Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007804.1 Hibiscus syriacus cultivar Beakdansim tig00110122_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: 1697051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:598808 original size:19 final size:19
Alignment explanation
Indices: 598743--598856 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
598733 GTCTTTGGTT
*
598743 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
598762 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
598784 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
598803 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
598820 G--A-GAGAATTGCAACGC
1 GAAATGAAAATCGCAACGC
*
598836 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
598855 GA
1 GA
598857 TTTTGGTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 32 0.43
20 12 0.16
21 12 0.16
22 4 0.05
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:598820 original size:40 final size:40
Alignment explanation
Indices: 598743--598851 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 40
598733 GTCTTTGGTT
* ***
598743 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGAGA
598784 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGA
598824 G-AAT-----T-GCAACGCGAAATGAAAATCGCAA
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
598852 TGCGATTTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
33 23 0.36
34 1 0.02
39 3 0.05
40 17 0.27
41 20 0.31
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (40 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGA
Found at i:598885 original size:19 final size:19
Alignment explanation
Indices: 598852--598960 Score: 84
Period size: 19 Copynumber: 5.8 Consensus size: 19
598842 AAAATCGCAA
**
598852 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
598871 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
598890 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
598904 TGCGATTTTCATTTTTCTCGT
1 TGCGATTTTCA--TTTCGCGT
** *
598925 TGCAGATAGTCATTTTCACGT
1 TGC-GATTTTCA-TTTCGCGT
598946 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
598961 TCTCGTTGCG
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 26 0.35
20 6 0.08
21 20 0.27
22 6 0.08
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:598923 original size:21 final size:21
Alignment explanation
Indices: 598898--598971 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
598888 GTTGCGATTC
598898 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
598919 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
598940 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
598961 TCTCGTTGCGA
1 TCTCGTTGCGA
598972 CTCTCTGCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:599091 original size:17 final size:17
Alignment explanation
Indices: 599066--599114 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
599056 CGCAACGAGA
*
599066 GAATAGCAACGCGAAAT
1 GAATCGCAACGCGAAAT
599083 GAATCGCAA--CG--A-
1 GAATCGCAACGCGAAAT
599095 GAATCGCAACGCGAAAT
1 GAATCGCAACGCGAAAT
599112 GAA
1 GAA
599115 ATCTAAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
12 9 0.35
13 1 0.04
14 2 0.08
15 2 0.08
16 1 0.04
17 11 0.42
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.10
Consensus pattern (17 bp):
GAATCGCAACGCGAAAT
Found at i:599106 original size:29 final size:30
Alignment explanation
Indices: 599053--599114 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
599043 ACTAACTTGA
599053 AATCGCAACGAGAGAATAGCAACGCGAAATG
1 AATCGCAAC-AGAGAATAGCAACGCGAAATG
*
599084 AATCGCAAC-GAGAATCGCAACGCGAAATG
1 AATCGCAACAGAGAATAGCAACGCGAAATG
599113 AA
1 AA
599115 ATCTAAGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 21 0.70
31 9 0.30
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (30 bp):
AATCGCAACAGAGAATAGCAACGCGAAATG
Found at i:599517 original size:20 final size:20
Alignment explanation
Indices: 599492--599684 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
599482 CTTTAAAAAT
599492 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
599512 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
599532 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
599553 CGCGTTGCGATATACGAATA
1 CGCGTTGCGATTTACGGATA
*
599573 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
599593 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
599613 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
599633 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
599653 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
599673 CGCGTTGCGATT
1 CGCGTTGCGATT
599685 CTGAAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:599745 original size:42 final size:43
Alignment explanation
Indices: 599652--599750 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 43
599642 ATTTATGTGT
* *
599652 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTGAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTCAAAAA
** * *
599693 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTCAAAAA
*
599735 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
599751 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 8 0.17
42 35 0.76
43 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTCAAAAA
Found at i:611225 original size:12 final size:12
Alignment explanation
Indices: 611208--611234 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
611198 TTATTGATTC
611208 TTGTAGGATCAG
1 TTGTAGGATCAG
611220 TTGTAGGATCAG
1 TTGTAGGATCAG
611232 TTG
1 TTG
611235 GAAGGTCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.33, T:0.37
Consensus pattern (12 bp):
TTGTAGGATCAG
Found at i:615722 original size:15 final size:15
Alignment explanation
Indices: 615702--615743 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
615692 ACGACATAAT
615702 GATCAAAATAAAATA
1 GATCAAAATAAAATA
615717 GATCAAAAATAAAAATA
1 GATC-AAAAT-AAAATA
*
615734 -ATTAAAATAA
1 GATCAAAATAA
615744 GATAACTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 7 0.29
17 6 0.25
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (15 bp):
GATCAAAATAAAATA
Found at i:621300 original size:24 final size:24
Alignment explanation
Indices: 621271--621324 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
621261 TATTAAATTA
621271 ATATTAAAT-ATATAATATTATTC
1 ATATTAAATAATATAATATTATTC
* *
621294 ATTATT-AATAATTTAATATTATTT
1 A-TATTAAATAATATAATATTATTC
621318 ATATTAA
1 ATATTAA
621325 CTTAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTAAATAATATAATATTATTC
Found at i:621324 original size:47 final size:46
Alignment explanation
Indices: 621271--621444 Score: 115
Period size: 47 Copynumber: 3.6 Consensus size: 46
621261 TATTAAATTA
621271 ATATTAAATATATAATATTATTCATTATTAATAATTTAATATTATTT
1 ATATTAAATATATAATATTATT-ATTATTAATAATTTAATATTATTT
* * *
621318 ATATTAACT-TAATAAATATAAATT-TTATTAATAATTTATTATATATTATT
1 ATATTAAATAT-AT-AATAT-TATTATTATTAATAATTTAATAT-TA-T-TT
* * * * *
621368 AAAATAAAAATATAATATTTTATATTATT-ATAATATAATTGATTATTT
1 ATATTAAATATATAATATTAT-TATTATTAATAATTTAA-T-ATTATTT
* *
621416 -TATTATAATAT-TAAAAATATATATTATTA
1 ATATTA-AATATATAATATTAT-TATTATTA
621445 GAAATATTAA
Statistics
Matches: 97, Mismatches: 17, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
46 1 0.01
47 44 0.45
48 14 0.14
49 18 0.19
50 17 0.18
51 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (46 bp):
ATATTAAATATATAATATTATTATTATTAATAATTTAATATTATTT
Found at i:621380 original size:44 final size:48
Alignment explanation
Indices: 621295--621390 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 48
621285 ATATTATTCA
* **
621295 TTATTAATAATTTAATATTATTTATATTAACTTAATAAATATAA-ATT
1 TTATTAATAATTTAATATTATATATATTAAAATAATAAATATAATATT
*
621342 TTATTAATAATTTATTA-TATAT-TATTAAAATAA-AAATATAATATT
1 TTATTAATAATTTAATATTATATATATTAAAATAATAAATATAATATT
621387 TTAT
1 TTAT
621391 ATTATTATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 8 0.18
45 16 0.36
46 4 0.09
47 16 0.36
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (48 bp):
TTATTAATAATTTAATATTATATATATTAAAATAATAAATATAATATT
Found at i:621406 original size:23 final size:23
Alignment explanation
Indices: 621376--621444 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
621366 TTAAAATAAA
621376 AATATAATATTTTATATTATTAT
1 AATATAATATTTTATATTATTAT
* *
621399 AATATAAT-TGATTATTTTATTAT
1 AATATAATAT-TTTATATTATTAT
* * *
621422 AATATTAAAAATATATATTATTA
1 AATA-TAATATTTTATATTATTA
621445 GAAATATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 1 0.03
23 23 0.64
24 12 0.33
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
AATATAATATTTTATATTATTAT
Found at i:621438 original size:16 final size:16
Alignment explanation
Indices: 621419--621456 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
621409 ATTATTTTAT
621419 TATAATATTAAAAATA
1 TATAATATTAAAAATA
* *
621435 TATATTATTAGAAATA
1 TATAATATTAAAAATA
621451 T-TAATA
1 TATAATA
621457 AATATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TATAATATTAAAAATA
Found at i:621440 original size:26 final size:26
Alignment explanation
Indices: 621411--621467 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
621401 TATAATTGAT
*
621411 TATTTTATTA-TAATATT-AAAAATA
1 TATTTTATTAGAAATATTAAAAAATA
* *
621435 TATATTATTAGAAATATTAATAAATA
1 TATTTTATTAGAAATATTAAAAAATA
621461 TATTTTA
1 TATTTTA
621468 AATATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 9 0.33
25 6 0.22
26 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
TATTTTATTAGAAATATTAAAAAATA
Found at i:621442 original size:21 final size:22
Alignment explanation
Indices: 621416--621473 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 22
621406 TTGATTATTT
621416 TATTATAATATTAA-AAATATA
1 TATTATAATATTAATAAATATA
621437 TATTATTAGAAATATTAATAAATATA
1 TATTA-T---AATATTAATAAATATA
*
621463 TTTTA-AATATT
1 TATTATAATATT
621474 TTAATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
21 11 0.35
22 1 0.03
25 8 0.26
26 11 0.35
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTATAATATTAATAAATATA
Found at i:629279 original size:84 final size:84
Alignment explanation
Indices: 629137--629304 Score: 300
Period size: 84 Copynumber: 2.0 Consensus size: 84
629127 ATTAAGTGCT
* *
629137 TGAAGAGTGAGTTAGTTGATAATGGGTGGAGCTATGTTCCAAAATGATTTATAGGTTTTTAGTAC
