Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006088.1 Hibiscus syriacus cultivar Beakdansim tig00014434_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: 126540
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2886 original size:2 final size:2
Alignment explanation
Indices: 2879--2935 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2869 TAAATATCAA
2879 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
2921 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2936 ACAATGAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4049 original size:20 final size:20
Alignment explanation
Indices: 4026--4139 Score: 192
Period size: 20 Copynumber: 5.7 Consensus size: 20
4016 GATTCTGACT
4026 ATCGCAATGCGAATAAGTAA
1 ATCGCAATGCGAATAAGTAA
*
4046 ATCGCAATGCGAATACGTAA
1 ATCGCAATGCGAATAAGTAA
*
4066 ATCGCAACGCGAATAAGTAA
1 ATCGCAATGCGAATAAGTAA
4086 ATCGCAATGCGAATAAGTAA
1 ATCGCAATGCGAATAAGTAA
*
4106 ATCGCAATGCGAATACGTAA
1 ATCGCAATGCGAATAAGTAA
*
4126 ATCGCAATACGAAT
1 ATCGCAATGCGAAT
4140 CTGACTATCG
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAATAAGTAA
Found at i:4051 original size:40 final size:40
Alignment explanation
Indices: 4026--4157 Score: 178
Period size: 40 Copynumber: 3.3 Consensus size: 40
4016 GATTCTGACT
4026 ATCGCAATGCGAATAAGTAAATCGCAATGCGAATAC-GTAA
1 ATCGCAATGCGAATAAGTAAATCGCAATGCGAAT-CTGTAA
* **
4066 ATCGCAACGCGAATAAGTAAATCGCAATGCGAATAAGTAA
1 ATCGCAATGCGAATAAGTAAATCGCAATGCGAATCTGTAA
* * *
4106 ATCGCAATGCGAATACGTAAATCGCAATACGAATCTG-ACT
1 ATCGCAATGCGAATAAGTAAATCGCAATGCGAATCTGTA-A
4146 ATCGCAATGCGA
1 ATCGCAATGCGA
4158 TTTACATAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.01
40 81 0.99
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
ATCGCAATGCGAATAAGTAAATCGCAATGCGAATCTGTAA
Found at i:4071 original size:60 final size:60
Alignment explanation
Indices: 4007--4157 Score: 232
Period size: 60 Copynumber: 2.5 Consensus size: 60
3997 GTTTCCAGAT
*
4007 TCGCAACGCGATTCTGACTATCGCAATGCGAATAAGTAAATCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATCTGACTATCGCAATGCGAATAAGTAAATCGCAATGCGAATACGTAAA
** *
4067 TCGCAACGCGAATAAGTA-AATCGCAATGCGAATAAGTAAATCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATCTG-ACTATCGCAATGCGAATAAGTAAATCGCAATGCGAATACGTAAA
**
4127 TCGCAATACGAATCTGACTATCGCAATGCGA
1 TCGCAACGCGAATCTGACTATCGCAATGCGA
4158 TTTACATAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 1 0.01
60 78 0.98
61 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (60 bp):
TCGCAACGCGAATCTGACTATCGCAATGCGAATAAGTAAATCGCAATGCGAATACGTAAA
Found at i:4358 original size:22 final size:22
Alignment explanation
Indices: 4333--4398 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
4323 GGCGACATCC
*
4333 GTCCCCATCTCCGACGAAATTA
1 GTCCCCATCTCCGACGAAATCA
* *
4355 GTCCCCATCGCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
4377 GTCTCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
4399 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:4771 original size:33 final size:34
Alignment explanation
Indices: 4723--4795 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
4713 ACTATCGCAA
** *
4723 TGCGATTCTGTCGTTGCGATTTTC-ATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
4756 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTCAAATTCGCGT
4790 TGCGAT
1 TGCGAT
4796 AGTCATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
Found at i:4812 original size:21 final size:21
Alignment explanation
Indices: 4766--4825 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
4756 TGCGATTCTT
**
4766 GCGTTGCGATAGTCA-AATTC
1 GCGTTGCGATAGTCATTTTTC
4786 GCGTTGCGATAGTCATTTTTC
1 GCGTTGCGATAGTCATTTTTC
* **
4807 GTGTTGCGATTTTCATTTT
1 GCGTTGCGATAGTCATTTT
4826 CATGTTGTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (21 bp):
GCGTTGCGATAGTCATTTTTC
Found at i:4831 original size:20 final size:21
Alignment explanation
Indices: 4788--4838 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
4778 TCAAATTCGC
** *
4788 GTTGCGATAGTCATTTTTCGT
1 GTTGCGATTTTCATTTTTCAT
4809 GTTGCGATTTTCA-TTTTCAT
1 GTTGCGATTTTCATTTTTCAT
*
4829 GTTGTGATTT
1 GTTGCGATTT
4839 AAAGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.14, C:0.12, G:0.22, T:0.53
Consensus pattern (21 bp):
GTTGCGATTTTCATTTTTCAT
Found at i:6805 original size:53 final size:53
Alignment explanation
Indices: 6719--6847 Score: 186
Period size: 53 Copynumber: 2.4 Consensus size: 53
6709 ATAGTTTACT
* ** * *
6719 ATCGTAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGCGAAAATGACTATCGCAAAGAAAGA
* *
6773 ATTGCAATGCGAAATGAAAATCGCAATGCGAAAATGACTATCGCAAAGAAAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAAAATGACTATCGCAAAGAAAGA
6826 ATCGCAATGCGAAATGAAAATC
1 ATCGCAATGCGAAATGAAAATC
6848 ATATTGCGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 58 0.87
54 9 0.13
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAAAATGACTATCGCAAAGAAAGA
Found at i:6815 original size:20 final size:20
Alignment explanation
Indices: 6716--6818 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
6706 AGAATAGTTT
*
6716 ACTATCGTAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
6736 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
6756 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
6772 A--ATTGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
6789 AAAATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
6809 ACTATCGCAA
1 ACTATCGCAA
6819 AGAAAGAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
14 6 0.09
16 6 0.09
17 4 0.06
