAA
1 GGGTATCGGTACCTCTATGGGGGTATCGGTACCCATTAGGCATTATATTTTTCTCGGAGCTAAAA
88496 ATTGACACAA
66 ATTGACACAA
* *
88506 GGGTATCGGTACCTCTATGGGGGTATCGGTACCCATTGGGCATTCTATTTTTCTCGGAGCTAAAA
1 GGGTATCGGTACCTCTATGGGGGTATCGGTACCCATTAGGCATTATATTTTTCTCGGAGCTAAAA
* * *
88571 ATTGGCATAG
66 ATTGACACAA
* *
88581 GGGTATCGGCACACCCTATGAGGGGTATCGGTACC
1 GGGTATCGGTAC-CTCTATG-GGGGTATCGGTACC
88616 TCCGTATTTA
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
74 55 0.57
75 21 0.22
76 6 0.06
77 14 0.15
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (75 bp):
GGGTATCGGTACCTCTATGGGGGTATCGGTACCCATTAGGCATTATATTTTTCTCGGAGCTAAAA
ATTGACACAA
Found at i:88897 original size:20 final size:20
Alignment explanation
Indices: 88868--88905 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
88858 CAATAATGAC
*
88868 CCTAGAGTATTGATACTCCA
1 CCTAGAGTATCGATACTCCA
*
88888 CCTAGGGTATCGATACTC
1 CCTAGAGTATCGATACTC
88906 ATCAGCTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (20 bp):
CCTAGAGTATCGATACTCCA
Found at i:91002 original size:31 final size:30
Alignment explanation
Indices: 90962--91021 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
90952 AATTAACTTT
*
90962 CGAAAAAAATTAAAAGTTTAGGTACTAAAA
1 CGAAAAAAATTAAAAGTTTAGATACTAAAA
* *
90992 CGAAATAAAATTGATAGTTTAGATACTAAA
1 CGAAA-AAAATTAAAAGTTTAGATACTAAA
91022 CACGTTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (30 bp):
CGAAAAAAATTAAAAGTTTAGATACTAAAA
Found at i:92483 original size:15 final size:16
Alignment explanation
Indices: 92463--92492 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
92453 AGAAAAACTC
92463 TAAATTTT-TGACGGG
1 TAAATTTTGTGACGGG
92478 TAAATTTTGTGACGG
1 TAAATTTTGTGACGG
92493 AACATGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (16 bp):
TAAATTTTGTGACGGG
Found at i:92577 original size:31 final size:31
Alignment explanation
Indices: 92537--92609 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
92527 AAGTAAATCT
*
92537 GTCAGAAATTTGTGACGGGTCCACACATTTC
1 GTCACAAATTTGTGACGGGTCCACACATTTC
* * * *
92568 GTCACAAATTTGTGATGTGTTCACATATTTC
1 GTCACAAATTTGTGACGGGTCCACACATTTC
*
92599 ATCACAAATTT
1 GTCACAAATTT
92610 AAAATATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (31 bp):
GTCACAAATTTGTGACGGGTCCACACATTTC
Found at i:95438 original size:3 final size:3
Alignment explanation
Indices: 95430--95463 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
95420 TATAGAGTTA
95430 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
95464 ATTCCTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:97423 original size:2 final size:2
Alignment explanation
Indices: 97416--97446 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
97406 CAATTTACAC
97416 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 T
97447 GAGAATACGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100188 original size:19 final size:20
Alignment explanation
Indices: 100142--100190 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
100132 TATATATAAA
* *
100142 ATTTTAATTCTTTTTCATAT
1 ATTTTTATTATTTTTCATAT
**
100162 ATCATTATTATTTTT-ATAT
1 ATTTTTATTATTTTTCATAT
100181 ATTTTTATTA
1 ATTTTTATTA
100191 CTATAATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTATTATTTTTCATAT
Found at i:100217 original size:17 final size:17
Alignment explanation
Indices: 100192--100234 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
100182 TTTTTATTAC
*
100192 TATAATTATATGTTATA
1 TATATTTATATGTTATA
*
100209 TATATTTATTATTTTATA
1 TATATTTA-TATGTTATA
100227 TAT-TTTAT
1 TATATTTAT
100235 TTTATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 11 0.48
18 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATATTTATATGTTATA
Found at i:100246 original size:7 final size:6
Alignment explanation
Indices: 100211--100270 Score: 50
Period size: 7 Copynumber: 9.2 Consensus size: 6
100201 ATGTTATATA
*
100211 TATTTAT TATTTT ATATATTT TA-TTT TATCTTT TATTTTT TATCTTC