1 TGAAGAGTGAGTTAGTTGATAATGGATGGAGCTATGTTCCAAAATGATTTATAAGTTTTTAGTAC
629202 AAAAAATGCAGTTCGCCTA
66 AAAAAATGCAGTTCGCCTA
629221 TGAAGAGTGAGTTAGTTGATAATGGATGGAGCTATGTTCCAAAATGATTTATAAGTTTTTAGTAC
1 TGAAGAGTGAGTTAGTTGATAATGGATGGAGCTATGTTCCAAAATGATTTATAAGTTTTTAGTAC
* *
629286 AAAAAGTGTAGTTCGCCTA
66 AAAAAATGCAGTTCGCCTA
629305 CGAAAGTTGC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (84 bp):
TGAAGAGTGAGTTAGTTGATAATGGATGGAGCTATGTTCCAAAATGATTTATAAGTTTTTAGTAC
AAAAAATGCAGTTCGCCTA
Found at i:629766 original size:9 final size:9
Alignment explanation
Indices: 629752--629783 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
629742 GAATAGAGTG
629752 AAATGAGAT
1 AAATGAGAT
629761 AAATGAGAT
1 AAATGAGAT
*
629770 AAATGAGAG
1 AAATGAGAT
629779 AAATG
1 AAATG
629784 GTCTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (9 bp):
AAATGAGAT
Found at i:632374 original size:4 final size:4
Alignment explanation
Indices: 632365--632410 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
632355 TTTTTCGGCA
* * * *
632365 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
632411 TCAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:632584 original size:21 final size:21
Alignment explanation
Indices: 632554--632651 Score: 101
Period size: 21 Copynumber: 4.7 Consensus size: 21
632544 GATGCACCTA
* *
632554 TCATCATTCAAGAGGCGCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
632575 TTATCGTTCAAGAGG-CCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
632595 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
632616 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
632637 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
632652 TCCTACCCGC
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.03
20 13 0.21
21 44 0.72
22 2 0.03
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:632599 original size:41 final size:42
Alignment explanation
Indices: 632554--632651 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 42
632544 GATGCACCTA
* ** *
632554 TCATCATTCAAGAGGCGCCTCTTATCGTTCAAGAGG-CCCTC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* *
632595 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
632637 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
632652 TCCTACCCGC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
40 2 0.04
41 28 0.61
42 14 0.30
43 2 0.04
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:632607 original size:20 final size:19
Alignment explanation
Indices: 632554--632612 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
632544 GATGCACCTA
632554 TCATCATTCAAGAGGCGCCTC
1 TCATCA-TCAAGAGGC-CCTC
* *
632575 TTATCGTTCAAGAGGCCCTC
1 TCATC-ATCAAGAGGCCCTC
*
632595 TCATCATCGAAGAAGCCC
1 TCATCATC-AAGAGGCCC
632613 CTCCCACCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.06
20 16 0.52
21 13 0.42
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (19 bp):
TCATCATCAAGAGGCCCTC
Found at i:634114 original size:20 final size:20
Alignment explanation
Indices: 634089--634128 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
634079 GATTTGTTTA
*
634089 CGAATTTGACTTTTGCGTTG
1 CGAATTTGACTTTCGCGTTG
634109 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
634129 ATTGCAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:634437 original size:18 final size:18
Alignment explanation
Indices: 634414--634449 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
634404 AAGCCGGTTG
*
634414 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
634432 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
634450 CCTTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:636549 original size:15 final size:12
Alignment explanation
Indices: 636514--636548 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
636504 CTTCGGGGAC
636514 TTTTTCTTCTTA
1 TTTTTCTTCTTA
636526 TTTTTCTTCTTA
1 TTTTTCTTCTTA
636538 TTTTTCTTCTT
1 TTTTTCTTCTT
636549 CAGGGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTCTTCTTA
Found at i:636763 original size:24 final size:24
Alignment explanation
Indices: 636736--636782 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
636726 CAAAATCCGA
*
636736 GTATTCCCCAAGATAAAAGTTTGG
1 GTATTCACCAAGATAAAAGTTTGG
* * *
636760 GTATTGACCAAGATCAAATTTTG
1 GTATTCACCAAGATAAAAGTTTG
636783 AATACTGACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (24 bp):
GTATTCACCAAGATAAAAGTTTGG
Found at i:636924 original size:12 final size:12
Alignment explanation
Indices: 636903--636936 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
636893 GGTTGTGGGT
*
636903 TTTGAGATTGTG
1 TTTGATATTGTG
636915 TTTGATATTGTG
1 TTTGATATTGTG
*
636927 TTTGGTATTG
1 TTTGATATTG
636937 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:637444 original size:2 final size:2
Alignment explanation
Indices: 637437--637463 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
637427 GAGGTTATTT
637437 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
637464 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:637468 original size:2 final size:2
Alignment explanation
Indices: 637463--637491 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
637453 TCTCTCTCTC
637463 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 T
637492 GGTGGCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:638948 original size:2 final size:2
Alignment explanation
Indices: 638941--638965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
638931 GAATAATAAT
638941 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 T
638966 TAATGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:638965 original size:69 final size:69
Alignment explanation
Indices: 638873--639011 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
638863 TTAATTTTTA
*
638873 ATATATATATATATATATATATATTAATGTGACTAAAATTAAATAAAGATAAAATGAAGAATAAT
1 ATATATATATATATATATATATATTAATGTAACTAAAATTAAATAAAGATAAAATGAAGAATAAT
638938 AATT
66 AATT
*
638942 ATATATATATATATATATATATATTAATGTAATTAAAATTAAATAAAGATAAAATGAAGAATAAT
1 ATATATATATATATATATATATATTAATGTAACTAAAATTAAATAAAGATAAAATGAAGAATAAT
639007 AATT
66 AATT
639011 A
1 A
639012 GAGTATTAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (69 bp):
ATATATATATATATATATATATATTAATGTAACTAAAATTAAATAAAGATAAAATGAAGAATAAT
AATT
Found at i:639592 original size:22 final size:22
Alignment explanation
Indices: 639544--639605 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
639534 GAGCTCTAGT
*
639544 CACCGGTCGGTCACTATTTCGAC
1 CACC-GTCGATCACTATTTCGAC
**
639567 CACC-TCCGATCACTATTTCGGT
1 CACCGT-CGATCACTATTTCGAC
*
639589 CACCGTCGGTCACTATT
1 CACCGTCGATCACTATT
639606 CACGGTGACC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 27 0.82
23 5 0.15
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.29
Consensus pattern (22 bp):
CACCGTCGATCACTATTTCGAC
Found at i:640268 original size:29 final size:29
Alignment explanation
Indices: 640234--640297 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
640224 AAAAATTTGG
*
640234 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
*
640263 TTAATTCGGTTCAGTTAGTAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
*
640292 TAAATT
1 TTAATT
640298 TTGGTTCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (29 bp):
TTAATTCGGTTCAGTTAATAATTTTCAAA
Found at i:640502 original size:132 final size:130
Alignment explanation
Indices: 640233--640541 Score: 329
Period size: 132 Copynumber: 2.3 Consensus size: 130
640223 AAAAAATTTG
* * * * *
640233 GTTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTC-AGTTAGTAATTTTCAAATAAAT
1 GTTAATTCAGTTCAGTTAATAATTTTCAAATTAATTTGGTTCGAGCTAATAATTTTCAAATAAAT
* * * * * *
640297 TTTGGTTCGATTAACCGAACCGACTGAATTTTTTCTTCGATTAATTCGGTTAATAATTAAAAAAA
66 TTTAGTTCAATTAACCGAACCAACCGAATTTTTGCTTCAATTAATTCGGTTAATAATTAAAAAAA
* *
640362 TTGGTTAATTCAGTTTAGTTAATAATGTTCAAATTAATTTGGTTCGA-CTAATAATTTTCAAATA
1 ---GTTAATTCAGTTCAGTTAATAATTTTCAAATTAATTTGGTTCGAGCTAATAATTTTCAAATA
*
640426 AATTTTAGTTCAATTAACCGAACCAAATTAACCGAATTTTTGCTTCAATTAATTTGGTTAATAAT
63 AATTTTAGTTCAATTAACCGAACC-----AACCGAATTTTTGCTTCAATTAATTCGGTTAATAAT
**
640491 T-TTAAAA
123 TAAAAAAA
* * * *
640498 -TTAATTCGGTTCGGATAATAATTTTCAAATAAATTTTGGTTCGA
1 GTTAATTCAGTTCAGTTAATAATTTTCAAATTAA-TTTGGTTCGA
640542 TTAAGCGAAC
Statistics
Matches: 148, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
132 101 0.68
133 11 0.07
136 4 0.03
137 32 0.22
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (130 bp):
GTTAATTCAGTTCAGTTAATAATTTTCAAATTAATTTGGTTCGAGCTAATAATTTTCAAATAAAT
TTTAGTTCAATTAACCGAACCAACCGAATTTTTGCTTCAATTAATTCGGTTAATAATTAAAAAAA
Found at i:640628 original size:68 final size:68
Alignment explanation
Indices: 640556--640683 Score: 211
Period size: 68 Copynumber: 1.9 Consensus size: 68
640546 GCGAACTGAA
* * * *
640556 TTTTTTTCTTTAACCGTTATTCAAACCGAAATTTATTTGAAAATTATTAATCGAACCGAATTAAA
1 TTTTTTTCTTTAACCATTAATCAAACCGAAATTTATTTGAAAATCATTAACCGAACCGAATTAAA
640621 CAG
66 CAG
*
640624 TTTTTTTCTTTAATCATTAATCAAACCGAAATTTATTTGAAAATCATTAACCGAACCGAA
1 TTTTTTTCTTTAACCATTAATCAAACCGAAATTTATTTGAAAATCATTAACCGAACCGAA
640684 CAAATTTTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (68 bp):
TTTTTTTCTTTAACCATTAATCAAACCGAAATTTATTTGAAAATCATTAACCGAACCGAATTAAA
CAG
Found at i:641668 original size:29 final size:29
Alignment explanation
Indices: 641636--641692 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
641626 ATTTGATGTT
641636 GTATACAAATTTAATTATAATTATTTATG
1 GTATACAAATTTAATTATAATTATTTATG
*
641665 GTATACAAATTTAATTATGATTATTTAT
1 GTATACAAATTTAATTATAATTATTTAT
641693 AGTAATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (29 bp):
GTATACAAATTTAATTATAATTATTTATG
Found at i:642121 original size:27 final size:27
Alignment explanation
Indices: 642084--642136 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
642074 TTTCAAATGA
642084 ATGATGGATTGAATAAATAAATAAATC
1 ATGATGGATTGAATAAATAAATAAATC
642111 ATGATGGATTGAATAAATAAATAAAT
1 ATGATGGATTGAATAAATAAATAAAT
642137 AAATCATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.15, T:0.30
Consensus pattern (27 bp):
ATGATGGATTGAATAAATAAATAAATC
Found at i:642153 original size:31 final size:31
Alignment explanation
Indices: 642095--642154 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
642085 TGATGGATTG
***
642095 AATAAATAAATAAATCATGATGGATTGAATA