18 2 0.03
19 10 0.14
20 41 0.59
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:6969 original size:73 final size:73
Alignment explanation
Indices: 6850--6987 Score: 231
Period size: 73 Copynumber: 1.9 Consensus size: 73
6840 TGAAAATCAT
* * *
6850 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGTGATAGTCATTTTCGCGTTGTGATTTT
1 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATTTT
6915 CATTTCGC
66 CATTTCGC
**
6923 ATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATTTT
1 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATTTT
6988 AAGTTTCAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (73 bp):
ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATTTT
CATTTCGC
Found at i:6981 original size:20 final size:20
Alignment explanation
Indices: 6865--6984 Score: 119
Period size: 20 Copynumber: 6.3 Consensus size: 20
6855 GATTCTCTCG
**
6865 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
6885 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
* **
6905 TTGTGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
6924 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
6938 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
6958 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
6978 TTGCGAT
1 TTGCGAT
6985 TTTAAGTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
17 2 0.02
18 4 0.05
19 12 0.14
20 53 0.63
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:6994 original size:20 final size:20
Alignment explanation
Indices: 6938--6994 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
6928 GATTCTCTCG
* *
6938 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTAAGTTTCGCA
* *
6958 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTAAGTTTCGCA
**
6978 TTGCGATTTTAAGTTTC
1 TTGCGATAGTAAGTTTC
6995 AGATTCTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTAAGTTTCGCA
Found at i:7509 original size:18 final size:19
Alignment explanation
Indices: 7470--7511 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
7460 CTCACCTGTC
7470 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
7491 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
7509 ATC
1 ATC
7512 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:7565 original size:42 final size:42
Alignment explanation
Indices: 7493--7575 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
7483 CCTCCCCTAT
*
7493 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
7535 CGTTCAATAGGCCACTATCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
7576 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:8971 original size:14 final size:14
Alignment explanation
Indices: 8952--9001 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
8942 ATTGTTTAAT
8952 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
8966 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
8980 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
8994 TGATTTGT
1 TGATTTGT
9002 TTAATTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:9193 original size:33 final size:33
Alignment explanation
Indices: 9136--9220 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
9126 TATCGCAACG
*
9136 CGTTGCAATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
9170 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
9203 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
9221 CACGTTGCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 34 0.72
34 13 0.28
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:9228 original size:20 final size:20
Alignment explanation
Indices: 9203--9291 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
9193 GCGATTCTCT
*
9203 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCG
*
9223 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
9243 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
9263 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
9283 CGTTGCGAT
1 CGTTGCGAT
9292 TTCCGCGTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 61 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:11780 original size:24 final size:24
Alignment explanation
Indices: 11729--11780 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
11719 ATCTGAGTAT
** *
11729 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
11753 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
11777 TGAC
1 TGAC
11781 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:12626 original size:20 final size:20
Alignment explanation
Indices: 12601--12647 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
12591 AAATTCAGTA
*
12601 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
12621 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
12641 TTGCGAT
1 TTGCGAT
12648 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:12657 original size:20 final size:20
Alignment explanation
Indices: 12634--12807 Score: 267
Period size: 20 Copynumber: 8.7 Consensus size: 20
12624 CGATAGTCAG
12634 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
12654 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
12674 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
12694 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
12714 ATTCGTGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
12734 ATTCGCATTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
* * * **
12754 AATCGCATTGCGATTTTCCAA
1 ATTCGCGTTGCGA-TTTACGT
12775 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
12795 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
