Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008033.1 Hibiscus syriacus cultivar Beakdansim tig00110515_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: 3048429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2220073 original size:20 final size:20
Alignment explanation
Indices: 2220045--2220158 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
2220035 AATTGGGAAA
2220045 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
2220065 ATCGTAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2220085 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
2220106 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
2220126 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
2220146 TTCGCAACGCGAT
1 ATCGCAATGCGAT
2220159 TTACATAGCA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2220109 original size:61 final size:61
Alignment explanation
Indices: 2220042--2220158 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
2220032 GCGAATTGGG
* * * * * *
2220042 AAAATCGCAATGCGATACTGACTATCGTAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
2220103 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
2220159 TTACATAGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2220716 original size:19 final size:19
Alignment explanation
Indices: 2220678--2220744 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2220668 TTCGAGAATG
2220678 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
2220698 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
2220717 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
2220736 AAAATCGCA
1 AAAATCGCA
2220745 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2220762 original size:19 final size:19
Alignment explanation
Indices: 2220740--2220829 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
2220730 GAAACCAAAA
*
2220740 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2220759 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2220778 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
2220797 TTGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
2220817 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2220830 GTCTGGTCGC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 48 0.74
20 17 0.26
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2220811 original size:39 final size:38
Alignment explanation
Indices: 2220740--2220829 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
2220730 GAAACCAAAA
*
2220740 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
2220778 TCGCGTTGCGATTTTTATTTTGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
2220817 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2220830 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 20 0.42
39 28 0.58
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:2220895 original size:34 final size:33
Alignment explanation
Indices: 2220812--2220899 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
2220802 GTTGCGATTT
* * *
2220812 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCAATAG
* *
2220845 TCATTTTGCGTTGCGATTCTCTCGTTGCAATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCAATAG
2220878 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
2220900 ATTATCTCGT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCAATAG
Found at i:2220901 original size:20 final size:20
Alignment explanation
Indices: 2220878--2220924 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2220868 GTTGCAATAG
2220878 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
2220898 TCATTAT-CTCGTTGCGATTG
1 TCATT-TCCGCGTTGCGATTC
2220918 TCATTTC
1 TCATTTC
2220925 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:2222988 original size:42 final size:42
Alignment explanation
Indices: 2222928--2223050 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2222918 GCCCGACTCG
* * *
2222928 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
2222970 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
2223012 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
2223051 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:2223008 original size:21 final size:21
Alignment explanation
Indices: 2222984--2223050 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2222974 TCATTCCTCG
2222984 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2223005 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2223026 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2223047 AGAG
1 AGAG
2223051 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2224430 original size:14 final size:14
Alignment explanation
Indices: 2224411--2224446 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2224401 ATTGTTTAAT
2224411 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2224425 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2224439 TGATTTGT
1 TGATTTGT
2224447 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2224671 original size:33 final size:32
Alignment explanation
Indices: 2224629--2224755 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
2224619 ATTAAATTTG
2224629 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
2224662 CGTTGCGATTTTCATTTCGCATTGTGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2224695 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
2224728 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2224756 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2224718 original size:66 final size:66
Alignment explanation
Indices: 2224622--2224751 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
2224612 ACGCGAAATT
*
2224622 AAATTTGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
2224687 G
66 G
*
2224688 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
2224752 CGATAGTAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
G
Found at i:2227060 original size:12 final size:12
Alignment explanation
Indices: 2227043--2227067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2227033 TCTTCAGGGA
2227043 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2227055 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2227067 C
1 C
2227068 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:2227276 original size:24 final size:24
Alignment explanation
Indices: 2227242--2227295 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2227232 CTGAAACATC
* *
2227242 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
2227266 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
2227290 ATCAAA
1 ATCAAA
2227296 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:2228380 original size:20 final size:20
Alignment explanation
Indices: 2228355--2228412 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2228345 ATTCATTTGA
*
2228355 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
2228375 CTATCGCAACGGGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
2228395 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
2228413 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:2228455 original size:14 final size:14
Alignment explanation
Indices: 2228436--2228489 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2228426 GAAAATCGCA
2228436 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
2228450 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
2228467 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
2228483 TTGCGAT
1 TTGCGAT
2228490 AGTCTGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:2228455 original size:33 final size:33
Alignment explanation
Indices: 2228418--2228488 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
2228408 AAAATCGCAA
2228418 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
2228451 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
2228484 TGCGA
1 TGCGA
2228489 TAGTCTGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:2228596 original size:14 final size:14
Alignment explanation
Indices: 2228577--2228613 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2228567 CATCAATTAA
2228577 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2228591 ACAAATCATCTTTT
1 ACAAATCAACATTT
2228605 ACAAATCAA
1 ACAAATCAA
2228614 TTAAATAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2230597 original size:13 final size:14
Alignment explanation
Indices: 2230536--2230597 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 14
2230526 TGCGAAATGA
*
2230536 AAATCGCAACGACA
1 AAATCGCAACGACG
*
2230550 AAATCGCAATGCGAAATG
1 AAATCGCAA--CG--ACG
2230568 AAATCGCAACGAC-
1 AAATCGCAACGACG