1 AATAAATAAATAAATCATGAAAAATTGAATA
642126 AATAAATAAATAAATCATGAAAAATTGAA
1 AATAAATAAATAAATCATGAAAAATTGAA
642155 CTACTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (31 bp):
AATAAATAAATAAATCATGAAAAATTGAATA
Found at i:643542 original size:40 final size:42
Alignment explanation
Indices: 643482--643669 Score: 113
Period size: 42 Copynumber: 4.5 Consensus size: 42
643472 TTTTGCGATG
* * *
643482 TCACATTTTATCTTTATAATTAAAG-TATCTA-TTTTTTAATC
1 TCACTTTTTAACTTTATAATTAAAGCT-CCTATTTTTTTAATC
* * * *
643523 T-ATTTTTTACCTTTATAATTGAGGCTCCTATTTTTTTAATC
1 TCACTTTTTAACTTTATAATTAAAGCTCCTATTTTTTTAATC
* * * *
643564 TCACTTTTTAACTTTATAATTGAGGC-CATCAAGTTTTTTCAATC
1 TCACTTTTTAACTTTATAATTAAAGCTC--CTA-TTTTTTTAATC
* * *
643608 TCACTTTCT-ACTTTTATAATTGAGGC-CCATAATTTTTTT-ATC
1 TCACTTTTTAAC-TTTATAATTAAAGCTCC-T-ATTTTTTTAATC
* *
643650 CCACTTCTTAACTTTA-AATT
1 TCACTTTTTAACTTTATAATT
643670 GAGGCCCTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
40 21 0.17
41 18 0.15
42 36 0.30
43 12 0.10
44 34 0.28
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.51
Consensus pattern (42 bp):
TCACTTTTTAACTTTATAATTAAAGCTCCTATTTTTTTAATC
Found at i:643556 original size:83 final size:84
Alignment explanation
Indices: 643428--643584 Score: 194
Period size: 83 Copynumber: 1.9 Consensus size: 84
643418 GGCCCATAAT
* * * * *
643428 TTTTTTAAATCTTATTTTATATCTTTATAATTGAGATCTTAATTTTTTGCGATGTCACATTTTAT
1 TTTTTTAAATCTTATTTTATACCTTTATAATTGAGATCCTAATTTTTT-CAATCTCACATTTTAA
643493 CTTTATAATTAAAGTATCTA
65 CTTTATAATTAAAGTATCTA
* * * *
643513 TTTTTT-AATC-TATTTTTTACCTTTATAATTGAGGCTCCT-ATTTTTTTAATCTCACTTTTTAA
1 TTTTTTAAATCTTATTTTATACCTTTATAATTGA-GATCCTAATTTTTTCAATCTCACATTTTAA
643575 CTTTATAATT
65 CTTTATAATT
643585 GAGGCCATCA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
82 21 0.34
83 27 0.44
84 8 0.13
85 6 0.10
ACGTcount: A:0.27, C:0.11, G:0.06, T:0.56
Consensus pattern (84 bp):
TTTTTTAAATCTTATTTTATACCTTTATAATTGAGATCCTAATTTTTTCAATCTCACATTTTAAC
TTTATAATTAAAGTATCTA
Found at i:643624 original size:44 final size:43
Alignment explanation
Indices: 643513--643906 Score: 270
Period size: 44 Copynumber: 8.9 Consensus size: 43
643503 AAAGTATCTA
* * *
643513 TTTTTT-AATCT-ATTTTTTACCTTTATAATTGAGG-CTCCTA-
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCT-CAAG
* * *
643553 TTTTTTTAATCTCACTTTTTAACTTTATAATTGAGGCCATCAAG
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCC-TCAAG
* *
643597 TTTTTTCAATCTCACTTTCTACTTTTATAATTGAGGCC-CATAA
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCTCA-AG
* * * *
643640 TTTTTT-TATCCCAC-TTCTTAACTTTA-AATTGAGGCCCTTAAG
1 TTTTTTCAATCTCACTTTC-TACCTTTATAATTGAGG-CCTCAAG
* *
643682 TTTTTTTTTTCAATCTCACTTTCTACATTTTCTACCTTTATAATTGAGACCCTTAAG
1 ----TTTTTTCAA--T--C--TC-AC--TTTCTACCTTTATAATTGAG-GCCTCAAG
* *
643739 TTCTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCCCTAAG
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCTC-AAG
* * * *
643783 TTTTTTCAATCTCAATTTCTTCCTTTATAATTTAGGCCCCTAA-
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCTC-AAG
* ** *
643826 TTTTTT-AATCCCACTCTT-TAAGTTTATAATTGAGGCCCTTAAG
1 TTTTTTCAATCTCACT-TTCTACCTTTATAATTGAGG-CCTCAAG
* *
643869 TTTTTTCAATCCCACTCTCTACCTTTATAATTGAGGCC
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCC
643907 CTTAAGGTAA
Statistics
Matches: 285, Mismatches: 37, Indels: 61
0.74 0.10 0.16
Matches are distributed among these distances:
40 6 0.02
41 16 0.06
42 60 0.21
43 32 0.11
44 121 0.42
46 8 0.03
47 3 0.01
49 2 0.01
51 2 0.01
53 9 0.03
54 2 0.01
56 7 0.02
57 17 0.06
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (43 bp):
TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCTCAAG
Found at i:643644 original size:86 final size:85
Alignment explanation
Indices: 643513--643908 Score: 386
Period size: 86 Copynumber: 4.5 Consensus size: 85
643503 AAAGTATCTA
* * * *
643513 TTTTTT-AATCT-ATTTTTTACCTTTATAATTGAGGCTCCTATTTTTTTAATCTCACTTTTTAAC
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGC-CCTAATTTTTTAATCCCACTTTTTAAC
*
643576 TTTATAATTGAGGCCATCAAG
65 TTTATAATTGAGGCCCTCAAG
* * *
643597 TTTTTTCAATCTCACTTTCTACTTTTATAATTGAGGCCCATAATTTTTTTATCCCACTTCTTAAC
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCC-TAATTTTTTAATCCCACTTTTTAAC
*
643662 TTTA-AATTGAGGCCCTTAAG
65 TTTATAATTGAGGCCCTCAAG
* *
643682 TTTTTTTTTTCAATCTCACTTTCTACATTTTCTACCTTTATAATTGAGACCCTTAAGTTCTTTCA
1 ----TTTTTTCAA--T--C--TC-AC--TTTCTACCTTTATAATTGAGGCCC-TAA-TT-TTTTA
* * *
643747 ATCTCACTTTCTACCTTTATAATTGAGGCCC-CTAAG
50 ATCCCACTTTTTAACTTTATAATTGAGGCCCTC-AAG
* * * * *
643783 TTTTTTCAATCTCAATTTCTTCCTTTATAATTTAGGCCCCTAATTTTTTAATCCCACTCTTTAAG
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGG-CCCTAATTTTTTAATCCCACTTTTTAAC
*
643848 TTTATAATTGAGGCCCTTAAG
65 TTTATAATTGAGGCCCTCAAG
* *
643869 TTTTTTCAATCCCACTCTCTACCTTTATAATTGAGGCCCT
1 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCCT
643909 TAAGGTAATT
Statistics
Matches: 255, Mismatches: 35, Indels: 43
0.77 0.11 0.13
Matches are distributed among these distances:
84 6 0.02
85 25 0.10
86 110 0.43
87 2 0.01
88 21 0.08
89 12 0.05
90 1 0.00
91 3 0.01
93 2 0.01
95 3 0.01
96 2 0.01
97 9 0.04
98 25 0.10
99 2 0.01
100 18 0.07
101 14 0.05
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (85 bp):
TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCCTAATTTTTTAATCCCACTTTTTAACT
TTATAATTGAGGCCCTCAAG
Found at i:643919 original size:18 final size:18
Alignment explanation
Indices: 643896--643930 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
643886 TCTACCTTTA
*
643896 TAATTGAGGCCCTTAAGG
1 TAATTGAGGCCCCTAAGG
*
643914 TAATTGATGCCCCTAAG
1 TAATTGAGGCCCCTAAG
643931 TTTTTCAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (18 bp):
TAATTGAGGCCCCTAAGG
Found at i:643965 original size:19 final size:19
Alignment explanation
Indices: 643943--643981 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
643933 TTTCAATCTC
643943 AATTATACTTTTATAATTG
1 AATTATACTTTTATAATTG
643962 AATTATACTTTTATAATTG
1 AATTATACTTTTATAATTG
643981 A
1 A
643982 GGCCCATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
AATTATACTTTTATAATTG
Found at i:646208 original size:29 final size:29
Alignment explanation
Indices: 646176--646236 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
646166 ATTTGACGTG
646176 GTATACAAATCTAATTATAATTATTTATA
1 GTATACAAATCTAATTATAATTATTTATA
* *
646205 GTATACAAATTTAATTATGATTATTTATA
1 GTATACAAATCTAATTATAATTATTTATA
646234 GTA
1 GTA
646237 ATTCAAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (29 bp):
GTATACAAATCTAATTATAATTATTTATA
Found at i:646685 original size:23 final size:23
Alignment explanation
Indices: 646659--646717 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
646649 ATGGATTGAA
646659 TAAATAAATAAATCATGATGGAT
1 TAAATAAATAAATCATGATGGAT
646682 TAAATAAATAAATCATGATGGAT
1 TAAATAAATAAATCATGATGGAT
646705 TAAATAAATAAAT
1 TAAATAAATAAAT
646718 AAATAAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (23 bp):
TAAATAAATAAATCATGATGGAT
Found at i:646687 original size:27 final size:26
Alignment explanation
Indices: 646646--646721 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 26
646636 TTTCAAATGA
646646 ATGATGGATTGAATAAATAAATAAATC
1 ATGATGGATT-AATAAATAAATAAATC
646673 ATGATGGA-T--TAAATAAATAAATC
1 ATGATGGATTAATAAATAAATAAATC
646696 ATGATGGATTAAATAAATAAATAAAT
1 ATGATGGATT-AATAAATAAATAAAT
646722 AAATCATGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
23 22 0.49
24 1 0.02
26 1 0.02
27 21 0.47
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (26 bp):
ATGATGGATTAATAAATAAATAAATC
Found at i:647485 original size:41 final size:42
Alignment explanation
Indices: 647416--647530 Score: 110
Period size: 43 Copynumber: 2.7 Consensus size: 42
647406 CGATGTCACA
* *
647416 TTTTATCTTTATAATTGAAGTATCTA-TTTT-TAATCTAAAT
1 TTTTAACTTTATAATTGAGGTATCTATTTTTGTAATCTAAAT
* * * *
647456 TTTTACCTTTTATAATTGAGG-CTCTTATTTTTGTAATCTCACT
1 TTTTAAC-TTTATAATTGAGGTATC-TATTTTTGTAATCTAAAT
* *
647499 TTTTAACTCTATAATTGAGGATATCAATTTTT
1 TTTTAACTTTATAATTGAGG-TATCTATTTTT
647531 TTCAATTTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
40 8 0.13
41 14 0.23
42 16 0.27
43 20 0.33
44 2 0.03
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (42 bp):
TTTTAACTTTATAATTGAGGTATCTATTTTTGTAATCTAAAT
Found at i:647691 original size:44 final size:44
Alignment explanation
Indices: 647641--648006 Score: 367
Period size: 44 Copynumber: 8.5 Consensus size: 44
647631 CTTTCTATAT
* * * *
647641 TTTCTACCTTTATAATTGAGACCCTTAAGTTCTTTCAATCTCAC
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
647685 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
* * * **
647729 TTTCTACCTTTATAATTTAGGCCCCTAA-TTTTTT-AACCCCGC
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
** * * * *
647771 TCTT-TAAGTTTATAATTGAGACTCTTAAGTTTTTTCAATCTCAC
1 T-TTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
* * * * *
647815 TCTCTACCTTTATAATTGAGGCCCTTAAGGTTTTTAAATCTTAA
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
* *
647859 TCTT-TACCTTTATAGTTGATGCCCCTAAG-TTTTTCAATCTCAA
1 T-TTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
* * **
647902 -TTATACTTTTATAATTGATTCCCCT-A-TTTTTTCAATCTCAA
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
* * *
647943 -TTATACTTTTATAATTGAGGCCACT-A-TTTTTTCAATCTCAA
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
*
647984 TTTCTACCTTTATAATTAAGGCC
1 TTTCTACCTTTATAATTGAGGCC
648007 TCTATTTTTT
Statistics
Matches: 272, Mismatches: 42, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
41 55 0.20
42 61 0.22
43 27 0.10
44 128 0.47
45 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (44 bp):
TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
Found at i:647883 original size:130 final size:130
Alignment explanation
Indices: 647649--648006 Score: 388
Period size: 130 Copynumber: 2.8 Consensus size: 130
647639 ATTTTCTACC
*
647649 TTTATAATTGAGACCCTTAAGTTCTTTCAATCTCACTTTCTACCTTTATAATTGAGGCCCCTAAG
1 TTTATAATTGAGACCCTTAAGTTCTTTCAATCTCACTCTCTACCTTTATAATTGAGGCCCCTAAG
* * * *
647714 TTTTTTCAATCTCAATTTCTACCTTTATAATTTAGGCCCCTAATTTTTTAACCCCGCTCTTTAAG
66 GTTTTTAAATCTCAATTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTAACCCCGCTCTTTAAG
* * *
647779 TTTATAATTGAGACTCTTAAGTTTTTTCAATCTCACTCTCTACCTTTATAATTGAGGCCCTTAAG
