Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_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: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3465247 original size:20 final size:20
Alignment explanation
Indices: 3465222--3465313 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
3465212 TTGAAGATGA
3465222 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
3465242 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
3465262 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
3465283 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
3465303 TTGCGATTTTC
1 TTGCGATTTTC
3465314 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:3465342 original size:20 final size:21
Alignment explanation
Indices: 3465298--3465349 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3465288 ATAGTCAGTA
*
3465298 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
3465319 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
3465339 TCGCATTGCGA
1 TCGCATTGCGA
3465350 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:3465565 original size:12 final size:12
Alignment explanation
Indices: 3465546--3465579 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3465536 CTCTCCGGTG
3465546 ACATCCGTTCCT
1 ACATCCGTTCCT
*
3465558 ATATCCGTTCCT
1 ACATCCGTTCCT
3465570 ACATCC-TTCC
1 ACATCCGTTCC
3465580 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:3466184 original size:24 final size:24
Alignment explanation
Indices: 3466133--3466186 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3466123 GTATTCGAAA
* * *
3466133 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGCCAATACCCAGAC
* *
3466157 TTTGATATTGGCCAATACTCAGAT
1 TTTGATATTGGCCAATACCCAGAC
3466181 TTTGAT
1 TTTGAT
3466187 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGCCAATACCCAGAC
Found at i:3468693 original size:19 final size:19
Alignment explanation
Indices: 3468671--3468801 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
3468661 GAAAATTACT
3468671 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3468690 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3468704 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3468723 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
3468737 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
3468756 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
3468770 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3468789 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3468802 TTTAATTTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 28 0.33
15 5 0.06
16 4 0.05
17 4 0.05
18 5 0.06
19 40 0.47
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3468713 original size:33 final size:33
Alignment explanation
Indices: 3468671--3468797 Score: 211
Period size: 33 Copynumber: 3.8 Consensus size: 33
3468661 GAAAATTACT
3468671 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3468704 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3468736 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3468770 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3468798 CGAATTTAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
32 1 0.01
33 85 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3468778 original size:66 final size:66
Alignment explanation
Indices: 3468672--3468804 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
3468662 AAAATTACTA
3468672 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
3468737 T
66 T
*
3468738 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
3468803 T
66 T
3468804 T
1 T
3468805 AATTTCGCGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:3468850 original size:19 final size:19
Alignment explanation
Indices: 3468826--3468886 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
3468816 GCGAATCTCT
3468826 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3468845 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
3468859 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3468878 CATTGCGAT
1 CGTTGCGAT
3468887 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3468864 original size:14 final size:14
Alignment explanation
Indices: 3468812--3468868 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3468802 TTTAATTTCG
*
3468812 CGTTGCGAATCTCT
1 CGTTGCGATTCTCT
*
3468826 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3468845 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3468859 CGTTGCGATT
1 CGTTGCGATT
3468869 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3468886 original size:33 final size:33
Alignment explanation
Indices: 3468797--3468886 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
3468787 AAATCGCAAC
* * *
3468797 GCGAATTTAATTTCGCGTTGCGAATCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
3468830 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
3468863 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
3468887 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.42
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:3469012 original size:14 final size:15
Alignment explanation
Indices: 3468993--3469029 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
3468983 CATCAATTAA
3468993 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
3469007 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
3469021 ACAAATCAA
1 ACAAATCAA
3469030 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:3470451 original size:21 final size:21
Alignment explanation
Indices: 3470385--3470451 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3470375 GTGAATCGGG
*
3470385 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3470405 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3470427 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3470448 CTCT
1 CTCT
3470452 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3470470 original size:42 final size:41
Alignment explanation
Indices: 3470385--3470507 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
3470375 GTGAATCGGG
* * * *
3470385 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
3470427 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
3470469 CTCTTTAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
3470508 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:3470903 original size:91 final size:90
Alignment explanation
Indices: 3470725--3470906 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 90
3470715 ATTTCAAACT
*
3470725 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTGAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
3470790 AGAATTGGCAGCAACCGAATAAATTTGC
63 AGAATTGGCAGCAACCGAATAAATTTGC
* *
3470818 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAATAGTTTAGTA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
3470882 GTATTGGCAGCAACCGAATAAATTT
64 GAATTGGCAGCAACCGAATAAATTT
3470907 ACTAAGCAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
91 37 0.45
93 19 0.23
95 27 0.33
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTGC
Found at i:3472664 original size:33 final size:33
Alignment explanation
Indices: 3472607--3472705 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
3472597 ACGAGATAAT
3472607 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
3472641 GAGAATCGCAACGCGAAATGACTATCGTAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
3472674 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
3472706 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:3472715 original size:19 final size:19
Alignment explanation
Indices: 3472582--3472727 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
3472572 TCTTTTGGTT
*
3472582 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3472601 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3472621 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
3472639 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
