Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006894.1 Hibiscus syriacus cultivar Beakdansim tig00017596_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: 213556
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:146877 original size:19 final size:19
Alignment explanation
Indices: 146855--146985 Score: 96
Period size: 19 Copynumber: 7.7 Consensus size: 19
146845 AGAAATTAAA
*
146855 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
146874 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
146890 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
146907 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
146921 TAC-CATATGCGATTTTCAT
1 TTCGCAT-TGCGATTTTCAT
146940 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
146956 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
146973 TTCGCATTGCGAT
1 TTCGCATTGCGAT
146986 AGTAATTTTC
Statistics
Matches: 86, Mismatches: 9, Indels: 34
0.67 0.07 0.26
Matches are distributed among these distances:
13 3 0.03
14 20 0.23
16 14 0.16
17 14 0.16
19 32 0.37
20 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:146901 original size:33 final size:33
Alignment explanation
Indices: 146859--146985 Score: 195
Period size: 33 Copynumber: 3.8 Consensus size: 33
146849 ATTAAATTCG
146859 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
146892 CGTTGCGATTTTCATTTCGCATTGCGAAAT-AC-
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCACT
* *
146924 CATATGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGT-TGCGATTTTCATTTCGCATTGCGATTCACT
146958 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
146986 AGTAATTTTC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
32 4 0.05
33 77 0.91
34 4 0.05
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:149294 original size:12 final size:12
Alignment explanation
Indices: 149277--149301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
149267 TCTTCGGGGA
149277 CTTTTTCTTCTT
1 CTTTTTCTTCTT
149289 CTTTTTCTTCTT
1 CTTTTTCTTCTT
149301 C
1 C
149302 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:150568 original size:33 final size:33
Alignment explanation
Indices: 150521--150614 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
150511 TCATTTGACC
** *
150521 ATCGCAATGTGAAATGAAAATCGCAACGATAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
150554 ATCGCAATACGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
150587 ATCGCAA-AGCGAAATGAAAATCGCAACG
1 ATCGCAATA-CGAAATGAAAATCGCAACG
150615 CGATTTTAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
32 1 0.02
33 55 0.98
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:150577 original size:19 final size:19
Alignment explanation
Indices: 150521--150579 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
150511 TCATTTGACC
**
150521 ATCGCAATGTGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
150540 ATCGC-A-ACG--AT-AGA
1 ATCGCAATACGAAATGAAA
150554 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
150573 ATCGCAA
1 ATCGCAA
150580 CGAGGGAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
16 3 0.10
17 1 0.03
18 3 0.10
19 14 0.45
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:150642 original size:18 final size:18
Alignment explanation
Indices: 150614--150657 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
150604 AAATCGCAAC
150614 GCGATTTTAGTTTCGCGTT
1 GCGA-TTTAGTTTCGCGTT
150633 GCGATTTAGTTTCGCGTT
1 GCGATTTAGTTTCGCGTT
150651 GCGATTT
1 GCGATTT
150658 TGTCGTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.45
Consensus pattern (18 bp):
GCGATTTAGTTTCGCGTT
Found at i:150684 original size:33 final size:33
Alignment explanation
Indices: 150629--150787 Score: 223
Period size: 33 Copynumber: 4.8 Consensus size: 33
150619 TTTAGTTTCG
* *
150629 CGTTGCGA-TTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCGTTGCGATTCTCT
*
150661 CGTTGTGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
150694 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
150727 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
150760 CGTTGCGATATTCAGTTTCGTGTTGCGA
1 CGTTGCGATTTTCA-TTTCGCGTTGCGA
150788 CATGCTATTT
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.06
33 97 0.84
34 12 0.10
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:150689 original size:19 final size:19
Alignment explanation
Indices: 150614--150755 Score: 86
Period size: 19 Copynumber: 8.3 Consensus size: 19
150604 AAATCGCAAC
150614 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
150633 GCGA-TTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
*
150651 GCGA-TTT--TGT--CGTT
1 GCGATTTTCATTTCGCGTT
*
150665 GTGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
150684 GCGA--TTC---TCTCGTT
1 GCGATTTTCATTTCGCGTT
*
150698 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
*
150717 GCGA--TTC---TCTCGTT
1 GCGATTTTCATTTCGCGTT
*
150731 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
150750 GCGATT
1 GCGATT
150756 CTCTCGTTGC
Statistics
Matches: 97, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
14 26 0.27
15 3 0.03
16 8 0.08
17 8 0.08
18 21 0.22
19 31 0.32
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:150699 original size:14 final size:14
Alignment explanation
Indices: 150680--150768 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
150670 TTTCATTTCG
150680 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
150694 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
150711 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
*
150727 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
150744 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
150760 CGTTGCGAT
1 CGTTGCGAT
150769 ATTCAGTTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 21 0.34