1 TATTT-T TATTTT -TAT-TTT TATTTT TAT-TTT TA-TTTT TAT-TTT
100258 TATTTT TATTTT T
1 TATTTT TATTTT T
100271 GTATTGTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
5 5 0.11
6 11 0.24
7 25 0.56
8 4 0.09
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:100270 original size:26 final size:25
Alignment explanation
Indices: 100211--100270 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
100201 ATGTTATATA
*
100211 TATTTATTATTTTATATATTTTATTT
1 TATTT-TTATTTTATATATTCTATTT
* *
100237 TATCTTTTATTTTTTATCTTCTATTTT
1 TAT-TTTTATTTTATATATTCTA-TTT
100264 TATTTTT
1 TATTTTT
100271 GTATTGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (25 bp):
TATTTTTATTTTATATATTCTATTT
Found at i:109223 original size:110 final size:106
Alignment explanation
Indices: 108881--109304 Score: 434
Period size: 106 Copynumber: 4.0 Consensus size: 106
108871 ATATCGTGCC
* * * * * ** * *
108881 ACTCGAGACAACACAAGTTCAACTTCACAACGAA-TGGACGACTGGTTGTCAAAAAACAATTTCC
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGA-GGCTGACTGTCAACAAACAACTTCC
* *
108945 AAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
* * *
108987 ACTCAAGACAGCACAAGCTCAACTTCATAGCGAAGGGGAGGCTGACTATCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGAGGCTGACTGTCAACAAACAACTTCCC
* *
109052 AGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
* * * * * * **
109093 ACTCAAGACAACACAAGCTCAACTTCACAACAAAGGGGTGACTGATTGTCAACAAATAACTTTTC
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGAGGCTGACTGTCAACAAACAACTTCCC
** * * *
109158 AGTTTCATTCAGATTCAATTTCAACTTCATAGTGAATGATATTGA
66 AG--T--TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
* *
109203 ACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAA--T---
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGAGGCTGACTGTCAACAAACAACTTCCC
* *
109263 --TTCCAGAGCCAATTTCAACTTCAC-GATGGAGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAG-TGAAGGATATTGG
109302 ACT
1 ACT
109305 TGGAACAATA
Statistics
Matches: 264, Mismatches: 48, Indels: 19
0.80 0.15 0.06
Matches are distributed among these distances:
98 1 0.00
99 32 0.12
101 1 0.00
106 142 0.54
107 3 0.01
108 2 0.01
110 83 0.31
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGAGGCTGACTGTCAACAAACAACTTCCC
AGTTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
Found at i:110690 original size:2 final size:2
Alignment explanation
Indices: 110685--110773 Score: 137
Period size: 2 Copynumber: 45.0 Consensus size: 2
110675 ATTCTTATTT
* *
110685 TA TA TA TA TA TA TA TA T- TC TA TCG T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
110726 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
110768 TA TA TA
1 TA TA TA
110774 CTTTTAATTC
Statistics
Matches: 82, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.02
2 79 0.96
3 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:110856 original size:14 final size:14
Alignment explanation
Indices: 110823--110951 Score: 55
Period size: 14 Copynumber: 8.4 Consensus size: 14
110813 TAATTATATG
110823 TTATATATATTTATT
1 TTATATAT-TTTATT
110838 ATTATATATTTTATT
1 -TTATATATTTTATT
* * *
110853 TTATCTTTTATTTTT
1 TTATATATT-TTATT
*
110868 TTATCTTCTATTTTTATT
1 TTA---TATA-TTTTATT
*
110886 TT-TGTATTGTTATT
1 TTATATATT-TTATT
*
110900 GTTATTATCTTCTTTATT
1 -TTA-TAT-AT-TTTATT
*
110918 TTATGTATTTTATT
1 TTATATATTTTATT
*
110932 TATATATATATT-TT
1 T-TATATATTTTATT
110946 TTATAT
1 TTATAT
110952 TTGTTTTTGT
Statistics
Matches: 89, Mismatches: 12, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
13 7 0.08
14 25 0.28
15 24 0.27
16 10 0.11
17 5 0.06
18 15 0.17
19 3 0.03
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (14 bp):
TTATATATTTTATT
Found at i:110869 original size:15 final size:15
Alignment explanation
Indices: 110851--110882 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
110841 ATATATTTTA
*