3472655 GAAATGACTATCGTAA--C
1 GAAATGAAAATCGCAACGC
*
3472672 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3472688 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3472707 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3472726 GA
1 GA
3472728 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 43 0.43
20 27 0.27
21 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3473345 original size:20 final size:20
Alignment explanation
Indices: 3473304--3473375 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3473294 GCTATGTAAA
* *
3473304 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
3473324 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
3473344 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
3473365 TCGCATTGCGA
1 TCGCATTGCGA
3473376 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.07
20 29 0.66
21 12 0.27
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:3473389 original size:21 final size:21
Alignment explanation
Indices: 3473365--3473437 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
3473355 TTTTCCTAAT
*
3473365 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTATGAAAA
* * *
3473386 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTATGAAAA
3473406 TCGCAATGCGAATT-TGGAAAA
1 TCGCAATGCGAATTAT-GAAAA
* *
3473427 TTGCATTGCGA
1 TCGCAATGCGA
3473438 TAGTCAGTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAATTATGAAAA
Found at i:3473477 original size:103 final size:103
Alignment explanation
Indices: 3473352--3473546 Score: 250
Period size: 103 Copynumber: 1.9 Consensus size: 103
3473342 ATTCGCGTTG
* * *
3473352 CGATTTTCCTAATTCGCATTGCGAATTA-TGAAAATCGCAACGCGAA-TACGTAAATCGCAATGC
1 CGATTTTCCAAATTCGCATTGCGAATTACT--AAATCGCAACGCGAATTACGAAAATCGCAACGC
* *
3473415 GAATTTGGAAAATTGCATTGCGATAGTCAGTATCGCATTA
64 GAAATTGGAAAATCGCATTGCGATAGTCAGTATCGCATTA
* * * ** **
3473455 CGATTTTCCAAATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAAAATCGCAACGCGA
1 CGATTTTCCAAATTCGCATTGCGAATTACTAAATCGCAACGCGAATTACGAAAATCGCAACGCGA
3473520 AATTGGAAAATCGCATTGCGATAGTCA
66 AATTGGAAAATCGCATTGCGATAGTCA
3473547 TAATCGCGTT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
102 11 0.14
103 66 0.85
104 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (103 bp):
CGATTTTCCAAATTCGCATTGCGAATTACTAAATCGCAACGCGAATTACGAAAATCGCAACGCGA
AATTGGAAAATCGCATTGCGATAGTCAGTATCGCATTA
Found at i:3473513 original size:41 final size:40
Alignment explanation
Indices: 3473360--3473513 Score: 114
Period size: 41 Copynumber: 3.8 Consensus size: 40
3473350 TGCGATTTTC
** *
3473360 CTAATTCGCATTGCGAATTAT-GAAAATCGCAACGCGAATA
1 CTAATTCGCATTGCGAATT-TGGAAAATCGCATTGCGATTA
* * *
3473400 CGTAAATCGCAATGCGAATTTGGAAAATTGCATTGCGA-TA
1 C-TAATTCGCATTGCGAATTTGGAAAATCGCATTGCGATTA
* * * * ** *
3473440 GTCAGTATCGCATTACGATTTTCCAAATTCGCATTGCGATTTA
1 CT-AAT-TCGCATTGCGAATTTGGAAAATCGCATTGCGA-TTA
* *
3473483 CTTATTCGCATTGCGAATTGGGAAAATCGCA
1 CTAATTCGCATTGCGAATTTGGAAAATCGCA
3473514 ACGCGAAATT
Statistics
Matches: 84, Mismatches: 24, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
39 1 0.01
40 5 0.06
41 74 0.88
42 1 0.01
43 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (40 bp):
CTAATTCGCATTGCGAATTTGGAAAATCGCATTGCGATTA
Found at i:3473540 original size:21 final size:22
Alignment explanation
Indices: 3473488--3473540 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3473478 ATTTACTTAT
3473488 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
3473509 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
3473530 TCGCATTGCGA
1 TCGCATTGCGA
3473541 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:3474674 original size:20 final size:20
Alignment explanation
Indices: 3474649--3474704 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
3474639 CTTATTCCTG
3474649 GGTAATCTTACATTCCCACT
1 GGTAATCTTACATTCCCACT
*
3474669 GGTAATCTTACATTCCTACT
1 GGTAATCTTACATTCCCACT
3474689 GGTAATCTTACATTCC
1 GGTAATCTTACATTCC
3474705 GTAAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.38
Consensus pattern (20 bp):
GGTAATCTTACATTCCCACT
Found at i:3478670 original size:18 final size:18
Alignment explanation
Indices: 3478647--3478716 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
3478637 TTCAGTATTC
*
3478647 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
3478665 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
3478687 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
*
3478705 ATCCCGAAGGAC
1 GTCCCGAAGGAC
3478717 TACTCCTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 27 0.61
22 17 0.39
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:3479811 original size:25 final size:25
Alignment explanation
Indices: 3479764--3479812 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3479754 TTACTTATGT
*
3479764 CTTATATCACATATTTATATTAAAA
1 CTTATATCACATATCTATATTAAAA
3479789 CTTATATCACATATACTAT-TTAAA
1 CTTATATCACATAT-CTATATTAAA
3479813 CCAGTTCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (25 bp):
CTTATATCACATATCTATATTAAAA
Found at i:3480292 original size:19 final size:19
Alignment explanation
Indices: 3480268--3480318 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
3480258 TATTATAGAG
3480268 ATGCATCGATGCATGACTT
1 ATGCATCGATGCATGACTT
3480287 ATGCATCGATGCATGACTT
1 ATGCATCGATGCATGACTT
3480306 ATGCATCGATGCA
1 ATGCATCGATGCA
3480319 CTAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCATGACTT
Found at i:3480356 original size:83 final size:83
Alignment explanation
Indices: 3480203--3480379 Score: 227
Period size: 83 Copynumber: 2.1 Consensus size: 83
3480193 TTAATGAAGG
* *
3480203 TATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTTATTATTATAGAG
1 TATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
*
3480268 ATGCATCGATGCATGACT
66 ATGCATCGATGCATGACC
* *
3480286 TATGCATCGATGCA-TGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA
1 TATGCATCGATGCACT-ACTGATGCATCGATGCA-TAAAATGCATTCGATGTTT-TATTATTAAA
*
3480348 -AGAGTGCATCGATGCATTACC
63 GAGA-TGCATCGATGCATGACC
*
3480369 AATGCATCGAT
1 TATGCATCGAT
3480380 ACACCTTCAA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
82 4 0.05
83 74 0.89
84 5 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (83 bp):
TATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
ATGCATCGATGCATGACC
Found at i:3483654 original size:22 final size:18
Alignment explanation
Indices: 3483611--3483680 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
3483601 TTCAGTATTC
*
3483611 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
3483629 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
3483651 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
3483669 GTCCCGAAGGAC
1 GTCCCGAAGGAC
3483681 TACTCCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 28 0.62
22 17 0.38
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:3485303 original size:64 final size:62
Alignment explanation
Indices: 3485195--3485351 Score: 156
Period size: 64 Copynumber: 2.5 Consensus size: 62
3485185 TAATGAAGGT
* * * * **
3485195 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGAATTCGATGTTTCTATT-TTA-AAAG
* *
3485259 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGAATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGAATTCGATGTTTCTATTTTAAAAG
*
3485322 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
3485352 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 4 0.05
64 67 0.85
65 8 0.10
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGAATTCGATGTTTCTATTTTAAAAG
Found at i:3487880 original size:3 final size:3
Alignment explanation
Indices: 3487872--3487896 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3487862 TTACCCGACC
3487872 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
3487897 CTACTACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3491077 original size:15 final size:17
Alignment explanation