16 14 0.23
17 14 0.23
19 12 0.20
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:152378 original size:21 final size:20
Alignment explanation
Indices: 152354--152413 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
152344 AACGGTGGGG
152354 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGG--A
* **
152375 GGGGCCTCTTGAACGATTGGA
1 GGGGACTCTTGAGGGA-TGGA
152396 GGGGACTCTTGAGGGATG
1 GGGGACTCTTGAGGGATG
152414 ACAGGTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
23 2 0.06
ACGTcount: A:0.20, C:0.13, G:0.45, T:0.22
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGGA
Found at i:152804 original size:20 final size:19
Alignment explanation
Indices: 152781--152848 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
152771 GAAACTTAAA
152781 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
152801 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
152821 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
152840 ATCGCAACG
1 ATCGCAACG
152849 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:152856 original size:14 final size:14
Alignment explanation
Indices: 152837--152957 Score: 98
Period size: 14 Copynumber: 7.7 Consensus size: 14
152827 ATGCGAAATG
152837 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
152851 AAAATCGCAAAGCGAAATG
1 AAAATCGC-AA-CG--A-C
152870 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
152884 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
152900 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
152916 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
152932 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
152948 AAAATCGCAA
1 AAAATCGCAA
152958 TGCGAAACAC
Statistics
Matches: 88, Mismatches: 6, Indels: 26
0.73 0.05 0.22
Matches are distributed among these distances:
14 36 0.41
15 3 0.03
16 18 0.20
17 2 0.02
18 21 0.24
19 8 0.09
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:152912 original size:32 final size:33
Alignment explanation
Indices: 152821--152964 Score: 256
Period size: 32 Copynumber: 4.4 Consensus size: 33
152811 GGAAATGGCT
152821 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
152854 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
152887 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
152919 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
152951 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
152965 CACAAATCGC
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
32 60 0.56
33 47 0.44
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:152972 original size:65 final size:64
Alignment explanation
Indices: 152821--152975 Score: 240
Period size: 65 Copynumber: 2.4 Consensus size: 64
152811 GGAAATGGCT
152821 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAAAGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAA--AAAATCGCAACGACAAAATCGCAAAGCGAAATGAAAATCGCAACGACAA
152886 A
64 A
* *
152887 ATCGCAATGCGAAATGAAATCGCAACGACAAAATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAA-AAAATCGCAACGACAAAATCGCAAAGCGAAATGAAAATCGCAACGACAAA
152951 ATCGCAATGCGAAACACAAATCGCA
1 ATCGCAATGCGAAA-A-AAATCGCA
152976 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
64 30 0.36
65 39 0.47
66 14 0.17
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (64 bp):
ATCGCAATGCGAAAAAAATCGCAACGACAAAATCGCAAAGCGAAATGAAAATCGCAACGACAAA
Found at i:152993 original size:19 final size:19
Alignment explanation
Indices: 152971--153053 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
152961 GAAACACAAA
152971 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
152990 TCGCGTTGCGATTATCATT
1 TCGCATTGCGATTTTCATT
*
153009 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
153025 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
153042 TCGCTTTGCGAT
1 TCGCATTGCGAT
153054 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.08
17 4 0.08
18 2 0.04
19 34 0.64
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:153060 original size:19 final size:20
Alignment explanation
Indices: 153038--153092 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
153028 TTGCGATTTT
*
153038 CATTT-CGCTTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
153057 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
* *
153077 CATTTTCGTGTTGCGA
1 CATTTCCGCGTTGCGA
153093 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:154968 original size:20 final size:20
Alignment explanation
Indices: 154920--154978 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
154910 AATAGTTTCT
** *
154920 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
154940 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
154960 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
154979 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:155032 original size:15 final size:15
Alignment explanation
Indices: 155012--155040 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
155002 AATCGCGTTG
155012 CGATTTTCATTTCGA
1 CGATTTTCATTTCGA
155027 CGATTTTCATTTCG
1 CGATTTTCATTTCG
155041 CGTTGCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (15 bp):
CGATTTTCATTTCGA
Found at i:155517 original size:20 final size:20
Alignment explanation
Indices: 155467--155601 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
155457 CGCTTTGAAA
*
155467 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
155488 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
155508 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
155528 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
155549 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
155569 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