2230581 AAATCGCAACG-CG
1 AAATCGCAACGACG
2230594 AAAT
1 AAAT
2230598 GAAAATCGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
12 1 0.03
13 15 0.38
14 10 0.25
16 4 0.10
18 10 0.25
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACG
Found at i:2230604 original size:32 final size:33
Alignment explanation
Indices: 2230519--2230605 Score: 151
Period size: 32 Copynumber: 2.7 Consensus size: 33
2230509 GGAAATGGCT
2230519 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2230552 ATCGCAATGCGAAATG-AAATCGCAACGAC-AA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2230583 ATCGCAACGCGAAATGAAAATCG
1 ATCGCAATGCGAAATGAAAATCG
2230606 TAATGCGATT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 17 0.33
32 19 0.37
33 16 0.31
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2230605 original size:19 final size:19
Alignment explanation
Indices: 2230461--2230605 Score: 89
Period size: 19 Copynumber: 8.2 Consensus size: 19
2230451 TAGTTTACTT
* *
2230461 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2230481 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
2230500 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
2230520 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2230539 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
2230553 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
2230571 TCGCAA--CG--A--CAAA
1 TCGCAACGCGAAATGAAAA
2230584 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2230603 TCG
1 TCG
2230606 TAATGCGATT
Statistics
Matches: 100, Mismatches: 12, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
13 9 0.09
14 11 0.11
15 3 0.03
16 4 0.04
17 3 0.03
18 10 0.10
19 31 0.31
20 29 0.29
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2230644 original size:14 final size:14
Alignment explanation
Indices: 2230625--2230682 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2230615 TTGTGTTTCG
2230625 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2230639 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2230655 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2230671 CGTTGCGATTTT
1 CGTTGCGATTTT
2230683 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2230659 original size:32 final size:33
Alignment explanation
Indices: 2230620--2230698 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2230610 GCGATTTGTG
2230620 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
2230652 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2230685 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2230699 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2230697 original size:19 final size:17
Alignment explanation
Indices: 2230620--2230698 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
2230610 GCGATTTGTG
2230620 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
2230636 TGTCG-TTGCGATTTCA
1 TTTCGCTTGCGATTTCA
2230652 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
2230668 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
2230685 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
2230699 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.30
15 3 0.06
16 12 0.24
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:2230717 original size:20 final size:19
Alignment explanation
Indices: 2230683--2230737 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2230673 TTGCGATTTT
*
2230683 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2230702 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2230722 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2230738 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2231245 original size:18 final size:18
Alignment explanation
Indices: 2231219--2231263 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2231209 GTCGATCAGA
**
2231219 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGACGAGG
*
2231237 TGATAGCTCTGGACGAGG
1 TGATGGCTCTGGACGAGG
2231255 TGATGGCTC
1 TGATGGCTC
2231264 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:2232607 original size:20 final size:20
Alignment explanation
Indices: 2232582--2232619 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2232572 AATAGTTTCT
2232582 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2232602 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2232620 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2233131 original size:20 final size:20
Alignment explanation
Indices: 2233106--2233220 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
2233096 AATTATGTAT
* *
2233106 TATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
* * *
2233126 TATCGCGTTGCGAAAGTAAG
1 TATCGCATTGCGATAGTCAG
* * ** * *
2233146 TATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGA-TAGTCAG
2233167 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
2233187 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
2233207 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2233221 TTTCCCAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 68 0.84
21 13 0.16
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAG
Found at i:2233198 original size:61 final size:61
Alignment explanation
Indices: 2233086--2233223 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
2233076 CGCTTTGAAA
* * * * *
2233086 ATCGCATTGCAATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGT
* * * * *
2233147 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGT
2233208 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2233224 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGT
Found at i:2233238 original size:21 final size:21
Alignment explanation
Indices: 2233209--2233301 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
2233199 ATAGTCAGTA
2233209 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
2233230 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
2233250 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
2233271 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
2233291 TCGCATTGCGA
1 TCGCATTGCGA
2233302 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:2233239 original size:41 final size:41
Alignment explanation
Indices: 2233209--2233301 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
2233199 ATAGTCAGTA
* *
2233209 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
2233250 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
2233291 TCGCATTGCGA
1 TCGCATTGCGA
2233302 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:2233239 original size:61 final size:61
Alignment explanation
Indices: 2233106--2233241 Score: 166
Period size: 61 Copynumber: 2.2 Consensus size: 61
2233096 AATTATGTAT
* * * * ** *
2233106 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTCCAA
* * *
2233167 TATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT-CCAA
2233229 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
2233242 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:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:2235131 original size:20 final size:20
Alignment explanation
Indices: 2235106--2235176 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
2235096 TATTGTCCAT
*
2235106 TACTATTCATACAGTATCGA
1 TACTATTCATACAGTATCGG
2235126 TACTATTCATACAGTATCGG
1 TACTATTCATACAGTATCGG
* *
2235146 TACTATTCATACAATATTGG
1 TACTATTCATACAGTATCGG
2235166 TACTATTCATA
1 TACTATTCATA
2235177 AAAAAAATTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
TACTATTCATACAGTATCGG
Found at i:2237912 original size:19 final size:19
Alignment explanation
Indices: 2237888--2237994 Score: 69
Period size: 19 Copynumber: 5.5 Consensus size: 19
2237878 AATTTTGGTA
2237888 CTATTCATACAATATCT-GT
1 CTATTCATACAATAT-TAGT
2237907 CTATTCATACAATATTAG-
1 CTATTCATACAATATTAGT
* ** *
2237925 CATTGGTTCCCACAATATTGGT
1 C--T-ATTCATACAATATTAGT
2237947 ACTATTCATACAATATCT-GT
1 -CTATTCATACAATAT-TAGT
* *
2237967 CTATTCATATAGTA-TAGT
1 CTATTCATACAATATTAGT
2237985 ACTATTCATA
1 -CTATTCATA
2237995 AAAACTTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
17 1 0.01
18 4 0.06
19 37 0.53
20 13 0.19
21 14 0.20
23 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (19 bp):
CTATTCATACAATATTAGT
Found at i:2239296 original size:50 final size:50
Alignment explanation
Indices: 2239184--2239288 Score: 183
Period size: 50 Copynumber: 2.1 Consensus size: 50
2239174 ACATCAATTC
* *
2239184 CATAATAGAAGCAACCTAAAATGGTGTTAACATGCATCAGGATATGAATG
1 CATAATACAAGCAACCTAAAATGGGGTTAACATGCATCAGGATATGAATG
*
2239234 CATAATACAAGCAACCTAAAATGGGGTTAACATGCATCAGGATATGACTG