Indices: 3491048--3491080 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3491038 TAAGTATATT
3491048 TTATCTTAATATAAAAA
1 TTATCTTAATATAAAAA
3491065 TTAT-TTAAT-TAAAAA
1 TTATCTTAATATAAAAA
3491080 T
1 T
3491081 AGAGGGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATCTTAATATAAAAA
Found at i:3491822 original size:8 final size:8
Alignment explanation
Indices: 3491809--3491835 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3491799 TTCGAGTCGA
3491809 TTTGAAAT
1 TTTGAAAT
3491817 TTTGAAAT
1 TTTGAAAT
3491825 TTTGAAAT
1 TTTGAAAT
3491833 TTT
1 TTT
3491836 CAGTTATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (8 bp):
TTTGAAAT
Found at i:3492364 original size:20 final size:21
Alignment explanation
Indices: 3492325--3492374 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3492315 TTCTTTAAAA
3492325 TATAATATTATAAATATATTT
1 TATAATATTATAAATATATTT
3492346 TATAAT-TTA-AAATTATATTT
1 TATAATATTATAAA-TATATTT
*
3492366 AAT-ATATTA
1 TATAATATTA
3492375 AATAATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 15 0.58
21 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATAATATTATAAATATATTT
Found at i:3492445 original size:2 final size:2
Alignment explanation
Indices: 3492398--3492437 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3492388 TATGAAATAA
3492398 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
3492438 CTTATATAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3492546 original size:18 final size:19
Alignment explanation
Indices: 3492510--3492547 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3492500 CACGAAATGT
3492510 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
3492530 AAGATTACCAG-GGAATAA
1 AAGATTACCAGAGGAATAA
3492548 GATTACTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:3492785 original size:21 final size:22
Alignment explanation
Indices: 3492761--3492802 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3492751 ACAAAATTAA
*
3492761 AAAT-ATAAAAAAAGTTTAATG
1 AAATGATAAAAAAAATTTAATG
*
3492782 AAATGGTAAAAAAAATTTAAT
1 AAATGATAAAAAAAATTTAAT
3492803 CCTGAACTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (22 bp):
AAATGATAAAAAAAATTTAATG
Found at i:3493409 original size:20 final size:20
Alignment explanation
Indices: 3493384--3493476 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
3493374 TTTTCCCAAT
3493384 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
3493404 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
3493424 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
3493445 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
3493466 TCGCAATGCGA
1 TCGCAATGCGA
3493477 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:3493426 original size:41 final size:41
Alignment explanation
Indices: 3493381--3493476 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
3493371 CGATTTTCCC
3493381 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
3493422 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
3493463 AAATCGCAATGCGA
1 AATTCGCAATGCGA
3493477 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:3493430 original size:21 final size:20
Alignment explanation
Indices: 3493384--3493476 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
3493374 TTTTCCCAAT
*
3493384 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
3493404 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
3493424 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
3493445 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
3493466 TCGCAATGCGA
1 TCGCAATGCGA
3493477 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:3493489 original size:41 final size:41
Alignment explanation
Indices: 3493403--3493537 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
3493393 GAATAAGTAA
* * *
3493403 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
3493444 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
3493485 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
3493526 TTCGCAACGCGA
1 ATCGCAACGCGA
3493538 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:3493490 original size:20 final size:20
Alignment explanation
Indices: 3493465--3493558 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
3493455 AATTGGGAAA
*
3493465 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
3493485 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
3493506 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3493526 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3493546 TTCGCAACGCGAT
1 ATCGCAACGCGAT
3493559 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3494117 original size:19 final size:19
Alignment explanation
Indices: 3494078--3494144 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
3494068 TTCGAGAATG
*
3494078 AAAATCGCAAAGCGTAAATA
1 AAAATCGCAACGCG-AAATA
**
3494098 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
3494117 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
3494136 AAAATCGCA
1 AAAATCGCA
3494145 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.49, C:0.24, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:3494162 original size:19 final size:19
Alignment explanation
Indices: 3494140--3494209 Score: 131
Period size: 19 Copynumber: 3.7 Consensus size: 19
3494130 GAAACCAAAA
*
3494140 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3494159 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3494178 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3494197 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3494210 CTCGTCGCGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3494227 original size:31 final size:31
Alignment explanation
Indices: 3494192--3494277 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 31
3494182 GTTGCGATTT
3494192 TCATTTCGCGTTGCGATTCTCGTC-GCGATAG
1 TCATTTCGCGTTGCGATTCTC-TCTGCGATAG
3494223 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTC--TGCGATAG
*
3494256 TCATTTCCGCGTTGCAATTCTC
1 TCATTT-CGCGTTGCGATTCTC
3494278 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
30 2 0.04
31 21 0.42
33 13 0.26
34 14 0.28
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (31 bp):
TCATTTCGCGTTGCGATTCTCTCTGCGATAG
Found at i:3494279 original size:20 final size:20
Alignment explanation
Indices: 3494256--3494302 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3494246 ATTGCGATAG
3494256 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
3494276 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
3494296 TCATTTC
1 TCATTTC
3494303 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:3496374 original size:42 final size:42
Alignment explanation
Indices: 3496328--3496416 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
3496318 CCTATCGTTG
* *
3496328 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCCTTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
3496370 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
3496412 AAGAG
1 AAGAG
3496417 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:3496415 original size:21 final size:20
Alignment explanation
Indices: 3496356--3496416 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
3496346 CTCGAGAGTC
*
3496356 CCCTCCCACCCTTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
** * * *
3496376 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCATTCAAGAGG
3496397 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTCAAGAG
3496417 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:3497789 original size:14 final size:14
Alignment explanation
Indices: 3497770--3497805 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3497760 ATTGTTTAAT
3497770 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3497784 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3497798 TGATTTGT
1 TGATTTGT
3497806 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3497936 original size:19 final size:19
Alignment explanation
