Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007895.1 Hibiscus syriacus cultivar Beakdansim tig00110280_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: 561701
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 3
Found at i:216855 original size:73 final size:72
Alignment explanation
Indices: 216726--216898 Score: 276
Period size: 73 Copynumber: 2.4 Consensus size: 72
216716 CGATTCTGTC
* *
216726 GTTGTGATTTTCATTTCGCGTTGTGATTCTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
216791 TTTTCGT
66 TTTTCGT
* *
216798 GTTGCGATTTTCATTTCGCGTTGCGATTCTTGCGTTGTGATAGTCAAATTCGTGTTGCGATAGTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTC-TGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
216863 ATTTTCGT
65 ATTTTCGT
*
216871 GTTGCGA-TTTCATTTTCGTGTTGCGATT
1 GTTGCGATTTTCA-TTTCGCGTTGCGATT
216899 TTAAGTTTCA
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
72 32 0.34
73 62 0.66
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (72 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTCTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
TTTTCGT
Found at i:219387 original size:20 final size:20
Alignment explanation
Indices: 219347--219467 Score: 125
Period size: 20 Copynumber: 5.6 Consensus size: 20
219337 AGAATAGTTT
*
219347 ACTATCGCAATGCGAAAAATG
1 ACTATCGCAACGCG-AAAATG
219368 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
219388 ACTATCGCAACGAGAAAATCG
1 ACTATCGCAACGCGAAAAT-G
*
219409 CAACAACAAAATCGCAACGCGAAAATG
1 -----AC--TATCGCAACGCGAAAATG
*
219436 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
219456 ACTATCGCAACG
1 ACTATCGCAACG
219468 AAAGAATCGC
Statistics
Matches: 85, Mismatches: 7, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
20 51 0.60
21 14 0.16
22 2 0.02
26 2 0.02
27 1 0.01
28 15 0.18
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:219410 original size:14 final size:14
Alignment explanation
Indices: 219391--219434 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
219381 GAAAATGACT
219391 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
* *
219405 ATCGCAACAACAAA
1 ATCGCAACGAGAAA
*
219419 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
219433 AT
1 AT
219435 GACTATCGCA
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:219460 original size:68 final size:69
Alignment explanation
Indices: 219350--219479 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 69
219340 ATAGTTTACT
*
219350 ATCGCAATGCGAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAA-AATCGCAACA
1 ATCGCAACGCGAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGA-AAGAATCGCAACA
219414 ACAAA
65 ACAAA
*
219419 ATCGCAACGCG-AAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAA
1 ATCGCAACGCGAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAA
219480 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
67 2 0.03
68 46 0.79
69 10 0.17
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (69 bp):
ATCGCAACGCGAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAACAA
CAAA
Found at i:219537 original size:20 final size:20
Alignment explanation
Indices: 219512--219790 Score: 276
Period size: 20 Copynumber: 14.3 Consensus size: 20
219502 GATTCTCTCG
**
219512 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
219532 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
* *
219552 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
219572 TTGCGATAGTCATTTTCGCGCA
1 TTGCGATAGTCATTTT--CGCA
*
219594 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
**
219608 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
219628 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
219648 TTGCGATAGTCATTTTCGCGCA
1 TTGCGATAGTCATTTT--CGCA
*
219670 TTGCGAT--TC-TCTT-G--
1 TTGCGATAGTCATTTTCGCA
**
219684 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
219704 TTGCGATAGTCATTTCCGCA
1 TTGCGATAGTCATTTTCGCA
* *
219724 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTTCGCA
* **
219744 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTTCGCA
219764 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
219784 TTGCGAT
1 TTGCGAT
219791 TTTAAGTTTC
Statistics
Matches: 219, Mismatches: 24, Indels: 32
0.80 0.09 0.12
Matches are distributed among these distances:
14 14 0.06
16 7 0.03
17 2 0.01
18 6 0.03
19 3 0.01
20 167 0.76
22 20 0.09
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:219632 original size:56 final size:54
Alignment explanation
Indices: 219550--219654 Score: 156
Period size: 56 Copynumber: 1.9 Consensus size: 54
219540 GTCATTTTCG
* ** *
219550 CGTTGTGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGCATTGCGATTCTCT
1 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCG--TTGCGATTCTCT
219606 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGAT
219655 AGTCATTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 7 0.16
56 38 0.84
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGATTCTCT
Found at i:219636 original size:76 final size:76
Alignment explanation
Indices: 219532--219750 Score: 352
Period size: 76 Copynumber: 2.9 Consensus size: 76
219522 CAAATTCGCA
** * *
219532 TTGCGATAGTCATTTTCGCGTTGTGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGCATTG
1 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGCATTG
219597 CGATTCTCTCG
66 CGATTCTCTCG
219608 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGCATTG
1 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGCATTG
*
219673 CGATTCTCTTG
66 CGATTCTCTCG
* * *
219684 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTCCGCATTGCGATAGTCA-TTTC-CGCGTTG
1 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGCATTG
219747 CGAT
66 CGAT
219751 AGTCATTTCC
Statistics
Matches: 135, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
74 10 0.07
75 4 0.03
76 121 0.90
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (76 bp):
TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGCATTG
CGATTCTCTCG
Found at i:219658 original size:96 final size:95
Alignment explanation
Indices: 219494--219791 Score: 399
Period size: 96 Copynumber: 3.1 Consensus size: 95
219484 AAATGAAAAT
*
219494 CGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGTGAT
1 CGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGAT
219559 AGTCATTTTCGCGTTGCGATAGTCATTTTCG
66 AGTCATTTTCGCGTTGCGATAGTCATTTT-G
219590 CGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGAT
1 CGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGAT
**
219655 AGTCATTTTCGCGCATTGCGATTCTC-TTGTTG
66 AGTCATTTTCGCG--TTGCGATAGTCATT-TTG
* * * * * * *
219687 CG-ATAGTCAAAT-TCGCATTGCGATAGTC-ATTTCCGCATTGCGATAGTCATTTCCGCGTTGCG
1 CGCATTG-CGATTCTCTCGTTGCGATAGTCAAATT-CGCATTGCGATAGTCATTTTCGCGTTGCG
* *
219749 ATAGTCATTTCCGTGTTGCGATAGTCATTTT-
64 ATAGTCATTTTCGCGTTGCGATAGTCATTTTG
219780 CGCATTGCGATT
1 CGCATTGCGATT
219792 TTAAGTTTCT
Statistics
Matches: 178, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
93 5 0.03
94 14 0.08
95 5 0.03
96 135 0.76
97 8 0.04
98 11 0.06
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (95 bp):
CGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGAT
AGTCATTTTCGCGTTGCGATAGTCATTTTG
Found at i:220339 original size:21 final size:20
Alignment explanation
Indices: 220265--220351 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
220255 GCCCGACTCA
220265 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGG-C
* ** *
220286 CCTATCATCCCTCAAGAGTC
1 CCTGTCATCGTTCAAGAGGC
*
220306 CCT-TCCCACCGTTCAAGAGGC
1 CCTGT--CATCGTTCAAGAGGC
*
220327 CACTGTCATCGTTGAAGAGGTC
1 C-CTGTCATCGTTCAAGAGG-C
220349 CCT
1 CCT
220352 CCCAACATTC
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.02
20 4 0.08
21 41 0.80
22 4 0.08
23 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.24
Consensus pattern (20 bp):
CCTGTCATCGTTCAAGAGGC
Found at i:220345 original size:42 final size:42
Alignment explanation
Indices: 220273--220355 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
220263 CACCTGTCAT
*
220273 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCTTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCC-TCCCAC
* ** *
220315 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
220356 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:221752 original size:14 final size:14
Alignment explanation
Indices: 221733--221768 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
221723 ATTGTTTAAT
221733 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
221747 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
221761 TGATTTGT
1 TGATTTGT
221769 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:221913 original size:14 final size:14
Alignment explanation