1 CATAATACAAGCAACCTAAAATGGGGTTAACATGCATCAGGATATGAATG
2239284 CATAA
1 CATAA
2239289 ATTAAGCACG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (50 bp):
CATAATACAAGCAACCTAAAATGGGGTTAACATGCATCAGGATATGAATG
Found at i:2246579 original size:21 final size:20
Alignment explanation
Indices: 2246551--2246589 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2246541 TATTATAGGA
*
2246551 ATTTATGGCATCGACAAAAG
1 ATTTATGGCATCAACAAAAG
*
2246571 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCATCAACAAA
2246590 GACATTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCATCAACAAAAG
Found at i:2260689 original size:20 final size:21
Alignment explanation
Indices: 2260651--2260689 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2260641 CATCATGGTC
* *
2260651 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCAATGAAATCT
2260672 TTTGTCGAGGCAAT-AAAT
1 TTTGTCGAGGCAATGAAAT
2260690 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGTCGAGGCAATGAAATCT
Found at i:2275093 original size:81 final size:81
Alignment explanation
Indices: 2274988--2275560 Score: 731
Period size: 81 Copynumber: 7.1 Consensus size: 81
2274978 ACTATTAGAG
* * * * * *
2274988 TTTTACCCAAAGGCATATAGCCTTTCATCTAACTTGCATGATTGACACC-TTCTTGTCAAATGCA
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTC-TGTCAAATGCA
* * *
2275052 TAGCTAGACCATTAATA
65 CAGCTAGGCCATTAATC
* * *
2275069 TTTTACTCAAAGTTATTTAACCTTTCATCTAACTAGCATAACTGACACCTTTCTGTCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
2275134 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
* * * * *
2275150 TTTTACTCAAATGTATTTAACCTTTCATCTAACTGGAAAAATTGACACATTT-TGTAAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
2275214 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
* *
2275230 TTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTTATGTCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
* * *
2275295 AGTTTGACCATTAATC
66 AGCTAGGCCATTAATC
* * *
2275311 TTTTACTTAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGACACCTTTATGTCAAATGCA-
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
*
2275375 A-CTCGAGGCCATTAATA
66 AGCT--AGGCCATTAATC
** * * * ** *
2275392 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATGTTTCTATCTATTAAAT
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
*
2275457 TGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
* * *
2275473 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATCTTTCTATCAAATGCAA
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
*
2275538 AACTAGGCCATTAATC
66 AGCTAGGCCATTAATC
*
2275554 GTTTACT
1 TTTTACT
2275561 TTGGAATAAT
Statistics
Matches: 430, Mismatches: 56, Indels: 12
0.86 0.11 0.02
Matches are distributed among these distances:
79 1 0.00
80 75 0.17
81 349 0.81
82 3 0.01
83 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (81 bp):
TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
AGCTAGGCCATTAATC
Found at i:2275437 original size:242 final size:242
Alignment explanation
Indices: 2274988--2275552 Score: 733
Period size: 242 Copynumber: 2.3 Consensus size: 242
2274978 ACTATTAGAG
* * * * *
2274988 TTTTACCCAAAGGCATATAGCCTTTCATCTAACTT-GCATGATTGACACCTTCTTGTCAAATGCA
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGGCATAATTGACACCTT-TTGTCAAATGCA
* *
2275052 TAGCTAGACCATTAATATTTTACTCAAAGTTATTTAACCTTTCATCTAACTAGCATAACTGACAC
64 CAGCTAGACCATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAACTGACAC
* * *
2275117 CTTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAATGTATTTAACCTTTCATCTAA
129 CTTTATGTCAAATGCACAGCTAGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAA
* **
2275182 CTGGAAAAATTGACACATTT-TGTAAAATGCACAGCTAGGCCATTAATC
194 CTGGAAAAATTGACACATTTCTATAAAATAAACAGCTAGGCCATTAATC
2275230 TTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTTATGTCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTT-TGTCAAATGCAC
* * * * * * *
2275295 AGTTTGACCATTAATCTTTTACTTAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGACACC
65 AGCTAGACCATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAACTGACACC
2275360 TTTATGTCAAATGCA-A-CTCGAGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTA
130 TTTATGTCAAATGCACAGCT--AGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTA
* * ** ** * **
2275423 ACTGGCATAATTGACATGTTTCTATCTATTAAATTGCTAGGCCATTAATC
193 ACTGGAAAAATTGACACATTTCTATAAAATAAACAGCTAGGCCATTAATC
* * * *
2275473 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATCTTTCTATCAAATGCAA
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTT-TGTCAAATGCAC
* *
2275538 AACTAGGCCATTAAT
65 AGCTAGACCATTAAT
2275553 CGTTTACTTT
Statistics
Matches: 280, Mismatches: 38, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
240 2 0.01
241 4 0.01
242 183 0.65
243 91 0.32
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (242 bp):
TTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTTTGTCAAATGCACA
GCTAGACCATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAACTGACACCT
TTATGTCAAATGCACAGCTAGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACT
GGAAAAATTGACACATTTCTATAAAATAAACAGCTAGGCCATTAATC
Found at i:2275772 original size:55 final size:55
Alignment explanation
Indices: 2275712--2275926 Score: 270
Period size: 55 Copynumber: 3.9 Consensus size: 55
2275702 TACCAATAGC
* *
2275712 GAAATTCATAAACTTGTTATGAATTTATTATTTTTGCACACAAAGTGCCCATGCA
1 GAAATTCATAAACTTATTATGAATTTATTATTTTTGCACACAAAGTGCCCATACA
* * * * * **
2275767 AAAATTCGTAAGCCTATTATGAATTTATTATTTTTTTCACACAAAGTGCCCATATG
1 GAAATTCATAAACTTATTATGAATTTATTA-TTTTTGCACACAAAGTGCCCATACA
* * * *
2275823 GAAATTGATAAACTCATTATAAATTTATTACTTTTGCACACAAAGTGCCCATACA
1 GAAATTCATAAACTTATTATGAATTTATTATTTTTGCACACAAAGTGCCCATACA
* *
2275878 GAAATTCATAAACTTATTATGAATTTCTT-TGTTTTGCACACATAGTGCC
1 GAAATTCATAAACTTATTATGAATTTATTAT-TTTTGCACACAAAGTGCC
2275927 ATTTGGTAAT
Statistics
Matches: 132, Mismatches: 26, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
55 88 0.67
56 44 0.33
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (55 bp):
GAAATTCATAAACTTATTATGAATTTATTATTTTTGCACACAAAGTGCCCATACA
Found at i:2275827 original size:111 final size:110
Alignment explanation
Indices: 2275712--2275926 Score: 295
Period size: 111 Copynumber: 1.9 Consensus size: 110
2275702 TACCAATAGC
** * * * *
2275712 GAAATTCATAAACTTGTTATGAATTTATTATTTTTGCACACAAAGTGCCCATGCAAAAATTCGTA
1 GAAATTCATAAACTCATTATAAATTTATTACTTTTGCACACAAAGTGCCCATACAAAAATTCATA
* * *
2275777 AGCCTATTATGAATTTATTATTTTTTTCACACAAAGTGCCCATATG
66 AACCTATTATGAATTTATT-TGTTTTGCACACAAAGTGCCCATATG
* *
2275823 GAAATTGATAAACTCATTATAAATTTATTACTTTTGCACACAAAGTGCCCATACAGAAATTCATA
1 GAAATTCATAAACTCATTATAAATTTATTACTTTTGCACACAAAGTGCCCATACAAAAATTCATA
* * *
2275888 AACTTATTATGAATTTCTTTGTTTTGCACACATAGTGCC
66 AACCTATTATGAATTTATTTGTTTTGCACACAAAGTGCC
2275927 ATTTGGTAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
110 17 0.19
111 73 0.81
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (110 bp):
GAAATTCATAAACTCATTATAAATTTATTACTTTTGCACACAAAGTGCCCATACAAAAATTCATA
AACCTATTATGAATTTATTTGTTTTGCACACAAAGTGCCCATATG
Found at i:2276272 original size:20 final size:20
Alignment explanation
Indices: 2276244--2276318 Score: 141
Period size: 20 Copynumber: 3.8 Consensus size: 20
2276234 GTTTCTGGCT
*
2276244 CCATAGTATCGATACCCCTA
1 CCATGGTATCGATACCCCTA
2276264 CCATGGTATCGATACCCCTA
1 CCATGGTATCGATACCCCTA
2276284 CCATGGTATCGATACCCCTA
1 CCATGGTATCGATACCCCTA
2276304 CCATGGTATCGATAC
1 CCATGGTATCGATAC
2276319 TACTATACTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (20 bp):
CCATGGTATCGATACCCCTA
Found at i:2277887 original size:2 final size:2
Alignment explanation
Indices: 2277880--2277914 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2277870 CCAGAAAAGC
2277880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2277915 GTTTCTGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2279330 original size:37 final size:37
Alignment explanation
Indices: 2279280--2279384 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
2279270 GTGCTTGTGC
* * * *
2279280 ATCTTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCTTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
2279317 ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCTTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
2279354 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCTTATTTTTAGGAGTTTGAATCCTAGTAG
2279385 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (37 bp):
ATCTTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:2280234 original size:105 final size:105