Indices: 3497912--3497978 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
3497902 AAAAAGTACT
*
3497912 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
3497931 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
3497945 ATCGCAACGCGAAAATG-AA
1 ATCGCAACGCG-AAATGAAA
3497964 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
3497979 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 4 0.10
19 20 0.50
20 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:3498005 original size:19 final size:19
Alignment explanation
Indices: 3497983--3498100 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
3497973 CGAAATTAAA
3497983 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3498002 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
3498017 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3498035 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
3498050 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
3498068 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
3498087 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
3498101 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:3498029 original size:33 final size:33
Alignment explanation
Indices: 3497987--3498080 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
3497977 ATTAAATTCG
3497987 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
3498020 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
3498053 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3498081 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:3501885 original size:14 final size:14
Alignment explanation
Indices: 3501866--3501902 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3501856 CATCAATTAA
3501866 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3501880 ACAAATCATCTTTT
1 ACAAATCAACATTT
3501894 ACAAATCAA
1 ACAAATCAA
3501903 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3503806 original size:20 final size:19
Alignment explanation
Indices: 3503771--3503837 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
3503761 GAAACTTAAA
3503771 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3503790 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
3503810 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3503829 ATCGCAACG
1 ATCGCAACG
3503838 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3503845 original size:14 final size:14
Alignment explanation
Indices: 3503826--3503915 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
3503816 ATGCGAAATG
3503826 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3503840 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3503856 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
3503872 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3503888 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3503904 AAAATCGCAACG
1 AAAATCGCAACG
3503916 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.48, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3503929 original size:18 final size:17
Alignment explanation
Indices: 3503841--3503930 Score: 75
Period size: 18 Copynumber: 5.5 Consensus size: 17
3503831 CGCAACGACA
*
3503841 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAA-C
*
3503859 AAATCGCAA--CGACA-
1 AAATCGCAACGCGAAAC
*
3503873 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAA-C
*
3503891 AAATCGCAA--CGACA-
1 AAATCGCAACGCGAAAC
3503905 AAATCGCAACGCGAAAC
1 AAATCGCAACGCGAAAC
3503922 ACAATCGCA
1 A-AATCGCA
3503931 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
14 18 0.30
16 16 0.27
17 1 0.02
18 25 0.42
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (17 bp):
AAATCGCAACGCGAAAC
Found at i:3503930 original size:32 final size:32
Alignment explanation
Indices: 3503810--3503920 Score: 204
Period size: 32 Copynumber: 3.4 Consensus size: 32
3503800 GGAAATGGCT
*
3503810 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
3503843 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3503875 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3503907 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3503921 CACAATCGCA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 62 0.81
33 15 0.19
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:3503953 original size:19 final size:19
Alignment explanation
Indices: 3503926--3504060 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
3503916 CGAAACACAA
*
3503926 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3503945 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
3503961 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
3503977 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
3503993 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
3504010 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
3504029 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATTTTCA-TT
*
3504050 TCGTGTTGCGA
1 TCGCGTTGCGA
3504061 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 19 0.20
15 3 0.03
16 6 0.06
17 2 0.02
18 14 0.15
19 23 0.25
20 23 0.25
21 3 0.03
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3503967 original size:14 final size:14
Alignment explanation
Indices: 3503948--3504005 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3503938 TTTCATTTCG
3503948 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3503962 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3503978 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
3503994 CGTTGCGATTTT
1 CGTTGCGATTTT
3504006 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3504012 original size:33 final size:33
Alignment explanation
Indices: 3503931--3504021 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3503921 CACAATCGCA
3503931 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
3503964 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
3503996 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
3504022 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:3504040 original size:20 final size:19
Alignment explanation
Indices: 3504006--3504060 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3503996 TTGCGATTTT
*
3504006 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3504025 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3504045 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
3504061 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3504559 original size:18 final size:18
Alignment explanation
Indices: 3504533--3504577 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3504523 GTCGATCAGA
*
3504533 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
3504551 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
3504569 TGATGGCTC
1 TGATGGCTC
3504578 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:3505921 original size:20 final size:20
Alignment explanation
Indices: 3505896--3505933 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3505886 AATAGTTTCT
3505896 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
3505916 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
3505934 GAAAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3506439 original size:21 final size:22
Alignment explanation
Indices: 3506409--3506504 Score: 69
Period size: 20 Copynumber: 4.6 Consensus size: 22
3506399 CGCTTTGAAA
*
3506409 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGATTATGTAAGT
* *
3506430 ATCGCGTTGCGA--AAGTAAGT
1 ATCGCATTGCGATTATGTAAGT
* * * * *
3506450 ATCTCGTTGCGATT-TTTTATT
1 ATCGCATTGCGATTATGTAAGT
*
3506471 ATCGCATTGCGA-TA-GTCAGT
1 ATCGCATTGCGATTATGTAAGT
3506491 ATCGCATTGCGATT
1 ATCGCATTGCGATT
3506505 TTCTCAATTC
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
19 3 0.05
20 29 0.51
21 25 0.44
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (22 bp):
ATCGCATTGCGATTATGTAAGT
Found at i:3506524 original size:41 final size:42