Indices: 221894--221947 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
221884 GGAAATGACT
221894 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
221908 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
221927 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
221941 ATCGCAA
1 ATCGCAA
221948 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:221924 original size:33 final size:33
Alignment explanation
Indices: 221874--221977 Score: 147
Period size: 33 Copynumber: 3.1 Consensus size: 33
221864 AAAACAGACT
* **
221874 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
221908 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
221941 ATCGCAATGCGAAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
221974 ATCG
1 ATCG
221978 TTGCAATAGT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
33 37 0.57
34 28 0.43
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:221965 original size:20 final size:19
Alignment explanation
Indices: 221907--221975 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
221897 GCAACGAGAG
221907 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
221926 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
221940 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
221960 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
221976 CGTTGCAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
19 13 0.32
20 13 0.32
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:222101 original size:33 final size:34
Alignment explanation
Indices: 222044--222119 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
222034 TTTAGTTTCG
222044 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
222078 CGTTGCGCTTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
222111 CGTTGCGAT
1 CGTTGCGAT
222120 AGTCATTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:222126 original size:33 final size:33
Alignment explanation
Indices: 222044--222128 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
222034 TTTAGTTTCG
222044 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
222078 CGTTGCGCTTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
**
222111 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
222129 CACGTTGCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 34 0.72
34 13 0.28
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:222136 original size:20 final size:20
Alignment explanation
Indices: 222111--222204 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
222101 GCGATTCTCT
*
222111 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCG
222131 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
222151 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
222171 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
222191 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
222205 AATGAATGTC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 68 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:224429 original size:3 final size:3
Alignment explanation
Indices: 224421--224450 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
224411 CTTTGGGGAT
224421 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
224451 AGGGTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:224692 original size:24 final size:24
Alignment explanation
Indices: 224641--224692 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
224631 ATCTGAGTAT
** *
224641 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
224665 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
224689 TGAC
1 TGAC
224693 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:225545 original size:20 final size:20
Alignment explanation
Indices: 225519--225626 Score: 128
Period size: 20 Copynumber: 5.4 Consensus size: 20
225509 GAAATTCAGT
*
225519 ATTGCGATAGTCAGAATCGC
1 ATTGCGATAGTCAGATTCGC
* * *
225539 GTTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGATTCGC
*
225559 GTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGATTCGC
* * *
225579 ATTGTGAT-TTACATATTCGC
1 ATTGCGATAGT-CAGATTCGC
225599 ATTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGATTCGC
225619 ATTGCGAT
1 ATTGCGAT
225627 TTACGTATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 73 0.97
21 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
ATTGCGATAGTCAGATTCGC
Found at i:225604 original size:40 final size:40
Alignment explanation
Indices: 225560--225686 Score: 186
Period size: 40 Copynumber: 3.2 Consensus size: 40
225550 CAGAATCTCG
* *
225560 TTGCGATAGTCAGATTCGCATTGTGATTTACATATTCGCA
1 TTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCA
*
225600 TTGCGATAGTCAGATTCGCATTGCGATTTACGTATTTGCA
1 TTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCA
*
225640 TTGCGAT--TTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATAGTCA-G-ATTCGCATTGCGATTTACGTATTCGCA
225680 TTGCGAT
1 TTGCGAT
225687 TTAGGAAAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 77 0.96
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (40 bp):
TTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCA
Found at i:225606 original size:60 final size:60
Alignment explanation
Indices: 225535--225666 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
225525 ATAGTCAGAA
* * * *
225535 TCGCGTTGCGATAGTCAGAATCTCGTTGCGATAGTCA-G-ATTCGCATTGTGATTTACATAT
1 TCGCATTGCGATAGTCAGAATCGCATTGCGAT--TCACGTATTCGCATTGCGATTTACATAT
* * * *
225595 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTTGCATTGCGATTTACGTAT
1 TCGCATTGCGATAGTCAGAATCGCATTGCGATTCACGTATTCGCATTGCGATTTACATAT
225655 TCGCATTGCGAT
1 TCGCATTGCGAT
225667 TTACGTATTC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 2 0.03
59 1 0.02
60 59 0.95
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (60 bp):
TCGCATTGCGATAGTCAGAATCGCATTGCGATTCACGTATTCGCATTGCGATTTACATAT
Found at i:225640 original size:20 final size:20
Alignment explanation
Indices: 225573--225689 Score: 166
Period size: 20 Copynumber: 5.8 Consensus size: 20
225563 CGATAGTCAG
* *
225573 ATTCGCATTGTGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
225593 ATTCGCATTGCGATAGT-CAG-
1 ATTCGCATTGCGAT-TTAC-GT
225613 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
225633 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
225653 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
225673 ATTCGCATTGCGATTTA
1 ATTCGCATTGCGATTTA
225690 GGAAAATCGC
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.02
20 84 0.97
21 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:228736 original size:12 final size:12
Alignment explanation
Indices: 228719--228750 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
228709 ATTACCGTTT
*
228719 TCCGTCCCTGTA
1 TCCGTCCCCGTA
228731 TCCGTCCCCGTA
1 TCCGTCCCCGTA
228743 TCCGTCCC
1 TCCGTCCC
228751 ACTTAGGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.50, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCGTCCCCGTA
Found at i:232806 original size:46 final size:46
Alignment explanation
Indices: 232753--232844 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
232743 TGAAGAAGAA
*
232753 ATATCCATGTTGACCAGCAAACTTTTTGTTATACTTATAACAAGCT
1 ATATCCATGTTGACCAGCAAACTTTTTATTATACTTATAACAAGCT
*
232799 ATATCCATGTTGACCAGCAAACTTTTTATTATACTTGTAACAAGCT
1 ATATCCATGTTGACCAGCAAACTTTTTATTATACTTATAACAAGCT
232845 TTGCTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (46 bp):
ATATCCATGTTGACCAGCAAACTTTTTATTATACTTATAACAAGCT
Found at i:234603 original size:21 final size:23
Alignment explanation
Indices: 234564--234622 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
234554 CCGAAATAAT
* *
234564 AATAAAAATATTAT-TTTTATTC
1 AATAAAAATAGTATATTTAATTC
*
234586 AATAAAAATAGTA-ATTTAATTG
1 AATAAAAATAGTATATTTAATTC
*
234608 AA-AAAAATAATATAT
1 AATAAAAATAGTATAT
234623 AGGTGATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.29
22 22 0.71
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (23 bp):
AATAAAAATAGTATATTTAATTC
Found at i:235102 original size:38 final size:38
Alignment explanation
Indices: 235049--235173 Score: 198
Period size: 38 Copynumber: 3.3 Consensus size: 38
235039 TTTTCACCCT
235049 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAAA
235088 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
* * *
235126 AAACTCGACCCGACTCAACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
*
235163 AACCCCGACCC
1 AAACCCGACCC
235174 AAACAAAATA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 12 0.15
38 62 0.77
39 7 0.09
ACGTcount: A:0.39, C:0.40, G:0.10, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:235768 original size:21 final size:21
Alignment explanation