Alignment explanation
Indices: 2279926--2280451 Score: 697
Period size: 105 Copynumber: 5.0 Consensus size: 105
2279916 GCATTGTTCT
* * * * * * *
2279926 GAGTCTAATATCCTCCG-TCGTGAAGTTGAAATTAGCTCTGGAACTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACA
* * * * *
2279990 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2280032 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTG-AA-TGA-AA--TATTGTCGACAAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
2280092 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2280132 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
2280197 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2280237 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
* *
2280302 CAGCGGTCCCTTCGTCATGAAGTTTAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2280342 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* * * *
2280407 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2280448 GAGT
1 GAGT
2280452 GTCACGATAT
Statistics
Matches: 376, Mismatches: 36, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
100 83 0.22
101 2 0.01
102 2 0.01
103 4 0.01
104 2 0.01
105 201 0.53
106 80 0.21
107 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2280697 original size:36 final size:36
Alignment explanation
Indices: 2280650--2280725 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
2280640 TGTTTGGAGA
* * *
2280650 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
2280686 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
2280722 GAAA
1 GAAA
2280726 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:2280742 original size:101 final size:103
Alignment explanation
Indices: 2280625--2280838 Score: 324
Period size: 104 Copynumber: 2.1 Consensus size: 103
2280615 TTCGTTAAAT
**
2280625 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA-TTC-GTTTCAAGGGA
1 TGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCTGTTTCAAGGGA
* * *
2280688 AACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AACTATCTCAAGAGAGAAAAAATTAATTTCAAGGGAAA
* *
2280726 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTCTGTTTCAAGGG
* *
2280791 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAGA
65 AAACTATCTCAAGAGAGAAAAAATTAATTTCAAGGGAAA
2280830 TGTTTTCAA
1 TGTTTTCAA
2280839 GAGAAACTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 46 0.46
103 3 0.03
104 52 0.51
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (103 bp):
TGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCTGTTTCAAGGGA
AACTATCTCAAGAGAGAAAAAATTAATTTCAAGGGAAA
Found at i:2280795 original size:39 final size:39
Alignment explanation
Indices: 2280741--2280815 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
2280731 TCAATGTTTA
* *
2280741 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
2280780 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
2280816 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:2281042 original size:36 final size:36
Alignment explanation
Indices: 2280926--2281042 Score: 90
Period size: 36 Copynumber: 3.1 Consensus size: 36
2280916 AATAGCCTTG
* *
2280926 AGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCA
1 AGTGAAAT-AAAT--CTTCTTTCGAG-AAAAACAGTCTCA
* * * * ** * * **
2280966 AGCGAGACAAATCTTGTTTTAAGAAAAATAATCTTG
1 AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
2281002 AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
1 AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
2281038 AGTGA
1 AGTGA
2281043 GACAAAGTAT
Statistics
Matches: 55, Mismatches: 22, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
36 38 0.69
37 8 0.15
39 4 0.07
40 5 0.09
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (36 bp):
AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
Found at i:2281046 original size:72 final size:74
Alignment explanation
Indices: 2280909--2281083 Score: 207
Period size: 72 Copynumber: 2.4 Consensus size: 74
2280899 TAAAATCTTC
** * *
2280909 TTAA-AAAAATAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAATAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
2280973 CAAA-TCTTGTT
64 CAAAGT-ATGTT
*
2280984 TTAAGAAAAATAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAATAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
2281047 AAGTATGTT
66 AAGTATGTT
* *
2281056 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAA-TAATCTTGAGTGAAATAA
2281084 TCATCTGCAT
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
72 47 0.53
73 15 0.17
75 8 0.09
76 19 0.21
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (74 bp):
TTAAGAAAAATAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
AAGTATGTT
Found at i:2282536 original size:183 final size:183
Alignment explanation
Indices: 2282226--2282566 Score: 621
Period size: 183 Copynumber: 1.9 Consensus size: 183
2282216 GAAGGGTTTA
2282226 TCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCAAGTGTCCGA
1 TCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCAAGTGTCCGA
**
2282291 GCAATGTCATGATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCCCTATAACCA
66 GCAATGTCATGATTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCCCTATAACCA
2282356 ATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTGAATGGTTCG
131 ATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTGAATGGTTCG
*
2282409 TCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCAAGTGTCCGA
1 TCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCAAGTGTCCGA
* *
2282474 GCAGTGTCAT-AGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCTCTATAACC
66 GCAATGTCATGA-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCCCTATAACC
2282538 AATTGCCTTAGTGGAATAGCTCAGCTTTA
130 AATTGCCTTAGTGGAATAGCTCAGCTTTA
2282567 CGGATTTAAT
Statistics
Matches: 152, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
182 1 0.01
183 151 0.99
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.27
Consensus pattern (183 bp):
TCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCAAGTGTCCGA
GCAATGTCATGATTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCCCTATAACCA
ATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTGAATGGTTCG
Found at i:2288088 original size:9 final size:9
Alignment explanation
Indices: 2288074--2288106 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
2288064 TACAAGGGAA
2288074 AAATAAAAT
1 AAATAAAAT
2288083 AAATAAAAT
1 AAATAAAAT
2288092 AAATAAAAT
1 AAATAAAAT
2288101 AAATAA
1 AAATAA
2288107 GTAAGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2288115 original size:18 final size:17
Alignment explanation
Indices: 2288074--2288128 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
2288064 TACAAGGGAA
*
2288074 AAATAAAATAAATAAAAT
1 AAATAAAATAAAT-AAGT
2288092 AAATAAAATAAATAAGT
1 AAATAAAATAAATAAGT
*
2288109 AAGATAAAAAAAAT-AGT
1 AA-ATAAAATAAATAAGT
2288126 AAA
1 AAA
2288129 GTAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 1 0.03
17 10 0.29
18 23 0.68
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (17 bp):
AAATAAAATAAATAAGT
Found at i:2288428 original size:37 final size:37
Alignment explanation
Indices: 2288378--2288482 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
2288368 GTTCTTGTGG
* * * *
2288378 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
2288415 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
2288452 ATCCTACTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
2288483 GAAGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:2296276 original size:81 final size:81
Alignment explanation
Indices: 2296170--2296345 Score: 246
Period size: 81 Copynumber: 2.2 Consensus size: 81
2296160 TGGGATATAG
* * * ***
2296170 CCTTTCATCTAACTTGCATGATTGACA-CTTTCCTATCAAATGCACGGTTAGGCCATTAATCTTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTT-CTACCAAATGCACAACTAGGCCATTAATCTTT
*
2296234 TGCTCAAAGGTATTTAA
65 TACTCAAAGGTATTTAA
* *
2296251 CCTTTTATCTAACTGGCATAATTGACACCTTTGTACCAAATGCACAACTAGGCCATTAATCTTTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACTAGGCCATTAATCTTTT
2296316 ACTCAAAGGTATTTAA
66 ACTCAAAGGTATTTAA
*
2296332 CATTTCATCTAACT
1 CCTTTCATCTAACT
2296346 AAAAATCATA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
81 79 0.95
82 4 0.05
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (81 bp):
CCTTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACTAGGCCATTAATCTTTT
ACTCAAAGGTATTTAA
Found at i:2308982 original size:22 final size:21
Alignment explanation
Indices: 2308940--2308979 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2308930 GAGTTTGTTT