1 TTTATAATTGAGACCCTTAAGTTCTTTCAATCTCACTCTCTACCTTTATAATTGAGGCCCCTAAG
* * * * * ** *
647844 GTTTTTAAATCTTAATCTT-TACCTTTATAGTTGATGCCCCTAAGTTTTTCAATCTCAAT-TATA
66 GTTTTTAAATCTCAAT-TTCTACCTTTATAATTGAGGCCCCTAAGTTTTT-AACCCCGCTCTTTA
**
647907 CT
129 AG
** * * * * * *
647909 TTTATAATTGATTCCCCT-A-TTTTTTCAATCTCAAT-TATACTTTTATAATTGAGGCCACT-A-
1 TTTATAATTGAGACCCTTAAGTTCTTTCAATCTCACTCTCTACCTTTATAATTGAGGCCCCTAAG
* * *
647969 TTTTTTCAATCTCAATTTCTACCTTTATAATTAAGGCC
66 GTTTTTAAATCTCAATTTCTACCTTTATAATTGAGGCC
648007 TCTATTTTTT
Statistics
Matches: 192, Mismatches: 33, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
124 2 0.01
125 29 0.15
126 1 0.01
127 20 0.10
128 15 0.08
129 1 0.01
130 117 0.61
131 7 0.04
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (130 bp):
TTTATAATTGAGACCCTTAAGTTCTTTCAATCTCACTCTCTACCTTTATAATTGAGGCCCCTAAG
GTTTTTAAATCTCAATTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTAACCCCGCTCTTTAAG
Found at i:647913 original size:86 final size:86
Alignment explanation
Indices: 647641--648006 Score: 375
Period size: 86 Copynumber: 4.3 Consensus size: 86
647631 CTTTCTATAT
* * *
647641 TTTCTACCTTTATAATTGAGACCCTTAAGTTCTTTCAATCTCACTTTCTACCTTTATAATTGAGG
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTT-TTTCAATCTCAATTT-TACCTTTATAATTGAGG
647706 CCCCTAAGTTTTTTCAATCTCAA
64 CCCCTAAGTTTTTTCAATCTCAA
* * * * ** ** *
647729 TTTCTACCTTTATAATTTAGGCCCCTAA-TTTTTTAACCCCGCTCTTTAAGTTTATAATTGAGAC
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTCAATCTCAAT-TTTACCTTTATAATTGAGGC
* * *
647793 TCTTAAGTTTTTTCAATCTCAC
65 CCCTAAGTTTTTTCAATCTCAA
* * * * * *
647815 TCTCTACCTTTATAATTGAGGCCCTTAAGGTTTTTAAATCTTAATCTTTACCTTTATAGTTGATG
1 TTTCTACCTTTATAATTGAGGCCCCTAA-GTTTTTCAATCTCAAT-TTTACCTTTATAATTGAGG
647880 CCCCTAAG-TTTTTCAATCTCAA
64 CCCCTAAGTTTTTTCAATCTCAA
* * ** * * *
647902 -TTATACTTTTATAATTGATTCCCCT-ATTTTTTCAATCTCAATTATACTTTTATAATTGAGGCC
1 TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTCAATCTCAATTTTACCTTTATAATTGAGGCC
*
647965 ACT-A-TTTTTTCAATCTCAA
66 CCTAAGTTTTTTCAATCTCAA
*
647984 TTTCTACCTTTATAATTAAGGCC
1 TTTCTACCTTTATAATTGAGGCC
648007 TCTATTTTTT
Statistics
Matches: 224, Mismatches: 49, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
82 15 0.07
83 36 0.16
84 13 0.06
85 1 0.00
86 87 0.39
87 17 0.08
88 55 0.25
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (86 bp):
TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTCAATCTCAATTTTACCTTTATAATTGAGGCC
CCTAAGTTTTTTCAATCTCAA
Found at i:649167 original size:2 final size:2
Alignment explanation
Indices: 649160--649200 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
649150 TTTGACTTCG
649160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
649201 CACACACCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:649772 original size:3 final size:3
Alignment explanation
Indices: 649764--649790 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
649754 CCTTTAACTT
649764 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
649791 GCTATAACAC
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:650431 original size:20 final size:20
Alignment explanation
Indices: 650408--650535 Score: 132
Period size: 20 Copynumber: 6.3 Consensus size: 20
650398 AACTCCAATT
* *
650408 TCGCAATGCGAATATGTAAA
1 TCGCAACGCAAATATGTAAA
*
650428 TCGCAACG-ATAATAGGTAAA
1 TCGCAACGCA-AATATGTAAA
* * **
650448 TCGCAACGCAATTTTCCAAAA
1 TCGCAACGCAAATAT-GTAAA
* *
650469 TCGCAATGCGAATATGTAAA
1 TCGCAACGCAAATATGTAAA
*
650489 TCGCAACGCAAATTTGTAAA
1 TCGCAACGCAAATATGTAAA
*
650509 TCGCAACGCAAATTTGTAAA
1 TCGCAACGCAAATATGTAAA
650529 TCGCAAC
1 TCGCAAC
650536 ACAGAAGTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
20 73 0.83
21 15 0.17
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.23
Consensus pattern (20 bp):
TCGCAACGCAAATATGTAAA
Found at i:650488 original size:41 final size:40
Alignment explanation
Indices: 650425--650535 Score: 134
Period size: 41 Copynumber: 2.8 Consensus size: 40
650415 GCGAATATGT
* *
650425 AAATCGCAACG-ATAATAGGTAAATCGCAACGCAATTTTCCA
1 AAATCGCAACGCA-AATATGTAAATCGCAACGCAAATTT-CA
* * **
650466 AAATCGCAATGCGAATATGTAAATCGCAACGCAAATTTGT
1 AAATCGCAACGCAAATATGTAAATCGCAACGCAAATTTCA
*
650506 AAATCGCAACGCAAATTTGTAAATCGCAAC
1 AAATCGCAACGCAAATATGTAAATCGCAAC
650536 ACAGAAGTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
40 27 0.45
41 33 0.55
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCAAATATGTAAATCGCAACGCAAATTTCA
Found at i:650552 original size:20 final size:20
Alignment explanation
Indices: 650529--650574 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
650519 AATTTGTAAA
650529 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
650549 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
650569 TCGCAA
1 TCGCAA
650575 AACGCGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:651136 original size:20 final size:20
Alignment explanation
Indices: 651113--651159 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
651103 AAACTTAAAT
*
651113 TCGCAACACGAAAATGAAAA
1 TCGCAACACAAAAATGAAAA
*
651133 TCGCAACGCAAAAATGAAAA
1 TCGCAACACAAAAATGAAAA
651153 TCGCAAC
1 TCGCAAC
651160 CCGATTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.11
Consensus pattern (20 bp):
TCGCAACACAAAAATGAAAA
Found at i:652657 original size:42 final size:42
Alignment explanation
Indices: 652596--652692 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
652586 ACCCCCACTT
* * * * *
652596 CGAGAGCCATCACCTGATCGACCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACATGATCGACCCGATTATACACCTCCACAA
* *
652638 CTAGAGCCATCACATGATCGAGCCGATTATACACCTCCACAA
1 CGAGAGCCATCACATGATCGACCCGATTATACACCTCCACAA
652680 CGAGAGCCATCAC
1 CGAGAGCCATCAC
652693 CTATTCCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.16
Consensus pattern (42 bp):
CGAGAGCCATCACATGATCGACCCGATTATACACCTCCACAA
Found at i:652836 original size:21 final size:21
Alignment explanation
Indices: 652809--652858 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
652799 GTTAGGGAAG
* *
652809 TTACGTGATGAGGTCAGTGCT
1 TTACGTGAGGAGGTCAGTACT
* *
652830 TTGCGTGAGGAGGTCGGTACT
1 TTACGTGAGGAGGTCAGTACT
652851 TTACGTGA
1 TTACGTGA
652859 CGATAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAGTACT
Found at i:652899 original size:21 final size:21
Alignment explanation
Indices: 652875--652924 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
652865 TGGTGCATGG
*
652875 CGTGATGAGGTA-CGGTCTTTA
1 CGTGATGAGGTAGAGGT-TTTA
*
652896 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
*
652917 TGTGATGA
1 CGTGATGA
652925 CAATGGTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.20, C:0.08, G:0.38, T:0.34
Consensus pattern (21 bp):
CGTGATGAGGTAGAGGTTTTA
Found at i:653318 original size:42 final size:42
Alignment explanation
Indices: 653266--653384 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
653256 GATTCACCTG
* * * *
653266 TCATCGTTCAAGAGGCCTCTCCTATCATTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTA
* *
653308 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTA
* * * * ** *
653350 CCATCGTTCAATAGGTCATTCCCACCGTTCAAGAG
1 TCATCATTCAAGAGGCCCCTCCCACCATTCAAGAG
653385 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTA
Found at i:653357 original size:21 final size:21
Alignment explanation
Indices: 653262--653360 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 21
653252 GCCCGATTCA
*
653262 CCTGTCATCGTTCAAGAGGCC
1 CCTGCCATCGTTCAAGAGGCC
* *
653283 TCT-CCTATCATTCAAGAGGCC
1 CCTGCC-ATCGTTCAAGAGGCC
** *
653304 CCTATCATCATTCAAGAGGCC
1 CCTGCCATCGTTCAAGAGGCC
* *
653325 CCTCCCACCGTTCAAGAGGCC
1 CCTGCCATCGTTCAAGAGGCC
653346 CCTGCCATCGTTCAA
1 CCTGCCATCGTTCAA
653361 TAGGTCATTC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.23
Consensus pattern (21 bp):
CCTGCCATCGTTCAAGAGGCC
Found at i:653378 original size:21 final size:21
Alignment explanation
Indices: 653270--653384 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 21
653260 CACCTGTCAT
* * *
653270 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCACTCCCAC
* * ** *
653291 CATTCAAGAGGCCCCTATCAT
1 CGTTCAAGAGGCCACTCCCAC
* *
653312 CATTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCACTCCCAC
* * *
653333 CGTTCAAGAGGCCCCTGCCAT
1 CGTTCAAGAGGCCACTCCCAC
* * *
653354 CGTTCAATAGGTCATTCCCAC
1 CGTTCAAGAGGCCACTCCCAC
653375 CGTTCAAGAG
1 CGTTCAAGAG
653385 CCCGATTCAC
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTCCCAC
Found at i:657778 original size:12 final size:12
Alignment explanation
Indices: 657757--657790 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
657747 GGTTGTGGGT
*
657757 TTTGAGATTGTG
1 TTTGATATTGTG
657769 TTTGATATTGTG
1 TTTGATATTGTG
*
657781 TTTGGTATTG
1 TTTGATATTG
657791 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:658405 original size:16 final size:15
Alignment explanation
Indices: 658383--658421 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
658373 GAAATCATTG
658383 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
658399 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
658414 AAAAATTA
1 AAAAATTA
658422 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:658642 original size:20 final size:20
Alignment explanation
Indices: 658578--658642 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
658568 AAATAAAAGC
* * **
658578 TGTTGCGAAATTAAAATTTG
1 TGTTGTGAAATCAAAATTCA
*
658598 TGTTGTGAATTCGAAAA-TCGA
1 TGTTGTGAAATC-AAAATTC-A
658619 -GTTGTGAAATCAAAATTCA
1 TGTTGTGAAATCAAAATTCA
658638 TGTTG
1 TGTTG
658643 CGATTTAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 5 0.14
20 26 0.74
21 4 0.11
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTTGTGAAATCAAAATTCA
Found at i:658642 original size:40 final size:40
Alignment explanation
Indices: 658579--658667 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
658569 AATAAAAGCT
* ** * *
658579 GTTGCGAAATTAAAATTTGTGTTGTGAATTCGAAAATCGA
1 GTTGCGAAATCAAAATTCATGTTGCGAATTAGAAAATCGA
* * **
658619 GTTGTGAAATCAAAATTCATGTTGCGATTTAGAAAATCTT
1 GTTGCGAAATCAAAATTCATGTTGCGAATTAGAAAATCGA
658659 GTTGCGAAA
1 GTTGCGAAA
658668 AGGAAACTTG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (40 bp):
GTTGCGAAATCAAAATTCATGTTGCGAATTAGAAAATCGA
Found at i:658763 original size:20 final size:20