Indices: 235743--235790 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
235733 AGTGCCAAAT
*
235743 AATAATAAAACCGGTAGAAAA
1 AATAATAAAACAGGTAGAAAA
* *
235764 AATAATAAAATAGGTAGAAAT
1 AATAATAAAACAGGTAGAAAA
235785 AATAAT
1 AATAAT
235791 GTTTCCGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.21
Consensus pattern (21 bp):
AATAATAAAACAGGTAGAAAA
Found at i:235966 original size:17 final size:16
Alignment explanation
Indices: 235944--235990 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
235934 GAATATGCGA
235944 AGGAATTAGAATCTGTC
1 AGGAATT-GAATCTGTC
*
235961 AGGAATTGAAATTTGTC
1 AGGAATTG-AATCTGTC
235978 AGGAATTGGAATC
1 AGGAATT-GAATC
235991 CAATTTCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (16 bp):
AGGAATTGAATCTGTC
Found at i:236027 original size:44 final size:41
Alignment explanation
Indices: 235979--236089 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 41
235969 AAATTTGTCA
235979 GGAATTGGAATCCAATTTCATATTCTGTTTGGTTGGCAAGAAAT
1 GGAATTGGAAT--AA-TTCATATTCTGTTTGGTTGGCAAGAAAT
*
236023 GGAATTGG--------ATATTCTGTTTGGTTGGCAGGAAAT
1 GGAATTGGAATAATTCATATTCTGTTTGGTTGGCAAGAAAT
236056 GGAATTGGAATATAATTCCATATTCTGTTTGGTT
1 GGAATTGG-A-ATAATT-CATATTCTGTTTGGTT
236090 CGCAGACATA
Statistics
Matches: 55, Mismatches: 1, Indels: 22
0.71 0.01 0.28
Matches are distributed among these distances:
33 32 0.58
44 23 0.42
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (41 bp):
GGAATTGGAATAATTCATATTCTGTTTGGTTGGCAAGAAAT
Found at i:236040 original size:33 final size:33
Alignment explanation
Indices: 235998--236064 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
235988 ATCCAATTTC
235998 ATATTCTGTTTGGTTGGCAAGAAATGGAATTGG
1 ATATTCTGTTTGGTTGGCAAGAAATGGAATTGG
*
236031 ATATTCTGTTTGGTTGGCAGGAAATGGAATTGG
1 ATATTCTGTTTGGTTGGCAAGAAATGGAATTGG
236064 A
1 A
236065 ATATAATTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.06, G:0.31, T:0.36
Consensus pattern (33 bp):
ATATTCTGTTTGGTTGGCAAGAAATGGAATTGG
Found at i:237227 original size:21 final size:21
Alignment explanation
Indices: 237201--237248 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
237191 AATGCCTAAT
237201 AATAATAAAATCGGTAGAAAA
1 AATAATAAAATCGGTAGAAAA
* *
237222 AATAATAAAATCTGTAGAAAT
1 AATAATAAAATCGGTAGAAAA
237243 AATAAT
1 AATAAT
237249 GTTTCCGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.25
Consensus pattern (21 bp):
AATAATAAAATCGGTAGAAAA
Found at i:237409 original size:18 final size:17
Alignment explanation
Indices: 237386--237430 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
237376 GTTTATGAGA
237386 GAATTGGAATATGTAAAG
1 GAATTGGAATATGT-AAG
* *
237404 GAATTGGAATCTGTCAG
1 GAATTGGAATATGTAAG
237421 GAATTGGAAT
1 GAATTGGAAT
237431 CCAATTCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.38, C:0.04, G:0.29, T:0.29
Consensus pattern (17 bp):
GAATTGGAATATGTAAG
Found at i:237424 original size:17 final size:18
Alignment explanation
Indices: 237386--237431 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
237376 GTTTATGAGA
*
237386 GAATTGGAATATGTAAAG
1 GAATTGGAATCTGTAAAG
*
237404 GAATTGGAATCTGT-CAG
1 GAATTGGAATCTGTAAAG
237421 GAATTGGAATC
1 GAATTGGAATC
237432 CAATTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (18 bp):
GAATTGGAATCTGTAAAG
Found at i:240424 original size:8 final size:8
Alignment explanation
Indices: 240409--240443 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
240399 TTTGAGAGGA
240409 ATATAGAT
1 ATATAGAT
*
240417 AGATAGAT
1 ATATAGAT
240425 ATATAGAT
1 ATATAGAT
240433 ATATAGAT
1 ATATAGAT
240441 ATA
1 ATA
240444 CTTCGTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (8 bp):
ATATAGAT
Found at i:241495 original size:7 final size:7
Alignment explanation
Indices: 241483--241543 Score: 104
Period size: 7 Copynumber: 8.4 Consensus size: 7
241473 GATTTCTCTC
241483 CTTTCTT
1 CTTTCTT
241490 CTTTCTT
1 CTTTCTT
241497 CTTTCTT
1 CTTTCTT
241504 CTTTCTT
1 CTTTCTT
241511 CTTTCTT
1 CTTTCTT
241518 CTTTCTT
1 CTTTCTT
241525 CTTTCTT
1 CTTTCTT
241532 CATCTTCTT
1 C-T-TTCTT
241541 CTT
1 CTT
241544 CTCCTAAACG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
7 44 0.85
8 2 0.04
9 6 0.12
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (7 bp):
CTTTCTT
Found at i:241498 original size:3 final size:3
Alignment explanation
Indices: 241485--241545 Score: 59
Period size: 3 Copynumber: 18.3 Consensus size: 3
241475 TTTCTCTCCT
241485 TTC TTC TTTC TTC TTTC TTC TTTC TTC TTTC TTC TTTC TTC TTTC TTC
1 TTC TTC -TTC TTC -TTC TTC -TTC TTC -TTC TTC -TTC TTC -TTC TTC
*
241533 ATC TTC TTC TTC T
1 TTC TTC TTC TTC T
241546 CCTAAACGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
3 32 0.64
4 18 0.36
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:242733 original size:22 final size:21
Alignment explanation
Indices: 242679--242742 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
242669 AGTCGAGGGT
242679 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
* * *
242700 CTCTTAGGTCCTTTGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
* *
242722 TTCACAGGTCCTTCAGGACAA
1 TTCATAGGTCCTTCGGGACAA
242743 AATTTCATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:244813 original size:3 final size:3
Alignment explanation
Indices: 244807--244856 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
244797 ATTATTTATT
* * *
244807 TAA TAA TAA TAA TATA TAA TAA TAT TAT TAA -AA CAA -AA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
244851 TAA TAA
1 TAA TAA
244857 ATAAAACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:244850 original size:22 final size:23
Alignment explanation
Indices: 244822--244866 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
244812 ATAATAATAT
* *
244822 ATAATAAT-ATTATTAAAACAAA
1 ATAATAATAATAAATAAAACAAA
244844 ATAATAATAATAAATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
244867 TGAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAATAATAATAAATAAAACAAA
Found at i:244857 original size:19 final size:19
Alignment explanation
Indices: 244807--244857 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
244797 ATTATTTATT
* * *
244807 TAATAATAATAATATATAA
1 TAATAATAATAAAACAAAA
* *
244826 TAATATTATTAAAACAAAA
1 TAATAATAATAAAACAAAA
244845 TAATAATAATAAA
1 TAATAATAATAAA
244858 TAAAACAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAATAATAAAACAAAA
Found at i:245046 original size:2 final size:2
Alignment explanation
Indices: 245039--245103 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
245029 ATTAGTATTG
245039 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
245081 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
245104 GAATCATAGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:247515 original size:18 final size:18
Alignment explanation
Indices: 247492--247529 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
247482 TCCTGTGACC
247492 CCCTGCTCAACTATGCCA
1 CCCTGCTCAACTATGCCA
247510 CCCTGCTCAACTATGCCA
1 CCCTGCTCAACTATGCCA
247528 CC
1 CC
247530 GATCAAGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.47, G:0.11, T:0.21
Consensus pattern (18 bp):
CCCTGCTCAACTATGCCA
Found at i:257880 original size:16 final size:15
Alignment explanation
Indices: 257859--257904 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
257849 CTTTATATTG
257859 TAATAATAATTGTGTT
1 TAATAATAATTGTG-T
* *
257875 TAATAATACTAAGTGT
1 TAATAATAAT-TGTGT
257891 TAATAATAATTGTG
1 TAATAATAATTGTG
257905 ATATTAACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (15 bp):
TAATAATAATTGTGT
Found at i:258762 original size:18 final size:19
Alignment explanation
Indices: 258739--258776 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
258729 AACATGTACT
*
258739 ACATTATAATCACCA-AAG
1 ACATTATAATAACCACAAG
258757 ACATTATAATAACCACAAG
1 ACATTATAATAACCACAAG
258776 A
1 A
258777 AAACTAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.53, C:0.21, G:0.05, T:0.21
Consensus pattern (19 bp):
ACATTATAATAACCACAAG
Found at i:263753 original size:24 final size:24
Alignment explanation
Indices: 263726--263797 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
263716 AAACGGAGAT
*
263726 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
263750 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
263774 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
263798 GTAATGTGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:263797 original size:12 final size:12
Alignment explanation
Indices: 263728--263797 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
263718 ACGGAGATAT
* *
263728 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
263740 CATAATTCAGAT
1 CAGAATTCAGAA
*
263752 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
263764 CAGAATCCAGAT