12808 ATTAGGAAAA
Statistics
Matches: 140, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
20 125 0.89
21 15 0.11
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACGT
Found at i:12828 original size:21 final size:21
Alignment explanation
Indices: 12804--12849 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12794 TATTCGCATT
12804 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
12825 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
12846 GCGA
1 GCGA
12850 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:32576 original size:12 final size:11
Alignment explanation
Indices: 32547--32579 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
32537 TTTAAATAAT
32547 AAAATTATTAA
1 AAAATTATTAA
32558 AAAATTATTAA
1 AAAATTATTAA
32569 AAATATTATTA
1 AAA-ATTATTA
32580 TTTTTATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAATTATTAA
Found at i:33341 original size:12 final size:12
Alignment explanation
Indices: 33312--33393 Score: 52
Period size: 12 Copynumber: 7.3 Consensus size: 12
33302 AGTTATTAAA
33312 ATATTTAA-AAT
1 ATATTTAATAAT
*
33323 ATATTTATTAAT
1 ATATTTAATAAT
*
33335 ATTTTTAATAAT
1 ATATTTAATAAT
* *
33347 ATA-AT-ATCAT
1 ATATTTAATAAT
33357 ATGA--T-ATAAT
1 AT-ATTTAATAAT
*
33367 A-ATATAATAAT
1 ATATTTAATAAT
*
33378 ATATTCAATAAT
1 ATATTTAATAAT
33390 ATAT
1 ATAT
33394 GATATTATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
8 1 0.02
10 13 0.23
11 15 0.27
12 27 0.48
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:33341 original size:23 final size:23
Alignment explanation
Indices: 33293--33349 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
33283 ATCATTTTAA
33293 TAAAATATTAGTTATTAAAATATT
1 TAAAATA-TAGTTATTAAAATATT
* * *
33317 TAAAATATATTTATTAATATTTT
1 TAAAATATAGTTATTAAAATATT
33340 TAATAATATA
1 TAA-AATATA
33350 ATATCATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAATATAGTTATTAAAATATT
Found at i:33371 original size:8 final size:8
Alignment explanation
Indices: 33340--33380 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
33330 TTAATATTTT
33340 TAATAATA
1 TAATAATA
33348 TAAT-ATCA
1 TAATAAT-A
*
33356 T-ATGATA
1 TAATAATA
33363 TAATAATA
1 TAATAATA
33371 TAATAATA
1 TAATAATA
33379 TA
1 TA
33381 TTCAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (8 bp):
TAATAATA
Found at i:33388 original size:23 final size:24
Alignment explanation
Indices: 33340--33438 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 24
33330 TTAATATTTT
*
33340 TAATAATATAAT-ATCATA-TGATA
1 TAATAATATAATAAT-ATATTCATA
33363 TAATAATATAATAATATATTCA-A
1 TAATAATATAATAATATATTCATA
* * *
33386 TAAT-ATATGATATTATATTCTTATTT
1 TAATAATATAATAATATATTC--A-TA
*
33412 TAATAATAT-ATAATAAATT-AT-
1 TAATAATATAATAATATATTCATA
33433 TAATAA
1 TAATAA
33439 AAAATATATT
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
21 6 0.10
22 15 0.24
23 21 0.33
24 5 0.08
26 12 0.19
27 4 0.06
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATAATATAATAATATATTCATA
Found at i:33703 original size:14 final size:14
Alignment explanation
Indices: 33674--33739 Score: 57
Period size: 15 Copynumber: 4.7 Consensus size: 14
33664 TATTTGTATT
*
33674 TATTTATAAAAATAA
1 TATTT-TAATAATAA
33689 TATTTTAATAATAA
1 TATTTTAATAATAA
*
33703 TA-TTGACATAAATAA
1 TATTTTA-AT-AATAA
*
33718 TA-TTAAATAA-AA
1 TATTTTAATAATAA
33730 TATTTTAATA
1 TATTTTAATA
33740 TTTTAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.09
13 11 0.25
14 14 0.32
15 15 0.34
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:33731 original size:15 final size:15
Alignment explanation
Indices: 33683--33728 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
33673 TTATTTATAA
**
33683 AAATAATATTTTAAT
1 AAATAATATTGAAAT
*
33698 -AATAATATTGACAT
1 AAATAATATTGAAAT
33712 AAATAATATT-AAAT
1 AAATAATATTGAAAT
33726 AAA
1 AAA
33729 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
AAATAATATTGAAAT
Found at i:34588 original size:130 final size:130
Alignment explanation
Indices: 34447--34694 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
34437 TATTTATATA
*
34447 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
34512 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
34577 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
34642 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
34695 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:34725 original size:130 final size:129
Alignment explanation
Indices: 34461--34725 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
34451 ATTTGGTCCT
* *
34461 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
34526 TGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
34591 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
34656 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
34720 -A
128 CA
34721 AAATT
1 AAATT
34726 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:35343 original size:21 final size:21
Alignment explanation
Indices: 35319--35361 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
35309 TATTACCTTA
35319 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
35340 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
35361 A
1 A
35362 GGGTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:41505 original size:2 final size:2
Alignment explanation
Indices: 41498--41526 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41488 TTTTTAAAAC
41498 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 A
41527 CCCCCATCCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41713 original size:12 final size:12