Alignment explanation
Indices: 658740--658829 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
658730 TGACTTCTGT
*
658740 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACATATTCGC
*
658760 GTTGCGATTTACATATTTGC
1 GTTGCGATTTACATATTCGC
* **
658780 TTTGCGATTTACATATTATC
1 GTTGCGATTTACATATTCGC
* *
658800 GTTGTGATTTACATATTCAC
1 GTTGCGATTTACATATTCGC
658820 GTTGCGATTT
1 GTTGCGATTT
658830 TGGAACATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:660541 original size:40 final size:40
Alignment explanation
Indices: 660489--660667 Score: 175
Period size: 41 Copynumber: 4.4 Consensus size: 40
660479 CGTTTATACA
* *
660489 AAAAAAGGCCACTATTGATTA-CACTATTGTGGCGTTTGTT
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
*
660529 AAAAAACGCCACTATTGATT-TAAACTATTGCGGCGTTTTT
1 AAAAAACGCCACTATTGATTAT-CACTATTGCGGCGTTTTT
* * *
660569 CTACAAATGCCACTATTGATTATCACTATTGCGGCGTTTATCT
1 -AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-T-T
* * * *
660612 -AAAAACACCACTATTTATTATCATTATTGCGGCGTTTTA
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTTT
*
660651 AGAATAAATGCCACTAT
1 A-AA-AAACGCCACTAT
660668 ATGTGTAATC
Statistics
Matches: 115, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
40 22 0.19
41 80 0.70
42 12 0.10
43 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (40 bp):
AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTTT
Found at i:660625 original size:82 final size:81
Alignment explanation
Indices: 660496--660649 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 81
660486 ACAAAAAAAG
* * *
660496 GCCACTATTGATTACACTATTGTGGCGTTTGTTAAAAAACGCCACTATTGATT-TAAACTATTGC
1 GCCACTATTGATTACACTATTGCGGCGTTTATTAAAAAACACCACTATTGATTAT-AACTATTGC
660560 GGCGTTTTTCTACAAAT
65 GGCGTTTTTCTACAAAT
* * *
660577 GCCACTATTGATTATCACTATTGCGGCGTTTATCT-AAAAACACCACTATTTATTATCATTATTG
1 GCCACTATTGATTA-CACTATTGCGGCGTTTAT-TAAAAAACACCACTATTGATTATAACTATTG
660641 CGGCGTTTT
64 CGGCGTTTT
660650 AAGAATAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
81 14 0.22
82 48 0.75
83 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (81 bp):
GCCACTATTGATTACACTATTGCGGCGTTTATTAAAAAACACCACTATTGATTATAACTATTGCG
GCGTTTTTCTACAAAT
Found at i:660700 original size:42 final size:41
Alignment explanation
Indices: 660654--660763 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 41
660644 CGTTTTAAGA
* *
660654 ATAAATGCCACTATATGTGTAATCTATTGTGGTGTTTGTGG-T
1 ATAAACGCCACTATATGT-TAATCTATTGCGGTGTTT-TGGCT
*
660696 ATAAACGCCGCTA-AT-TTACCGATCTATTGCGGTGTTTTGGCT
1 ATAAACGCCACTATATGTTA---ATCTATTGCGGTGTTTTGGCT
660738 A-AAACGCCACTATATGTTAATCTATT
1 ATAAACGCCACTATATGTTAATCTATT
660764 ACGACGTTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
39 2 0.03
40 8 0.14
41 15 0.26
42 30 0.52
43 3 0.05
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (41 bp):
ATAAACGCCACTATATGTTAATCTATTGCGGTGTTTTGGCT
Found at i:662386 original size:81 final size:80
Alignment explanation
Indices: 662139--662389 Score: 218
Period size: 81 Copynumber: 3.1 Consensus size: 80
662129 TCAATTGCGA
* * * * * *
662139 CGTTTGTAAAAAAACTCCGCTAAAGCACTACTCTGTTGTGGCGTTTGTCGAAAAAATGACATTAT
1 CGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGTGGCGTTTGTTGAAAAAACGACACTAT
*
662204 A-TATGAACCCTATTATGG
66 AGT-T--A-CCTTTTATGG
* * * ** * *
662222 CATTTTTATACAAACGCCGCTAAAGTACTACTCTGTCATGGCGTTTGTTG-AGAAACGCCACTAT
1 CGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGTGGCGTTTGTTGAAAAAACGACACTAT
* * * **
662286 GGATGAACTTATTGCGG
66 AG-TTACCTT-TTATGG
* * * *
662303 CGTTTGTATAAAAACGCCACTAAAATACTACTCTGTTGCGGCATTTGTTGAAAAAACGACACTAT
1 CGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGTGGCGTTTGTTGAAAAAACGACACTAT
662368 AGTTACCATTTTATGG
66 AGTTACC-TTTTATGG
662384 CGTTTG
1 CGTTTG
662390 GAATGTAAAC
Statistics
Matches: 128, Mismatches: 35, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
80 2 0.02
81 59 0.46
82 25 0.20
83 41 0.32
84 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (80 bp):
CGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGTGGCGTTTGTTGAAAAAACGACACTAT
AGTTACCTTTTATGG
Found at i:663804 original size:22 final size:22
Alignment explanation
Indices: 663776--663826 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
663766 GGATCGATCA
663776 AACGTGTTGAGTCAGCTGATTT
1 AACGTGTTGAGTCAGCTGATTT
663798 AACGTGTTGAGTCAGCTGATTT
1 AACGTGTTGAGTCAGCTGATTT
663820 AACGTGT
1 AACGTGT
663827 CACGTCACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (22 bp):
AACGTGTTGAGTCAGCTGATTT
Found at i:675599 original size:191 final size:191
Alignment explanation
Indices: 675275--675655 Score: 726
Period size: 191 Copynumber: 2.0 Consensus size: 191
675265 ACACCAAAAT
675275 TCAAATTTAAGACTATGGACATCTTCACTTCATCTTTCCACCGTGAAGTATATTCAAGTATTATT
1 TCAAATTTAAGACTATGGACATCTTCACTTCATCTTTCCACCGTGAAGTATATTCAAGTATTATT
675340 TTATAAATTTATTTTATTTTTTAGATTAAATCTTGAGTTCAACCATTTTATGATACTCTTTCGAC
66 TTATAAATTTATTTTATTTTTTAGATTAAATCTTGAGTTCAACCATTTTATGATACTCTTTCGAC
675405 AATACAGAGATAATTTATTATACCTCTATAAATATTATTCCCCCACCAATCTATCAACAAC
131 AATACAGAGATAATTTATTATACCTCTATAAATATTATTCCCCCACCAATCTATCAACAAC
*
675466 TCAAATTTAAGACTATGGACATCTTCACTTCATCTTTCCACCGTGAAGTATATTCAAGTCTTATT
1 TCAAATTTAAGACTATGGACATCTTCACTTCATCTTTCCACCGTGAAGTATATTCAAGTATTATT
*
675531 TTATAAATTTATTTTATTTTTTAGATTAAATCTTGAGTTCAGCCATTTTATGATACTCTTTCGAC
66 TTATAAATTTATTTTATTTTTTAGATTAAATCTTGAGTTCAACCATTTTATGATACTCTTTCGAC
* *
675596 AATACATATATAATTTATTATACCTCTATAAATATTATTCCCCCACCAATCTATCAACAA
131 AATACAGAGATAATTTATTATACCTCTATAAATATTATTCCCCCACCAATCTATCAACAA
675656 TCATCTCTAG
Statistics
Matches: 186, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 186 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (191 bp):
TCAAATTTAAGACTATGGACATCTTCACTTCATCTTTCCACCGTGAAGTATATTCAAGTATTATT
TTATAAATTTATTTTATTTTTTAGATTAAATCTTGAGTTCAACCATTTTATGATACTCTTTCGAC
AATACAGAGATAATTTATTATACCTCTATAAATATTATTCCCCCACCAATCTATCAACAAC
Found at i:681135 original size:35 final size:34
Alignment explanation
Indices: 681084--681154 Score: 106
Period size: 35 Copynumber: 2.1 Consensus size: 34
681074 ATATCCATTC
*
681084 ATAGGGGTATCAGTACCCGTTCATAAGAGGTATTG
1 ATAGGGGTATCAGTACCCATTCAT-AGAGGTATTG
* *
681119 ATAGGGGTATCGGTACCCATTCATAGGGGTATTG
1 ATAGGGGTATCAGTACCCATTCATAGAGGTATTG
681153 AT
1 AT
681155 GCCCATTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 11 0.33
35 22 0.67
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (34 bp):
ATAGGGGTATCAGTACCCATTCATAGAGGTATTG
Found at i:681147 original size:22 final size:22
Alignment explanation
Indices: 681119--681179 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
681109 AGAGGTATTG
681119 ATAGGGGTATCGGTACCCATTC
1 ATAGGGGTATCGGTACCCATTC
* * *
681141 ATAGGGGTATTGATGCCCATTC
1 ATAGGGGTATCGGTACCCATTC
**
681163 ATAGATGTATCGGTACC
1 ATAGGGGTATCGGTACC
681180 TCTTAATATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (22 bp):
ATAGGGGTATCGGTACCCATTC
Found at i:684408 original size:20 final size:22
Alignment explanation
Indices: 684383--684422 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
684373 AGTGGTATAT
684383 AGCCG-TTGGGGA-TATTTTGG
1 AGCCGTTTGGGGATTATTTTGG
684403 AGCCGTTTGGGGATTATTTT
1 AGCCGTTTGGGGATTATTTT
684423 TTTTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.15, C:0.10, G:0.35, T:0.40
Consensus pattern (22 bp):
AGCCGTTTGGGGATTATTTTGG
Found at i:685141 original size:35 final size:35
Alignment explanation
Indices: 685038--685141 Score: 102
Period size: 35 Copynumber: 3.0 Consensus size: 35
685028 ACCTTAGATC
*
685038 CGTAAGGAATTACCAGCTCGATCCG-TCTAAACCTA
1 CGTAAGGAATTACCAGTTCGAT-CGATCTAAACCTA
** * * * ** *
685073 TATAAGGAATTACCAATTTGACCGAGATGAACCTA
1 CGTAAGGAATTACCAGTTCGATCGATCTAAACCTA
*
685108 CGTAAGGAAATACCAGTTCGATCGATCTAAACCT
1 CGTAAGGAATTACCAGTTCGATCGATCTAAACCT
685142 TATATCTAAA
Statistics
Matches: 50, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
34 2 0.04
35 48 0.96
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (35 bp):
CGTAAGGAATTACCAGTTCGATCGATCTAAACCTA
Found at i:686293 original size:25 final size:26
Alignment explanation
Indices: 686265--686315 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
686255 TTTTTTACAA
*
686265 CATAAGGGTA-TTTTGTAATTTTACC
1 CATAAGGGTATTTTTATAATTTTACC
686290 CATAAGGGTATTTTTATAATTTTACC
1 CATAAGGGTATTTTTATAATTTTACC
686316 TAACCGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (26 bp):
CATAAGGGTATTTTTATAATTTTACC
Found at i:686913 original size:22 final size:22
Alignment explanation
Indices: 686888--686939 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
686878 TGACTTTTTT
686888 GGTCAAAGTCAACGGTCA-ATCC
1 GGTCAAAGTCAACGGTCAGA-CC
*
686910 GGTCAAAGTTAACGGTCAGACC
1 GGTCAAAGTCAACGGTCAGACC
686932 GGTCAAAG
1 GGTCAAAG
686940 GTTAATGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (22 bp):
GGTCAAAGTCAACGGTCAGACC
Found at i:686973 original size:19 final size:19
Alignment explanation
Indices: 686910--686975 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
686900 CGGTCAATCC
686910 GGTCAAAGTTAACGG-TCAGA
1 GGTCAAAGTTAACGGTTC--A
*
686930 CCGGTCAAAGGTTAATGGGTT-A
1 --GGTCAAA-GTTAA-CGGTTCA
686952 GGTCAAAGTTAACGGTTCA
1 GGTCAAAGTTAACGGTTCA
686971 GGTCA
1 GGTCA
686976 GGTTGACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
18 4 0.11
19 11 0.29
20 7 0.18
22 8 0.21
23 5 0.13
24 2 0.05
25 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (19 bp):
GGTCAAAGTTAACGGTTCA
Found at i:688965 original size:36 final size:35
Alignment explanation
Indices: 688866--688987 Score: 95
Period size: 35 Copynumber: 3.5 Consensus size: 35
688856 CTTTGATCTG
* * * *
688866 TAAGGAATTACCAGATCGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCAGTTTGAACCTACA
* ** * *
688901 TAAGGAATTACCAATTTAACTGAG-TTGAACCTGCCA
1 TAAGGAATTACCAGTTCGA-TCAGTTTGAACCT-ACA
* *
688937 TAAGGAATTACCAGTTCGATCAGTTTGAA-ATAATA
1 TAAGGAATTACCAGTTCGATCAGTTTGAACCT-ACA
*
688972 TAATGAATTACCAGTT
1 TAAGGAATTACCAGTT
688988 TGATTGAACT
Statistics
Matches: 66, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
35 42 0.64
36 24 0.36
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (35 bp):
TAAGGAATTACCAGTTCGATCAGTTTGAACCTACA
Found at i:689003 original size:71 final size:71
Alignment explanation
Indices: 688866--689005 Score: 165