*
2308940 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2308961 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2308980 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2310972 original size:64 final size:64
Alignment explanation
Indices: 2310902--2311131 Score: 227
Period size: 65 Copynumber: 3.6 Consensus size: 64
2310892 TTGGAACACT
* *** *
2310902 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTTGATGTTTGAAAA-ATAGCA
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCA
* * *
2310966 TGATGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATGCA
* * * *
2311031 -GAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-T-
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATATG
2311092 CA
63 CA
* * *
2311094 TCGATGCATCGATGCATGGACTGATGCATTGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
2311132 CCTTTGAATA
Statistics
Matches: 141, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
63 6 0.04
64 63 0.45
65 70 0.50
66 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCA
Found at i:2311054 original size:19 final size:19
Alignment explanation
Indices: 2311030--2311080 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2311020 GAAAATATTC
2311030 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2311049 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2311068 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2311081 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2314567 original size:65 final size:65
Alignment explanation
Indices: 2314425--2314602 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 65
2314415 TGGAACACTT
* * *
2314425 GATGCATCGGTGCACT-AAGTGTGCATCGATG--TGAAATGCATTTGATG-TTTGAAAAATAGCC
1 GATGCATCGATGCA-TGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCC
*
2314486 T
65 A
* * **
2314487 GATGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCA
1 GATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCA
* * *
2314551 GAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 GA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
2314603 CAATTAATTC
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
61 1 0.01
62 26 0.27
64 23 0.23
65 48 0.49
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (65 bp):
GATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCA
Found at i:2314574 original size:19 final size:19
Alignment explanation
Indices: 2314550--2314600 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2314540 GAAAATATTC
2314550 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2314569 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2314588 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2314601 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2314642 original size:65 final size:63
Alignment explanation
Indices: 2314456--2314651 Score: 193
Period size: 65 Copynumber: 3.0 Consensus size: 63
2314446 TGCATCGATG
* * ** * *
2314456 TGAAATGCATTTGATGTTTGAAAAATAGCCTGATGCATCGATGCATGGATTG-TGCATCGATGCA
1 TGAAATGCATTCGATGTTT-CAAAATATTCAGATGCATCGATGCATGGA-TGATGCATCGGTGCA
* *
2314520 TCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA-GAGTGCATCGGTGC
1 TGAAATGCATTCGATG-TTTCAAAATATTCAGA-TGCATCGATGCATGGATGA-TGCATCGGTGC
2314584 A
63 A
* *
2314585 TGGAATGCATTCGATG-TTC-AATTAATTCATCGATGCATCGATGCATGGACTGATGCATCGGTG
1 TGAAATGCATTCGATGTTTCAAAAT-ATTCA--GATGCATCGATGCATGGA-TGATGCATCGGTG
2314648 CA
62 CA
2314650 TG
1 TG
2314652 CCTTTGAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 39 0.35
65 60 0.54
66 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (63 bp):
TGAAATGCATTCGATGTTTCAAAATATTCAGATGCATCGATGCATGGATGATGCATCGGTGCA
Found at i:2316218 original size:31 final size:31
Alignment explanation
Indices: 2316158--2316218 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
2316148 CTGAATCGAG
*
2316158 CTTTTCTTAGTGTTTTATGAGCTGTCATGTA
1 CTTTTCTTAGTGTTTTATGAGCTGACATGTA
*
2316189 CTTTT-TTAGCTG-TTTGTGAGCTGCACATGT
1 CTTTTCTTAG-TGTTTTATGAGCTG-ACATGT
2316219 CGTCCAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (31 bp):
CTTTTCTTAGTGTTTTATGAGCTGACATGTA
Found at i:2319287 original size:25 final size:26
Alignment explanation
Indices: 2319231--2319287 Score: 91
Period size: 24 Copynumber: 2.3 Consensus size: 26
2319221 TCTTTTCTTT
*
2319231 ACTTTTTCTTCTTTTTTGAGTGCTTG
1 ACTTTTTCTTCTTTTTGGAGTGCTTG
2319257 AC-TTTTCTTC-TTTTGGAGTGCTTG
1 ACTTTTTCTTCTTTTTGGAGTGCTTG
2319281 ACTTTTT
1 ACTTTTT
2319288 ATTTGCTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 15 0.52
25 12 0.41
26 2 0.07
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.60
Consensus pattern (26 bp):
ACTTTTTCTTCTTTTTGGAGTGCTTG
Found at i:2322274 original size:54 final size:54
Alignment explanation
Indices: 2322131--2322275 Score: 193
Period size: 53 Copynumber: 2.7 Consensus size: 54
2322121 GCACTATGTT
* * ** *
2322131 TGCAAAACTAAGAAATTTATAATAAGTTTATGAATTTCCGTATGGGCTTTTTGTG
1 TGCAAAA-TAAAAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTCTG
* *
2322186 TGCAAAA-AAAAAATTCACAATAAGTTTATGAATTTCTGTATGGGCACTTTCTG
1 TGCAAAATAAAAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTCTG
* *
2322239 TGTAAAATAATAAATTCATAATAAGTTTATGAATTTC
1 TGCAAAATAAAAAATTCATAATAAGTTTATGAATTTC
2322276 GGTACTGGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 45 0.57
54 27 0.34
55 7 0.09
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (54 bp):
TGCAAAATAAAAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTCTG
Found at i:2322638 original size:81 final size:81
Alignment explanation
Indices: 2322427--2323058 Score: 815
Period size: 81 Copynumber: 7.8 Consensus size: 81
2322417 ACTATTCCAA
* * * * * **
2322427 AGTAAAAGATTAATGGCCAAACTTTGCATTTGATAAAAAACTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2322492 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
2322508 AGTAAAAG---AATGGCCTAG-TTTCGAATTTGACAGAAATGTGTCAATTATGCCATTTAGATGA
1 AGTAAAAGATTAATGGCCTAGCTGT-GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGA
*
2322569 AAAGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * * * *
2322586 AGTAAAATATTAATAGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTGGATAAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* * *
2322651 AGGTTAAACATCTTTA
66 AGGTTAAATACCTTTG
* * * * ** *
2322667 AGTAAAATATTAATGGCCT-GATTGTGCATTTGACAAAAAGGTGTTAATTATGTGAGTTATATGA
1 AGTAAAAGATTAATGGCCTAG-CTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGA
* *
2322731 AATGTTAAATACCTTTT
65 AAGGTTAAATACCTTTG
* * * * *
2322748 AGTAAAATATTAATGGCCTAGCTATGTATTTAACAAAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
2322813 AGGATAAATACCTTTG
66 AGGTTAAATACCTTTG
2322829 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2322894 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* *
2322910 AGTAAAAGATTAATGGCCTAGCTGTGTATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATTAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
2322975 AGGTTAAATACCTTTT
66 AGGTTAAATACCTTTG
* * * * * *
2322991 AGTAAAAAATTAATGGCATTGCTGTGCATTTGACAGGAAGGTGTCAATCATGCAAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2323056 AGG
66 AGG
2323059 CTATATTCCT
Statistics
Matches: 481, Mismatches: 63, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
77 3 0.01
78 64 0.13
80 1 0.00
81 410 0.85
82 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:2326233 original size:26 final size:26
Alignment explanation
Indices: 2326199--2326328 Score: 206
Period size: 26 Copynumber: 5.0 Consensus size: 26
2326189 CACTATGTGT
*
2326199 TTATGGTGGGCACGACCTTATGTATA
1 TTATAGTGGGCACGACCTTATGTATA
2326225 TTATAGTGGGCACGACCTTATGTATA
1 TTATAGTGGGCACGACCTTATGTATA
*
2326251 TTATAGTGGGCACGACCTTATATATA
1 TTATAGTGGGCACGACCTTATGTATA
* *
2326277 TTATAGTGGGCACGACCTTAAGTGTA
1 TTATAGTGGGCACGACCTTATGTATA
* *
2326303 TTATGGTGGGCACAACCTTATGTATA
1 TTATAGTGGGCACGACCTTATGTATA
2326329 AGCACTACGA
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 95 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (26 bp):
TTATAGTGGGCACGACCTTATGTATA
Found at i:2330618 original size:19 final size:20
Alignment explanation
Indices: 2330594--2330631 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2330584 GATTTTCTTA
2330594 TTTTGAATTAA-TTAAATTT
1 TTTTGAATTAATTTAAATTT
2330613 TTTTGAATTAATTTAAATT
1 TTTTGAATTAATTTAAATT
2330632 AAATATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTGAATTAATTTAAATTT
Found at i:2339470 original size:11 final size:11
Alignment explanation
Indices: 2339456--2339506 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