Alignment explanation
Indices: 41688--41780 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
41678 ACAGAGATAT
* *
41688 CAGAAATCAAAA
1 CAGAATTCAGAA
41700 CAGAATTCAGAA
1 CAGAATTCAGAA
41712 CAGATATT-AGAA
1 CAGA-ATTCAGAA
* * *
41724 CAGAATCCATAT
1 CAGAATTCAGAA
*
41736 CAGAAATCAGAA
1 CAGAATTCAGAA
* **
41748 TAGAATTCAGGT
1 CAGAATTCAGAA
*
41760 CATGTA-TCAGAA
1 CA-GAATTCAGAA
41772 CAGAATTCA
1 CAGAATTCA
41781 AGTCGAAAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
11 4 0.07
12 50 0.85
13 5 0.08
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:41725 original size:24 final size:24
Alignment explanation
Indices: 41686--41780 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
41676 AAACAGAGAT
* *
41686 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* * * *
41710 AACAGATATTAGAACAGAATCCAT
1 ATCAGATATCAGAACAGAATTCAG
* *
41734 ATCAGAAATCAGAATAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
*
41758 GTCATG-TATCAGAACAGAATTCA
1 ATCA-GATATCAGAACAGAATTCA
41781 AGTCGAAAAT
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 54 0.98
25 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATTCAG
Found at i:41772 original size:48 final size:48
Alignment explanation
Indices: 41684--41777 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
41674 TTAAACAGAG
*
41684 ATATCAGAAATCAAAACAGAATTCAGAACAGATATTAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
* * **
41732 ATATCAGAAATCAGAATAGAATTCAGGTCATG-TATCAGAACAGAAT
1 ATATCAGAAATCAAAACAGAATTCAGAACA-GATATCAGAACAGAAT
41778 TCAAGTCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
Found at i:41792 original size:24 final size:24
Alignment explanation
Indices: 41720--41794 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
41710 AACAGATATT
* *
41720 AGAACAGAATCCATA-TCAGAAATC
1 AGAACAGAATTCA-AGTCATAAATC
* * **
41744 AGAATAGAATTCAGGTCATGTATC
1 AGAACAGAATTCAAGTCATAAATC
41768 AGAACAGAATTCAAGTCGA-AAATC
1 AGAACAGAATTCAAGTC-ATAAATC
41792 AGA
1 AGA
41795 TAAAATAATT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
24 38 0.97
25 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (24 bp):
AGAACAGAATTCAAGTCATAAATC
Found at i:48729 original size:4 final size:4
Alignment explanation
Indices: 48722--48754 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
48712 TGCACTTCCT
*
48722 TCCA TCCA TCCA TCCA TCCA TCCA TCAA TCCA T
1 TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA T
48755 ACATACATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.27, C:0.45, G:0.00, T:0.27
Consensus pattern (4 bp):
TCCA
Found at i:48759 original size:4 final size:4
Alignment explanation
Indices: 48752--48793 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
48742 TCCATCAATC
* *
48752 CATA CATA CATA CACA CATA CAGA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
48794 CACAGACACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.19
Consensus pattern (4 bp):
CATA
Found at i:48770 original size:12 final size:12
Alignment explanation
Indices: 48755--48805 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
48745 ATCAATCCAT
*
48755 ACATACATACAC
1 ACATACAGACAC
*
48767 ACATACAGACAT
1 ACATACAGACAC
* *
48779 ACATACATACAT
1 ACATACAGACAC
*
48791 ACACACAGACAC
1 ACATACAGACAC
48803 ACA
1 ACA
48806 GACACACAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.51, C:0.31, G:0.04, T:0.14
Consensus pattern (12 bp):
ACATACAGACAC
Found at i:48802 original size:8 final size:8
Alignment explanation
Indices: 48771--48816 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
48761 ATACACACAT
*
48771 ACAGACAT
1 ACAGACAC
* *
48779 ACATACAT
1 ACAGACAC
*
48787 ACATACAC
1 ACAGACAC
48795 ACAGACAC
1 ACAGACAC
48803 ACAGACAC
1 ACAGACAC
48811 ACAGAC
1 ACAGAC
48817 GCACGCACGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.50, C:0.33, G:0.09, T:0.09
Consensus pattern (8 bp):
ACAGACAC
Found at i:51318 original size:27 final size:27
Alignment explanation
Indices: 51280--51344 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
51270 ATAATGACTC
51280 TGAATCATTCAGAATGTACTTCTGTAT
1 TGAATCATTCAGAATGTACTTCTGTAT
* *
51307 TGAATTATTCAGAATGTACTTCTGTGT
1 TGAATCATTCAGAATGTACTTCTGTAT
51334 TGAATCATTCA
1 TGAATCATTCA
51345 TAGATGCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (27 bp):
TGAATCATTCAGAATGTACTTCTGTAT
Found at i:51488 original size:7 final size:7
Alignment explanation
Indices: 51478--51505 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
51468 GACTTTATAT
51478 TTTAAAA
1 TTTAAAA
51485 TTTAAAA
1 TTTAAAA
51492 TTTAAAA
1 TTTAAAA
51499 TTTAAAA
1 TTTAAAA
51506 ACAATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TTTAAAA
Found at i:64014 original size:21 final size:21
Alignment explanation
Indices: 63972--64015 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
63962 ACTCAGGGAG
* *
63972 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
63993 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
64014 CT
1 CT
64016 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:64278 original size:16 final size:16
Alignment explanation
Indices: 64254--64285 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
64244 TTTCAACGGC
*
64254 AGATGCTTGCACGTAT
1 AGATACTTGCACGTAT
64270 AGATACTTGCACGTAT
1 AGATACTTGCACGTAT
64286 GGATGCTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (16 bp):
AGATACTTGCACGTAT
Found at i:65248 original size:64 final size:64
Alignment explanation
Indices: 65146--65268 Score: 178