1 CAGAATTCAGAA
*
263776 CAGAAATCAGAA
1 CAGAATTCAGAA
263788 CAGAATTCAG
1 CAGAATTCAG
263798 GTAATGTGTC
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:263814 original size:48 final size:47
Alignment explanation
Indices: 263726--263834 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 47
263716 AAACGGAGAT
* * * *
263726 ATCAGAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
* * *
263773 GATCAGAAATCAGAACAGAATTCAGGTAATG-TGTCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAATCCA
*
263821 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
263835 TAAAATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 1 0.02
48 49 0.96
49 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
Found at i:264984 original size:18 final size:18
Alignment explanation
Indices: 264963--265003 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
264953 CTGCCATCTG
*
264963 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
264981 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
*
264999 GTCTT
1 ATCTT
265004 TTCGAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:267104 original size:2 final size:2
Alignment explanation
Indices: 267097--267140 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
267087 AATAATTATC
267097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
267139 AT
1 AT
267141 CCAATTACGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267485 original size:17 final size:18
Alignment explanation
Indices: 267454--267487 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
267444 ATATATAATT
*
267454 TAATTGAAATTATTTAAA
1 TAATTGAAATAATTTAAA
267472 TAATT-AAATAATTTAA
1 TAATTGAAATAATTTAA
267488 TCAATAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TAATTGAAATAATTTAAA
Found at i:271394 original size:138 final size:137
Alignment explanation
Indices: 271091--271414 Score: 327
Period size: 138 Copynumber: 2.4 Consensus size: 137
271081 CTCAGTTACT
* *
271091 AGTCCAAGTCTTTGTCTTCTTGATG-A-CAGGTTTGGCATCCTTCATTTTAAAGGCACTGATCGT
1 AGTCCAAGTCTTTGTC-TCTTGATGAATCAGATTTGGCATCCTTCATTTTAAAGGCACTGATCAT
* * * *
271154 CTTTCCCTTAGCATCTTCATACGTAGGAACCGGAGGATTTTTCACATGCCGCTCTCCAAATTCCC
65 CTTTCCCTCAACATCTTCACACGTAGGAACCGGAGGATTTTTCACATGCCGCACTCCAAATTCCC
271219 TAGTTCCA
130 TAGTTCCA
** * * * * * * *
271227 AAACGAAGTCTTTTTCCTCTTGATAAATCAGATCTGACATCCTTCATTTTAAAGTCACTGATTAT
1 AGTCCAAGTCTTTGT-CTCTTGATGAATCAGATTTGGCATCCTTCATTTTAAAGGCACTGATCAT
* * * ** *
271292 CTTTTCCTCAACATGTTCACCCGTAGGAATTGGAGGATTTTTCACATTTTCCG-ACT-CAAAGTT
65 CTTTCCCTCAACATCTTCACACGTAGGAACCGGAGGATTTTTCACA--TGCCGCACTCCAAA-TT
*
271355 CCC-GGTTCCA
127 CCCTAGTTCCA
* *
271365 AGTCCAAGTCCTTGTCTGCTAGATGAATCA-AGTTTGGCATCCTTCATTTT
1 AGTCCAAGTCTTTGTCT-CTTGATGAATCAGA-TTTGGCATCCTTCATTTT
271415 GGAGTAAATG
Statistics
Matches: 149, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
136 18 0.12
137 5 0.03
138 115 0.77
139 7 0.05
140 4 0.03
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (137 bp):
AGTCCAAGTCTTTGTCTCTTGATGAATCAGATTTGGCATCCTTCATTTTAAAGGCACTGATCATC
TTTCCCTCAACATCTTCACACGTAGGAACCGGAGGATTTTTCACATGCCGCACTCCAAATTCCCT
AGTTCCA
Found at i:271538 original size:17 final size:17
Alignment explanation
Indices: 271518--271551 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
271508 AAGGGAAGTG
*
271518 GTTAATCAGCTGTTATA
1 GTTAATCAGCTGATATA
271535 GTTAATCAGCTGATATA
1 GTTAATCAGCTGATATA
271552 AATGAGCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (17 bp):
GTTAATCAGCTGATATA
Found at i:271770 original size:15 final size:15
Alignment explanation
Indices: 271752--271792 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
271742 GTCTTCTGCC
271752 TTCCTTGCTTCATTG
1 TTCCTTGCTTCATTG
271767 TTCCTTGCTTCATTG
1 TTCCTTGCTTCATTG
271782 TTCCTTGCTTC
1 TTCCTTGCTTC
271793 TTGGTTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.05, C:0.29, G:0.12, T:0.54
Consensus pattern (15 bp):
TTCCTTGCTTCATTG
Found at i:279101 original size:21 final size:21
Alignment explanation
Indices: 279025--279123 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
279015 AGTCGAGGGT
* *
279025 TACAGTGGTCCTACGAGAC-A
1 TACAGTGGTCCTTCGGGACAA
* *
279045 T--AGTGGTCTTTCGAGACAA
1 TACAGTGGTCCTTCGGGACAA
279064 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
*
279085 TACAGTGGTCCTACGGG---A
1 TACAGTGGTCCTTCGGGACAA
*
279103 TATAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
279124 ATTTCAGTGC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 30 0.45
19 2 0.03
20 1 0.02
21 33 0.50
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (21 bp):
TACAGTGGTCCTTCGGGACAA
Found at i:280216 original size:21 final size:21
Alignment explanation
Indices: 280183--280223 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
280173 TGTAACTAAA
*
280183 GTTGTTAAGAATTGGTTAAGT
1 GTTGTTAAGAATTAGTTAAGT
**
280204 GTTGTTACTAATTAGTTAAG
1 GTTGTTAAGAATTAGTTAAG
280224 GGAAGTTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (21 bp):
GTTGTTAAGAATTAGTTAAGT
Found at i:280253 original size:17 final size:17
Alignment explanation
Indices: 280231--280264 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
280221 AAGGGAAGTT
* *
280231 GTTAATTGGTTGTTATA
1 GTTAATTAGTTGATATA
280248 GTTAATTAGTTGATATA
1 GTTAATTAGTTGATATA
280265 AATGAGCTGC
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:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (17 bp):
GTTAATTAGTTGATATA
Found at i:284657 original size:18 final size:17
Alignment explanation
Indices: 284634--284671 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
284624 TTTATAAATA
284634 AAAATATAAAATATATTT
1 AAAATATAAAATA-ATTT
*
284652 AAAATATATAATAATTT
1 AAAATATAAAATAATTT
284669 AAA
1 AAA
284672 TTTTTTAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATATAAAATAATTT
Found at i:284818 original size:30 final size:31
Alignment explanation
Indices: 284757--284818 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
284747 AGTGGGTGAA
* **
284757 TTTAAACTTTTAAAATTTTAAGAATTTAAAC
1 TTTAAACTTATAAAATTTTAAGAATGAAAAC
284788 TTTAAA-TTATAAAATTTTAA-AAGTGAAAAC
1 TTTAAACTTATAAAATTTTAAGAA-TGAAAAC
284818 T
1 T
284819 AATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.07
30 19 0.70
31 6 0.22
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (31 bp):
TTTAAACTTATAAAATTTTAAGAATGAAAAC
Found at i:286763 original size:21 final size:21
Alignment explanation
Indices: 286734--286774 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
286724 CATCGTCTGC
*
286734 CGCCACTCGATCTCCTTCGAA
1 CGCCACTCGATCTCCCTCGAA
* *
286755 CGCCGCTCGTTCTCCCTCGA
1 CGCCACTCGATCTCCCTCGA
286775 CTGGAACGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.46, G:0.17, T:0.24
Consensus pattern (21 bp):
CGCCACTCGATCTCCCTCGAA
Found at i:289024 original size:14 final size:14
Alignment explanation
Indices: 289005--289036 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
288995 AAATATCATT
289005 TATTTTTTGTTAAA
1 TATTTTTTGTTAAA
289019 TA-TTTTTGTTAAA
1 TATTTTTTGTTAAA
289032 -ATTTT
1 TATTTT
289037 ATTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.06
13 14 0.82
14 2 0.12
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (14 bp):
TATTTTTTGTTAAA
Found at i:292727 original size:35 final size:34
Alignment explanation
Indices: 292642--292728 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
292632 ATTTGGTATT
*
292642 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
292676 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
292714 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
292729 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:295982 original size:15 final size:15
Alignment explanation
Indices: 295964--295998 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
295954 CGAGGGTATT
295964 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
295979 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
295994 GTAGT
1 GTAGT
295999 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:296009 original size:18 final size:18
Alignment explanation
Indices: 295982--296029 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
295972 TCGGGACGTA
*
295982 GTCCTTCGGGACGTAGTG
1 GTCCTACGGGACGTAGTG
296000 GTCCTACGGGACGTAGTG
1 GTCCTACGGGACGTAGTG
296018 GTCCTACGGGAC
1 GTCCTACGGGAC
296030 ATATATAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.23
Consensus pattern (18 bp):
GTCCTACGGGACGTAGTG
Found at i:296173 original size:3 final size:3
Alignment explanation
Indices: 296167--296196 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
296157 TATACATGGG
296167 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
296197 TGACAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:302176 original size:80 final size:80