110851 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
110866 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
110881 TT
1 TT
110883 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:110882 original size:21 final size:20
Alignment explanation
Indices: 110846--110921 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 20
110836 TTATTATATA
110846 TTTTATTTTATCTTTTATTT
1 TTTTATTTTATCTTTTATTT
110866 TTTTATCTTCTAT-TTTTATTT
1 TTTTAT-TT-TATCTTTTATTT
* *
110887 TTGTATTGTTATTGTTATTATCTT
1 TTTTATT-TTA-TCTT-TTAT-TT
*
110911 CTTTATTTTAT
1 TTTTATTTTAT
110922 GTATTTTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
20 9 0.20
21 17 0.37
22 6 0.13
23 7 0.15
24 7 0.15
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTTATTTTATCTTTTATTT
Found at i:110949 original size:33 final size:32
Alignment explanation
Indices: 110878--110955 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
110868 TTATCTTCTA
*
110878 TTTTTATTTTTGTATTGTTATTGTTATTATCT
1 TTTTTATTTTTGTATTGTTATTGTTATTATAT
*
110910 TCTTTATTTTATGTATT-TTATT-TATATATATAT
1 TTTTTATTTT-TGTATTGTTATTGT-TAT-TATAT
*
110943 TTTTTATATTTGT
1 TTTTTATTTTTGT
110956 TTTTGTGCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.03
32 20 0.51
33 18 0.46
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (32 bp):
TTTTTATTTTTGTATTGTTATTGTTATTATAT
Found at i:111867 original size:20 final size:21
Alignment explanation
Indices: 111829--111867 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
111819 AAAAAAATAA
* *
111829 AAAAATAAAAGAAGTAAAAGT
1 AAAAATAAAACAAGAAAAAGT
111850 AAAAAT-AAACAAGAAAAA
1 AAAAATAAAACAAGAAAAA
111868 AGAATGAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAATAAAACAAGAAAAAGT
Found at i:112092 original size:2 final size:2
Alignment explanation
Indices: 112085--112135 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
112075 AGTTATATGA
112085 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
112127 AT AT AT AT A
1 AT AT AT AT A
112136 CAACTTATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112835 original size:35 final size:35
Alignment explanation
Indices: 112796--112867 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
112786 CTAAAAAACC
*
112796 CTATTTTATACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
112831 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
112866 CT
1 CT
112868 TCTTTGTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:113536 original size:106 final size:106
Alignment explanation
Indices: 113352--113557 Score: 252
Period size: 106 Copynumber: 1.9 Consensus size: 106
113342 TGTGTTACTC
* **
113352 CGAGTCTAATATCCTCCGTAATGAAGTTGAAATTGGCTATGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCTAATATCCTCCGTAATGAAGTTGAAATTGACTATAAAACTGGGAAATTGTTTGTTGACA
** * *
113417 GTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTATCT
66 ACCAGCCGCCCCTTCACTGTGAAGTTGAACTTGTGCTATCT
* * * * * *
113458 CGAGTCTAATATCCTTCGCT-GTGAAGTTGAAATTGATTCTAAAATTGGGAAGTTGTTTGTTGAC
1 CGAGTCTAATATCCTCCG-TAATGAAGTTGAAATTGACTATAAAACTGGGAAATTGTTTGTTGAC
* **
113522 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG
65 AACCAGCCGCCCCTTCACTGTGAAGTTGAACTTGTG
113558 TTGTCTTGAG
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
106 82 0.99
107 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCTAATATCCTCCGTAATGAAGTTGAAATTGACTATAAAACTGGGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCACTGTGAAGTTGAACTTGTGCTATCT
Found at i:113803 original size:280 final size:281
Alignment explanation
Indices: 113288--113849 Score: 824
Period size: 280 Copynumber: 2.0 Consensus size: 281
113278 TCGTCGTGAA
* * *
113288 GTTGAGCCTGAGAATTGGATATCCTTCATTGTGAAATTGAAATTCAATGTAAGTTGTGTTACTCC
1 GTTGAGCCTGAGAATTGGATATCCTTCATCGTGAAATTGAAATCCAATGTAAGTTGTATTACTCC
* * *
113353 GAGTCTAATATCCTCCGTAATGAAGTTGAAATTGGCTATGGAACTGGGAAATTGTTTGTTGACAG
66 GAGTCCAATATCCTCCGTAATGAAGTCGAAATTGGCTATGGAACTGGGAAATTGTTTGTTAACAG