Period size: 64 Copynumber: 1.9 Consensus size: 64
65136 AATGCATTTT
* *
65146 ATGCATCGATGCACTCAGGTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACAAAAC
1 ATGCATCGATGCACTCAGGTTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAAAC
* *
65210 ATGCATCGATGCACTCAGGCTGTTT-TG-AAATATTGAATGCACTTCATGCATCGATGCAC
1 ATGCATCGATGCACTCAGG-T-TTTATGAAAACATCGAATGCACTTCATGCATCGATGCAC
65269 TCTTAGTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
64 47 0.89
65 3 0.06
66 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACTCAGGTTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAAAC
Found at i:65268 original size:17 final size:19
Alignment explanation
Indices: 65246--65288 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
65236 GAAATATTGA
*
65246 ATGCACT-TCA-TGCATCG
1 ATGCACTCTCAGTGCACCG
*
65263 ATGCACTCTTAGTGCACCG
1 ATGCACTCTCAGTGCACCG
65282 ATGCACT
1 ATGCACT
65289 AAAGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (19 bp):
ATGCACTCTCAGTGCACCG
Found at i:68745 original size:37 final size:37
Alignment explanation
Indices: 68646--68747 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 37
68636 CCTTTTCGTC
68646 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
*
68683 -T--TAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
68717 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
68748 TTACATGCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 32 0.56
35 1 0.02
36 1 0.02
37 23 0.40
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:69262 original size:33 final size:35
Alignment explanation
Indices: 69224--69307 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
69214 TTTACACTAT
*
69224 ATATTATTATTATATATACATA-A-ATTTTTTTAG
1 ATATTATTATTATATATACATATACATTTTTTTAA
* *
69257 ATATTATTTATATATATATATATATACTTTTTTTTAA
1 ATATTA-TTAT-TATATATACATATACATTTTTTTAA
69294 ATATT-TTACTTATA
1 ATATTATTA-TTATA
69308 AGCGTATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
33 6 0.14
34 4 0.09
35 18 0.42
36 2 0.05
37 13 0.30
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
ATATTATTATTATATATACATATACATTTTTTTAA
Found at i:69562 original size:2 final size:2
Alignment explanation
Indices: 69555--69595 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
69545 TTTACTCATT
*
69555 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69596 TTCCTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:69596 original size:8 final size:8
Alignment explanation
Indices: 69552--69597 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
69542 TATTTTACTC
69552 ATTTATAT
1 ATTTATAT
69560 ATATATATAT
1 AT-T-TATAT
*
69570 ATATATAT
1 ATTTATAT
*
69578 ATATATAT
1 ATTTATAT
69586 ATTTATAT
1 ATTTATAT
69594 ATTT
1 ATTT
69598 CCTATTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 26 0.76
9 1 0.03
10 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
ATTTATAT
Found at i:69693 original size:16 final size:16
Alignment explanation
Indices: 69648--69700 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
69638 TCTTTTTTTA
69648 TTAT-TATTTACTTAT
1 TTATATATTTACTTAT
* *
69663 ATATATGCTTTTACTTAT
1 TTATAT--ATTTACTTAT
*
69681 TTATATATTTACTCAT
1 TTATATATTTACTTAT
69697 TTAT
1 TTAT
69701 TTATCTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 3 0.10
16 13 0.43
18 14 0.47
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (16 bp):
TTATATATTTACTTAT
Found at i:74411 original size:18 final size:17
Alignment explanation
Indices: 74385--74418 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
74375 ATCCAATCAA
74385 AAACAAAGAAAAAAGAG
1 AAACAAAGAAAAAAGAG
74402 AAACAGAAGAAAAAAGA
1 AAACA-AAGAAAAAAGA
74419 AAAAACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (17 bp):
AAACAAAGAAAAAAGAG
Found at i:74424 original size:19 final size:18
Alignment explanation
Indices: 74383--74441 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
74373 AGATCCAATC
74383 AAAAACAAAGAAAAAAG-
1 AAAAACAAAGAAAAAAGA
*
74400 AGAAACAGAAGAAAAAAGA
1 AAAAACA-AAGAAAAAAGA
74419 AAAAACAAA-ATCAAAAAGA
1 AAAAACAAAGA--AAAAAGA
74438 AAAA
1 AAAA
74442 GGGACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 7 0.19
18 12 0.33
19 17 0.47
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAACAAAGAAAAAAGA
Found at i:75072 original size:22 final size:22
Alignment explanation
Indices: 75044--75120 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
75034 GCTACCCCAT
75044 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
*
75066 CAAACCTTTGAACATCAAAT-A
1 CAAACCTTTGAGCATCAAATGA
* *
75087 CCAAACATTTGAGCATCAAATGC
1 -CAAACCTTTGAGCATCAAATGA
75110 CAAACCTTTGA
1 CAAACCTTTGA
75121 CCAAACACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:75974 original size:36 final size:36
Alignment explanation
Indices: 75865--75998 Score: 144
Period size: 36 Copynumber: 3.7 Consensus size: 36
75855 TTTCCAATAT
* *
75865 AAATTTTGTCTCGCTTGAGACAGTC-TCATTTAAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTTC-TTTGAAAC
* * * * *
75901 AAGATTTTATCTCGCTTGAGATAATTTTTCTTTGAAAC
1 AA-ATTTTGTCTCCCTTGAGA-CAGTCTTCTTTGAAAC
* *
75939 AAATTTCGTCTCCCTTGAGACAGTCTTCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTTCTTTGAAAC
*
75975 AAATTTTGTCTCCTTTGAGACAGT
1 AAATTTTGTCTCCCTTGAGACAGT
75999 TTTTCTCCAG
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
36 36 0.44
37 32 0.40
38 11 0.14
39 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTCTTCTTTGAAAC
Found at i:76854 original size:106 final size:106
Alignment explanation
Indices: 76003--76853 Score: 1292