Alignment explanation
Indices: 302070--302222 Score: 281
Period size: 80 Copynumber: 1.9 Consensus size: 80
302060 TAGTGATGGA
302070 GTTACTATGGTAAAAAGTGACTCTTAAAATGTTAATGATTTGTGATTCTTATATATGCATGAATA
1 GTTACTATGGTAAAAAGTGACTCTTAAAATGTTAATGATTTGTGATTCTTATATATGCATGAATA
302135 CATGAAATGGGTATAG
66 CAT-AAATGGGTATAG
*
302151 GTTACTATGGT-AAAAGTGACTCTTAAAATGTTATTGATTTGTGATTCTTATATATGCATGAATA
1 GTTACTATGGTAAAAAGTGACTCTTAAAATGTTAATGATTTGTGATTCTTATATATGCATGAATA
302215 CATAAATG
66 CATAAATG
302223 ATAGGTTATA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
79 5 0.07
80 55 0.77
81 11 0.15
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (80 bp):
GTTACTATGGTAAAAAGTGACTCTTAAAATGTTAATGATTTGTGATTCTTATATATGCATGAATA
CATAAATGGGTATAG
Found at i:302529 original size:15 final size:15
Alignment explanation
Indices: 302511--302545 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
302501 CGAGGGTATT
302511 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
* *
302526 GTAGTCCTTTGGGAT
1 GTAGTCCTTCGGGAC
302541 GTAGT
1 GTAGT
302546 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.34, T:0.34
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:302703 original size:3 final size:3
Alignment explanation
Indices: 302697--302723 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
302687 ATACATGGGA
302697 AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC
302724 GATAATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:303639 original size:111 final size:112
Alignment explanation
Indices: 303502--303723 Score: 401
Period size: 111 Copynumber: 2.0 Consensus size: 112
303492 TTACAAAAAA
*
303502 TAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAA
1 TAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAA
* *
303567 ATTAAAACGTTAAAATGTTAATGTATCAGCAAAGTGTCGAG-ATATT
66 ATTAAAACGTTAAAATGTTAACGTATCAGCAAAGTGTAGAGTATATT
303613 TAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAA
1 TAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAA
*
303678 ATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGTATAT
66 ATTAAAACGTTAAAATGTTAACGTATCAGCAAAGTGTAGAGTATAT
303724 GATTTCCATC
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 102 0.96
112 4 0.04
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (112 bp):
TAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAA
ATTAAAACGTTAAAATGTTAACGTATCAGCAAAGTGTAGAGTATATT
Found at i:303826 original size:17 final size:18
Alignment explanation
Indices: 303785--303823 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
303775 ATTATATTAT
303785 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
303802 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
303820 TAAA
1 TAAA
303824 TACATAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:306351 original size:101 final size:103
Alignment explanation
Indices: 306174--306384 Score: 261
Period size: 101 Copynumber: 2.1 Consensus size: 103
306164 TTTGTCACCT
* * *
306174 TTGAGATTGTTTATCTCAAAACAAAGTTTCGTCTCGCTTGAGACAGTTTCCCTTGAAGCCCAAAT
1 TTGAGATTGTTTATCCCAAAACAAAATTTCGTCTCGCTTGAGACAGTTTCCCTTGAAACCCAAAT
*
306239 TTCAAACTTGTTTCACTTGAAACAAAA-TTGATCTCAC
66 TTCAAACTTGTTTCACATGAAACAAAATTTGATCTCAC
* **
306276 TTGAGATTGTTT-TCCCAAAA-ATAAATTT-GTCTCGCTTGAGATAGTTTTCCCTTGAAATGCAA
1 TTGAGATTGTTTATCCCAAAACA-AAATTTCGTCTCGCTTGAGACAG-TTTCCCTTGAAACCCAA
* * *
306338 ATTTTGAAA-TTGTTTCCCATGAAACAAAATTTTATCTCAC
64 A-TTTCAAACTTGTTTCACATGAAACAAAATTTGATCTCAC
*
306378 CTGAGAT
1 TTGAGAT
306385 AGCTTCTCTA
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
100 16 0.17
101 45 0.48
102 33 0.35
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (103 bp):
TTGAGATTGTTTATCCCAAAACAAAATTTCGTCTCGCTTGAGACAGTTTCCCTTGAAACCCAAAT
TTCAAACTTGTTTCACATGAAACAAAATTTGATCTCAC
Found at i:308059 original size:20 final size:20
Alignment explanation
Indices: 308036--308075 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
308026 AAAATTGGAA
308036 TCAAAAGGTAAAATAATTTT
1 TCAAAAGGTAAAATAATTTT
308056 TCAAAAGGTAAAATAATTTT
1 TCAAAAGGTAAAATAATTTT
308076 ACTCCATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
TCAAAAGGTAAAATAATTTT
Found at i:311136 original size:20 final size:19
Alignment explanation
Indices: 311103--311161 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
311093 GTTTTTTAAA
*
311103 TTTTAGAAAAATAAGTTTTT
1 TTTTAGAAAAATAA-TATTT
* *
311123 TTTTATAAATATAATATTT
1 TTTTAGAAAAATAATATTT
* *
311142 TTTTAAAAAAATAAAATTT
1 TTTTAGAAAAATAATATTT
311161 T
1 T
311162 CAATTACTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTTTAGAAAAATAATATTT
Found at i:318568 original size:21 final size:20
Alignment explanation
Indices: 318482--318639 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
318472 AAATGACCAA
**
318482 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
318501 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
318521 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
318541 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
318562 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
318583 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
318603 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
318624 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
318640 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:318701 original size:20 final size:20
Alignment explanation
Indices: 318607--318835 Score: 248
Period size: 20 Copynumber: 11.4 Consensus size: 20
318597 GATTTTCCAG
* ** *
318607 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
318627 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
318647 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
318667 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
318687 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
318707 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
318727 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
318747 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
318767 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
318787 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
318807 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
318827 AATCACAAC
1 AATCGCAAC
318836 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:319567 original size:24 final size:24
Alignment explanation
Indices: 319528--319574 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
319518 AAATTTGGTC
319528 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
319552 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
319575 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:319766 original size:12 final size:12
Alignment explanation
Indices: 319749--319773 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
319739 ATATAATCCT
319749 GAAGAAGAAAAA
1 GAAGAAGAAAAA
319761 GAAGAAGAAAAA
1 GAAGAAGAAAAA
319773 G
1 G
319774 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:322109 original size:33 final size:34
Alignment explanation
Indices: 322058--322237 Score: 156
Period size: 33 Copynumber: 5.2 Consensus size: 34
322048 CGGAAATTAC
* *
322058 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
322091 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * *
322125 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
322164 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* * *
322197 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
322230 AATCGCAA
1 AATCGCAA
322238 TGCGGAAATG
Statistics
Matches: 120, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
32 2 0.02
33 56 0.47
34 35 0.29
36 1 0.01
38 4 0.03
39 21 0.17
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:322123 original size:20 final size:19
Alignment explanation
Indices: 322072--322257 Score: 204
Period size: 19 Copynumber: 10.4 Consensus size: 19
322062 GCAACGAGAG
322072 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
322091 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
322105 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
322125 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
322144 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
322158 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
322178 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
322197 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
322211 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
322230 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
322250 AATCGCAA
1 AATCGCAA
322258 CGAGAGAATC
Statistics
Matches: 141, Mismatches: 8, Indels: 35
0.77 0.04 0.19
Matches are distributed among these distances:
14 32 0.23
15 2 0.01
16 4 0.03
17 6 0.04
18 1 0.01
19 52 0.37
20 44 0.31
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:322215 original size:86 final size:84
Alignment explanation
Indices: 322058--322237 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
322048 CGGAAATTAC
322058 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
322123 AAAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
322144 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
* *
322207 -A-GAGAATCGCAATGCGAAATTAA
60 AATGAAAATCGCAATGCGAAATGAA
322230 AATCGCAA
1 AATCGCAA
322238 TGCGGAAATG
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 53 0.62
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:322289 original size:53 final size:53
Alignment explanation
Indices: 322072--322275 Score: 349
Period size: 53 Copynumber: 3.8 Consensus size: 53
322062 GCAACGAGAG
* *
322072 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
322125 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
322178 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
322230 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCG
322276 ATTTTAATTT
Statistics
Matches: 145, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
52 18 0.12
53 126 0.87
54 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:322329 original size:52 final size:52
Alignment explanation
Indices: 322266--322400 Score: 252
Period size: 52 Copynumber: 2.6 Consensus size: 52
322256 AACGAGAGAA
* *
322266 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
322318 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
322370 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
322401 AGTCATTTTT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:322408 original size:19 final size:19
Alignment explanation
Indices: 322266--322400 Score: 164
Period size: 19 Copynumber: 7.6 Consensus size: 19
322256 AACGAGAGAA
* *
322266 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
322285 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
322301 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
322318 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
322337 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
322353 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
322370 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
322389 TCGCATTGCGAT
1 TCGCATTGCGAT
322401 AGTCATTTTT
Statistics
Matches: 100, Mismatches: 6, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
14 12 0.12
16 14 0.14
17 13 0.13
19 61 0.61
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:322526 original size:14 final size:14
Alignment explanation
Indices: 322507--322543 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
322497 CATCAATTAC
322507 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
322521 ACAAATCATCTTTT
1 ACAAATCAACTTTT
322535 ACAAATCAA
1 ACAAATCAA
322544 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:324508 original size:19 final size:19
Alignment explanation
Indices: 324466--324605 Score: 155
Period size: 19 Copynumber: 7.6 Consensus size: 19
324456 TAGTTTACTT
* *
324466 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
324486 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
324505 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
324524 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
324543 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
324557 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
324576 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
324595 TCGCAATGCGA
1 TCGCAACGCGA
324606 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
19 71 0.70
20 12 0.12
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:324568 original size:33 final size:35
Alignment explanation
Indices: 324482--324583 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 35
324472 CACGAAACTT
*
324482 AAAATCGCAACGCGAAATGATAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC--G-AACC
324520 AAAATCGCAACGCGAAATGAAAATCGCAACG-A-C
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAACC
* *
324553 AGAATCGCAATGCGAAATGAAAATCGCAACG
1 AAAATCGCAACGCGAAATGAAAATCGCAACG
324584 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
33 30 0.49
34 1 0.02
36 1 0.02
38 29 0.48
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.11
Consensus pattern (35 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAACC
Found at i:324636 original size:14 final size:14
Alignment explanation
Indices: 324617--324643 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
324607 TTTGGTTTCG
324617 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
324631 CGTTGCGATTTTG
1 CGTTGCGATTTTG
324644 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:324643 original size:33 final size:33
Alignment explanation
Indices: 324601--324695 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
324591 AAAATCGCAA
324601 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
324634 TGCGATTTTGGTTTCGCGTTGCGATTATT-TTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTGTCGT
**
324667 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
324696 GTTTCGCGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.08, C:0.15, G:0.27, T:0.49
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:324655 original size:19 final size:19
Alignment explanation
Indices: 324601--324729 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
324591 AAAATCGCAA
324601 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
324620 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
324634 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
324653 TGCGATTAT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
**
324667 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
324686 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
324705 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
324725 TGCGA
1 TGCGA
324730 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 48 0.52
20 13 0.14
ACGTcount: A:0.09, C:0.15, G:0.28, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:325051 original size:92 final size:93
Alignment explanation
Indices: 324774--325055 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
324764 ATGGATTGCA
324774 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
324838 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
324866 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
324931 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
324959 TTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
325023 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
325051 TTACT
1 TTACT
325056 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 76 0.40
93 112 0.60
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:326834 original size:33 final size:36
Alignment explanation
Indices: 326752--326843 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 36
326742 TCTTTTGGTT
326752 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGA
1 GAAATGAAAATCGCAACGAGAGAA-GAC--TCGCAACGA
*
326791 GATAAATGAAAATCGCAACGAGAG-A-A-TCGCAACGC
1 G--AAATGAAAATCGCAACGAGAGAAGACTCGCAACGA
326826 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
326844 CGAAATGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
33 17 0.34
35 9 0.18
38 1 0.02
39 1 0.02
40 1 0.02
41 21 0.42
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (36 bp):
GAAATGAAAATCGCAACGAGAGAAGACTCGCAACGA
Found at i:326839 original size:19 final size:19
Alignment explanation
Indices: 326752--326865 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
326742 TCTTTTGGTT
*
326752 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
326771 GAGAATGACTGTCGCAACGA
1 GA-AATGAAAATCGCAACGC
326791 GATAAATGAAAATCGCAA--C
1 G--AAATGAAAATCGCAACGC
*
326810 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
326826 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
326845 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
326864 GA
1 GA
326866 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
18 1 0.01
19 36 0.47
20 15 0.19
21 11 0.14
22 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:326896 original size:14 final size:14
Alignment explanation
Indices: 326877--326933 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
326867 TTTGGTTTCG
326877 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
326891 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
326908 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
326924 CGTTGCGATT
1 CGTTGCGATT
326934 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 17 0.47
16 6 0.17
17 6 0.17
19 7 0.19