Period size: 71 Copynumber: 2.0 Consensus size: 71
688856 CTTTGATCTG
* * ** *
688866 TAAGGAATTACCAGATCGATCGGTCTGAACCTATATAAGGAATTACCAATTTAACTGAGTTGAAC
1 TAAGGAATTACCAGATCGATCAGTCTGAACATATATAAGGAATTACCAATTTAACTGAACTAAAC
688931 CTGCCA
66 CTGCCA
* * * * * *
688937 TAAGGAATTACCAGTTCGATCAGTTTGAA-ATAATATAATGAATTACCAGTTTGATTGAACTAAA
1 TAAGGAATTACCAGATCGATCAGTCTGAACAT-ATATAAGGAATTACCAATTTAACTGAACTAAA
689001 CCTGC
65 CCTGC
689006 AAAGACTTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
70 1 0.02
71 56 0.98
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (71 bp):
TAAGGAATTACCAGATCGATCAGTCTGAACATATATAAGGAATTACCAATTTAACTGAACTAAAC
CTGCCA
Found at i:690660 original size:20 final size:20
Alignment explanation
Indices: 690637--690677 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
690627 TGGACTTTGG
690637 ATTCGGACTCAAGACTTCGA
1 ATTCGGACTCAAGACTTCGA
*
690657 ATTCGGACTCAGGACTTCGA
1 ATTCGGACTCAAGACTTCGA
690677 A
1 A
690678 AAACATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (20 bp):
ATTCGGACTCAAGACTTCGA
Found at i:690765 original size:22 final size:23
Alignment explanation
Indices: 690740--690783 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
690730 GGTCAACGAG
*
690740 CAGACCAGTTAAAGTT-AACGGT
1 CAGACCAGTCAAAGTTCAACGGT
*
690762 CAGACTAGTCAAAGTTCAACGG
1 CAGACCAGTCAAAGTTCAACGG
690784 GTTAGGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (23 bp):
CAGACCAGTCAAAGTTCAACGGT
Found at i:690810 original size:19 final size:20
Alignment explanation
Indices: 690769--690810 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
690759 GGTCAGACTA
* *
690769 GTCAAAGTTCAACGGGTTAG
1 GTCAAAGTTCAAAGGGTCAG
*
690789 GTCAAAG-TCAAAGGGTCGG
1 GTCAAAGTTCAAAGGGTCAG
690808 GTC
1 GTC
690811 GGGTTGACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (20 bp):
GTCAAAGTTCAAAGGGTCAG
Found at i:691635 original size:20 final size:20
Alignment explanation
Indices: 691593--691635 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
691583 CTCAGTCCTT
* *
691593 AAATTTCCTATAAATTTCTA
1 AAATTGCCTATAAATTTCAA
*
691613 AAATTGCCTATAAGTTTCAA
1 AAATTGCCTATAAATTTCAA
691633 AAA
1 AAA
691636 CTCATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (20 bp):
AAATTGCCTATAAATTTCAA
Found at i:703955 original size:75 final size:76
Alignment explanation
Indices: 703866--704027 Score: 220
Period size: 76 Copynumber: 2.1 Consensus size: 76
703856 ATCTCATTGG
**
703866 AGATTGTTTTTCTTAAAA-TGGACTTTGTCTCACTTGAGA-ATGTTTTACTCGAAAGAAGACATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACATGTTTTACTCGAAAGAAGACATT
*
703929 TCATTTGACTCA
65 TCATTTCACTCA
** * * *
703941 AGATTGTTTTTCTTAAAACAAGATTTGTCTTGCTTGAGACATTTTTTACTCGAAATAATACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACATGTTTTACTCGAAAGAAGACATTT
*
704006 TATTTCACTCA
66 CATTTCACTCA
704017 AGATTGTTTTT
1 AGATTGTTTTT
704028 AAAGAATATT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
75 32 0.42
76 44 0.58
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACATGTTTTACTCGAAAGAAGACATTT
CATTTCACTCA
Found at i:704085 original size:39 final size:39
Alignment explanation
Indices: 704030--704225 Score: 209
Period size: 39 Copynumber: 5.0 Consensus size: 39
704020 TTGTTTTTAA
* *
704030 AGAATATTGTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * *
704069 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * * *
704108 AGAAGAGTTTGTCTCGTTTGAGATAATTTCTCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * **
704147 AGAATATTTTATCTCGTTTAAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
704186 AGAAGATCTTGTATCT--CTTGAGGA-AGTTTCCCTTGAAAC
1 AGAAGAT-TT-TATCTCGCTTGA-GATAGTTTCCCTTGAAAC
704225 A
1 A
704226 CCAATCTTTG
Statistics
Matches: 128, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
39 119 0.93
40 4 0.03
41 5 0.04
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
Found at i:704146 original size:78 final size:78
Alignment explanation
Indices: 704041--704225 Score: 230
Period size: 78 Copynumber: 2.4 Consensus size: 78
704031 GAATATTGTA
* * *
704041 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
1 TCTCGCTTGAGATAATTTCCCTTGAAACAAAAGATTTTATCTCGCTTAAGATAGTTTCCCTCAAA
*
704106 ATAGAAGAGTTTG
66 ACAGAAGAGTTTG
* * * * *
704119 TCTCGTTTGAGATAATTTCTCTTGAAACAGAATATTTTATCTCGTTTAAGATAGTTTCCCTCAAA
1 TCTCGCTTGAGATAATTTCCCTTGAAACAAAAGATTTTATCTCGCTTAAGATAGTTTCCCTCAAA
704184 ACAGAAGA-TCTTG
66 ACAGAAGAGT-TTG
* * *
704197 TATCTCTTGAGGA-AGTTTCCCTTGAAACA
1 TCTCGCTTGA-GATAATTTCCCTTGAAACA
704226 CCAATCTTTG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
77 1 0.01
78 88 0.97
79 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (78 bp):
TCTCGCTTGAGATAATTTCCCTTGAAACAAAAGATTTTATCTCGCTTAAGATAGTTTCCCTCAAA
ACAGAAGAGTTTG
Found at i:704237 original size:30 final size:31
Alignment explanation
Indices: 704198--704255 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
704188 AAGATCTTGT
704198 ATCTCTTGAGGA-AGTTTCCCTTGAAACACCA
1 ATCTCTTGA-GATAGTTTCCCTTGAAACACCA
*
704229 ATCT-TTGAGATTGTTTCCCTTGAAACA
1 ATCTCTTGAGATAGTTTCCCTTGAAACA
704256 AATTTTGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 2 0.08
30 19 0.76
31 4 0.16
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (31 bp):
ATCTCTTGAGATAGTTTCCCTTGAAACACCA
Found at i:704446 original size:36 final size:36
Alignment explanation
Indices: 704403--704567 Score: 183
Period size: 36 Copynumber: 4.6 Consensus size: 36
704393 TAAACTTTGA
* *
704403 AAAC-GTTTCCCTTGAAACGAA-TTTTATCACTCTTG
1 AAACAGTTTCCCTTGAAAC-AAGTTTTGTCTCTCTTG
* *
704438 AAACCGTTTCCCTTGAAACAAGTTTTGTCTCCCTTG
1 AAACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTG
* * *
704474 AGACATTTTCTCTTGAAACAAGTTTTGTCTCTCTTG
1 AAACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTG
* *
704510 AGACAGTTTCTCTTGAAACAAAGTTTTGTCTCT-TTAG
1 AAACAGTTTCCCTTGAAAC-AAGTTTTGTCTCTCTT-G
* *
704547 AGACAGTTTCCCTCGAAACAA
1 AAACAGTTTCCCTTGAAACAA
704568 ATCTCATTTG
Statistics
Matches: 115, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
35 6 0.05
36 78 0.68
37 31 0.27
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (36 bp):
AAACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTG
Found at i:704472 original size:21 final size:20
Alignment explanation
Indices: 704448--704541 Score: 73
Period size: 21 Copynumber: 5.0 Consensus size: 20
704438 AAACCGTTTC
704448 CCTTGAAACAAGTTTTGTCT
1 CCTTGAAACAAGTTTTGTCT
*
704468 CCCTTGAGAC-A--TTT-TCT
1 -CCTTGAAACAAGTTTTGTCT
704485 -CTTGAAACAAGTTTTGTCT
1 CCTTGAAACAAGTTTTGTCT
*
704504 CTCTTGAGAC-AG--TT-TCT
1 C-CTTGAAACAAGTTTTGTCT
704521 -CTTGAAACAAAGTTTTGTCT
1 CCTTGAAAC-AAGTTTTGTCT
704541 C
1 C
704542 TTTAGAGACA
Statistics
Matches: 57, Mismatches: 4, Indels: 24
0.67 0.05 0.28
Matches are distributed among these distances:
15 14 0.25
16 1 0.02
17 8 0.14
18 8 0.14
19 5 0.09
20 6 0.11
21 15 0.26
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (20 bp):
CCTTGAAACAAGTTTTGTCT
Found at i:704554 original size:20 final size:20
Alignment explanation
Indices: 704494--704555 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
704484 TCTTGAAACA
704494 AGTTTTGTCTCTCTT-GAGAC
1 AGTTTTGTCTCT-TTAGAGAC
* * * *
704514 AG--TT-TCTCTTGAAACAA
1 AGTTTTGTCTCTTTAGAGAC
704531 AGTTTTGTCTCTTTAGAGAC
1 AGTTTTGTCTCTTTAGAGAC
704551 AGTTT
1 AGTTT
704556 CCCTCGAAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
16 1 0.03
17 9 0.30
18 2 0.07
19 2 0.07
20 16 0.53
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.44
Consensus pattern (20 bp):
AGTTTTGTCTCTTTAGAGAC
Found at i:705430 original size:263 final size:264
Alignment explanation
Indices: 704902--705973 Score: 1451
Period size: 263 Copynumber: 4.1 Consensus size: 264
704892 TGTTCAATTG
* * * *
704902 TTTGCTCGATTCTATCATAGAAGGAGGTAGATCAGCACCAACATTTCGTTTGATTCCATCACAAA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCATCACAGA
* * *
704967 AGGAGGTA-GATCGACA--TTT-GTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCAA
66 AGGAGG-AGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAA
* * * *
705028 ATTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAACATCGACGTATCGTTCAATTTCCATCA
130 CTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCAA-TTCCATCA
* * * * * *
705093 TAGAAGGAGGTGAATCAACATTTTTATTTTTGCTCAAATCCATCGTAGAAGGATTTGGATCAGCG
194 CAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCG
*
705158 TTAACTT
259 TCAAC-T
* * * * * *
705165 TTTTCTCGTTTCTATCACAGAAGGAGGTAGATCAACA-CAACATCTCATTCAATTCCATCGCAGA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCATCACAGA
* * * * *
705229 AGGAGGAGGATCGATATTTTTATTTCGCTCAAATCTATCGTAGAAGGAGTTGGATCAGCATCAAC
66 AGGAGGAGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAAC
* * * * * *
705294 TTTTAGCGT-GATTCTATCATAGAAGGAGGTAGATCAGCATCGATATGTTGTTCGATTCCATCAC
131 TTTTAGC-TCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCAATTCCATCAC
* * *
705358 AGAAGGAGGTGGATCGACAATTTTA-TTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAGCAT
195 AGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGT
705422 CAACT
260 CAACT
* * *
705427 TTTTCTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACGTCTCGTTCGATTCCATCACAGA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCATCACAGA
*
705492 AGGAGGTGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAAC
66 AGGAGGAGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAAC
** * *
705557 TTTTTTCTCGATTATATCACAGAAGGAGGTAGATCAACATCGACATCTTGTTCAATTCCATCACA
131 TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCAATTCCATCACA
* *
705622 GAAGGAGGTGGATTGACATTTTTA-TTTCGCTCAAATCCATCGCAGAAGGAGTTAGATCAGCGTC
196 GAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTC
705686 AACT
261 AACT
* * *
705690 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGGATCGACATCTCGTTCGATTCCATCACAGA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCATCACAGA
* * * * *
705755 AGGAGGCGGATCAACATTTTTATTTTCACTCAAATCCATTGCAGAAGAAGTTAGATCAGCGTCAA
66 AGGAGGAGGATCGACATTTTTA-TTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAA
* * * * * *
705820 CTTTTTGCTCGATTTTATCACAGAAGGAGGTAGATCAACATCAACATCTCGTTCGATTTCATCAT
130 CTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCAATTCCATCAC
* *
705885 AGAAGGAGGTGGATCGACATTTTTATTTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCATCGT
195 AGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGT
705950 CAACT
260 CAACT
705955 TCTTGCTCGATTC-ATCACA
1 T-TTGCTCGATTCTATCACA
705974 TATGGAGTTG
Statistics
Matches: 719, Mismatches: 80, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
261 1 0.00
262 72 0.10
263 349 0.49
264 154 0.21
265 131 0.18
266 12 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (264 bp):
TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCATCACAGA
AGGAGGAGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAAC
TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCAATTCCATCACA
GAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTC
AACT
Found at i:705756 original size:44 final size:44
Alignment explanation
Indices: 704907--705899 Score: 324
Period size: 44 Copynumber: 22.6 Consensus size: 44
704897 AATTGTTTGC
* * *
704907 TCGATTCTATCATAGAAGGAGGTAGATCAGCACCAACATTTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
* * ** *
704951 TTGATTCCATCACAAAAGGAGGTAGATC-G-A-C-ATTTGTTCGC
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACAT-TTCGT
* * * * * * * *
704992 TCAAATCCATCGCAGAAGGAGTTGGATCAACGTCAA-ATTTTAGCT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACA-TTTCG-T
* * * * *
705037 T-GATTCTATCACAGAAGGAGGTAGATCAACATCGACGTATCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
* * * **** * *
705080 TCAATTTCCATCATAGAAGGAGGT-GAATCAACATTTTTATTTTTGC
1 TCGA-TTCCATCACAGAAGGAGGTAG-ATCAGCATCAACA-TTTCGT
* * ** ** * * * **
705126 TCAAATCCATCGTAGAAGGATTTGGATCAGCGTTAAC-TTTTTT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
* * * * *
705169 CTCGTTTCTATCACAGAAGGAGGTAGATCAACA-CAACATCTCAT
1 -TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
* * * **** *
705213 TCAATTCCATCGCAGAAGGAGG-AGGATC-GATATTTTTATTTCGC
1 TCGATTCCATCACAGAAGGAGGTA-GATCAG-CATCAACATTTCGT
* * * ** * * *
705257 TCAAATCTATCGTAGAAGGAGTTGGATCAGCATCAACTTTTAGCG-
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTT--CGT
* * * *
705302 T-GATTCTATCATAGAAGGAGGTAGATCAGCATCGATATGTT-GT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACAT-TTCGT
* * **
705345 TCGATTCCATCACAGAAGGAGGTGGATC-G-A-CAATTTTATTTCAC
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAA---CATTTCGT
* * * * * *
705389 TCAAATCCATCGCAGAAGGAGTTGGATCAGCATCAAC-TTT-TT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
* * * * *
705431 CTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACGTCTCGT
1 -TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
* **** **
705476 TCGATTCCATCACAGAAGGAGGTGGATC-GACATTTTTATTTCAC
1 TCGATTCCATCACAGAAGGAGGTAGATCAG-CATCAACATTTCGT
* * * * * * **
705520 TCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAAC-TTTTTT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
** * *
705563 CTCGATTATATCACAGAAGGAGGTAGATCAACATCGACATCTT-GT
1 -TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACAT-TTCGT
* * * **** *
705608 TCAATTCCATCACAGAAGGAGGTGGAT-TGACATTTTTATTTCGC
1 TCGATTCCATCACAGAAGGAGGTAGATCAG-CATCAACATTTCGT
* * * * * * *
705652 TCAAATCCATCGCAGAAGGAGTTAGATCAGCGTCAAC-TTTTGC
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
* * * *
705695 TCGATTCTATCACAGAAGGAGGTAGATCAGGATCGACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
** * **** **
705739 TCGATTCCATCACAGAAGGAGGCGGATCAACATTTTTATTTTCAC
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACA-TTTCGT
* * ** * * * * * *
705784 TCAAATCCATTGCAGAAGAAGTTAGATCAGCGTCAACTTTTTGC
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
** * *
705828 TCGATTTTATCACAGAAGGAGGTAGATCAACATCAACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
* * *
705872 TCGATTTCATCATAGAAGGAGGTGGATC
1 TCGATTCCATCACAGAAGGAGGTAGATC
705900 GACATTTTTA
Statistics
Matches: 668, Mismatches: 236, Indels: 90
0.67 0.24 0.09
Matches are distributed among these distances:
40 2 0.00
41 28 0.04
42 4 0.01
43 109 0.16
44 423 0.63
45 86 0.13
46 13 0.02
47 3 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
TCGATTCCATCACAGAAGGAGGTAGATCAGCATCAACATTTCGT
Found at i:708442 original size:12 final size:12
Alignment explanation
Indices: 708427--708470 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
708417 AATTTTTACT
708427 TTAACTTTAAAA
1 TTAACTTTAAAA
*
708439 TTAACTTTGAAA
1 TTAACTTTAAAA
*
708451 TCAACATATTAAAA
1 TTAAC-T-TTAAAA
708465 TTAACT
1 TTAACT
708471 CAATACAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 15 0.58
13 2 0.08
14 9 0.35
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (12 bp):
TTAACTTTAAAA
Found at i:708730 original size:29 final size:29
Alignment explanation
Indices: 708695--708751 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
708685 GCAATACACC
708695 TAAATGCTTAAACATTTAACCCATAAACT
1 TAAATGCTTAAACATTTAACCCATAAACT
*
708724 TAAATGCTTAAACATTTAACTCATAAAC
1 TAAATGCTTAAACATTTAACCCATAAAC
708752 ACCAATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.32
Consensus pattern (29 bp):
TAAATGCTTAAACATTTAACCCATAAACT
Found at i:708752 original size:15 final size:15
Alignment explanation
Indices: 708703--708752 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
708693 CCTAAATGCT
*
708703 TAAACATTTAACCCA
1 TAAACATTTAACTCA
* *
708718 TAAAC--TTAAATGCT
1 TAAACATTTAACT-CA
708732 TAAACATTTAACTCA
1 TAAACATTTAACTCA
708747 TAAACA
1 TAAACA
708753 CCAATACAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 4 0.15
14 6 0.22
15 12 0.44
16 5 0.19
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (15 bp):
TAAACATTTAACTCA
Found at i:709119 original size:83 final size:83
Alignment explanation
Indices: 708980--709152 Score: 337
Period size: 83 Copynumber: 2.1 Consensus size: 83
708970 CTCTTTCAGA
*
708980 TATTTCTTCATATACCATTTGAAGAACATACAATCTGAATTCTTGAAATTAGAACAACTAAAAAA
1 TATTTTTTCATATACCATTTGAAGAACATACAATCTGAATTCTTGAAATTAGAACAACTAAAAAA
709045 GCTTTCACCTGCATTTTT
66 GCTTTCACCTGCATTTTT
709063 TATTTTTTCATATACCATTTGAAGAACATACAATCTGAATTCTTGAAATTAGAACAACTAAAAAA
1 TATTTTTTCATATACCATTTGAAGAACATACAATCTGAATTCTTGAAATTAGAACAACTAAAAAA
709128 GCTTTCACCTGCATTTTT
66 GCTTTCACCTGCATTTTT
709146 TATTTTT
1 TATTTTT
709153 CAGTTGTCCA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 89 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (83 bp):
TATTTTTTCATATACCATTTGAAGAACATACAATCTGAATTCTTGAAATTAGAACAACTAAAAAA
GCTTTCACCTGCATTTTT
Found at i:711410 original size:28 final size:26
Alignment explanation
Indices: 711379--711459 Score: 117
Period size: 28 Copynumber: 3.0 Consensus size: 26
711369 TATAAGTTTA
711379 TATATAAACTATATATATAAACTATG
1 TATATAAACTATATATATAAACTATG
*
711405 TTTATATGAACTATATATATAAACTATG
1 --TATATAAACTATATATATAAACTATG
711433 TATATAAACTATATACGTATAAACTAT
1 TATATAAACTATATA--TATAAACTAT
711460 AAAAAGTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 14 0.29
28 35 0.71
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (26 bp):
TATATAAACTATATATATAAACTATG
Found at i:711458 original size:41 final size:41
Alignment explanation
Indices: 711377--711460 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
711367 AATATAAGTT
* ** *
711377 TATATATAAACTATATATATAAACTATGTTTATATGAACTA
1 TATATATAAACTATATATATAAACTATATACATATAAACTA
* *
711418 TATATATAAACTATGTATATAAACTATATACGTATAAACTA
1 TATATATAAACTATATATATAAACTATATACATATAAACTA
711459 TA
1 TA
711461 AAAAGTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (41 bp):
TATATATAAACTATATATATAAACTATATACATATAAACTA
Found at i:711517 original size:2 final size:2
Alignment explanation
Indices: 711496--712065 Score: 227
Period size: 2 Copynumber: 285.0 Consensus size: 2
711486 GTTTGTATTA
* * * * *
711496 AT AT AGT AT AT AT TT TT AT AT AT AT GT AT AT AA ACT AT AT AT GT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * * *
711540 AT AA AC A- AT AT AT GT AT AA ACT AT AT AGT TT AT AA AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* * *
711581 AT TT AT AT -T A- AT AT AGT AT AT AT AT GT AT GT AT A- ACT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
711621 AT AT GT -T AT TT AT AG AT -T 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
* * * * * *
711661 AT AA AT AT AT AG AT -T AT AT AT AA AGT TT AT AC AT AT AT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT
* * * * ** * *
711704 AT AG AA AC ACC AT GC AT AA ACT AT AT AT AT A- AT AT AA AT -T AT
1 AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * *
711746 AT AT AT TT AT -T AT AA ACT AT AT AT AT AA ACT AT AT GGT -T AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT -AT AT AT
* * *
711787 -T AT A- AT AT AT AT AT -T AT AA ACT AT AT AT GT AT AA ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT
* * * * * *
711828 AT A- AT CT AT AT AT AT A- AG CT AC AT AT GT AT AA AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
711867 AT GT A- AT CT AT AT AGT TT AT AT AA ACT AT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT
* * * *
711909 AT AA AT CAT AT AGT TT AT A- AA AT AT A- AT TT AT AT AT AT AT AT
1 AT AT AT -AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
711951 GT AT AT AT AT AGT -T AT AT AA ACT AT AT AGT -T AGT TT AT AA ACT
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT A-T AT A-T AT AT AT A-T
711994 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
712036 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
712066 GTAACCTATA
Statistics
Matches: 416, Mismatches: 102, Indels: 100
0.67 0.17 0.16
Matches are distributed among these distances:
1 25 0.06
2 363 0.87
3 28 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:711534 original size:17 final size:15
Alignment explanation
Indices: 711514--711911 Score: 85
Period size: 13 Copynumber: 27.4 Consensus size: 15
711504 TATATTTTTA
711514 TATATATGTATATAAAC
1 TATATATG--TATAAAC
711531 TATATATGTATAAAC
1 TATATATGTATAAAC
*
711546 AATATATGTATAAAC
1 TATATATGTATAAAC
* *
711561 TATATAGTTTATAAAT
1 TATATA-TGTATAAAC
* *
711577 TATA-AT-T-TATAT
1 TATATATGTATAAAC
*
711589 TA-ATATAGTATATA-
1 TATATAT-GTATAAAC
*
711603 TATGTATGTAT-AAC
1 TATATATGTATAAAC
*
711617 TAATATATGTTATTTATAGAT
1 T-ATATATG-TA--TA-A-AC
* *
711638 TATATATATATATA-
1 TATATATGTATAAAC
*
711652 TATATATATATAAA-
1 TATATATGTATAAAC
*
711666 TATATA-G-AT-TA-
1 TATATATGTATAAAC
* * *
711677 TATATAAAGTTTATAC
1 TATAT-ATGTATAAAC
*
711693 ATATATAGTTTATAGAAAC
1 -TATATA-TGTAT--AAAC
** *
711712 -A-CCATGCATAAAC
1 TATATATGTATAAAC
711725 TATATA--TAT-AA-