Period size: 106 Copynumber: 8.0 Consensus size: 106
75993 GACAGTTTTT
* * * * *
76003 CTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAATAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
76068 ATTTCAAAGCCAAGTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * * * ** *
76109 CTCAAGACAGCACAAGCTCAACTTCAC-AGCGAAGGGGCAGCTGACTGTCAACAAACAACTTCTC
1 CTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
76173 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * *
76215 CTCGAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGTTCTCAACAAACAATTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
76280 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
76321 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
76386 ATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
76427 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
76492 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
76533 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* * *
76598 ATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTCGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
76639 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACAACTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
76704 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * * *
76745 CTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCG
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
76810 ATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGA
76851 CTC
1 CTC
76854 GGAACAATCC
Statistics
Matches: 680, Mismatches: 62, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
105 2 0.00
106 677 1.00
107 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
Found at i:78233 original size:37 final size:36
Alignment explanation
Indices: 78169--78264 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 36
78159 TCAATTGATT
*
78169 TTTTTTACACTATATATTATTAT-TATATATACATAAA
1 TTTTTTA-AATAT-TATTATTATATATATATACATAAA
* * **
78206 TTTTTTAGATATTATTATTTATATATATATATATACC
1 TTTTTTAAATATTATTA-TTATATATATATACATAAA
78243 TTTTTTAAATATT-TTACTTATA
1 TTTTTTAAATATTATTA-TTATA
78265 AGCGTATTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
35 5 0.10
36 15 0.30
37 30 0.60
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.56
Consensus pattern (36 bp):
TTTTTTAAATATTATTATTATATATATATACATAAA
Found at i:78624 original size:38 final size:39
Alignment explanation
Indices: 78582--78664 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 39
78572 ATTTTTGATT
* *
78582 TTTTTATTAT-TATTTTACTTATATATATATGC-TTTTAC
1 TTTTTATTATATATTTTACTCATATATATATCCATTTT-C
* * *
78620 TTTTT-TTTTATATTTTACTCATTTATTTATCCATTTTC
1 TTTTTATTATATATTTTACTCATATATATATCCATTTTC
78658 TTTTTAT
1 TTTTTAT
78665 CTTTATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
37 3 0.08
38 29 0.78
39 5 0.14
ACGTcount: A:0.22, C:0.10, G:0.01, T:0.67
Consensus pattern (39 bp):
TTTTTATTATATATTTTACTCATATATATATCCATTTTC
Found at i:79732 original size:20 final size:20
Alignment explanation
Indices: 79707--79787 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
79697 TCTAATTTCA
*
79707 CAACACAGGTTCCAAAATCG
1 CAACACAGTTTCCAAAATCG
79727 CAACACAGTTTCCAAAATCG
1 CAACACAGTTTCCAAAATCG
* * **
79747 CAACGCGAATTT-GTAAATCG
1 CAACAC-AGTTTCCAAAATCG
79767 CAACACAGTTTCCAAAATCG
1 CAACACAGTTTCCAAAATCG
79787 C
1 C
79788 GTTGCGATAG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
19 4 0.08
20 42 0.84
21 4 0.08
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (20 bp):
CAACACAGTTTCCAAAATCG
Found at i:79878 original size:57 final size:57
Alignment explanation
Indices: 79780--80136 Score: 509
Period size: 57 Copynumber: 6.3 Consensus size: 57
79770 CACAGTTTCC
* * *
79780 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTCGCGTTGCGAATTTG
1 AAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTG
** * * * * *
79837 AAAATCGTATTGCGATAACATTGTTTACCTACATCGATAATTAGTGTTGCGAATTTA
1 AAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTG
*
79894 AAAATCGCGTTGCGGTAATACTGTTTACCTATATCGGTAATTAGTGTTGCG-ATTTGG
1 AAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTT-G
* * *
79951 AAAATCGCGTTGCGATAACACTGTTTACTTATATCGGTAATTAGCGTTGCGAATTTG
1 AAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTG
* * * *
80008 TAAATCGTGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTT
1 AAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTG
* *
80065 TAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTG
1 AAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTG
*
80122 AAAATCTCGTTGCGA
1 AAAATCGCGTTGCGA
80137 ATTTGTAAAT
Statistics
Matches: 265, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
56 4 0.02
57 257 0.97
58 4 0.02
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (57 bp):
AAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTG
Found at i:80135 original size:20 final size:20
Alignment explanation
Indices: 80110--80156 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
80100 GGTAATTAGT
*
80110 GTTGCGAATTTGAAAATCTC
1 GTTGCGAATTTGAAAATCGC
*
80130 GTTGCGAATTTGTAAATCGC
1 GTTGCGAATTTGAAAATCGC
80150 GTTGCGA
1 GTTGCGA
80157 TAATACTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:80148 original size:77 final size:77
Alignment explanation
Indices: 80053--80466 Score: 371
Period size: 77 Copynumber: 5.4 Consensus size: 77
80043 GGTAATTAGT
** * *
80053 GTTGCGAATTTTTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGTGTTGCGAA
1 GTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGAA
80118 TTTGAAAATCTC