155589 ATCACATTGCGAT
1 ATCGCATTGCGAT
155602 TTTCCCAATT
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.05
20 63 0.68
21 23 0.25
22 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:155573 original size:61 final size:61
Alignment explanation
Indices: 155471--155604 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 61
155461 TTGAAAATCG
* * * *
155471 CATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCT
1 CATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCA
* * * *
155532 CGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCA
1 CATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCA
155593 CATTGCGATTTT
1 CATTGCGATTTT
155605 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (61 bp):
CATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCA
Found at i:155620 original size:61 final size:61
Alignment explanation
Indices: 155487--155622 Score: 166
Period size: 61 Copynumber: 2.2 Consensus size: 61
155477 GATTATGTAT
* * * * ** *
155487 TATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCACATTGCGATTTTCCAA
* * *
155548 TATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCACATTGCGATTTT-CCAA
155610 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
155623 TTACTTATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 61 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCACATTGCGATTTTCCAA
Found at i:158193 original size:21 final size:21
Alignment explanation
Indices: 158169--158214 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
158159 ATTCTGACTA
158169 TCGCGTTGCGACTTTCCAAAT
1 TCGCGTTGCGACTTTCCAAAT
* *
158190 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGACTTTCCAAAT
158211 TCGC
1 TCGC
158215 AATGTGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.20, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGACTTTCCAAAT
Found at i:158236 original size:20 final size:20
Alignment explanation
Indices: 158211--158303 Score: 141
Period size: 20 Copynumber: 4.7 Consensus size: 20
158201 TTTTCCTAAT
*
158211 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
**
158231 TCGCAATGCGAATATATAAA
1 TCGCAATGCGAATACGTAAA
* *
158251 TCTCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
158271 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
158291 TCGCAATGCGAAT
1 TCGCAATGCGAAT
158304 CTGACTATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:158313 original size:20 final size:20
Alignment explanation
Indices: 158290--158341 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
158280 GAATACGTAA
158290 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
158310 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
*
158330 ATCACAATGCGA
1 ATCGCAATGCGA
158342 TTTACATAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:158318 original size:60 final size:59
Alignment explanation
Indices: 158211--158323 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
158201 TTTTCCTAAT
* * *
158211 TCGCAATGTGAATACGTAAATCGCAATGCGAATATATAAATCTCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATATAT-AATCGCAATGCGAATACGTAAA
*
158271 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACT-ATCGCAATGCGAAT
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAT-A-TAATCGCAATGCGAAT
158324 CTGACTATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
60 45 0.96
61 1 0.02
62 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (59 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATATATAATCGCAATGCGAATACGTAAA
Found at i:158546 original size:22 final size:22
Alignment explanation
Indices: 158521--158586 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
158511 GGCGACATCC
158521 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
158543 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* **
158565 GTCTCCATCTCCGGTGAAATCA
1 GTCCCCATCTCCGACGAAATCA
158587 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:158946 original size:19 final size:19
Alignment explanation
Indices: 158922--158969 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
158912 GCGATTCTGT
158922 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
158941 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
158960 CGTTGCGATT
1 CGTTGCGATT
158970 CTTGCGTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:160596 original size:31 final size:31
Alignment explanation
Indices: 160558--160713 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
160548 AGGGTCGAGG
160558 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
160589 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
160620 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
160651 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
160682 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
160713 G
1 G
160714 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:163919 original size:21 final size:21
Alignment explanation
Indices: 163893--163937 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
163883 GATTTCTGGG
* *
163893 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
163914 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
163935 CAA
1 CAA
163938 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:164779 original size:31 final size:31
Alignment explanation
Indices: 164741--164896 Score: 244
Period size: 31 Copynumber: 5.0 Consensus size: 31
164731 AGGGTCGAGG
164741 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
164772 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
164803 GTTTACCTATGTTCTTCGGGACATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
164834 GTTTACCTATG-TCATTCGGGACATATGGACT
1 GTTTACCTATGTTC-TTCGGGACATATGGACT
* * *
164865 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