* ** * *
113418 TCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTATCTCGAGTCTAATATCCTTCGCTGTGAA
131 CCAACCGCCCCTTCACCGTGAAGTTGAGCTTGTGCTATCTCGAGTCCAATATCCTTCGCTGTGAA
* * ** * *
113483 GTTGAAATTGATTCTAAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
196 GTTGAAATTGATTCTAAAACTGGGAAATTGTTCATTGACAACCAGCCATCCCTTCGTTATGAAGT
113548 TGAACTTGTGTTGTCTTGAGT
261 TGAACTTGTGTTGTCTTGAGT
* * *
113569 GTTGAGCCTG-GTAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-GTAAGTTGTATTGCTC
1 GTTGAGCCTGAG-AATTGGATATCCTTCATCGTGAAATTGAAATCCAATGTAAGTTGTATTACTC
** *
113632 CGAGTCCAATATCCTCCGTCGTGAAGTCGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTAACA
65 CGAGTCCAATATCCTCCGTAATGAAGTCGAAATTGGCTATGGAACTGGGAAATTGTTTGTTAACA
* *
113697 GCCAACCGCCCCTTCACCGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGCTGTGA
130 GCCAACCGCCCCTTCACCGTGAAGTTGAGCTTGTGCTATCTCGAGTCCAATATCCTTCGCTGTGA
* * * *
113762 AGTTGAAATTG-TCTTTGAAACTGTGAAATTGTTCATTGACAACCAGCCATCCCTTCGTTATTAA
195 AGTTGAAATTGAT-TCTAAAACTGGGAAATTGTTCATTGACAACCAGCCATCCCTTCGTTATGAA
113826 GTTGAACTTGTGTTGTCTTGAGT
259 GTTGAACTTGTGTTGTCTTGAGT
113849 G
1 G
113850 GCACGATATC
Statistics
Matches: 250, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
279 1 0.00
280 208 0.83
281 41 0.16
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (281 bp):
GTTGAGCCTGAGAATTGGATATCCTTCATCGTGAAATTGAAATCCAATGTAAGTTGTATTACTCC
GAGTCCAATATCCTCCGTAATGAAGTCGAAATTGGCTATGGAACTGGGAAATTGTTTGTTAACAG
CCAACCGCCCCTTCACCGTGAAGTTGAGCTTGTGCTATCTCGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGATTCTAAAACTGGGAAATTGTTCATTGACAACCAGCCATCCCTTCGTTATGAAGT
TGAACTTGTGTTGTCTTGAGT
Found at i:122484 original size:9 final size:9
Alignment explanation
Indices: 122461--122536 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
122451 AACGAAAAGA
122461 AAAATAAAT
1 AAAATAAAT
122470 -AAATAAAT
1 AAAATAAAT
122478 AAAATAAA-
1 AAAATAAAT
*
122486 AGACATAAA-
1 A-AAATAAAT
122495 ATAAATAAAT
1 A-AAATAAAT
**
122505 AAAATCCAT
1 AAAATAAAT
*
122514 AAAAGAAAAT
1 AAAA-TAAAT
*
122524 GAAATAAAT
1 AAAATAAAT
122533 AAAA
1 AAAA
122537 ACTAGAAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
8 9 0.17
9 37 0.71
10 6 0.12
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:122516 original size:31 final size:32
Alignment explanation
Indices: 122461--122535 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
122451 AACGAAAAGA
*
122461 AAAATAAATAAATAAATAAAATAAAAG-ACAT
1 AAAATAAATAAATAAATAAAATAAAAGAAAAT
**
122492 AAAATAAATAAATAAA-ATCCATAAAAGAAAAT
1 AAAATAAATAAATAAATA-AAATAAAAGAAAAT
*
122524 GAAATAAATAAA
1 AAAATAAATAAA
122536 AACTAGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 1 0.03
31 23 0.61
32 14 0.37
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (32 bp):
AAAATAAATAAATAAATAAAATAAAAGAAAAT
Found at i:122522 original size:27 final size:27
Alignment explanation
Indices: 122466--122536 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
122456 AAAGAAAAAT
*
122466 AAATAAATAAATAAAATAAAAGACATA
1 AAATAAATAAATAAAATAAAAGACAGA
*
122493 AAATAAATAAATAAAATCCATAA-A-AGA
1 AAATAAATAAATAAAAT--AAAAGACAGA
122520 AAATGAAATAAATAAAA
1 AAAT-AAATAAATAAAA
122537 ACTAGAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 23 0.59
28 13 0.33
29 3 0.08
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (27 bp):
AAATAAATAAATAAAATAAAAGACAGA
Found at i:122545 original size:28 final size:27
Alignment explanation
Indices: 122458--122545 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
122448 AGAAACGAAA
**
122458 AGAAAA-ATAAATAAATAAATAAAATAAA
1 AGAAAAGA-AAATAAATAAATAAAA-ACC
* * *
122486 AG-ACATAAAATAAATAAATAAAATCC
1 AGAAAAGAAAATAAATAAATAAAAACC
* *
122512 ATAAAAGAAAATGAAATAAATAAAAACT
1 AGAAAAGAAAAT-AAATAAATAAAAACC
122540 AGAAAA
1 AGAAAA
122546 TAATGGTGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
26 1 0.02
27 25 0.53
28 21 0.45