2339446 AAATTTTGGA
2339456 TTTTTTGTTTT
1 TTTTTTGTTTT
*
2339467 TTTTTTGTTTG
1 TTTTTTGTTTT
* *
2339478 TTTTTTGCCTCT
1 TTTTTTG-TTTT
2339490 TTTTTTGTTTT
1 TTTTTTGTTTT
2339501 TTTTTT
1 TTTTTT
2339507 TGAAAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:2344191 original size:11 final size:11
Alignment explanation
Indices: 2344175--2344246 Score: 76
Period size: 11 Copynumber: 6.6 Consensus size: 11
2344165 AAATTTTGGA
2344175 TTTTTTGTTTT
1 TTTTTTGTTTT
2344186 TTTTTTGTTTT
1 TTTTTTGTTTT
2344197 TTTTTTGTTTT
1 TTTTTTGTTTT
*** *
2344208 TTGCCT-CTTT
1 TTTTTTGTTTT
*
2344218 TTTGTTG-TTT
1 TTTTTTGTTTT
2344228 TTTTTTGTTGTT
1 TTTTTTGTT-TT
2344240 TTTTTTG
1 TTTTTTG
2344247 AAAAAATAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
10 15 0.30
11 26 0.52
12 9 0.18
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.83
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:2344200 original size:29 final size:31
Alignment explanation
Indices: 2344168--2344243 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
2344158 GTTTTTGAAA
*
2344168 TTTTGGATTTTTTG-T-TTTTTTTTTGTTTTT
1 TTTTGG-TTTTTTGCTCTTTTTTGTTGTTTTT
*
2344198 TTTTTGTTTTTTGCCTCTTTTTTGTTGTTTTT
1 TTTTGGTTTTTTG-CTCTTTTTTGTTGTTTTT
2344230 TTTTGTTGTTTTTT
1 TTTTG--GTTTTTT
2344244 TTGAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 7 0.18
30 5 0.13
31 1 0.03
32 18 0.47
34 7 0.18
ACGTcount: A:0.01, C:0.04, G:0.13, T:0.82
Consensus pattern (31 bp):
TTTTGGTTTTTTGCTCTTTTTTGTTGTTTTT
Found at i:2351644 original size:39 final size:39
Alignment explanation
Indices: 2351585--2351664 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
2351575 CTAAAGGTAG
*
2351585 CTGGGAGAGTAGCTGAGGAGCTGAGAAGACCAAAGCTAA
1 CTGGCAGAGTAGCTGAGGAGCTGAGAAGACCAAAGCTAA
*
2351624 CTGGCAGAGTAGCTGAGGAGCTGAGAAGACTAAAGCTAA
1 CTGGCAGAGTAGCTGAGGAGCTGAGAAGACCAAAGCTAA
2351663 CT
1 CT
2351665 AGCTTGAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.34, T:0.15
Consensus pattern (39 bp):
CTGGCAGAGTAGCTGAGGAGCTGAGAAGACCAAAGCTAA
Found at i:2360758 original size:16 final size:16
Alignment explanation
Indices: 2360737--2360768 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2360727 AAGTGCTGGT
2360737 TTGCTTTTCTTTACCC
1 TTGCTTTTCTTTACCC
2360753 TTGCTTTTCTTTACCC
1 TTGCTTTTCTTTACCC
2360769 ATTTGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.31, G:0.06, T:0.56
Consensus pattern (16 bp):
TTGCTTTTCTTTACCC
Found at i:2364980 original size:19 final size:20
Alignment explanation
Indices: 2364956--2364998 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2364946 AGAATGTATC
2364956 TTCATT-AAAATCATGCATT
1 TTCATTAAAAATCATGCATT
*
2364975 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGCATT
2364995 TTCA
1 TTCA
2364999 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (20 bp):
TTCATTAAAAATCATGCATT
Found at i:2367860 original size:38 final size:42
Alignment explanation
Indices: 2367775--2367875 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 42
2367765 TTAGGATTAG
*
2367775 AGTTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACATTTTTTT
1 AGTTATTATTTTATTAGGAATTAA-G--GAGTTAAAACA-TTGTTT
2367821 AGTTATTA-TTTATTAGGAATT-A-GAGTTAAAACA-TGTTT
1 AGTTATTATTTTATTAGGAATTAAGGAGTTAAAACATTGTTT
*
2367859 AGTTTGTTATTTTATTA
1 AG-TTATTATTTTATTA
2367876 ATTAGTTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
38 6 0.12
39 5 0.10
40 18 0.35
44 1 0.02
45 13 0.25
46 8 0.16
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (42 bp):
AGTTATTATTTTATTAGGAATTAAGGAGTTAAAACATTGTTT
Found at i:2374760 original size:24 final size:24
Alignment explanation
Indices: 2374733--2374787 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2374723 AAAATCAGCA
* *
2374733 AAGAAAAGTCAAGCACTCCAAAAG
1 AAGAAAACTCAAGCACTCAAAAAG
*
2374757 AAGAAAACTTAAGCACTCAAAAAG
1 AAGAAAACTCAAGCACTCAAAAAG
*
2374781 ATGAAAA
1 AAGAAAA
2374788 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.58, C:0.16, G:0.15, T:0.11
Consensus pattern (24 bp):
AAGAAAACTCAAGCACTCAAAAAG
Found at i:2376103 original size:12 final size:11
Alignment explanation
Indices: 2376073--2376107 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2376063 AGAAAGGAAT
*
2376073 ATGATTAATAA
1 ATGAATAATAA
2376084 ATGAATAATAA
1 ATGAATAATAA
2376095 ATGGAATAATAA
1 AT-GAATAATAA
2376107 A
1 A
2376108 GATAAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (11 bp):
ATGAATAATAA
Found at i:2383219 original size:12 final size:12
Alignment explanation
Indices: 2383194--2383239 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
2383184 TTAGGAGTCA
*
2383194 TTTTCTTTTCTTT
1 TTTTC-TTTATTT
2383207 TTTTCTTTATTT
1 TTTTCTTTATTT
2383219 TTCTTCTTTATTT
1 TT-TTCTTTATTT
*
2383232 TTCTCTTT
1 TTTTCTTT
2383240 TTGTTGCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 13 0.43
13 17 0.57
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTTATTT
Found at i:2383482 original size:15 final size:15
Alignment explanation
Indices: 2383445--2383474 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2383435 GGAATATGGA
2383445 ATAAGAAAGAAAATG
1 ATAAGAAAGAAAATG
2383460 ATAAGAAAGAAAATG
1 ATAAGAAAGAAAATG
2383475 GATAGAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (15 bp):
ATAAGAAAGAAAATG
Found at i:2392376 original size:38 final size:37
Alignment explanation
Indices: 2392291--2392365 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
2392281 GGCTTGGTGA
2392291 TGAGAATTTTTAACGAGTGCTTCAACTTTCTTTCTTT
1 TGAGAATTTTTAACGAGTGCTTCAACTTTCTTTCTTT
* *
2392328 TGAGAATTTTTAATGAGTGCTTCTACTTTCTTTCTTT
1 TGAGAATTTTTAACGAGTGCTTCAACTTTCTTTCTTT
2392365 T
1 T
2392366 TGTTCCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (37 bp):
TGAGAATTTTTAACGAGTGCTTCAACTTTCTTTCTTT
Found at i:2397818 original size:26 final size:26
Alignment explanation
Indices: 2397784--2397850 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
2397774 AAATGGTTAG
2397784 GGATAGAAATGGTTATGATAGGGGTA
1 GGATAGAAATGGTTATGATAGGGGTA
2397810 GGATAGAAATGGTTATGATAGGGGTA
1 GGATAGAAATGGTTATGATAGGGGTA
*
2397836 GGATAGAAAAGGTTA
1 GGATAGAAATGGTTA
2397851 AGAAAAAGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.25
Consensus pattern (26 bp):
GGATAGAAATGGTTATGATAGGGGTA
Found at i:2398369 original size:16 final size:15
Alignment explanation
Indices: 2398350--2398388 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
2398340 TTTGATAATT
2398350 AAGAAATGAAAATGGA
1 AAGAAATG-AAATGGA
*
2398366 AAGAATTGAAATGGA
1 AAGAAATGAAATGGA
2398381 AAGAAATG
1 AAGAAATG
2398389 TTATCAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:2398627 original size:36 final size:36
Alignment explanation
Indices: 2398534--2398645 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 36
2398524 TTGGTGGTTA
** * * *
2398534 TATAGGCGTGA-AATGGTGATATAAGATGGTAAGGA
1 TATAGGCGTGACAATGGTGATGGAAGATGGTGATGT
* *
2398569 TATAGGCGTG-CAATGGTAATGGAATATGGTGATGT
1 TATAGGCGTGACAATGGTGATGGAAGATGGTGATGT
2398604 TATAGGCGTGACAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGACAATGGTGATGGAAGATGGTGATGT
2398640 TATAGG
1 TATAGG
2398646 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
35 37 0.56
36 29 0.44
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (36 bp):
TATAGGCGTGACAATGGTGATGGAAGATGGTGATGT
Found at i:2415446 original size:13 final size:14
Alignment explanation
Indices: 2415423--2415452 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2415413 AAGTGAAGAA
2415423 AAACTAAAGAAAGG
1 AAACTAAAGAAAGG
2415437 AAAC-AAAGAAAGG
1 AAACTAAAGAAAGG
2415450 AAA
1 AAA
2415453 ATGCAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.70, C:0.07, G:0.20, T:0.03
Consensus pattern (14 bp):
AAACTAAAGAAAGG
Found at i:2418978 original size:168 final size:168
Alignment explanation
Indices: 2418700--2419035 Score: 663
Period size: 168 Copynumber: 2.0 Consensus size: 168
2418690 GAGAACGACA
2418700 AGAACTGCAACTGGATCTACCAAACCAGAATCCAAGACCAAACAATGATGAACTTTTGGTACCCA
1 AGAACTGCAACTGGATCTACCAAACCAGAATCCAAGACCAAACAATGATGAACTTTTGGTACCCA
2418765 GGCGAGAACAACCACGTTTCAAGCACCTAAAATCTTTGCAAAACCAAAGTTCATGGTCCCGTCTT
66 GGCGAGAACAACCACGTTTCAAGCACCTAAAATCTTTGCAAAACCAAAGTTCATGGTCCCGTCTT
2418830 TCAAATGAGACAATGATCCGGATAGGTACATCGATTGG
131 TCAAATGAGACAATGATCCGGATAGGTACATCGATTGG
2418868 AGAACTGCAACTGGATCTACCAAACCAGAATCCAAGACCAAACAATGATGAACTTTTGGTACCCA
1 AGAACTGCAACTGGATCTACCAAACCAGAATCCAAGACCAAACAATGATGAACTTTTGGTACCCA
*
2418933 GGCGAGAACAACCACGTTTCAAGCACCTAAACTCTTTGCAAAACCAAAGTTCATGGTCCCGTCTT
66 GGCGAGAACAACCACGTTTCAAGCACCTAAAATCTTTGCAAAACCAAAGTTCATGGTCCCGTCTT