164896 G
1 G
164897 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
30 2 0.02
31 112 0.96
32 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:167543 original size:20 final size:20
Alignment explanation
Indices: 167518--167637 Score: 114
Period size: 20 Copynumber: 5.6 Consensus size: 20
167508 AGAATAGTTT
*
167518 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
167538 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
167558 ACTATCGCAACGAGAAAATCG
1 ACTATCGCAACGCGAAAAT-G
*
167579 CAACAACAAAATCGCAACGCGAAAATG
1 -----AC--TATCGCAACGCGAAAATG
* * *
167606 ACTATCGTAATGCAAAAATG
1 ACTATCGCAACGCGAAAATG
167626 ACTATCGCAACG
1 ACTATCGCAACG
167638 AAAGAATCGC
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
20 61 0.74
21 1 0.01
22 2 0.02
26 2 0.02
27 1 0.01
28 15 0.18
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.16
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:167580 original size:14 final size:14
Alignment explanation
Indices: 167561--167604 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
167551 GAAAATGACT
167561 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
* *
167575 ATCGCAACAACAAA
1 ATCGCAACGAGAAA
*
167589 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
167603 AT
1 AT
167605 GACTATCGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:167630 original size:68 final size:68
Alignment explanation
Indices: 167521--167649 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 68
167511 ATAGTTTACT
* *
167521 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAA-AATCGCAACAA
1 ATCGCAACGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGA-AAGAATCGCAACAA
167585 CAAA
65 CAAA
* *
167589 ATCGCAACGCGAAAATGACTATCGTAATGCAAAAATGACTATCGCAACGAAAGAATCGCAA
1 ATCGCAACGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAAAGAATCGCAA
167650 TGCGAAATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
67 2 0.04
68 54 0.96
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.15
Consensus pattern (68 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAAAGAATCGCAACAAC
AAA
Found at i:167741 original size:20 final size:20
Alignment explanation
Indices: 167680--167745 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
167670 GCGATTCTCT
167680 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
167700 CATCGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
167720 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
167740 CGTTGC
1 CGTTGC
167746 AATTTTAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:168271 original size:18 final size:19
Alignment explanation
Indices: 168232--168273 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
168222 CTCACCTGTC
168232 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
168253 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
168271 ATC
1 ATC
168274 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:169740 original size:14 final size:14
Alignment explanation
Indices: 169721--169756 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
169711 ATTGTTTAAT
169721 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
169735 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
169749 TGATTTGT
1 TGATTTGT
169757 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:169980 original size:14 final size:14
Alignment explanation
Indices: 169961--170014 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
169951 CATTTTCGCA
169961 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
169975 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
169992 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
170008 TTGCGAT
1 TTGCGAT
170015 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:169982 original size:34 final size:34
Alignment explanation
Indices: 169939--170034 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
169929 ACTAATTTTG
169939 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
169973 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
170006 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
170035 AGTCATTTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:170031 original size:20 final size:20
Alignment explanation
Indices: 170006--170079 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
169996 GCGATTCTCT
170006 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
**
170026 CGTTGCGATAGTCATTTCTA
1 CGTTGCGATAGTCATTTCCG
*
170046 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
170066 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
170080 AATGAATGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:173419 original size:20 final size:20
Alignment explanation
Indices: 173394--173452 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
173384 TTCAGTATTA
173394 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
* *
173414 CGATAGTCATAATCTCGTTG
1 CGATAGTCAGAATCGCGTTG
*
173434 CGATAGTCAGATTCGCGTT
1 CGATAGTCAGAATCGCGTT
173453 ATAATTTACG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (20 bp):
CGATAGTCAGAATCGCGTTG
Found at i:173479 original size:20 final size:20
Alignment explanation
Indices: 173456--173496 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
173446 TCGCGTTATA
173456 ATTTACGTATTCACATTGCG
1 ATTTACGTATTCACATTGCG
*
173476 ATTTACGTATTCGCATTGCG
1 ATTTACGTATTCACATTGCG
173496 A
1 A
173497 ATTAGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
ATTTACGTATTCACATTGCG
Found at i:173517 original size:21 final size:21
Alignment explanation
Indices: 173493--173538 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
173483 TATTCGCATT
173493 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
173514 GCGAATTTGGAAAATTGCAAT