66 TTTGAAAATCTC
* * **
80130 GTTGCGAATTTGTAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCGTTTTGAA
1 GTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGAA
80195 TTTGAAAATCTC
66 TTTGAAAATCTC
* * * * * ** * * *
80207 ATTGAGAATTTGAAAATCTCATTGCGA-A-T-TTGTAAATCGCGT-T-GCGAT-AGTA-CTGTTT
1 GTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTA-C-C-TATATCGGTAATTAGC-G-TT
** * **
80265 ACCTATATCGGTAAT-TAGC
61 ACGAAT-TTGAAAATCT--C
* * * *
80284 GTTGCGAATTTGTAAATTGCGTTGCGATAGTACTGTTTACTTATATCGGTAATTAGCGTTGCGAA
1 GTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGAA
80349 TTTGAAAATCTC
66 TTTGAAAATCTC
* *
80361 GTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATCAGCGTTACG-A
1 GTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGAA
* *
80425 TTT-ATATATTCGC
66 TTTGA-A-AATCTC
*
80438 GTTGCGAATTTAGAAAACCGCGTTGCGAT
1 GTTGCGAATTT-GAAAATCGCGTTGCGAT
80467 TTACATATTA
Statistics
Matches: 267, Mismatches: 51, Indels: 37
0.75 0.14 0.10
Matches are distributed among these distances:
73 1 0.00
74 8 0.03
75 11 0.04
76 13 0.05
77 191 0.72
78 23 0.09
79 11 0.04
80 8 0.03
81 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (77 bp):
GTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGAA
TTTGAAAATCTC
Found at i:80242 original size:97 final size:97
Alignment explanation
Indices: 80115--80300 Score: 327
Period size: 97 Copynumber: 1.9 Consensus size: 97
80105 TTAGTGTTGC
*
80115 GAATTTGAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAATACTGTTTACCTATATCGGT
1 GAATTTGAAAATCTCATTGCGAATTTGTAAATCGCGTTGCGATAATACTGTTTACCTATATCGGT
**
80180 AATTAGCGTTTTGAATTTGAAAATCTCATTGA
66 AATTAGCGTTGCGAATTTGAAAATCTCATTGA
*
80212 GAATTTGAAAATCTCATTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGT
1 GAATTTGAAAATCTCATTGCGAATTTGTAAATCGCGTTGCGATAATACTGTTTACCTATATCGGT
*
80277 AATTAGCGTTGCGAATTTGTAAAT
66 AATTAGCGTTGCGAATTTGAAAAT
80301 TGCGTTGCGA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (97 bp):
GAATTTGAAAATCTCATTGCGAATTTGTAAATCGCGTTGCGATAATACTGTTTACCTATATCGGT
AATTAGCGTTGCGAATTTGAAAATCTCATTGA
Found at i:80253 original size:20 final size:20
Alignment explanation
Indices: 80192--80244 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
80182 TTAGCGTTTT
*
80192 GAATTTGAAAATCTCATTGA
1 GAATTTGAAAATCTCATTGC
80212 GAATTTGAAAATCTCATTGC
1 GAATTTGAAAATCTCATTGC
*
80232 GAATTTGTAAATC
1 GAATTTGAAAATC
80245 GCGTTGCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (20 bp):
GAATTTGAAAATCTCATTGC
Found at i:80290 original size:231 final size:231
Alignment explanation
Indices: 79997--80420 Score: 758
Period size: 231 Copynumber: 1.8 Consensus size: 231
79987 GTAATTAGCG
* *
79997 TTGCGAATTTGTAAATCGTGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGTGTTGCGAAT
1 TTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAAT
* *
80062 TTTTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGTGTTGCGAATTTGAAAAT
66 TTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAAT
* * *
80127 CTCGTTGCGAATTTGTAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCGTTTT
131 CTCGTTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTACATCGGTAATCAGCGTTTT
80192 GAATTTGAAAATCTCATTGAGAATTTGAAAATCTCA
196 GAATTTGAAAATCTCATTGAGAATTTGAAAATCTCA
80228 TTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAAT
1 TTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAAT
* *
80293 TTGTAAATTGCGTTGCGATAGTACTGTTTACTTATATCGGTAATTAGCGTTGCGAATTTGAAAAT
66 TTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAAT
*
80358 CTCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATCAGCGTT
131 CTCGTTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTACATCGGTAATCAGCGTT
80421 ACGATTTATA
Statistics
Matches: 183, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
231 183 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (231 bp):
TTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAAT
TTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAAT
CTCGTTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTACATCGGTAATCAGCGTTTT
GAATTTGAAAATCTCATTGAGAATTTGAAAATCTCA
Found at i:80297 original size:57 final size:57
Alignment explanation
Indices: 80228--80367 Score: 244
Period size: 57 Copynumber: 2.5 Consensus size: 57
80218 GAAAATCTCA
80228 TTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
1 TTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
* *
80285 TTGCGAATTTGTAAATTGCGTTGCGATAGTACTGTTTACTTATATCGGTAATTAGCG
1 TTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
* *
80342 TTGCGAATTTGAAAATCTCGTTGCGA
1 TTGCGAATTTGTAAATCGCGTTGCGA
80368 ATTTGAAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 78 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (57 bp):
TTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
Found at i:80365 original size:20 final size:20
Alignment explanation
Indices: 80339--80387 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
80329 TCGGTAATTA
80339 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
*
80359 TCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
80379 GCGTTGCGA
1 GCGTTGCGA
80388 TAGTACTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:80475 original size:41 final size:39
Alignment explanation
Indices: 80416--80507 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 39
80406 TCGGTAATCA
* * *
80416 GCGTTACGATTTATATATTCGCGTTGCGAATTTAGAAAACC
1 GCGTTGCGATTTACATATTAGCGTTGCG-ATTTA-AAAACC
* * * *
80457 GCGTTGCGATTTACATATTATCGTTGCGATTTACATATC
1 GCGTTGCGATTTACATATTAGCGTTGCGATTTAAAAACC