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.17
Consensus pattern (27 bp):
AGAAAAGAAAATAAATAAATAAAAACC
Found at i:122801 original size:2 final size:2
Alignment explanation
Indices: 122796--122822 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
122786 TATATATATA
122796 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
122823 AATCTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:122954 original size:14 final size:15
Alignment explanation
Indices: 122935--122973 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
122925 AAATGTGCGT
*
122935 ATAAATAAAATTA-A
1 ATAAATAAAATAATA
122949 ATAAATAAAATAATA
1 ATAAATAAAATAATA
*
122964 ATAATTAAAA
1 ATAAATAAAA
122974 CGTAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:124285 original size:110 final size:110
Alignment explanation
Indices: 124131--124329 Score: 317
Period size: 110 Copynumber: 1.8 Consensus size: 110
124121 AACTGGGAAA
* *
124131 TTGTTTGTTGACAGCCAGCCGCCCCTTCACTGTGAAGTTAAGCTTGTGTTGTCTCGAGTTCAATA
1 TTGTTTGTTGACAACCAGCCGCCCCTTCACTGTGAAGTTAAGCTTGTGTTGTCTCGAGTCCAATA
*
124196 TCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAG
66 TCCCTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAG
* * ** * *
124241 TTGTTTGTTGACAATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAACCAGCCGCCCCTTCACTGTGAAGTTAAGCTTGTGTTGTCTCGAGTCCAATA
124306 TCCCTCGATGTGAAGTTGAAATTG
66 TCCCTCGATGTGAAGTTGAAATTG
124330 GCTTTGAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 80 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (110 bp):
TTGTTTGTTGACAACCAGCCGCCCCTTCACTGTGAAGTTAAGCTTGTGTTGTCTCGAGTCCAATA
TCCCTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAG
Found at i:125212 original size:65 final size:65
Alignment explanation
Indices: 125054--125436 Score: 279
Period size: 65 Copynumber: 5.8 Consensus size: 65
125044 TATATCTGTC
* * * * * **
125054 GTTTCATGA-AAACGGTCTC-AGGGGGA-AAAATTTTGTTTTAAGGGAAATAAATTTGAAACTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATAAA-TTCAAAGATT
125116 TGT
64 T-T
* * *
125119 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTT
* * * * ***
125184 GTTTCAAGTGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA-----T-AA-A-TTCA
* * *
125249 AAAACTTA
58 AAGATTTT
* * ** *** * * * *
125257 GTTCCAAAAGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTT
* * *** *
125322 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATGTTTTCAATG-TTTA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTT-
125386 T
65 T
*
125387 GTTGCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAA
125437 CTATCTCAAG
Statistics
Matches: 250, Mismatches: 55, Indels: 25
0.76 0.17 0.08
Matches are distributed among these distances:
64 2 0.01
65 134 0.54
66 33 0.13
67 26 0.10
68 4 0.02
70 1 0.00
71 2 0.01
72 1 0.00
73 47 0.19
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTT
Found at i:125233 original size:36 final size:36
Alignment explanation
Indices: 125181--125457 Score: 167
Period size: 36 Copynumber: 8.0 Consensus size: 36
125171 ATTCAAAGAT
* *
125181 TTTGTTTCAAGTGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
125217 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * **
125253 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
125290 TTTGTTTCAA-ATAAAACATAT-TC-----A-A-ATAA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACAAAA
*
125319 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
125355 TTTGTTTCAAGGGAAA-TGTTTTC-A-A-TG-----T
1 TTTGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAA
* *
125383 TTATGTTGCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
125420 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
125457 T
1 T
125458 CTTCTTTTTA
Statistics
Matches: 184, Mismatches: 33, Indels: 48
0.69 0.12 0.18
Matches are distributed among these distances:
28 4 0.02
29 33 0.18
30 4 0.02
31 1 0.01
32 1 0.01
33 1 0.01