1 GCGAATTAGGAAAATCGCAAC
173535 GCGA
1 GCGA
173539 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:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:175055 original size:2 final size:2
Alignment explanation
Indices: 175050--175103 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
175040 AGAGAAATGT
175050 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
175092 TA TA TA TA TA TA
1 TA TA TA TA TA TA
175104 CTCTGAATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:179445 original size:2 final size:2
Alignment explanation
Indices: 179440--179475 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
179430 TTTTTTCTTC
179440 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
179476 TGAATAAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:179792 original size:20 final size:20
Alignment explanation
Indices: 179764--179803 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
179754 CGTCGTGATT
*
179764 ATTTTATAACAATTTGATAA
1 ATTTAATAACAATTTGATAA
* *
179784 ATTTAATAACTATTTTATAA
1 ATTTAATAACAATTTGATAA
179804 CTTTTAAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTTAATAACAATTTGATAA
Found at i:181076 original size:2 final size:2
Alignment explanation
Indices: 181069--181125 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
181059 GCTAGAAAGT
181069 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
181111 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
181126 TGTTTTCTTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:193185 original size:21 final size:21
Alignment explanation
Indices: 193161--193230 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
193151 ATTTTTCAAA
193161 ATCGCAACGCGAACTTTGACT
1 ATCGCAACGCGAACTTTGACT
**
193182 ATCGCAA--CGAA-TTTGAAAA
1 ATCGCAACGCGAACTTTG-ACT
* *
193201 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTTGACT
193222 ATCGCAACG
1 ATCGCAACG
193231 AATTTGGACT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
21 20 0.51
22 3 0.08
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTTGACT
Found at i:193215 original size:40 final size:40
Alignment explanation
Indices: 193158--193236 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
193148 GCGATTTTTC
*
193158 AAAATCGCAACGCGAACTTTGACTATCGCAACGAATTTGA
1 AAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGA
*
193198 AAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTG
1 AAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTG
193237 GACTAACGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (40 bp):
AAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGA
Found at i:193239 original size:19 final size:19
Alignment explanation
Indices: 193178--193241 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
193168 CGCGAACTTT
193178 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
* ** *
193197 AAAAATCGCAACGTGAACTTG
1 GACTATCGCAAC--GAATTTG
193218 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
193237 GACTA
1 GACTA
193242 ACGTAAATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 20 0.57
21 15 0.43
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (19 bp):
GACTATCGCAACGAATTTG
Found at i:193438 original size:19 final size:19
Alignment explanation
Indices: 193406--193453 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
193396 GGAAACTGAT
*
193406 TTGCGATATTAGAGATCGCG
1 TTGCGAT-TTAGAGATCGCA
193426 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
193445 TTGCGATTT
1 TTGCGATTT
193454 TGTTGGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Found at i:200350 original size:17 final size:17
Alignment explanation
Indices: 200317--200350 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
200307 AATGAATAAT
*
200317 TTTAAAATATTAGAATA
1 TTTAAAATATTAAAATA
*
200334 TTTAAAATTTTAAAATA
1 TTTAAAATATTAAAATA
200351 GATAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAAATATTAAAATA
Found at i:204464 original size:21 final size:20
Alignment explanation
Indices: 204378--204532 Score: 80
Period size: 21 Copynumber: 7.7 Consensus size: 20
204368 AAATGACCAA
**
204378 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
204397 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
204417 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
204437 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
204458 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
204479 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
204499 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
204520 GAAAATCGCAACG
1 CAAAATCGCAACG
204533 TGAACACATA
Statistics
Matches: 101, Mismatches: 29, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 39 0.39
21 46 0.46
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:204528 original size:20 final size:20
Alignment explanation
Indices: 204503--204554 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
204493 GATTTTCAAG
* *
204503 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
*
204523 AATCGCAACGTGAACACATA
1 AATCGCAACGCGAACACATA
204543 AATCGCAACGCG
1 AATCGCAACGCG
204555 TATCCGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:204564 original size:20 final size:20
Alignment explanation
Indices: 204541--204731 Score: 224
Period size: 20 Copynumber: 9.6 Consensus size: 20
204531 CGTGAACACA
204541 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
204561 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
*
204581 TAAATAGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
204601 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
204621 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
204641 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
204661 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