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:326909 original size:33 final size:33
Alignment explanation
Indices: 326861--326941 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
326851 AAAATCGCAA
**
326861 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
326894 TGCGATTTTCATTTCGTGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
326927 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
326942 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:326944 original size:21 final size:21
Alignment explanation
Indices: 326918--326993 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
326908 CGTGTTGCGA
326918 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
326939 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
326959 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
326980 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
326994 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:326974 original size:41 final size:41
Alignment explanation
Indices: 326917--326994 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
326907 TCGTGTTGCG
*
326917 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
326958 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
326995 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:327115 original size:33 final size:33
Alignment explanation
Indices: 327073--327143 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
327063 AATACTAACT
327073 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
327106 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
327139 TGAAA
1 TGAAA
327144 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:327527 original size:20 final size:20
Alignment explanation
Indices: 327502--327694 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
327492 CTTTAAATAT
327502 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
327522 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
327544 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
327563 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
327583 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
327603 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
327623 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
327643 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
327663 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
327683 CGCGTTGCGATT
1 CGCGTTGCGATT
327695 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.01
20 131 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:329070 original size:21 final size:21
Alignment explanation
Indices: 329046--329085 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
329036 TTTTTGTTCA
329046 ACCGAAAATGTTAATTTTCTT
1 ACCGAAAATGTTAATTTTCTT
*
329067 ACCGAAAATGTTATTTTTC
1 ACCGAAAATGTTAATTTTC
329086 ATGTAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
ACCGAAAATGTTAATTTTCTT
Found at i:331940 original size:6 final size:6
Alignment explanation
Indices: 331929--332438 Score: 956
Period size: 6 Copynumber: 85.0 Consensus size: 6
331919 TAACTTAACC
331929 CATATA CATATA CATATA CATATA CATATA CATATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA C--ATATA CATATA CATATA
331979 CATACATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CAT--ATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332029 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332077 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332125 CATATA CATATA CATATA CATATA CATATA CATATA C--ATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332171 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332219 CATATA CATATA CATATA CATATA CATATA CATATA C--ATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332265 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332313 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332361 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
332409 CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA
332439 TTAGTTTATT
Statistics
Matches: 496, Mismatches: 0, Indels: 16
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.02
6 476 0.96
8 12 0.02
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:333404 original size:16 final size:17
Alignment explanation
Indices: 333377--333408 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
333367 ATCCTTTTGT
333377 TAAATCGTCAACAATTA
1 TAAATCGTCAACAATTA
333394 TAAAT-GTCAACAATT
1 TAAATCGTCAACAATT
333409 TGTATTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (17 bp):
TAAATCGTCAACAATTA
Found at i:333679 original size:31 final size:31
Alignment explanation
Indices: 333641--333704 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
333631 TCATTGTCAC
333641 CGCTATAATCATCAATATCTAATATATTAAT
1 CGCTATAATCATCAATATCTAATATATTAAT
* *
333672 CGCTATAATTATCAATATCTGATATATTAAT
1 CGCTATAATCATCAATATCTAATATATTAAT
333703 CG
1 CG
333705 AGGTTATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (31 bp):
CGCTATAATCATCAATATCTAATATATTAAT
Found at i:337079 original size:227 final size:226
Alignment explanation
Indices: 336685--337139 Score: 851
Period size: 227 Copynumber: 2.0 Consensus size: 226
336675 TCAATGAATG
336685 ATTATACAAATTATAATGCATAAATTATTCATAATTTTTAAAATCAGCAGAAGCATGAATGCACT
1 ATTATACAAATTATAATGCATAAATTATTCATAATTTTTAAAATCAGCAGAAGCATGAATGCACT
336750 CAAATTCAAAAGAATAACAAAATCGATAATTCAATAATCATATACGTACATATAATGTGTTTCTT
66 CAAATTCAAAAGAATAACAAAATCGATAATTCAATAATCATATACGTACATATAA-GTGTTTCTT
*
336815 AAAACTCAAATCAATATACGAATGCTCTTAGATTCAGCAGAATATCAAAATCAAAATAATGGAGT
130 AAAAATCAAATCAATATACGAATGCTCTTAGATTCAGCAGAATATCAAAATCAAAATAATGGAGT
336880 ATTGACTATGGTCTTGTATATTG-ATAGAACT
195 ATTGACTATGGTCTTGTATATTGAATAGAACT
336911 ATTATACAAATTATAATGCATAAATTATTCATAATTTTTAAAATCAGCAGAATGCATGAATGCAC
1 ATTATACAAATTATAATGCATAAATTATTCATAATTTTTAAAATCAGCAGAA-GCATGAATGCAC
336976 TCAAATTCAAAAGAATAACAAAATCGATAATTCAATAATCAATATACGTACATATAA-TGTTTCT
65 TCAAATTCAAAAGAATAACAAAATCGATAATTCAATAATC-ATATACGTACATATAAGTGTTTCT
337040 TAAAAATCAAAATCAATATACGAATGCTCTTAGATTCAGCAGAATATCAAAATCAAAATAATGGA
129 TAAAAATC-AAATCAATATACGAATGCTCTTAGATTCAGCAGAATATCAAAATCAAAATAATGGA
337105 GTATTGACTATGGTCTTGTATATTGAATAGAACT
193 GTATTGACTATGGTCTTGTATATTGAATAGAACT
337139 A
1 A
337140 AGTGGATTAG
Statistics
Matches: 224, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
226 66 0.29
227 133 0.59
228 25 0.11
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (226 bp):
ATTATACAAATTATAATGCATAAATTATTCATAATTTTTAAAATCAGCAGAAGCATGAATGCACT
CAAATTCAAAAGAATAACAAAATCGATAATTCAATAATCATATACGTACATATAAGTGTTTCTTA
AAAATCAAATCAATATACGAATGCTCTTAGATTCAGCAGAATATCAAAATCAAAATAATGGAGTA
TTGACTATGGTCTTGTATATTGAATAGAACT
Found at i:340190 original size:24 final size:24
Alignment explanation
Indices: 340162--340238 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
340152 GAATATTTTA
*
340162 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGT
* * * *
340186 TCTGATATCTGATCTGAAATATGT
1 TCTGATTTCCGATCTGAATTCTGT
* * *
340210 TCTGA-TTCCTAACTGGATTCTGT
1 TCTGATTTCCGATCTGAATTCTGT
340233 TCTGAT
1 TCTGAT
340239 ATCTGATCAC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
23 16 0.40
24 24 0.60
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (24 bp):
TCTGATTTCCGATCTGAATTCTGT
Found at i:341036 original size:76 final size:75
Alignment explanation
Indices: 340885--341036 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 75
340875 GTTTTTATAA
340885 AAGTTTTAAATTTTGAGATTTTTACAGTGGGTCGCTCCGGTGGCCCTAATGTGATACCCCAGATT
1 AAGTTTTAAATTTTGAGATTTTTACAGTGGGTCGCTCCGGTGGCCCTAATGTGATACCCCAGATT
340950 GGATCGGGTT
66 GGATCGGGTT
340960 AAGTTTTAAATTTTCTGAGATTTTTACAGTGGGTCGCTCCGGTGG-CCTAATGTGATACCCCAGA
1 AAGTTTTAAA-TTT-TGAGATTTTTACAGTGGGTCGCTCCGGTGGCCCTAATGTGATACCCCAGA
341024 TTGGATCGGGTT
64 TTGGATCGGGTT
341036 A
1 A
341037 CCGCATCGGT
Statistics
Matches: 75, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
75 10 0.13
76 35 0.47
77 30 0.40
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (75 bp):
AAGTTTTAAATTTTGAGATTTTTACAGTGGGTCGCTCCGGTGGCCCTAATGTGATACCCCAGATT
GGATCGGGTT
Found at i:349713 original size:11 final size:11
Alignment explanation
Indices: 349697--349766 Score: 70
Period size: 11 Copynumber: 6.3 Consensus size: 11
349687 AATTACTTAC
349697 TGTTTATTTGT
1 TGTTTATTTGT
349708 TGTTTATTTGCT
1 TGTTTATTTG-T
*
349720 AT-TTTAGTTGT
1 -TGTTTATTTGT
349731 TGTTTATTTGT
1 TGTTTATTTGT
* *
349742 TATTTATTTGC
1 TGTTTATTTGT
* *
349753 TATTTAGTTGT
1 TGTTTATTTGT
349764 TGT
1 TGT
349767 GAATTCAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
10 1 0.02
11 39 0.80
12 8 0.16
13 1 0.02
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (11 bp):