34 2 0.01
35 5 0.03
36 70 0.38
37 61 0.33
38 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:125278 original size:37 final size:36
Alignment explanation
Indices: 125193--125284 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
125183 TGTTTCAAGT
** * * *
125193 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGAAAAAATTAGTTCCAAAA
125229 GAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGAAAAAA-TTAGTTCCAAAA
*
125266 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
125285 TGAAATTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 22 0.45
37 27 0.55
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGAAAAAATTAGTTCCAAAA
Found at i:125446 original size:37 final size:37
Alignment explanation
Indices: 125386--125457 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
125376 TCAATGTTTA
* *
125386 TGTTGCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTGCAAGAGAAACTATCTCAAGCGAGACAAAATTT
* * *
125423 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTGCAAGAGAAACTATCTCAAGCGAGACAAAAT
125458 CTTCTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (37 bp):
TGTTGCAAGAGAAACTATCTCAAGCGAGACAAAATTT
Found at i:126966 original size:20 final size:20
Alignment explanation
Indices: 126943--126998 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
126933 TCCCTTTTTC
126943 TTTTTTCTTTTTGTTATTTA
1 TTTTTTCTTTTTGTTATTTA
* *
126963 TTTTTT-TCTTTTGTTTTTTT
1 TTTTTTCT-TTTTGTTATTTA
*
126983 TTTTTTGCTTCTTGTT
1 TTTTTT-CTTTTTGTT
126999 CTTGATTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 22 0.73
21 6 0.20
22 1 0.03
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTGTTATTTA
Found at i:126969 original size:21 final size:20
Alignment explanation
Indices: 126943--126998 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
126933 TCCCTTTTTC
126943 TTTTTTCTTTTTGTTATTTAT
1 TTTTTTCTTTTTGTT-TTTAT
*
126964 TTTTTTC-TTTTGTTTTTTT
1 TTTTTTCTTTTTGTTTTTAT
*
126983 TTTTTTGCTTCTTGTT
1 TTTTTT-CTTTTTGTT
126999 CTTGATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 10 0.32
20 8 0.26
21 13 0.42
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTGTTTTTAT
Found at i:130113 original size:9 final size:9
Alignment explanation
Indices: 130095--130167 Score: 53
Period size: 9 Copynumber: 8.1 Consensus size: 9
130085 ACGAAAAGAA
130095 AAAT-AAAT
1 AAATAAAAT
130103 AAATAAAAT
1 AAATAAAAT
*
130112 AAA-AGACAT
1 AAATA-AAAT
130121 AAA-ATAAAT
1 AAATA-AAAT
130130 AAATAAAAT
1 AAATAAAAT
** *
130139 CCATAAAAGC
1 AAATAAAA-T
*
130149 AAATGAAAT
1 AAATAAAAT
130158 AAATAAAAT
1 AAATAAAAT
130167 A
1 A
130168 CTAGAAAATA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
8 5 0.10
9 39 0.78
10 6 0.12
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:130129 original size:23 final size:22
Alignment explanation
Indices: 130099--130160 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
130089 AAAGAAAAAT
130099 AAATAAATAAAATAAAAGACATA
1 AAATAAAT-AAATAAAAGACATA
**
130122 AAATAAATAAATAAAATCCATA
1 AAATAAATAAATAAAAGACATA
*
130144 AAAGCAAATGAAATAAA
1 AAA-TAAAT-AAATAAA
130161 TAAAATACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.44
23 12 0.35
24 7 0.21
ACGTcount: A:0.71, C:0.06, G:0.05, T:0.18
Consensus pattern (22 bp):
AAATAAATAAATAAAAGACATA
Found at i:130403 original size:2 final size:2
Alignment explanation
Indices: 130398--130430 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
130388 CTAAAAAAAC
*
130398 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
130431 CTAAAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:131381 original size:20 final size:19
Alignment explanation
Indices: 131356--131398 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
131346 TAAATTAAAT
131356 AAAAATAAAGAAATGAAAAG
1 AAAAATAAAGAAAT-AAAAG
* *
131376 AAAAATAAATAAATAAAAT
1 AAAAATAAAGAAATAAAAG
131395 AAAA
1 AAAA