Alignment explanation
Indices: 3506409--3506565 Score: 135
Period size: 41 Copynumber: 3.8 Consensus size: 42
3506399 CGCTTTGAAA
* * * *
3506409 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCTCAATATCGCGTTGCGATAGTAAGT
* * * * * *
3506450 ATCTCGTTGCGATTTT-TTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCTCAATATCGCGTTGCGATAGTAAGT
* **
3506491 ATCGCATTGCGATTTTCTCAAT-TCGCGTTGCGAT-TTACTT
1 ATCGCATTGCGATTTTCTCAATATCGCGTTGCGATAGTAAGT
* *
3506531 ATTCGCATTGCGAATTTCCCAAT-TCGCGTTGCGAT
1 A-TCGCATTGCGATTTTCTCAATATCGCGTTGCGAT
3506566 TTACTTATTC
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
40 4 0.04
41 89 0.93
42 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (42 bp):
ATCGCATTGCGATTTTCTCAATATCGCGTTGCGATAGTAAGT
Found at i:3506536 original size:20 final size:20
Alignment explanation
Indices: 3506492--3506581 Score: 99
Period size: 21 Copynumber: 4.4 Consensus size: 20
3506482 ATAGTCAGTA
*
3506492 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
3506513 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
3506533 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
3506554 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
3506574 TCGCATTG
1 TCGCATTG
3506582 TAAATTAGGA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
20 25 0.45
21 31 0.55
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:3506566 original size:41 final size:41
Alignment explanation
Indices: 3506492--3506581 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
3506482 ATAGTCAGTA
* *
3506492 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
3506533 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
3506574 TCGCATTG
1 TCGCATTG
3506582 TAAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:3506929 original size:24 final size:23
Alignment explanation
Indices: 3506886--3506931 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3506876 ACTCATCAAC
*
3506886 AAATTTCGCACCCTGAAATTTTA
1 AAATTTCACACCCTGAAATTTTA
3506909 AAATTTCACATCCCT-ACAATTTT
1 AAATTTCACA-CCCTGA-AATTTT
3506932 TAGTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (23 bp):
AAATTTCACACCCTGAAATTTTA
Found at i:3509078 original size:16 final size:16
Alignment explanation
Indices: 3509053--3509083 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3509043 AACCGAATAA
3509053 ATAAAAGAACAAAAAC
1 ATAAAAGAACAAAAAC
*
3509069 ATAAACGAACAAAAA
1 ATAAAAGAACAAAAA
3509084 AAAAATTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.13, G:0.06, T:0.06
Consensus pattern (16 bp):
ATAAAAGAACAAAAAC
Found at i:3510709 original size:30 final size:30
Alignment explanation
Indices: 3510656--3510731 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
3510646 AGCAGTCCAA
* *
3510656 ACACTTAAATGAATAATAGAATAAAACGTTAA-
1 ACAC-TAAATTAA-AATAAAAT-AAACGTTAAG
*
3510688 ACCCTAAATTAAAATAAAATAAACGTTAAG
1 ACACTAAATTAAAATAAAATAAACGTTAAG
*
3510718 ACATTAAATTAAAA
1 ACACTAAATTAAAA
3510732 CGGATGATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 9 0.24
30 19 0.50
31 7 0.18
32 3 0.08
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.25
Consensus pattern (30 bp):
ACACTAAATTAAAATAAAATAAACGTTAAG
Found at i:3512395 original size:22 final size:22
Alignment explanation
Indices: 3512367--3512416 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
3512357 AATAGAATCA
3512367 TTCAGCGTTGAATGTTGAACCG
1 TTCAGCGTTGAATGTTGAACCG
*
3512389 TTCAGCGTTGAATGTTGAATCG
1 TTCAGCGTTGAATGTTGAACCG
3512411 TTCAGC
1 TTCAGC
3512417 ATTCAGCGCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (22 bp):
TTCAGCGTTGAATGTTGAACCG
Found at i:3514539 original size:17 final size:17
Alignment explanation
Indices: 3514485--3514539 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
3514475 AATTTAAACT
3514485 TTTTATTAA-AATATAATA
1 TTTTATTAATAATA-AA-A
* *
3514503 TCTTATT-ATAATCAATA
1 TTTTATTAATAAT-AAAA
3514520 TTTTATTAATAATAAAA
1 TTTTATTAATAATAAAA
3514537 TTT
1 TTT
3514540 AAACTGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.47
18 15 0.50
19 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTATTAATAATAAAA
Found at i:3514651 original size:5 final size:6
Alignment explanation
Indices: 3514637--3514661 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3514627 TTATTTTCAA
3514637 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
3514662 GAGGTTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:3515305 original size:36 final size:37
Alignment explanation
Indices: 3515265--3515338 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
3515255 ATTAAACCTT
3515265 TTTTAT-ATATTT-AATTTTGTAAA-AAAATTATATAAA
1 TTTTATGA-ATTTAAATTTTGTAAAGAAAA-TATATAAA
*
3515301 TTTTATGAATTTAAATTTTTTAAAGAAAATATATAAA
1 TTTTATGAATTTAAATTTTGTAAAGAAAATATATAAA
3515338 T
1 T
3515339 ATTTCCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 10 0.29
37 20 0.59
38 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTTATGAATTTAAATTTTGTAAAGAAAATATATAAA
Found at i:3515519 original size:20 final size:20
Alignment explanation
Indices: 3515491--3515530 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3515481 AGTAATCTTA
*
3515491 TCCACTGGTAATCTTTTATT
1 TCCACTGGTAATCTTATATT
*
3515511 TCCATTGGTAATCTTATATT
1 TCCACTGGTAATCTTATATT
3515531 CCGTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (20 bp):
TCCACTGGTAATCTTATATT
Found at i:3517080 original size:23 final size:23
Alignment explanation
Indices: 3517006--3517115 Score: 86
Period size: 23 Copynumber: 4.8 Consensus size: 23
3516996 TTTAGTGAAA
*
3517006 TAATATATTATAAAT-TA-T-AT
1 TAATATATTTTAAATATATTAAT
*
3517026 TAAT-TATTATTAAAGTATAGT-AT
1 TAATATATT-TTAAA-TATATTAAT
*
3517049 TATATTATATTTTAAAAATATTAAT
1 TA-A-TATATTTTAAATATATTAAT
* * *
3517074 TAGTATATTTTAAATATCTTTAT
1 TAATATATTTTAAATATATTAAT
*
3517097 TAAAATATTTTAAATATAT
1 TAATATATTTTAAATATAT
3517116 AAATATATTA
Statistics
Matches: 72, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
19 4 0.06
20 8 0.11
21 1 0.01
22 2 0.03
23 38 0.53
24 5 0.07
25 10 0.14
26 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
TAATATATTTTAAATATATTAAT
Found at i:3517138 original size:35 final size:34
Alignment explanation
Indices: 3517095--3517176 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 34
3517085 AAATATCTTT
* *
3517095 ATTAAAATATTTTAAA-TATATAAATATATTATTC
1 ATTAAAATATATAAAATTATAT-AATATATTATTC
* *
3517129 ATTATAAATATATAAAATTATATTATATATTATTA
1 ATTA-AAATATATAAAATTATATAATATATTATTC
*
3517164 AATAAAA-ATATAA
1 ATTAAAATATATAA
3517177 TATCTTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 6 0.15
34 7 0.17
35 23 0.56
36 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (34 bp):
ATTAAAATATATAAAATTATATAATATATTATTC
Found at i:3517150 original size:28 final size:27
Alignment explanation
Indices: 3517101--3517263 Score: 95
Period size: 28 Copynumber: 5.8 Consensus size: 27
3517091 CTTTATTAAA
3517101 ATATT-TTAAATATATAAATATATTAT
1 ATATTATTAAATATATAAATATATTAT
3517127 -TCATTA-TAAATATATAAAATTATATTAT
1 AT-ATTATTAAATATAT-AAA-TATATTAT
*
3517155 ATATTATTAAATA-A-AAATATAATATCTT
1 ATATTATTAAATATATAAATAT-AT-T-AT
* * *
3517183 ATATTATTATAATATAATTGATTATTTTAT
1 ATATTATTA-AATAT-A-TAAATATATTAT
* *
3517213 ATAATATTAAAAATATAATATTATATTATT
1 ATATTATTAAATATATAA-A-TATATTA-T
* *
3517243 ATAAATATT-AATAAATAAATA
1 AT-ATTATTAAATATATAAATA
3517264 AATAATATTT
Statistics
Matches: 107, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
25 4 0.04
26 17 0.16
27 6 0.06
28 26 0.24
29 22 0.21
30 19 0.18
31 8 0.07
32 1 0.01
33 4 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATTATTAAATATATAAATATATTAT
Found at i:3517237 original size:22 final size:23
Alignment explanation
Indices: 3517212--3517255 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3517202 GATTATTTTA
3517212 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
3517234 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