TGTTTATTTGT
Found at i:349725 original size:23 final size:22
Alignment explanation
Indices: 349699--349751 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
349689 TTACTTACTG
349699 TTTATTTGTTGTTTATTTGCTA
1 TTTATTTGTTGTTTATTTGCTA
* *
349721 TTTTAGTTGTTGTTTATTTGTTA
1 -TTTATTTGTTGTTTATTTGCTA
349744 TTTATTTG
1 TTTATTTG
349752 CTATTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.13, C:0.02, G:0.15, T:0.70
Consensus pattern (22 bp):
TTTATTTGTTGTTTATTTGCTA
Found at i:349740 original size:34 final size:33
Alignment explanation
Indices: 349697--349766 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 33
349687 AATTACTTAC
*
349697 TGTTTATTTGTTGTTTATTTGCTATTTTAGTTGT
1 TGTTTATTTGTTATTTATTTGCTA-TTTAGTTGT
349731 TGTTTATTTGTTATTTATTTGCTATTTAGTTGT
1 TGTTTATTTGTTATTTATTTGCTATTTAGTTGT
349764 TGT
1 TGT
349767 GAATTCAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 12 0.34
34 23 0.66
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (33 bp):
TGTTTATTTGTTATTTATTTGCTATTTAGTTGT
Found at i:350005 original size:22 final size:23
Alignment explanation
Indices: 349959--350019 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
349949 GAATTCAATA
349959 TTATTGGATA-TTA--TGTCTGT
1 TTATTGGATATTTAGTTGTCTGT
*
349979 TTATTGGATGTTTAGTTGTC-GT
1 TTATTGGATATTTAGTTGTCTGT
* *
350001 TTATTTGCTATTTAGTTGT
1 TTATTGGATATTTAGTTGT
350020 TGTGAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.26
21 3 0.09
22 18 0.53
23 4 0.12
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.57
Consensus pattern (23 bp):
TTATTGGATATTTAGTTGTCTGT
Found at i:350094 original size:74 final size:72
Alignment explanation
Indices: 349912--350094 Score: 269
Period size: 74 Copynumber: 2.5 Consensus size: 72
349902 TATTTTAGTT
* *
349912 GATGTTTATTTGTTATTTTTTGCTATTTAGTTATTGTGAATTCAATATTATTGGATATTATGTCT
1 GATGTTTAGTTG-TATTTTTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATATTATGTCT
349977 GTTTATTG
65 GTTTATTG
* *
349985 GATGTTTAGTTGTCGTTTATTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATATTATGTT
1 GATGTTTAGTTGT-ATTT-TTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATATTATGTC
350050 TGTTTATTG
64 TGTTTATTG
350059 GATGTTTAGTTGCTATTTTGGTTGCTATTTA-TTGTT
1 GATGTTTAGTTG-TATTTT--TTGCTATTTAGTTGTT
350095 ATTTTCTATT
Statistics
Matches: 100, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
72 1 0.01
73 15 0.15
74 73 0.73
75 11 0.11
ACGTcount: A:0.20, C:0.04, G:0.19, T:0.57
Consensus pattern (72 bp):
GATGTTTAGTTGTATTTTTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATATTATGTCTG
TTTATTG
Found at i:353744 original size:29 final size:29
Alignment explanation
Indices: 353702--353764 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
353692 AGCTTCAATA
* *
353702 TGTGTTGATGGATGTTA-ACTGCCATTTTT
1 TGTGTTGATAGATGTTACA-TGCCATCTTT
*
353731 TGTGTTGATAGATGTTACATGTCATCTTT
1 TGTGTTGATAGATGTTACATGCCATCTTT
353760 TGTGT
1 TGTGT
353765 CATTTTTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.17, C:0.10, G:0.24, T:0.49
Consensus pattern (29 bp):
TGTGTTGATAGATGTTACATGCCATCTTT
Found at i:353780 original size:40 final size:40
Alignment explanation
Indices: 353727--353811 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
353717 TAACTGCCAT
* * *
353727 TTTTTGTGTTGATAGATGTTACA-TGTCATCTTTTGTGTCA
1 TTTTTGTGTTGATAAATG-TAAAGTGTCATCTTTAGTGTCA
353767 TTTTTGTGTTGATAAATGTAAAGTGTCATCTTTAGTGTCA
1 TTTTTGTGTTGATAAATGTAAAGTGTCATCTTTAGTGTCA
353807 TTTTT
1 TTTTT
353812 TGTATATGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.07
40 38 0.93
ACGTcount: A:0.20, C:0.08, G:0.19, T:0.53
Consensus pattern (40 bp):
TTTTTGTGTTGATAAATGTAAAGTGTCATCTTTAGTGTCA
Found at i:354199 original size:35 final size:35
Alignment explanation
Indices: 354144--354255 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
354134 TCTAAACCTT
* *
354144 AAATTGAAGTATTTTAGAATTTGAGGTTTAGAATG
1 AAATTAAATTATTTTAGAATTTGAGGTTTAGAATG
* *
354179 TAATTAAATTATTTTAGAATTT-AGGGTTTAGAATA
1 AAATTAAATTATTTTAGAATTTGA-GGTTTAGAATG
* * * *
354214 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTAAATTATTTTAGAATTTGAGGTTTAGAATG
354249 AAATTAA
1 AAATTAA
354256 GGAATGTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.02
35 63 0.98
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
AAATTAAATTATTTTAGAATTTGAGGTTTAGAATG
Found at i:359882 original size:208 final size:208
Alignment explanation
Indices: 359524--359939 Score: 800
Period size: 208 Copynumber: 2.0 Consensus size: 208
359514 TGGGTTGACC
359524 TTCGTTTATTATATTGCATTTGTAAGTTTCAGCTACCTCTACATTTCTCTCTTTTTCATTTTTCT
1 TTCGTTTATTATATTGCATTTGTAAGTTTCAGCTACCTCTACATTTCTCTCTTTTTCATTTTTCT
359589 GAGGATTTGCCTGCTTGTGCTCACTAGATTTCAAGATTTGGTTCTAACTTCTTTTCTGTTTGGAA
66 GAGGATTTGCCTGCTTGTGCTCACTAGATTTCAAGATTTGGTTCTAACTTCTTTTCTGTTTGGAA
359654 ATTTCAGGGTGGAGGAGAAAAAAGCCTAGCGGTAAATTCCAACTTTCATCTTAAGAAGGTTTTCC
131 ATTTCAGGGTGGAGGAGAAAAAAGCCTAGCGGTAAATTCCAACTTTCATCTTAAGAAGGTTTTCC
359719 GTGGAAGATGAGG
196 GTGGAAGATGAGG
359732 TTCGTTTATTATATTGCATTTGTAAGTTTCAGCTACCTCTACA-TT-TCTCTTTTTCATTTTTCT
1 TTCGTTTATTATATTGCATTTGTAAGTTTCAGCTACCTCTACATTTCTCTCTTTTTCATTTTTCT
359795 GAGGATTTGCCTGCTTGTGCTCACTAGATTTCAAGATTTGGTTTCTAACTTCTTTTCTGTTTGGA
66 GAGGATTTGCCTGCTTGTGCTCACTAGATTTCAAGATTTGG-TTCTAACTTCTTTTCTGTTTGGA
359860 AATTTCAGGGGTGGAGGAGAAAAAAGCCTAGCGGTAAATTCCAACTTTCATCTTAAGAAGGTTTT
130 AATTTCA-GGGTGGAGGAGAAAAAAGCCTAGCGGTAAATTCCAACTTTCATCTTAAGAAGGTTTT
359925 CCGTGGAAGATGAGG
194 CCGTGGAAGATGAGG
359940 CATCCTCTCG
Statistics
Matches: 206, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
206 59 0.29
207 32 0.16
208 115 0.56
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (208 bp):
TTCGTTTATTATATTGCATTTGTAAGTTTCAGCTACCTCTACATTTCTCTCTTTTTCATTTTTCT
GAGGATTTGCCTGCTTGTGCTCACTAGATTTCAAGATTTGGTTCTAACTTCTTTTCTGTTTGGAA
ATTTCAGGGTGGAGGAGAAAAAAGCCTAGCGGTAAATTCCAACTTTCATCTTAAGAAGGTTTTCC
GTGGAAGATGAGG
Found at i:360899 original size:24 final size:24
Alignment explanation
Indices: 360867--360915 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
360857 AGCTGCCTTC
**
360867 ATTGGTTGCTGTACTATTATCAAT
1 ATTGGTTGCTCCACTATTATCAAT
*
360891 ATTGGTTGCTCCAGTATTATCAAT
1 ATTGGTTGCTCCACTATTATCAAT
360915 A
1 A
360916 AGCAGGATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (24 bp):
ATTGGTTGCTCCACTATTATCAAT
Found at i:362637 original size:14 final size:15
Alignment explanation
Indices: 362614--362644 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
362604 TTTTTTTTAA
362614 AAATATTTTAATTTT
1 AAATATTTTAATTTT
362629 AAATA-TTTAATTTT
1 AAATATTTTAATTTT
362643 AA
1 AA
362645 GATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATATTTTAATTTT
Found at i:368711 original size:19 final size:19
Alignment explanation
Indices: 368674--368711 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
368664 TCACAATTAG
*
368674 GTATCTAATTTTTTATGGT
1 GTATCTAATCTTTTATGGT
368693 GTATCTAACTCTTTT-TGGT
1 GTATCTAA-TCTTTTATGGT
368712 ATAGTTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (19 bp):
GTATCTAATCTTTTATGGT
Found at i:376623 original size:3 final size:3
Alignment explanation
Indices: 376615--376658 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
376605 ATAGTGTTTG
376615 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
376659 GACAGCTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:378463 original size:16 final size:16
Alignment explanation
Indices: 378444--378539 Score: 66
Period size: 16 Copynumber: 5.9 Consensus size: 16
378434 AACCATAACT
378444 GAAATTAACCCGAACC
1 GAAATTAACCCGAACC
** * *
378460 GAAAGCAACCCCAACT
1 GAAATTAACCCGAACC
* * *
378476 GAATTTTAACTCGATCC
1 GAA-ATTAACCCGAACC
* *
378493 GAAAATAACCCGAACT
1 GAAATTAACCCGAACC
* *
378509 GAATTTAACCCGACCC
1 GAAATTAACCCGAACC
**
378525 GAAAGCAACCCGAAC
1 GAAATTAACCCGAAC
378540 AAATTGAAAT
Statistics
Matches: 55, Mismatches: 24, Indels: 2
0.68 0.30 0.02
Matches are distributed among these distances:
16 46 0.84
17 9 0.16
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.15
Consensus pattern (16 bp):
GAAATTAACCCGAACC
Found at i:378536 original size:32 final size:32
Alignment explanation
Indices: 378440--378539 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
378430 AATCAACCAT
* *
378440 AACTGAAATTAACCCGAACCGAAAGCAACCCC
1 AACTGAATTTAACCCGAACCGAAAGCAACCCG
* * **
378472 AACTGAATTTTAACTCGATCCGAAAATAACCCG
1 AACTGAA-TTTAACCCGAACCGAAAGCAACCCG
*
378505 AACTGAATTTAACCCGACCCGAAAGCAACCCG
1 AACTGAATTTAACCCGAACCGAAAGCAACCCG
378537 AAC
1 AAC
378540 AAATTGAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 31 0.54
33 26 0.46
ACGTcount: A:0.41, C:0.31, G:0.13, T:0.15
Consensus pattern (32 bp):
AACTGAATTTAACCCGAACCGAAAGCAACCCG
Done.