2418998 TCAAATGAGACAATGATCCGGATAGGTACATCGATTGG
131 TCAAATGAGACAATGATCCGGATAGGTACATCGATTGG
2419036 GAAGGAAAAG
Statistics
Matches: 167, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 167 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.21
Consensus pattern (168 bp):
AGAACTGCAACTGGATCTACCAAACCAGAATCCAAGACCAAACAATGATGAACTTTTGGTACCCA
GGCGAGAACAACCACGTTTCAAGCACCTAAAATCTTTGCAAAACCAAAGTTCATGGTCCCGTCTT
TCAAATGAGACAATGATCCGGATAGGTACATCGATTGG
Found at i:2424295 original size:19 final size:20
Alignment explanation
Indices: 2424257--2424307 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
2424247 GAAACCCCTT
2424257 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
2424277 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
2424296 TGAAGATACATG
1 TGAAAATACATG
2424308 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:2428259 original size:17 final size:16
Alignment explanation
Indices: 2428227--2428265 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2428217 AAGCATTCAA
2428227 AAAAAGTAAAAGAAAG
1 AAAAAGTAAAAGAAAG
2428243 AAAAA-TAAATAGCAAAG
1 AAAAAGTAAA-AG-AAAG
2428260 AAAAAG
1 AAAAAG
2428266 AAGTTGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (16 bp):
AAAAAGTAAAAGAAAG
Found at i:2430444 original size:22 final size:21
Alignment explanation
Indices: 2430416--2430457 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
2430406 AGCTACGAAA
2430416 TTGATGGTCTTGATGGATGAAG
1 TTGATGGTCTTGAT-GATGAAG
*
2430438 TTGATGGTGTTGATGATGAA
1 TTGATGGTCTTGATGATGAA
2430458 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGAAG
Found at i:2435144 original size:24 final size:24
Alignment explanation
Indices: 2435117--2435171 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
2435107 CCTCAATGAT
* *
2435117 CACAACTTGTGGCACTTCAAGTTG
1 CACAACTTGTGGAACTTCAAGTGG
* * *
2435141 CACATCTTTTTGAACTTCAAGTGG
1 CACAACTTGTGGAACTTCAAGTGG
*
2435165 CATAACT
1 CACAACT
2435172 GTTGGAATGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (24 bp):
CACAACTTGTGGAACTTCAAGTGG
Found at i:2443414 original size:13 final size:13
Alignment explanation
Indices: 2443398--2443445 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
2443388 CTTTTTGAAC
2443398 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
*
2443411 TTCTTTTCTTCTT
1 TTCTTTTTTTCTT
* *
2443424 TTCTGATTTTTCTC
1 TTCT-TTTTTTCTT
2443438 TTCTTTTT
1 TTCTTTTT
2443446 GCACTCTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:2443817 original size:20 final size:21
Alignment explanation
Indices: 2443780--2443818 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2443770 GATGGTCTTG
*
2443780 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
2443801 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
2443819 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:2457496 original size:14 final size:14
Alignment explanation
Indices: 2457469--2457509 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
2457459 TTGCATTTTG
2457469 CTTTCTTT-GTTTC
1 CTTTCTTTAGTTTC
2457482 CTTTCTTTAGTTTC
1 CTTTCTTTAGTTTC
2457496 CTTTCTTTAGTTTC
1 CTTTCTTTAGTTTC
2457510 TCTTCACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.05, C:0.22, G:0.07, T:0.66
Consensus pattern (14 bp):
CTTTCTTTAGTTTC
Found at i:2473275 original size:38 final size:38
Alignment explanation
Indices: 2473224--2473299 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
2473214 GATGTCCGTA
*
2473224 TTCCATTTTAAAGATGGGAGAATTGCTAGTGAAAAATT
1 TTCCATTTTAAAGACGGGAGAATTGCTAGTGAAAAATT
2473262 TTCCATTTTAAAGACGGGAGAATTGCTAGTGAAAAATT
1 TTCCATTTTAAAGACGGGAGAATTGCTAGTGAAAAATT
2473300 AATGGTTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (38 bp):
TTCCATTTTAAAGACGGGAGAATTGCTAGTGAAAAATT
Found at i:2493994 original size:22 final size:23
Alignment explanation
Indices: 2493951--2493994 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2493941 TTTTTATTCT
*
2493951 TTTTGAGTGCATTCAATTTCTTC
1 TTTTGAATGCATTCAATTTCTTC
*
2493974 TTTTGAATGC-TTCGATTTCTT
1 TTTTGAATGCATTCAATTTCTT
2493995 TGCTGGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.55
Consensus pattern (23 bp):
TTTTGAATGCATTCAATTTCTTC
Found at i:2506671 original size:21 final size:21
Alignment explanation
Indices: 2506647--2506689 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2506637 TGTAGAGCTA
* *
2506647 GCTAGTAAGCTTGGGCTGTTT
1 GCTAGCAAGCATGGGCTGTTT
2506668 GCTAGCAAGCATGGGCTGTTT
1 GCTAGCAAGCATGGGCTGTTT
2506689 G
1 G
2506690 TGAACAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.33
Consensus pattern (21 bp):
GCTAGCAAGCATGGGCTGTTT
Found at i:2506697 original size:21 final size:21
Alignment explanation
Indices: 2506653--2506698 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2506643 GCTAGCTAGT
* *
2506653 AAGCTTGGGCTGTTTGCTAGC
1 AAGCATGGGCTGTTTGCTAAC
2506674 AAGCATGGGCTGTTTG-TGAAC
1 AAGCATGGGCTGTTTGCT-AAC
2506695 AAGC
1 AAGC
2506699 TTACTAGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (21 bp):
AAGCATGGGCTGTTTGCTAAC
Found at i:2515581 original size:17 final size:17
Alignment explanation
Indices: 2515544--2515585 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2515534 TCTTTTTGAA
2515544 TTTC-TTTT-TCTTTTC
1 TTTCTTTTTGTCTTTTC
2515559 -TTCTTTTTGTCTTTTC
1 TTTCTTTTTGTCTTTTC
2515575 TTTCTTTTTGT
1 TTTCTTTTTGT
2515586 ACTCCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 4 0.17
16 7 0.29
17 10 0.42
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTGTCTTTTC
Found at i:2515908 original size:22 final size:21
Alignment explanation
Indices: 2515880--2515921 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
2515870 AGCTGCGGAA
2515880 TTGATGGTCTTGATGGATGAAG
1 TTGATGGTCTTGAT-GATGAAG
*
2515902 TTGATGGTGTTGATGATGAA
1 TTGATGGTCTTGATGATGAA
2515922 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGAAG
Found at i:2517180 original size:2 final size:2
Alignment explanation
Indices: 2517163--2517196 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2517153 TCATAATAAC
*
2517163 TA TA GA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2517197 GAAAATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2518313 original size:17 final size:17
Alignment explanation
Indices: 2518291--2518340 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
2518281 CAAAAGAGTT
2518291 AGGGTAATGGATATAAA
1 AGGGTAATGGATATAAA
2518308 AGGGT-AT--AT-T---
1 AGGGTAATGGATATAAA
2518318 AGGGTAATGGATATAAA
1 AGGGTAATGGATATAAA
2518335 AGGGTA
1 AGGGTA
2518341 TATTAGGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 14
0.65 0.00 0.35
Matches are distributed among these distances:
10 5 0.19
11 2 0.08
13 3 0.12
14 3 0.12
16 2 0.08
17 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (17 bp):
AGGGTAATGGATATAAA
Found at i:2518319 original size:27 final size:27
Alignment explanation
Indices: 2518289--2518347 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
2518279 AACAAAAGAG
2518289 TTAGGGTAATGGATATAAAAGGGTATA
1 TTAGGGTAATGGATATAAAAGGGTATA
2518316 TTAGGGTAATGGATATAAAAGGGTATA
1 TTAGGGTAATGGATATAAAAGGGTATA
2518343 TTAGG
1 TTAGG
2518348 TCTAGCAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (27 bp):
TTAGGGTAATGGATATAAAAGGGTATA
Found at i:2521520 original size:11 final size:11
Alignment explanation
Indices: 2521483--2521545 Score: 65
Period size: 13 Copynumber: 5.3 Consensus size: 11
2521473 GATACTATTT
2521483 TCATCACCATA
1 TCATCACCATA
2521494 GTCCATCACCATTA
1 -T-CATCACCA-TA
2521508 TCA-CACCTATA
1 TCATCACC-ATA
2521519 TCATCACCATA
1 TCATCACCATA
2521530 TTCCATCACCATA
1 -T-CATCACCATA
2521543 TCA
1 TCA
2521546 CGCCAATAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 19 0.42
14 2 0.04
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:2521574 original size:33 final size:33
Alignment explanation
Indices: 2521530--2521598 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2521520 CATCACCATA
*
2521530 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
2521563 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
2521596 TTC
1 TTC
2521599 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:2522540 original size:28 final size:29
Alignment explanation
Indices: 2522486--2522560 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
2522476 TTCAACTTTC
*
2522486 TTTCTTTTCTTTACTTTTTGGTAAGTGCTGGAA
1 TTTC-TTTCTTT-C-TTTTGG-AAGTGCTGCAA
*
2522519 TTTCTTTCTTTCTTTTGG-AGTGCTTCAA
1 TTTCTTTCTTTCTTTTGGAAGTGCTGCAA
2522547 TTTCTTT-TTT-TTTT
1 TTTCTTTCTTTCTTTT
2522561 ATTTTCTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.10
27 3 0.08
28 15 0.38
30 6 0.15