3517256 AATAAATAAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:3520916 original size:9 final size:9
Alignment explanation
Indices: 3520902--3520934 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
3520892 AAAAATAAAC
3520902 AATATTAAT
1 AATATTAAT
3520911 AATATTAAT
1 AATATTAAT
3520920 AATA-TAAT
1 AATATTAAT
3520928 AATATTA
1 AATATTA
3520935 TATCCCGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATATTAAT
Found at i:3521428 original size:35 final size:36
Alignment explanation
Indices: 3521333--3521479 Score: 224
Period size: 36 Copynumber: 4.1 Consensus size: 36
3521323 CAAATGATGC
* *
3521333 TTCAAGAGAAACTGTCTCAAAAGAGATAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
3521369 TTCAAGGGAAACTGTCTCATGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
3521405 TTCAAGA-AAAATGTCTCAAGAGAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
3521440 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
3521477 TTC
1 TTC
3521480 GTGGATGGCT
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 32 0.32
36 59 0.60
37 8 0.08
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:3521429 original size:71 final size:73
Alignment explanation
Indices: 3521333--3521479 Score: 226
Period size: 71 Copynumber: 2.0 Consensus size: 73
3521323 CAAATGATGC
* * * *
3521333 TTCAAGAGAAACTGTCTCAAAAGAGATAAAATTTGTTTCAAGGGAAACTGTCTCATGAGAGACAA
1 TTCAAGAGAAAATGTCTCAAAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
3521398 AA-TTTGT
66 AACTTTGT
* *
3521405 TTCAAGA-AAAATGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 TTCAAGAGAAAATGTCTCAAAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
3521469 AACTTTGT
66 AACTTTGT
3521477 TTC
1 TTC
3521480 GTGGATGGCT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 53 0.78
72 15 0.22
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (73 bp):
TTCAAGAGAAAATGTCTCAAAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
AACTTTGT
Found at i:3522114 original size:292 final size:294
Alignment explanation
Indices: 3521574--3522157 Score: 895
Period size: 292 Copynumber: 2.0 Consensus size: 294
3521564 GGTACGATTC
*
3521574 CCTTCGTCGTGAAGTTGAACCTTGAATTGAATATCATTCGTCGTGAAGTTGAAATCCAAGTTAAG
1 CCTTCATCGTGAAGTTGAACCTTGAATTGAATATCATTCGTCGTGAAGTTGAAATCCAAGTT-AG
* *
3521639 TTGCGTTGTTTCGAGGCCAATATCCTTCGACGTTAAGTTGAAATTGACTCTGAAACTGGAAAGTT
65 TT-CGTTGTTTCGAGGCCAATATCCTTCGACGTGAAGTTAAAATTGACTCTGAAACTGGAAAGTT
3521704 TATTGACAGACACTCCTTCTTCGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAG
129 TATTGACAGACACTCCTTCTTCGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAG
** * * * * * *
3521769 ATGGATGTTGCTTGTGTGTATGATTCCCTTCATCGTGAAGTTGAAATCGTGGATGTGTGGGCACG
194 ATAAATGCTGCTTGTGGGTACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGTATGAGCACG
* * *
3521834 ATATCCTCTGTCGTGGAGTTGGAATCATGGATGGCG
259 ATATCCTCCGTCGTAGAGTTGAAATCATGGATGGCG
** * *
3521870 CCTTCATCGTGAAGTTGGGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTT-G
1 CCTTCATCGTGAAGTTGAACCTTGAATTGAATATCATTCGTCGTGAAGTTGAAATCCAAG-TTAG
* * * *
3521934 -T-GTTGTTTCGAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAACTGGAAATTTT
65 TTCGTTGTTTCGAGGCCAATATCCTTCGACGTGAAGTTAAAATTGACTCTGAAACTGGAAAGTTT
*
3521997 ATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGA
130 ATTGACAGACACTCCTTCTTCGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGA
* *
3522062 TAAATGCTGCTTGTGGGTACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTATGAGCACGA
195 TAAATGCTGCTTGTGGGTACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGTATGAGCACGA
3522127 TATCCTCCGTCGTAGAGTTGAAATCATGGAT
260 TATCCTCCGTCGTAGAGTTGAAATCATGGAT
3522158 CCATTGGTAC
Statistics
Matches: 262, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
292 203 0.77
294 1 0.00
295 1 0.00
296 55 0.21
297 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (294 bp):
CCTTCATCGTGAAGTTGAACCTTGAATTGAATATCATTCGTCGTGAAGTTGAAATCCAAGTTAGT
TCGTTGTTTCGAGGCCAATATCCTTCGACGTGAAGTTAAAATTGACTCTGAAACTGGAAAGTTTA
TTGACAGACACTCCTTCTTCGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGAT
AAATGCTGCTTGTGGGTACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGTATGAGCACGAT
ATCCTCCGTCGTAGAGTTGAAATCATGGATGGCG
Found at i:3522146 original size:43 final size:42
Alignment explanation
Indices: 3522080--3522188 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 42
3522070 GCTTGTGGGT
* * * **
3522080 ACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTA-TGAGC
1 ACGATATCCTCCGTCGTG-AGTTGAAACCATGGATCCATTG-GC
* *
3522123 ACGATATCCTCCGTCGTAGAGTTGAAATCATGGATCCATTGGT
1 ACGATATCCTCCGTCGT-GAGTTGAAACCATGGATCCATTGGC
3522166 ACGATATCCTCCGTCGTGGAGTT
1 ACGATATCCTCCGTCGT-GAGTT
3522189 AAAATTATGG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 53 0.95
44 3 0.05
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (42 bp):
ACGATATCCTCCGTCGTGAGTTGAAACCATGGATCCATTGGC
Found at i:3522419 original size:335 final size:334
Alignment explanation
Indices: 3521807--3522986 Score: 1822
Period size: 335 Copynumber: 3.5 Consensus size: 334
3521797 TTCATCGTGA
** * * * *
3521807 AGTTGAAATCGTGGATGTGTGGGCACGATATCCTCTGTCGTGGAGTTGGAATCATGGATGGCGCC
1 AGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCATGGATGGCGCC
* * *
3521872 TTCATCGTGAAGTTGGGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGT
66 TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGC
*
3521937 TGTTTCGAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAACTGGAAATTTTATTGA
131 TGTTTCGAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAACTGGAAAGTTTATTGA
3522002 CAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATAAAT
196 CAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGAT-AAT
*
3522067 GCTGCTTGTGGGTACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTATGAGCACGATATCC
260 GCTGCTTGTGTGTACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTATGAGCACGATATCC
3522132 TCCGTCGTAG
325 TCCGTCGTAG
* * * * *
3522142 AGTTGAAATCATGGATCCATTGGTACGATATCCTCCGTCGTGGAGTTAAAATTATGGATGGTGCC
1 AGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCATGGATGGCGCC
* *
3522207 TTCGTCGTGAAGTTGAGCTTTGACTTGAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTGC
66 TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGC
* *
3522272 TGTTTCGAGTCCAATATCCTTCGCCATTAAGTTAAAATTGGCTCTGAAACTGGAAAGTTTATTGA
131 TGTTTCGAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAACTGGAAAGTTTATTGA
* *
3522337 CAGACACTCATTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCTAGAGATGAAT
196 CAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGAT-AAT
* *
3522402 GCTGCTTGTGTGTACGATTTCCTTCATCGTGAAGTTGAAACCGTGGATGTATGGGCACGATATCC
260 GCTGCTTGTGTGTACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTATGAGCACGATATCC
*
3522467 TCCGTCGTGG
325 TCCGTCGTAG
* * * *
3522477 AGTTGAAATCGTGGATCCGTTGGTACGATATCCTCTGTCGTGGAGTTGAAATCGTGGATGACCCC
1 AGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCATGGATGGCGCC
* * *
3522542 TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTAAAGTTGAAATCCAAGCTTTTGT
66 TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGC
* * *
3522607 TGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTTTATTGA
131 TGTTTCGAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAACTGGAAAGTTTATTGA
* *
3522672 CAGACACTCCTTCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAGATAGAT
196 CAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATA-AT
* * * * *
3522737 GTTGTTTGTGTGTACGATTCCCTTCGTCGTGAAGTTGAAACCGTGAATGTGT-AGGCACGATATC
260 GCTGCTTGTGTGTACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTATGA-GCACGATATC
* *
3522801 CTCCATCGTTG
324 CTCCGTCGTAG
* * *
3522812 AGTTGAAATCGTGGATCCGTTGGTATGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGGCACC
1 AGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCATGGATGGCGCC
*
3522877 TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCATGAAGTTGAAATCCAAGCTTGTGC
66 TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGC
* * *** * *
3522942 TATTTTGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCT
131 TGTTTCGAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCT
3522987 AAAAGCTGCA
Statistics
Matches: 773, Mismatches: 70, Indels: 4
0.91 0.08 0.00
Matches are distributed among these distances:
334 1 0.00
335 772 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (334 bp):
AGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCATGGATGGCGCC
TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGC
TGTTTCGAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAACTGGAAAGTTTATTGA
CAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATAATG
CTGCTTGTGTGTACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTATGAGCACGATATCCT
CCGTCGTAG
Found at i:3522481 original size:43 final size:41
Alignment explanation
Indices: 3522428--3522536 Score: 146
Period size: 43 Copynumber: 2.6 Consensus size: 41
3522418 ATTTCCTTCA
* *
3522428 TCGTGAAGTTGAAACCGTGGATGTATGGGCACGATATCCTCCG
1 TCGTGGAGTTGAAATCGTGGATGT-T-GGCACGATATCCTCCG
* *
3522471 TCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCTG
1 TCGTGGAGTTGAAATCGTGGAT--GTTGGCACGATATCCTCCG
3522514 TCGTGGAGTTGAAATCGTGGATG
1 TCGTGGAGTTGAAATCGTGGATG
3522537 ACCCCTTCGT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
41 1 0.02
43 56 0.93
44 1 0.02
45 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.29
Consensus pattern (41 bp):
TCGTGGAGTTGAAATCGTGGATGTTGGCACGATATCCTCCG
Found at i:3522816 original size:43 final size:43
Alignment explanation
Indices: 3522763--3522867 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
3522753 ATTCCCTTCG
* * **
3522763 TCGTGAAGTTGAAACCGTGAATGTGTAGGCACGATATCCTCCA
1 TCGTGGAGTTGAAATCGTGAATCCGTAGGCACGATATCCTCCA
* * * * * *
3522806 TCGTTGAGTTGAAATCGTGGATCCGTTGGTATGATATCCTCCG
1 TCGTGGAGTTGAAATCGTGAATCCGTAGGCACGATATCCTCCA
3522849 TCGTGGAGTTGAAATCGTG
1 TCGTGGAGTTGAAATCGTG
3522868 GATGGCACCT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (43 bp):
TCGTGGAGTTGAAATCGTGAATCCGTAGGCACGATATCCTCCA
Found at i:3523220 original size:32 final size:32
Alignment explanation
Indices: 3523146--3523220 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
3523136 TTGCATCAGG
* * *
3523146 ATGTTGAATCCCCAAATATGCCCCAATATTCA
1 ATGTTGAATCTCCAAATATCCCCCAACATTCA
*
3523178 ATGTTAAATCTCCAAATATCCCCCAACATAT-A
1 ATGTTGAATCTCCAAATATCCCCCAACAT-TCA
*
3523210 TTGTTGAATCT
1 ATGTTGAATCT
3523221 TTGACGATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATCCCCCAACATTCA
Found at i:3524261 original size:10 final size:10
Alignment explanation
Indices: 3524246--3524324 Score: 63
Period size: 10 Copynumber: 7.9 Consensus size: 10
3524236 ATTATCATCC
3524246 CTTTTTTTTT
1 CTTTTTTTTT
3524256 C-TTTTTTTT
1 CTTTTTTTTT
* *
3524265 CTCTTTGTTT
1 CTTTTTTTTT
*
3524275 CTCTTTTTTT
1 CTTTTTTTTT
* *
3524285 CTTTTCTTTA
1 CTTTTTTTTT
*
3524295 ATTTCTTTTTT
1 CTTT-TTTTTT
*
3524306 ATTTTTTTTAT
1 CTTTTTTTT-T
3524317 -TTTTTTTT
1 CTTTTTTTT
3524325 GCTCTGTGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
9 9 0.16
10 39 0.68
11 9 0.16
ACGTcount: A:0.05, C:0.11, G:0.01, T:0.82
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:3524262 original size:9 final size:9
Alignment explanation
Indices: 3524248--3524323 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
3524238 TATCATCCCT
3524248 TTTTTTTTC
1 TTTTTTTTC
3524257 TTTTTTTTC
1 TTTTTTTTC
*
3524266 TCTTTGTTTC
1 T-TTTTTTTC
3524276 TCTTTTTTTC
1 T-TTTTTTTC
3524286 TTTTCTTTAAT-
1 TTTT-TTT--TC
*
3524297 TTCTTTTTTA
1 TT-TTTTTTC
*
3524307 TTTTTTTTA
1 TTTTTTTTC
3524316 TTTTTTTT
1 TTTTTTTT
3524324 TGCTCTGTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
9 29 0.49
10 22 0.37
11 5 0.08
12 3 0.05
ACGTcount: A:0.05, C:0.11, G:0.01, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3524281 original size:19 final size:18
Alignment explanation
Indices: 3524253--3524288 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3524243 TCCCTTTTTT
*
3524253 TTTCTTTTTTTTCTCTTTG
1 TTTCTCTTTTTT-TCTTTG
3524272 TTTCTCTTTTTTTCTTT
1 TTTCTCTTTTTTTCTTT
3524289 TCTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTCTCTTTTTTTCTTTG
Found at i:3530519 original size:13 final size:14
Alignment explanation
Indices: 3530501--3530529 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3530491 ACTATACTAC
3530501 AATATATA-CATAT
1 AATATATAGCATAT
3530514 AATATATAGCATAT
1 AATATATAGCATAT
3530528 AA
1 AA
3530530 AATTTATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (14 bp):
AATATATAGCATAT
Found at i:3533163 original size:16 final size:16
Alignment explanation
Indices: 3533142--3533173 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3533132 AATAAATAAG
3533142 CGAACATAAACGAACA
1 CGAACATAAACGAACA
3533158 CGAACATAAACGAACA
1 CGAACATAAACGAACA
3533174 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:3533254 original size:10 final size:10
Alignment explanation
Indices: 3533239--3533313 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
3533229 CATTTAATAA
3533239 ATAAACGAAC
1 ATAAACGAAC
3533249 ATAAACGAAC
1 ATAAACGAAC
*
3533259 ----ACAAAC
1 ATAAACGAAC
3533265 ATAAACGAAC
1 ATAAACGAAC
** *
3533275 ACGAAC-ATAA
1 ATAAACGA-AC
3533285 ATGAACACGAAC
1 AT-AA-ACGAAC
3533297 ATAAACGAAC
1 ATAAACGAAC
3533307 ATAAACG
1 ATAAACG
3533314 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3533267 original size:16 final size:16
Alignment explanation
Indices: 3533246--3533312 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
3533236 TAAATAAACG
3533246 AACATAAACGAACACA
1 AACATAAACGAACACA
*
3533262 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
3533278 AACATAAATGAACACG
1 AACATAAACGAACACA
*
3533294 AACATAAACGAACATA
1 AACATAAACGAACACA
3533310 AAC
1 AAC
3533313 GTTGGAGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:3533279 original size:32 final size:32
Alignment explanation
Indices: 3533243--3533307 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
3533233 TAATAAATAA
3533243 ACGAACATAAACGAACACAAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
* *
3533275 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
3533307 A
1 A
3533308 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACGAAC
Found at i:3534876 original size:24 final size:24
Alignment explanation
Indices: 3534815--3534876 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
3534805 TATTAGGTTA
*
3534815 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
3534839 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
3534863 AACATAACCGAACG
1 AACATAACTGAACG
3534877 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:3535506 original size:29 final size:31
Alignment explanation
Indices: 3535450--3535511 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
3535440 AACGTATGTC
* *
3535450 TTTGGTTATAGTTTGGTGCTTAATG-TTTAT
1 TTTGGTTATAGTTTAGTGCTTAACGTTTTAT
3535480 TTTGGTT-TAGTTTAGTG-TCTAACGTTTTAT
1 TTTGGTTATAGTTTAGTGCT-TAACGTTTTAT
3535510 TT
1 TT
3535512 CGTTACTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.04
29 13 0.46
30 14 0.50
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.58
Consensus pattern (31 bp):
TTTGGTTATAGTTTAGTGCTTAACGTTTTAT
Found at i:3538607 original size:20 final size:21
Alignment explanation
Indices: 3538571--3538609 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3538561 GGTCTTATCC
3538571 CATTTAAGTGAATATTATATT
1 CATTTAAGTGAATATTATATT
*
3538592 CATTTAAGTGGA-ATTATA
1 CATTTAAGTGAATATTATA
3538610 ATGTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (21 bp):
CATTTAAGTGAATATTATATT
Found at i:3555544 original size:36 final size:36
Alignment explanation
Indices: 3555503--3555578 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
3555493 TTTGAGTTTT
* *
3555503 AGTCTAGCTTAAAAATTTTAGCCTCTC-AAGTTTTCG
1 AGTCTAGCTTAAAAATTTCAGCCTCACGAA-TTTTCG
*
3555539 AGTCTAGCTTAAAAATTTCAGGCTCACGAATTTTCG
1 AGTCTAGCTTAAAAATTTCAGCCTCACGAATTTTCG
3555575 AGTC
1 AGTC