80496 GCGTTGCGATTT
1 GCGTTGCGATTT
80508 TGGAACCTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 15 0.34
40 5 0.11
41 24 0.55
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (39 bp):
GCGTTGCGATTTACATATTAGCGTTGCGATTTAAAAACC
Found at i:80481 original size:20 final size:19
Alignment explanation
Indices: 80457--80507 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
80447 TTAGAAAACC
80457 GCGTTGCGATTTACATATTA
1 GCGTTGCGATTTACATA-TA
* *
80477 TCGTTGCGATTTACATATC
1 GCGTTGCGATTTACATATA
80496 GCGTTGCGATTT
1 GCGTTGCGATTT
80508 TGGAACCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (19 bp):
GCGTTGCGATTTACATATA
Found at i:80556 original size:19 final size:19
Alignment explanation
Indices: 80524--80560 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
80514 CTGTTTTGCG
*
80524 AAATTAGAGTTCGCGTTGT
1 AAATTAGAGATCGCGTTGT
*
80543 AAATTTGAGATCGCGTTG
1 AAATTAGAGATCGCGTTG
80561 CGAATTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (19 bp):
AAATTAGAGATCGCGTTGT
Found at i:80566 original size:19 final size:19
Alignment explanation
Indices: 80519--80568 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
80509 GGAACCTGTT
* *
80519 TTGCGAAATTAGAGTTCGCG
1 TTGCG-AATTTGAGATCGCG
**
80539 TTGTAAATTTGAGATCGCG
1 TTGCGAATTTGAGATCGCG
80558 TTGCGAATTTG
1 TTGCGAATTTG
80569 TTGGTCATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (19 bp):
TTGCGAATTTGAGATCGCG
Found at i:103198 original size:45 final size:47
Alignment explanation
Indices: 103125--103230 Score: 162
Period size: 45 Copynumber: 2.3 Consensus size: 47
103115 TTTATTTTCG
*
103125 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTTGAAT-AATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
103172 TTTTTTGAATAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
103218 TTTTTGTGAATAA
1 TTTTT-TGAATAA
103231 CAAAGCATGG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
45 28 0.51
46 11 0.20
47 16 0.29
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:112907 original size:21 final size:20
Alignment explanation
Indices: 112865--113078 Score: 114
Period size: 21 Copynumber: 9.8 Consensus size: 20
112855 TCGCTTGAAG
112865 AAAAATGAAAAATAATG-AAAA
1 AAAAATGAAAAA-AA-GAAAAA
*
112886 AAATA-GAAAAAAAGAAAGAA
1 AAAAATGAAAAAAAGAAA-AA
*
112906 AAAAATGAAGAAAAGAAAAAAA
1 AAAAATGAA-AAAA-AGAAAAA
*
112928 TGAAAAATG-AAAAATGAAAAA
1 --AAAAATGAAAAAAAGAAAAA
*
112949 TGAAAAATG-AAAAATGAAAAA
1 --AAAAATGAAAAAAAGAAAAA
*
112970 TGAAAAATGAAAAATGAAAAAAATA
1 --AAAAATGAAAAA--AAGAAAA-A
112995 AAAAATGAAAAAAATGAAAAAA
1 AAAAATGAAAAAAA-G-AAAAA
*
113017 TGAAAAATG-AAAAATGAAAAA
1 --AAAAATGAAAAAAAGAAAAA
113038 TGAAAAATGAAAAAAGAAGAAAAA
1 --AAAAATG-AAAAA-AAGAAAAA
*
113062 AGAAAAAGAAATAAAAG
1 A-AAAATGAAA-AAAAG
113079 GAGGGTTCAA
Statistics
Matches: 162, Mismatches: 11, Indels: 39
0.76 0.05 0.18
Matches are distributed among these distances:
18 1 0.01
19 4 0.02
20 12 0.07
21 58 0.36
22 23 0.14
23 37 0.23
24 26 0.16
25 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAAATGAAAAAAAGAAAAA
Found at i:113068 original size:7 final size:7
Alignment explanation
Indices: 112923--113051 Score: 204
Period size: 7 Copynumber: 17.7 Consensus size: 7
112913 AAGAAAAGAA
112923 AAAAATG
1 AAAAATG
112930 AAAAATG
1 AAAAATG
112937 AAAAATG
1 AAAAATG
112944 AAAAATG
1 AAAAATG
112951 AAAAATG
1 AAAAATG
112958 AAAAATG
1 AAAAATG
112965 AAAAATG
1 AAAAATG
112972 AAAAATG
1 AAAAATG
112979 AAAAATG
1 AAAAATG
*
112986 AAAAAAATA
1 --AAAAATG
112995 AAAAATG
1 AAAAATG
113002 AAAAAAATG
1 --AAAAATG
113011 AAAAAATG
1 -AAAAATG
113019 AAAAATG
1 AAAAATG
113026 AAAAATG
1 AAAAATG
113033 AAAAATG
1 AAAAATG
113040 AAAAATG
1 AAAAATG
113047 AAAAA
1 AAAAA
113052 AGAAGAAAAA
Statistics
Matches: 116, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
7 95 0.82
8 8 0.07
9 13 0.11
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:114357 original size:37 final size:36
Alignment explanation
Indices: 114300--114371 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
114290 AAACAGGTCA
*
114300 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAACC
*
114336 ATCTATAAGCCTTCACAGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACAGAAGAGTAGTGAAGCAAAC
114372 TCATTTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAACC
Found at i:114437 original size:51 final size:51
Alignment explanation
Indices: 114373--114631 Score: 211
Period size: 51 Copynumber: 4.9 Consensus size: 51
114363 GAAGCAAACT
*
114373 CATTTTATGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CATTTTATAAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
114424 CATTTTATAAAGATCGAGTCCTATACGCTTTAAATGAATAGGGAGCGGACA
1 CATTTTATAAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
114475 CGTTTGT-TCAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGG--A
1 CATTT-TATAAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * *
114524 CTTGTTTATTGAAGATTTTCCGAGTTCTATACTCTCTGAAGGAATAGAGAGCTGACC
1 CAT-TTTA-TAAAGA---T-CGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
114581 CGTTTTATTAAAGATTGTTCAAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 CATTTTA-TAAAGA----TCGAGTCCTATACTCT-CTGAAGGAATAGGGAGC
114632 ATGCTCGTCA
Statistics
Matches: 169, Mismatches: 27, Indels: 19
0.79 0.13 0.09
Matches are distributed among these distances:
49 4 0.02
50 2 0.01
51 90 0.53
52 1 0.01
54 1 0.01
55 30 0.18
56 36 0.21
57 5 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (51 bp):
CATTTTATAAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Done.