1 TATATATGTATAAAC
* *
711736 TATAAAT-TATATA-
1 TATATATGTATAAAC
*
711749 TATTTAT-TATAAAC
1 TATATATGTATAAAC
711763 TATATA--TATAAAC
1 TATATATGTATAAAC
711776 TATATGGTTAT-TATAATA-
1 TATA----TATGTATAA-AC
711794 TATATAT-TATAAAC
1 TATATATGTATAAAC
711808 TATATATGTATAAAC
1 TATATATGTATAAAC
*
711823 --TATA--TATAATC
1 TATATATGTATAAAC
*
711834 TATATA--TATAAGC
1 TATATATGTATAAAC
* *
711847 TACATATGTATAAAT
1 TATATATGTATAAAC
*
711862 TATATATG--TAATC
1 TATATATGTATAAAC
*
711875 TATATAGTTTATATAAAC
1 TATATA---TGTATAAAC
711893 TATATA--TATAAAC
1 TATATATGTATAAAC
711906 TATATA
1 TATATA
711912 AATCATATAG
Statistics
Matches: 294, Mismatches: 42, Indels: 94
0.68 0.10 0.22
Matches are distributed among these distances:
11 18 0.06
12 16 0.05
13 73 0.25
14 50 0.17
15 66 0.22
16 16 0.05
17 20 0.07
18 20 0.07
19 6 0.02
20 7 0.02
21 2 0.01
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (15 bp):
TATATATGTATAAAC
Found at i:711592 original size:95 final size:89
Alignment explanation
Indices: 711429--711603 Score: 251
Period size: 95 Copynumber: 1.9 Consensus size: 89
711419 ATATATAAAC
* * *
711429 TATGTATATAAACTATATACGTATAAACTATAAAAAGTATATAGTTTATAAACTATAGTTTGTAT
1 TATGTATATAAACTATATACGTATAAACTATAAAAACTATATAGTTTATAAACTATAATTTATAT
711494 TAATATAGTATATATTTTTATATA
66 TAATATAGTATATATTTTTATATA
* *
711518 TATGTATATAAACTATATATGTATAAACAATATATGTATAAACTATATAGTTTATAAATTATAAT
1 TATGTATATAAACTATATACGTATAAAC--TATA---A-AAACTATATAGTTTATAAACTATAAT
711583 TTATATTAATATAGTATATAT
60 TTATATTAATATAGTATATAT
711604 ATGTATGTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
89 27 0.36
91 4 0.05
94 1 0.01
95 43 0.57
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (89 bp):
TATGTATATAAACTATATACGTATAAACTATAAAAACTATATAGTTTATAAACTATAATTTATAT
TAATATAGTATATATTTTTATATA
Found at i:711806 original size:45 final size:45
Alignment explanation
Indices: 711741--711827 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
711731 TATAATATAA
*
711741 ATTATATATATTTATTATAAACTATATA-TATAAACTATATGGTT
1 ATTATATATATATATTATAAACTATATAGTATAAACTATATGGTT
711785 ATTATAATATATATATTATAAACTATATATGTATAAACTATAT
1 ATTAT-ATATATATATTATAAACTATATA-GTATAAACTATAT
711828 ATAATCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 5 0.13
45 22 0.56
47 12 0.31
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (45 bp):
ATTATATATATATATTATAAACTATATAGTATAAACTATATGGTT
Found at i:712097 original size:54 final size:53
Alignment explanation
Indices: 711993--712173 Score: 173
Period size: 54 Copynumber: 3.5 Consensus size: 53
711983 GTTTATAAAC
* * *
711993 TATATATAT-ATATATATATA-TATATATAT-A--TATA-TATATATATATA-
1 TATATATATAATATATATAAACTATATATATAACCTATAGTATATAAAAATAG
* * *
712039 TATATATAT-ATATATATATA-TATATATGTAACCTATAGTTTATAAAGAATAG
1 TATATATATAATATATATAAACTATATATATAACCTATAGTATATAAA-AATAG
* * * *
712091 TTTATATATAATTTATATAAACTATATAAATAACCTATAGTCTATAAACAATAG
1 TATATATATAATATATATAAACTATATATATAACCTATAGTATATAAA-AATAG
* *
712145 TAGATATATAATTTATATAAACTATATAT
1 TATATATATAATATATATAAACTATATAT
712174 GTATAGACAC
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
46 28 0.25
47 1 0.01
49 4 0.04
50 6 0.05
51 3 0.03
52 8 0.07
53 9 0.08
54 54 0.48
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (53 bp):
TATATATATAATATATATAAACTATATATATAACCTATAGTATATAAAAATAG
Found at i:712305 original size:20 final size:20
Alignment explanation
Indices: 712288--712326 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
712278 ACATGTATGT
*
712288 ATAAACTATGTATAGTATAA
1 ATAAACTATATATAGTATAA
712308 ATAAACTATATATA-TATAA
1 ATAAACTATATATAGTATAA
712327 CGTATAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
ATAAACTATATATAGTATAA
Found at i:712373 original size:13 final size:13
Alignment explanation
Indices: 712303--712394 Score: 55
Period size: 13 Copynumber: 6.8 Consensus size: 13
712293 CTATGTATAG
*
712303 TATAAATAAACTA
1 TATATATAAACTA
712316 TATATATATAACGTA
1 TATATATA-AAC-TA
*
712331 TAGTATAT---GTA
1 TA-TATATAAACTA
* *
712342 TATATACAATCTA
1 TATATATAAACTA
712355 TTTATATATAAACTA
1 --TATATATAAACTA
*
712370 TATATGTAAACTA
1 TATATATAAACTA
*
712383 TAGTTTATAAAC
1 TA-TATATAAAC
712395 AATGATTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
10 4 0.07
11 4 0.07
13 23 0.38
14 10 0.16
15 15 0.25
16 5 0.08
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:712440 original size:21 final size:21
Alignment explanation
Indices: 712415--712462 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
712405 ATTAGTGTAC
*
712415 TATATAGTTTAT-AACATATAG
1 TATATAATTTATAAAC-TATAG
712436 TATATAATTTATAAACTATAG
1 TATATAATTTATAAACTATAG
*
712457 TTTATA
1 TATATA
712463 TTAGTGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:712556 original size:36 final size:36
Alignment explanation
Indices: 712502--712593 Score: 130
Period size: 36 Copynumber: 2.6 Consensus size: 36
712492 TAATTATCTT
*
712502 AACTATAATTTATGTTAATAAAGTATATAGTTTATA
1 AACTATAATTTATATTAATAAAGTATATAGTTTATA
* **
712538 AACTATAATTTGTATTAATGTAGTATATAGTTTATA
1 AACTATAATTTATATTAATAAAGTATATAGTTTATA
* *
712574 AACTATAGTTTACATTAATA
1 AACTATAATTTATATTAATA
712594 TTAACTATAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (36 bp):
AACTATAATTTATATTAATAAAGTATATAGTTTATA
Found at i:712603 original size:36 final size:35
Alignment explanation
Indices: 712502--712609 Score: 101
Period size: 36 Copynumber: 3.0 Consensus size: 35
712492 TAATTATCTT
** **
712502 AACTATAATTTATGTTAATAAAGTATATAGTTTATA
1 AACTATAATTTACATTAATGTAG-ATATAGTTTATA
**
712538 AACTATAATTTGTATTAATGTAGTATATAGTTTATA
1 AACTATAATTTACATTAATGTAG-ATATAGTTTATA
* *
712574 AACTATAGTTTACATTAATATTA-ACTATAGTTTATA
1 AACTATAATTTACATTAAT-GTAGA-TATAGTTTATA
712610 TTAATATAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.02
36 59 0.95
37 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (35 bp):
AACTATAATTTACATTAATGTAGATATAGTTTATA
Found at i:712624 original size:22 final size:22
Alignment explanation
Indices: 712574--712656 Score: 80
Period size: 22 Copynumber: 3.6 Consensus size: 22
712564 ATAGTTTATA
*
712574 AACTATAGTTTACATTAATATT
1 AACTATAGTTTATATTAATATT
712596 AACTATAGTTTATATTAATA-T
1 AACTATAGTTTATATTAATATT
712617 AGTA-TATAGTATATAGTATTAATATT
1 A--ACTATAGT-T-TA-TATTAATATT
* *
712643 AATTATAGTCTATA
1 AACTATAGTTTATA
712657 AACCATATAC
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.04
22 27 0.52
23 4 0.08
24 3 0.06
25 14 0.27
26 2 0.04
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (22 bp):
AACTATAGTTTATATTAATATT
Found at i:712745 original size:6 final size:6
Alignment explanation
Indices: 712734--712867 Score: 75
Period size: 6 Copynumber: 22.2 Consensus size: 6
712724 AATATAGTTT
* * * **
712734 ATATTA ATATTA ATTTTA TAGATT- ATATTTT ATATTA ATATTA ATTACAA
1 ATATTA ATATTA ATATTA -ATATTA ATA-TTA ATATTA ATATTA A-TATTA
* * *
712784 ATTATAA ACTATATT ATATTA ATA-TA A-GTTA ATATTA ATATTA ATATTA
1 A-TATTA A-TAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
712833 AT-TATA ATATATA AT-TT- ATATTA ATATTA AT-TTA A
1 ATAT-TA ATAT-TA ATATTA ATATTA ATATTA ATATTA A
712868 ATGATAGTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
4 2 0.02
5 16 0.16
6 56 0.54
7 28 0.27
8 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:712753 original size:24 final size:25
Alignment explanation
Indices: 712726--712772 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
712716 ATTTATAAAA
*
712726 TATAGTTTATA-TTAATATTAATTT
1 TATAGATTATATTTAATATTAATTT
*
712750 TATAGATTATATTTTATATTAAT
1 TATAGATTATATTTAATATTAAT
712773 ATTAATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TATAGATTATATTTAATATTAATTT
Found at i:712766 original size:31 final size:30
Alignment explanation
Indices: 712714--712866 Score: 149
Period size: 29 Copynumber: 5.2 Consensus size: 30
712704 CTATACTATA
* *
712714 TAATTTATAAAATATAGTTTATATTAATAT
1 TAATTTATAAATTATAATTTATATTAATAT
* *
712744 TAATTTTATAGATTATATTTTATATTAATAT
1 TAA-TTTATAAATTATAATTTATATTAATAT
* **
712775 TAA-TTACAAATTATAAACTATATT-ATAT
1 TAATTTATAAATTATAATTTATATTAATAT
* *
712803 TAA--TATAAGTTA-ATATTAATATTAATAT
1 TAATTTATAAATTATA-ATTTATATTAATAT
712831 TAA-TTAT-AATATATAATTTATATTAATAT
1 TAATTTATAAAT-TATAATTTATATTAATAT
712860 TAATTTA
1 TAATTTA
712867 AATGATAGTT
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
26 1 0.01
27 13 0.13
28 16 0.16
29 37 0.37
30 7 0.07
31 27 0.27
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (30 bp):
TAATTTATAAATTATAATTTATATTAATAT
Found at i:723521 original size:6 final size:6
Alignment explanation
Indices: 723510--723597 Score: 79
Period size: 6 Copynumber: 14.7 Consensus size: 6
723500 ACAGTAACCT
* * * *
723510 AACCCA AACCCA AACTCG AACCCG AACCCG AACCCG AACCCA AACCCG
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
* * * * *
723558 AACCCG AACAC- AAACCA ATACTCG AACCCG AACCCA AACC
1 AACCCG AACCCG AACCCG A-ACCCG AACCCG AACCCG AACC
723598 TAAATCTGAG
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
5 3 0.04
6 61 0.91
7 3 0.04
ACGTcount: A:0.42, C:0.45, G:0.09, T:0.03
Consensus pattern (6 bp):
AACCCG
Found at i:723537 original size:18 final size:18
Alignment explanation
Indices: 723510--723597 Score: 97
Period size: 18 Copynumber: 4.9 Consensus size: 18
723500 ACAGTAACCT
*
723510 AACCCAAACCCAAACTCG
1 AACCCAAACCCAAACCCG
* *
723528 AACCCGAACCCGAACCCG
1 AACCCAAACCCAAACCCG
*
723546 AACCCAAACCCGAACCCG
1 AACCCAAACCCAAACCCG
* *
723564 AACACAAA-CCAATACTCG
1 AACCCAAACCCAA-ACCCG
*
723582 AACCCGAACCCAAACC
1 AACCCAAACCCAAACC
723598 TAAATCTGAG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
17 3 0.05
18 51 0.88
19 4 0.07
ACGTcount: A:0.42, C:0.45, G:0.09, T:0.03
Consensus pattern (18 bp):
AACCCAAACCCAAACCCG
Found at i:723537 original size:24 final size:24
Alignment explanation
Indices: 723511--723597 Score: 104
Period size: 24 Copynumber: 3.6 Consensus size: 24
723501 CAGTAACCTA
* * *
723511 ACCCAAACCCAAACTCGAACCCGA
1 ACCCGAACCCAAACCCAAACCCGA
*
723535 ACCCGAACCCGAACCCAAACCCGA
1 ACCCGAACCCAAACCCAAACCCGA
* *
723559 ACCCGAACACAAA-CCAATACTCGA
1 ACCCGAACCCAAACCCAA-ACCCGA
723583 ACCCGAACCCAAACC
1 ACCCGAACCCAAACC
723598 TAAATCTGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 4 0.08
24 48 0.91
25 1 0.02
ACGTcount: A:0.41, C:0.46, G:0.09, T:0.03
Consensus pattern (24 bp):
ACCCGAACCCAAACCCAAACCCGA
Done.