131399 GACATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (19 bp):
AAAAATAAAGAAATAAAAG
Found at i:131710 original size:2 final size:2
Alignment explanation
Indices: 131649--131690 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
131639 GAAAATTAAC
131649 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
131691 GTAATCTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133223 original size:106 final size:106
Alignment explanation
Indices: 132973--133446 Score: 530
Period size: 106 Copynumber: 4.5 Consensus size: 106
132963 CTGGAAATTG
* * * *
132973 TTTGTTGACAGTCAGTCGCTCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCC
1 TTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
* * *
133038 TTCGTTGTGAAGTTGAAATTGACTCT-TAA-T--GAA-AT-
66 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTA
* * * *
133073 TTTGTTGACAATCAGCCTCCTCTTCG-TCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATC
1 TTTGTTGACAATCAGCCGCCCCTTCGCT-GTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATC
* *
133137 CTTCGTTGGGAAGTTGAAATTGGCCCTGAAATTGGGAAGTTA
65 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTA
* * * *
133179 TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCC
1 TTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
* * *
133244 TTCGGTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTG
66 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTA
* * * * ** * *
133285 TTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAATTTGTGTTATCTCGAATCCAATATCC
1 TTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
* * * *
133350 TTCGCTGTGAAGTTGAAATTGGTTCTGAAACTGGGAAATTA
66 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTA
* * * * * * * *
133391 TTTATTTACAACCAGCTGTCCCTTCGTTGAGAAGTTGAACTTGTGTTGTCTCGAGT
1 TTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
133447 TTTGGCATTT
Statistics
Matches: 318, Mismatches: 48, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
99 1 0.00
100 78 0.25
101 2 0.01
102 1 0.00
104 3 0.01
105 1 0.00
106 231 0.73
107 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (106 bp):
TTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTA
Found at i:134222 original size:14 final size:13
Alignment explanation
Indices: 134190--134232 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
134180 TTTTCCATTG
134190 TTTTTTCTCTTTT
1 TTTTTTCTCTTTT
*
134203 TATTTTCTCTTTT
1 TTTTTTCTCTTTT
134216 CTTTTTTCTCTTTT
1 -TTTTTTCTCTTTT
134230 TTT
1 TTT
134233 CTCTTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTCTCTTTT
Found at i:134239 original size:7 final size:7
Alignment explanation
Indices: 134192--134229 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
134182 TTCCATTGTT
134192 TTTTCTC
1 TTTTCTC
*
134199 TTTT-TA
1 TTTTCTC
134205 TTTTCTC
1 TTTTCTC
*
134212 TTTTCTT
1 TTTTCTC
134219 TTTTCTC
1 TTTTCTC
134226 TTTT
1 TTTT
134230 TTTCTCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTCTC
Found at i:137758 original size:2 final size:2
Alignment explanation
Indices: 137751--137822 Score: 123
Period size: 2 Copynumber: 37.5 Consensus size: 2
137741 AATTAAAGTA
137751 AT AT AT AT AT AT A- AT A- AT AT AT -T 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
137790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
137823 ATGGAAATAT
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 64 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:138336 original size:35 final size:35
Alignment explanation
Indices: 138297--138368 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
138287 CAAAAAAACC
*
138297 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCCAATCCAACT
*
138332 CTATTTTAGACTAGTATTTGAGTCCCAATTCAACT
1 CTATTTTAGACTAGTATTTGAGTCCCAATCCAACT
138367 CT
1 CT
138369 TCTTTGTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCCAATCCAACT
Found at i:140753 original size:60 final size:58
Alignment explanation