31 1 0.03
32 7 0.17
33 4 0.10
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.63
Consensus pattern (29 bp):
TTTCTTTCTTTCTTTTGGAAGTGCTGCAA
Found at i:2527277 original size:153 final size:153
Alignment explanation
Indices: 2527000--2527305 Score: 587
Period size: 153 Copynumber: 2.0 Consensus size: 153
2526990 GAAATGGCAA
2527000 TGGTGGTGATGTTGTATCTCAAACAAGCCAAAGAGGAAACTATGCTATGAAGCACAATCCGGTCT
1 TGGTGGTGATGTTGTATCTCAAACAAGCCAAAGAGGAAACTATGCTATGAAGCACAATCCGGTCT
2527065 TCACAAACTTGCTTGACGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATCTAGGAATTTT
66 TCACAAACTTGCTTGACGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATCTAGGAATTTT
2527130 GGAATC-AAATGGAAGGAATGAC
131 GGAATCAAAATGGAAGGAATGAC
2527152 TGGTGGTGATGTTGTATCTCAAACAAGCCAAAGAGGAAACTATGCTATGAAGCACAATCCCGGTC
1 TGGTGGTGATGTTGTATCTCAAACAAGCCAAAGAGGAAACTATGCTATGAAGCACAAT-CCGGTC
*
2527217 TTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATCTAGGAATTT
65 TTCACAAACTTGCTTGACGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATCTAGGAATTT
2527282 TGGAATCAAAATGGAAGGAATGAC
130 TGGAATCAAAATGGAAGGAATGAC
2527306 ACCACAAGTA
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
152 58 0.38
153 77 0.51
154 16 0.11
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (153 bp):
TGGTGGTGATGTTGTATCTCAAACAAGCCAAAGAGGAAACTATGCTATGAAGCACAATCCGGTCT
TCACAAACTTGCTTGACGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATCTAGGAATTTT
GGAATCAAAATGGAAGGAATGAC
Found at i:2528743 original size:19 final size:21
Alignment explanation
Indices: 2528700--2528743 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2528690 GAAACCCCTT
2528700 TGAAAATACATGAATTTTAAA
1 TGAAAATACATGAATTTTAAA
2528721 TGAAAATACATG-ATTTT-AA
1 TGAAAATACATGAATTTTAAA
2528740 TGAA
1 TGAA
2528744 GATAAATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 12 0.52
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (21 bp):
TGAAAATACATGAATTTTAAA
Found at i:2529585 original size:30 final size:31
Alignment explanation
Indices: 2529544--2529603 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2529534 ACATGTTTCC
**
2529544 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
2529575 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
2529604 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:2531135 original size:21 final size:21
Alignment explanation
Indices: 2531073--2531138 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
2531063 CTTGGCTTAC
* *
2531073 TTTC-TCTTTT-TGAATATCT
1 TTTCTTCTTTTCTGATTTTCT
*
2531092 TTTTTTCTTTTCTGATTTT-T
1 TTTCTTCTTTTCTGATTTTCT
*
2531112 TTTCTTCTTTT-TGTCTTTTCT
1 TTTCTTCTTTTCTG-ATTTTCT
2531133 TTTCTT
1 TTTCTT
2531139 TTTGCACTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.13
20 21 0.55
21 12 0.32
ACGTcount: A:0.06, C:0.15, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTCTTCTTTTCTGATTTTCT
Found at i:2531970 original size:21 final size:20
Alignment explanation
Indices: 2531921--2531973 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
2531911 TCGAATTTCT
2531921 TTTTTTTTCCTTCTTTTTTGA
1 TTTTTTTT-CTTCTTTTTTGA
*
2531942 ATTTTTTTCTTCTTTTTGTG-
1 TTTTTTTTCTTCTTTTT-TGA
2531962 TTTTCTTTTCTT
1 TTTT-TTTTCTT
2531974 TTTGCACTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (20 bp):
TTTTTTTTCTTCTTTTTTGA
Found at i:2532730 original size:19 final size:20
Alignment explanation
Indices: 2532683--2532733 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2532673 GAAACCCCTT
* *
2532683 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTGTAA
2532703 TGAAAATACATGA-TTGTAA
1 TGAAAATACATGATTTGTAA
*
2532722 TGAAGATACATG
1 TGAAAATACATG
2532734 CTCTTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTGTAA
Found at i:2536065 original size:29 final size:29
Alignment explanation
Indices: 2536010--2536078 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
2536000 CTTGGCTTGC
*
2536010 TTTC-TCTTTT-TGAATTTCTTTTTTTCT
1 TTTCTTCTTTTCTAAATTTCTTTTTTTCT
2536037 TTTCTTCTTTTCTAAATTT-TTTTTCTTCT
1 TTTCTTCTTTTCTAAATTTCTTTTT-TTCT
2536066 TTT-TGTCTTTTCT
1 TTTCT-TCTTTTCT
2536079 TTTCTTTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 4 0.11
28 12 0.32
29 21 0.57
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (29 bp):
TTTCTTCTTTTCTAAATTTCTTTTTTTCT
Found at i:2536634 original size:20 final size:19
Alignment explanation
Indices: 2536609--2536659 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
2536599 GAAACCCCTT
2536609 TGAAAATACATGATTTTTAA
1 TGAAAATACATGA-TTTTAA
*
2536629 TGAAAATACAAGATTTTAA
1 TGAAAATACATGATTTTAA
*
2536648 TGAAGATACATG
1 TGAAAATACATG
2536660 CTCTTAGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:2536701 original size:100 final size:100
Alignment explanation
Indices: 2536582--2536788 Score: 369
Period size: 100 Copynumber: 2.1 Consensus size: 100
2536572 TAAACACATC
* *
2536582 ATGGTTCGGCTAAGGTTGAAACCCCTTTGAAAATACATGATTTTTAATGAAAATACAAGATTTTA
1 ATGGTTCAGCTAAGGTTGAAACCCCTTTGAAAATACATGATTTATAATGAAAATACAAGATTTTA
2536647 ATGAAGATACATGCTCTTAGCCGAATGGTTAGGTG
66 ATGAAGATACATGCTCTTAGCCGAATGGTTAGGTG
2536682 ATGGTTCAGCTAAGGTTGAAACCCCTTTGAAAATACATGATTTATAATGAAAATACAAGATTTTA
1 ATGGTTCAGCTAAGGTTGAAACCCCTTTGAAAATACATGATTTATAATGAAAATACAAGATTTTA
* * *
2536747 ATTAAGATACATGCTCTTGGCCGAATGGTTAGGTT
66 ATGAAGATACATGCTCTTAGCCGAATGGTTAGGTG
2536782 ATGGTTC
1 ATGGTTC
2536789 GGCCCTAAGG
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (100 bp):
ATGGTTCAGCTAAGGTTGAAACCCCTTTGAAAATACATGATTTATAATGAAAATACAAGATTTTA
ATGAAGATACATGCTCTTAGCCGAATGGTTAGGTG
Found at i:2536734 original size:20 final size:19
Alignment explanation
Indices: 2536709--2536759 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2536699 GAAACCCCTT
2536709 TGAAAATACATGATTTATAA
1 TGAAAATACATGATTT-TAA
*
2536729 TGAAAATACAAGATTTTAA
1 TGAAAATACATGATTTTAA
* *
2536748 TTAAGATACATG
1 TGAAAATACATG
2536760 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:2548544 original size:19 final size:19
Alignment explanation
Indices: 2548516--2548565 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
2548506 GAAACCCCTT
*
2548516 TGAAAATACATGATTTTTA
1 TGAAAATACATGATTTTAA
*
2548535 TGAAATTACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
2548554 TGAAGATACATG
1 TGAAAATACATG
2548566 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:2549501 original size:30 final size:31
Alignment explanation
Indices: 2549462--2549521 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2549452 ACATGCTTCC
**
2549462 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
2549493 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
2549522 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:2551868 original size:8 final size:8
Alignment explanation
Indices: 2551857--2551881 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2551847 TATTTTTCTT
2551857 TTCTTTTC
1 TTCTTTTC
2551865 TTCTTTTC
1 TTCTTTTC
2551873 TTCTTTTC
1 TTCTTTTC
2551881 T
1 T
2551882 GATTTTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:2552637 original size:19 final size:20
Alignment explanation
Indices: 2552596--2552645 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2552586 GAAACCCCTT
*
2552596 TGAAAATACATAATTTTTGA
1 TGAAAATACATAATTTTTAA
* *
2552616 TGAAAATATATGA-TTTTAA
1 TGAAAATACATAATTTTTAA
*
2552635 TGAAGATACAT
1 TGAAAATACAT
2552646 GCTCTTGGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (20 bp):
TGAAAATACATAATTTTTAA
Found at i:2553582 original size:30 final size:31
Alignment explanation
Indices: 2553543--2553602 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2553533 ACAAGCTTCC
**
2553543 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
2553574 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
2553603 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:2572670 original size:19 final size:20
Alignment explanation
Indices: 2572623--2572673 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2572613 GAAACCCCTT
* *
2572623 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTGTAA
2572643 TGAAAATACATGA-TTGTAA
1 TGAAAATACATGATTTGTAA
*
2572662 TGAAGATACATG
1 TGAAAATACATG
2572674 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTGTAA
Found at i:2573407 original size:20 final size:21
Alignment explanation
Indices: 2573369--2573408 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2573359 GATCATCTAG
* *
2573369 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
2573390 AAGCT-AGATAAAAGGTATA
1 AAGCTAAGATAAAAGGTATA
2573409 CGACGTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Done.