204681 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
204701 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
204721 TAAATCACAAC
1 TAAATCGCAAC
204732 ACTGAAATTT
Statistics
Matches: 146, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:204570 original size:40 final size:38
Alignment explanation
Indices: 204503--204731 Score: 215
Period size: 40 Copynumber: 5.8 Consensus size: 38
204493 GATTTTCAAG
* ** * *
204503 AATCGCAACGCGAATATGAAAATCGCAACGTGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGT-AAC-CGTA
* *
204543 AATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAAC--GTAACCGTA
* *
204583 AATAGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAA--CGTAACCGTA
*
204623 TATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-TAA-CCGTA
* * *
204663 AATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-TAA-CCGTA
* * * *
204703 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
204732 ACTGAAATTT
Statistics
Matches: 166, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 157 0.95
41 2 0.01
42 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (38 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGTAACCGTA
Found at i:205461 original size:24 final size:24
Alignment explanation
Indices: 205422--205468 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
205412 AAATTTGGTC
205422 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
205446 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
205469 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:205660 original size:12 final size:12
Alignment explanation
Indices: 205643--205667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
205633 ATATAATCCT
205643 GAAGAAGAAAAA
1 GAAGAAGAAAAA
205655 GAAGAAGAAAAA
1 GAAGAAGAAAAA
205667 G
1 G
205668 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:208016 original size:34 final size:33
Alignment explanation
Indices: 207948--208127 Score: 261
Period size: 33 Copynumber: 5.2 Consensus size: 33
207938 CGGAAATTAC
207948 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * *
207981 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAA
*
208015 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
208053 AATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAA
208087 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
208120 AATCGCAA
1 AATCGCAA
208128 TGCGAAATGA
Statistics
Matches: 134, Mismatches: 6, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
33 51 0.38
34 49 0.37
36 3 0.02
38 17 0.13
39 14 0.10
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:208025 original size:53 final size:52
Alignment explanation
Indices: 207962--208198 Score: 313
Period size: 53 Copynumber: 4.5 Consensus size: 52
207952 GCAACGAGAG
*
207962 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGC-GAAATGAA
*
208015 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AA-GAAAATCGCAATGCGAAATGAA
* *
208067 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
208120 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGC-GAAATGAA
208173 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
208199 TTGCAATTCT
Statistics
Matches: 167, Mismatches: 5, Indels: 24
0.85 0.03 0.12
Matches are distributed among these distances:
48 10 0.06
49 1 0.01
50 2 0.01
51 1 0.01
52 47 0.28
53 90 0.54
55 2 0.01
56 1 0.01
57 2 0.01
58 11 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:208055 original size:72 final size:72
Alignment explanation
Indices: 207962--208198 Score: 298
Period size: 72 Copynumber: 3.4 Consensus size: 72
207952 GCAACGAGAG
*
207962 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
208027 AAATGAA
66 AAATGAA
* *
208034 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
*
208097 --A-GAG
66 AAATGAA
*
208101 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAGAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AA-GAAAATCGCAATGCGGAAATGAAAATCGCA
208160 ATGCGGAAATGAA
61 ATGC-GAAATGAA
208173 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
208199 TTGCAATTCT
Statistics
Matches: 146, Mismatches: 8, Indels: 22
0.83 0.05 0.12
Matches are distributed among these distances:
66 10 0.07
67 30 0.21
68 2 0.01
69 3 0.02
70 3 0.02
71 2 0.01
72 96 0.66
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:208105 original size:86 final size:86
Alignment explanation
Indices: 208015--208180 Score: 332
Period size: 86 Copynumber: 1.9 Consensus size: 86
208005 CGGAAATGAA
208015 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
208080 AAATGAAAATCGCAACGAGAG
66 AAATGAAAATCGCAACGAGAG
208101 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
208166 AAATGAAAATCGCAA
66 AAATGAAAATCGCAA
208181 TGCGAAATGA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.13
Consensus pattern (86 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
AAATGAAAATCGCAACGAGAG
Found at i:208218 original size:86 final size:86
Alignment explanation
Indices: 208034--208205 Score: 251
Period size: 86 Copynumber: 2.0 Consensus size: 86
208024 GCGAAATGAA
* *
208034 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
* *
208099 AGAATCG-CAATGCGAAATG-AA-
66 A-AAT-GAAAAT-CGCAATGCAAT
208120 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
*
208185 AAATGAAAATCGCATTGCAAT
66 AAATGAAAATCGCAATGCAAT
208206 TCTCTCATTG
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
84 6 0.08
85 8 0.10
86 64 0.82
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (86 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAATGCAAT
Found at i:208238 original size:53 final size:52
Alignment explanation
Indices: 208175--208290 Score: 142
Period size: 53 Copynumber: 2.2 Consensus size: 52
208165 GAAATGAAAA