Indices: 140599--140763 Score: 183
Period size: 57 Copynumber: 2.8 Consensus size: 58
140589 ATATTATTGG
* * **
140599 ATGTTCAAAAGTTTGGAGACTAATTTAGAATAAGAATCATAGTTTGAGGATGAATTTTTA
1 ATGTTCAAAAGTTTGG-GACTAATTTAGAATAAGAGTCATAGTTT-AGGATGAAATTAAA
* * * **
140659 ATGTTCGAAA--TTGGGACCAGTTTAGAATTGGAGTCATAGTTTAGTGAT-ACAATTAAA
1 ATGTTCAAAAGTTTGGGACTAATTTAGAATAAGAGTCATAGTTTAG-GATGA-AATTAAA
140716 ATGTTCAAAAGTTTAGGGACTAATTTAGAATAAGAGTCATAGTTTAGG
1 ATGTTCAAAAGTTT-GGGACTAATTTAGAATAAGAGTCATAGTTTAGG
140764 GGTGTATTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
56 3 0.03
57 39 0.45
58 4 0.05
59 3 0.03
60 37 0.43
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (58 bp):
ATGTTCAAAAGTTTGGGACTAATTTAGAATAAGAGTCATAGTTTAGGATGAAATTAAA
Found at i:141118 original size:21 final size:21
Alignment explanation
Indices: 141089--141129 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
141079 GATATTTTTA
141089 TATTCATTTTAAATTTAAATT
1 TATTCATTTTAAATTTAAATT
* *
141110 TATTTATTTTAATTTTAAAT
1 TATTCATTTTAAATTTAAAT
141130 ATTAATCCAT
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:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTCATTTTAAATTTAAATT
Found at i:144318 original size:36 final size:35
Alignment explanation
Indices: 144246--144337 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 35
144236 TTTTTATATT
* *
144246 TTTAA-TTTATAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAATATATAAATATTATCAA
*
144280 TTTAATTTTTTAAAGAAAATATATAAATATT-TACAA
1 TTTAATTTTATAAA-AAAATATATAAATATTAT-CAA
* * *
144316 TTTAATATTATACAAATATATA
1 TTTAATTTTATAAAAAAATATA
144338 ATAAGGACAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 5 0.10
35 15 0.31
36 28 0.58
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (35 bp):
TTTAATTTTATAAAAAAATATATAAATATTATCAA
Found at i:144494 original size:20 final size:20
Alignment explanation
Indices: 144458--144495 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
144448 ATCCTATTCT
**
144458 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
144478 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
144496 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:150653 original size:15 final size:15
Alignment explanation
Indices: 150617--150647 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
150607 TACGTAATTT
150617 ATCTTATTATTATTA
1 ATCTTATTATTATTA
150632 ATCTTATTATTATTA
1 ATCTTATTATTATTA
150647 A
1 A
150648 ATTTATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
ATCTTATTATTATTA
Found at i:151006 original size:2 final size:2
Alignment explanation
Indices: 150999--151042 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
150989 CTAAATGTTT
150999 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
151041 TA
1 TA
151043 ATAAAAGTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:151945 original size:18 final size:18
Alignment explanation
Indices: 151922--151956 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
151912 TTTTTTTAAA
151922 TTATTTTTAAAAAATATT
1 TTATTTTTAAAAAATATT
151940 TTATTTTTAAAAAATAT
1 TTATTTTTAAAAAATAT
151957 AAACTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTTTTAAAAAATATT
Found at i:152423 original size:16 final size:16
Alignment explanation
Indices: 152402--152434 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
152392 TATAAGCATC
152402 ATTTT-AATTTATAAAA
1 ATTTTAAATTTA-AAAA
152418 ATTTTAAATTTAAAAA
1 ATTTTAAATTTAAAAA
152434 A
1 A
152435 ACTCAACGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTAAATTTAAAAA
Found at i:152435 original size:17 final size:16
Alignment explanation
Indices: 152402--152435 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
152392 TATAAGCATC
*
152402 ATTTTAATTTATAAAA
1 ATTTTAATTTAAAAAA
152418 ATTTTAAATTTAAAAAA
1 ATTTT-AATTTAAAAAA
152435 A
1 A
152436 CTCAACGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTAATTTAAAAAA
Done.