*
208175 TCGCAATGCGAAATGAAAATCGCATTGCAATTCTCTCATTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCAATTCTCTCATTGCGATTTTCATT
** ** ** * *
208227 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCAATTCTCTCATTGCGATTTTCATT
208280 TCGCATTGCGA
1 TCGCATTGCGA
208291 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
52 11 0.20
53 43 0.80
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCAATTCTCTCATTGCGATTTTCATT
Found at i:208253 original size:19 final size:19
Alignment explanation
Indices: 208211--208300 Score: 127
Period size: 19 Copynumber: 4.9 Consensus size: 19
208201 GCAATTCTCT
208211 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
208231 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
208250 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
208266 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
208283 CATTGCGATTTTCATTTC
1 CATTGCGATTTTCATTTC
208301 AACATAATGC
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.41
20 17 0.27
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:208410 original size:14 final size:14
Alignment explanation
Indices: 208391--208427 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
208381 CATCAATTAC
208391 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
208405 ACAAATCATCTTTT
1 ACAAATCAACTTTT
208419 ACAAATCAA
1 ACAAATCAA
208428 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:210387 original size:19 final size:19
Alignment explanation
Indices: 210345--210503 Score: 175
Period size: 19 Copynumber: 8.6 Consensus size: 19
210335 TAGTTTACTT
* *
210345 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
210365 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
210384 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
210403 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
210422 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
210441 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
210455 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
210474 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
210493 TCGCAATGCGA
1 TCGCAACGCGA
210504 TTTTGGTTCG
Statistics
Matches: 120, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
14 8 0.07
16 5 0.04
17 5 0.04
19 90 0.75
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:210479 original size:52 final size:55
Alignment explanation
Indices: 210345--210498 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 55
210335 TAGTTTACTT
* * *
210345 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGAAAATCGCAAC-AG-AACCAAAA
*
210403 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAAC-G-A-CAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
* **
210455 TCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAA
210499 TGCGATTTTG
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
52 45 0.51
53 1 0.01
55 1 0.01
57 29 0.33
58 13 0.15
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (55 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
Found at i:210552 original size:19 final size:17
Alignment explanation
Indices: 210499--210589 Score: 77
Period size: 14 Copynumber: 5.4 Consensus size: 17
210489 AAAATCGCAA
210499 TGCGATTTTGGTTCGCGT
1 TGCGATTTT-GTTCGCGT
210517 TGCGATTTTG-T--CGT
1 TGCGATTTTGTTCGCGT
210531 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-G-TTCGCGT
*
210550 TGCGATTCTG-T--CGT
1 TGCGATTTTGTTCGCGT
*
210564 TGCGATTTTCATTTCGCGT
1 TGCGATTTT--GTTCGCGT
210583 TGCGATT
1 TGCGATT
210590 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 3 0.05
18 10 0.17
19 21 0.35
ACGTcount: A:0.08, C:0.18, G:0.29, T:0.46
Consensus pattern (17 bp):
TGCGATTTTGTTCGCGT
Found at i:210552 original size:33 final size:33
Alignment explanation
Indices: 210499--210621 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
210489 AAAATCGCAA
*
210499 TGCGATTTTGG-TTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
210531 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
210564 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
210597 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
210622 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 11 0.13
33 59 0.72
34 12 0.15
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:210599 original size:14 final size:14
Alignment explanation
Indices: 210547--210603 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
210537 TTTGGTTTCG
*
210547 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
210561 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
210580 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
210594 CGTTGCGATT
1 CGTTGCGATT
210604 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:210785 original size:83 final size:87
Alignment explanation
Indices: 210669--210941 Score: 315
Period size: 93 Copynumber: 3.1 Consensus size: 87
210659 ATGGATTGCA
* **
210669 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ACTTACAGTGAGATACACAGTTTAGCA
* *
210728 GAATTGGTAGCAACTGAACAAAT
65 GAATTGGCAGCAACCGAACAAAT
*
210751 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
210816 TAGCAGAATTGGCAGCAACCGAACAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
*
210844 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
*
210909 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
210937 TTACT
1 TTACT
210942 AAGCAATCTA
Statistics
Matches: 172, Mismatches: 7, Indels: 13
0.90 0.04 0.07
Matches are distributed among these distances:
82 7 0.04
83 31 0.18
84 3 0.02
85 1 0.01
90 1 0.01
92 2 0.01
93 127 0.74
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTTACAGTGAGATACACAGTTTAGCAG
AATTGGCAGCAACCGAACAAAT
Found at i:210878 original size:93 final size:93
Alignment explanation
Indices: 210719--210941 Score: 419
Period size: 93 Copynumber: 2.4 Consensus size: 93
210709 TCAGGGTATT
* *
210719 AGTTTAGCAGAATTGGTAGCAACTGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
210784 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
210812 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
210877 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
210905 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
210942 AAGCAATCTA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 127 1.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:212642 original size:12 final size:12
Alignment explanation
Indices: 212625--212650 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
212615 TTGAAATGAA
212625 AATCGCAACGAG
1 AATCGCAACGAG
212637 AATCGCAACGAG
1 AATCGCAACGAG
212649 AA
1 AA
212651 ATGAAAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.08
Consensus pattern (12 bp):
AATCGCAACGAG
Found at i:212655 original size:31 final size:31
Alignment explanation
Indices: 212617--212719 Score: 188
Period size: 31 Copynumber: 3.3 Consensus size: 31
212607 TCTTTTGGTT
*
212617 GAAATGAAAATCGCAACGAGAATCGCAACGA
1 GAAATGAAAATCGCAACGAGAATCGCAACGC
212648 GAAATGAAAATCGCAACGAAGAATCGCAACGC
1 GAAATGAAAATCGCAACG-AGAATCGCAACGC
212680 GAAATGAAAATCGCAACGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAATCGCAACGC
212711 GAAATGAAA
1 GAAATGAAA
212720 TGCATGCGAT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 40 0.57
32 30 0.43
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.10
Consensus pattern (31 bp):
GAAATGAAAATCGCAACGAGAATCGCAACGC
Found at i:212661 original size:19 final size:19
Alignment explanation
Indices: 212637--212701 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
212627 TCGCAACGAG
212637 AATCGCAACGAGAAATGAA
1 AATCGCAACGAGAAATGAA
212656 AATCGCAAC--G-AA-G--
1 AATCGCAACGAGAAATGAA
*
212669 AATCGCAACGCGAAATGAA
1 AATCGCAACGAGAAATGAA
212688 AATCGCAACGAGAA
1 AATCGCAACGAGAA
212702 TCGCAACGCG
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.23
15 2 0.05
16 4 0.10
17 2 0.05
19 22 0.56
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.09
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAA
Found at i:212758 original size:14 final size:14
Alignment explanation
Indices: 212739--212795 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
212729 TTTGGTTTCG
212739 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
212753 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
212772 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
212786 CGTTGCGATT
1 CGTTGCGATT
212796 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:212774 original size:33 final size:33
Alignment explanation
Indices: 212734--212802 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
212724 TGCGATTTGG
212734 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
212767 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
212800 TTT
1 TTT
212803 TTCTCGTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.09, C:0.23, G:0.20, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:212808 original size:21 final size:21
Alignment explanation
Indices: 212783--212856 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
212773 GTTGCGATTC
212783 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
212804 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
212825 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
212846 TCTCGTTGCGA
1 TCTCGTTGCGA
212857 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:212976 original size:33 final size:33
Alignment explanation
Indices: 212934--213004 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
212924 AATACTAACT
212934 TGAAAATCGCAACGAGAGAATAGCAACGCCAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCCAAA
* * *
212967 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCCAAA
213000 TGAAA
1 TGAAA
213005 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCCAAA
Found at i:213401 original size:20 final size:20
Alignment explanation
Indices: 213376--213528 Score: 175
Period size: 20 Copynumber: 7.6 Consensus size: 20
213366 CTTTAAAAAT
213376 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
213396 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
213416 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
213437 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
213457 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
213477 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
213497 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
213517 CGCGTTGCGATT
1 CGCGTTGCGATT
213529 CTGGAAAATC
Statistics
Matches: 114, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
20 96 0.84
21 18 0.16
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:213547 original size:81 final size:83
Alignment explanation
Indices: 213371--213547 Score: 213
Period size: 81 Copynumber: 2.2 Consensus size: 83
213361 TGGCGCTTTA
* *
213371 AAAATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGAT
1 AAAATCGCATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGAT
213436 ACGCGTTGCGATATACGG
66 ACGCGTTGCGATATACGG
* * * * *
213454 -ATA-CGCATTGCGATTTACGGATACGCGTTGCGA-TTTATGTGTTCG-CGTTGCGATTTTCATA
1 AAAATCGCATTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GTCGTTGCGATTTACAGA
*
213515 TTCGCGTTGCGAT-T-CTGG
65 TACGCGTTGCGATATAC-GG
*
213533 AAAATCGCAATGCGA
1 AAAATCGCATTGCGA
213548 ATTTGTACT
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
78 1 0.01
79 3 0.04
80 35 0.44
81 39 0.49
82 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (83 bp):
AAAATCGCATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGAT
ACGCGTTGCGATATACGG
Done.