3555579 GAGTCGAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (36 bp):
AGTCTAGCTTAAAAATTTCAGCCTCACGAATTTTCG
Found at i:3563667 original size:42 final size:42
Alignment explanation
Indices: 3563608--3563692 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
3563598 CGACTGTAAT
3563608 GTATTTGAGTTTTTATTGTTAAACGATAAAATATTTGAAATA
1 GTATTTGAGTTTTTATTGTTAAACGATAAAATATTTGAAATA
*
3563650 GTATTTGAGTTTTTATTGTTAAACGATAAAGTATTTGAAATA
1 GTATTTGAGTTTTTATTGTTAAACGATAAAATATTTGAAATA
3563692 G
1 G
3563693 ATACTACCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.45
Consensus pattern (42 bp):
GTATTTGAGTTTTTATTGTTAAACGATAAAATATTTGAAATA
Found at i:3566109 original size:3 final size:3
Alignment explanation
Indices: 3566051--3566096 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
3566041 TTCATTTAAA
3566051 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3566095 TA
1 TA
3566097 ATAAATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 3 0.08
3 36 0.90
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3568324 original size:19 final size:19
Alignment explanation
Indices: 3568300--3568342 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3568290 TAATTCTTTC
* *
3568300 TTTTCAAATTTTTTATATA
1 TTTTCAAAGTATTTATATA
*
3568319 TTTTCATAGTATTTATATA
1 TTTTCAAAGTATTTATATA
3568338 TTTTC
1 TTTTC
3568343 TTATTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTCAAAGTATTTATATA
Found at i:3571655 original size:15 final size:15
Alignment explanation
Indices: 3571635--3571666 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3571625 ATCAATACCT
3571635 TTTTGCATACATACA
1 TTTTGCATACATACA
*
3571650 TTTTGCATACATTCA
1 TTTTGCATACATACA
3571665 TT
1 TT
3571667 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:3579013 original size:11 final size:10
Alignment explanation
Indices: 3579000--3579080 Score: 85
Period size: 11 Copynumber: 7.7 Consensus size: 10
3578990 AGAAAATAAC
3579000 AAAAAAGAAA
1 AAAAAAGAAA
3579010 CAAAAAAGAAA
1 -AAAAAAGAAA
3579021 AAGAAAAGAAA
1 AA-AAAAGAAA
3579032 AAAAAGAGAAGA
1 AAAAA-AGAA-A
3579044 ACAAAAA-AAA
1 A-AAAAAGAAA
3579054 AAAAAAGAAA
1 AAAAAAGAAA
*
3579064 AAAGAAA-AAG
1 AAA-AAAGAAA
3579074 AAAAAAG
1 AAAAAAG
3579081 GGGGTCAAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 15
0.79 0.01 0.19
Matches are distributed among these distances:
9 8 0.13
10 18 0.29
11 29 0.47
12 3 0.05
13 4 0.06
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:3579015 original size:1 final size:1
Alignment explanation
Indices: 3579000--3579079 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
3578990 AGAAAATAAC
* * * * * * * * * *
3579000 AAAAAAGAAACAAAAAAGAAAAAGAAAAGAAAAAAAAGAGAAGAACAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
3579065 AAGAAAAAGAAAAAA
1 AAAAAAAAAAAAAAA
3579080 GGGGGTCAAG
Statistics
Matches: 55, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:3579023 original size:6 final size:6
Alignment explanation
Indices: 3579001--3579078 Score: 72
Period size: 6 Copynumber: 12.8 Consensus size: 6
3578991 GAAAATAACA
* *
3579001 AAAAAG AAACA- AAAAAG AAAAAG -AAAAG AAAAAA AAGAGAAG AACAAA-
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-A-AAG AA-AAAG
*
3579049 AAAAAA AAAAAG AAAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG -AAAAAG AAAAAG AAAAA
3579079 AGGGGGTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
5 12 0.20
6 34 0.57
7 9 0.15
8 5 0.08
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3579049 original size:17 final size:15
Alignment explanation
Indices: 3578987--3579080 Score: 72
Period size: 16 Copynumber: 6.2 Consensus size: 15
3578977 ATTATGCTTG
3578987 AAGAGAAAATAACAAAA
1 AAGAGAAAA-AA-AAAA
3579004 AAGA-AACAAAAAAGAA
1 AAGAGAA-AAAAAA-AA
3579020 AA-AGAAAAGAAAAAA
1 AAGAGAAAA-AAAAAA
*
3579035 AAGAGAAGAACAAAAA
1 AAGAGAA-AAAAAAAA
*
3579051 AA-A-AAAAAAGAAA
1 AAGAGAAAAAAAAAA
*
3579064 AA-AGAAAAAGAAAA
1 AAGAGAAAAAAAAAA
3579078 AAG
1 AAG
3579081 GGGGTCAAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
13 9 0.14
14 12 0.19
15 10 0.16
16 25 0.39
17 8 0.12
ACGTcount: A:0.82, C:0.03, G:0.14, T:0.01
Consensus pattern (15 bp):
AAGAGAAAAAAAAAA
Found at i:3580226 original size:93 final size:93
Alignment explanation
Indices: 3579983--3580765 Score: 1390
Period size: 93 Copynumber: 8.4 Consensus size: 93
3579973 GTCTCTATAC
3579983 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
* *
3580048 TATCTGATCTGGTTTGGTAT-AAACCTA
66 TATCTGATCTGGTTTGGTATGAACCCCA
*
3580075 AAACCCCATCATTGGACTTGAAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
3580140 TATCTGATCTGGTTTGGTATAAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
* *
3580168 AAACCCCATCATTAGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
3580233 TATCTGATCTGGTTTGGTATGAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
3580261 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
3580326 TATCTGATCTGGTTTGGTATGAACCCTA
66 TATCTGATCTGGTTTGGTATGAACCCCA
* *
3580354 AAACCCCATCATTAGACTTGAAAGATGAGTGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
3580419 TATTTGATCTGGTTTGGTATGAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
*
3580447 AAACCCCATCATTGGACTTGAAAGATGAGTGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
3580512 TATCTGATCTGGTTTGGTATGAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
*
3580540 AAACCCCATCATTGGACTTGAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
3580605 TATCTGATCTGGTTTGGTATGAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
3580633 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
**
3580698 TATCTGATCTGGTTTGGTATGAAACTACA
66 TATCTGATCTGGTTTGGTATG-AACCCCA
* * *
3580727 GAA-CCAATCATTGGATTTGAAAGATGAATGTGCTCATAG
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAG
3580766 TACAAATAAA
Statistics
Matches: 665, Mismatches: 24, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
92 84 0.13
93 574 0.86
94 7 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (93 bp):
AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGGTTTGGTATGAACCCCA
Found at i:3581887 original size:113 final size:113
Alignment explanation
Indices: 3581560--3582242 Score: 691
Period size: 113 Copynumber: 6.0 Consensus size: 113
3581550 GCAAAGATTC
* * * * * *
3581560 AAATCCATCATTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATATGAAG
1 AAATTCATCATTTGATGGATCAACATTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
3581625 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * *
3581673 AAATTCATTATTTGATGGATTAACATTGCCAG-TAGAGTTCATAATGAGAAGAACTCATCATCTA
1 AAATTCATCATTTGATGGATCAACATTGCCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTG
* *
3581737 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* ** * * * * *
3581788 GAATTCATCATTCAATGGACCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAACATTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
3581853 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * *
3581901 AAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAACATTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
3581966 AAGGAAGACGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * *** ***
3582014 AAATCCATCACTTGATGGATCAGTTTTTTTAG--AGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCATTTGATGGATCAACATTGCCAGTTAG-AGTTCATAATGAGAAGAACTCATCTGAA
* ** * *
3582077 GAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCAT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * ** *
3582122 -AATTCTATCACAGAAGTAGATAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGA
1 AAATTC-AT--C---A-T---TTGA-T-GGATCAACATTGCCAGTTAGAGTTCATAATGAGAAGA
* ** *
3582186 ACTCATCTGAAGAA-GAATGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
54 ACTCATCTGAAGAAGGAA-GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
3582243 AATGACTCTA
Statistics
Matches: 476, Mismatches: 71, Indels: 35
0.82 0.12 0.06
Matches are distributed among these distances:
107 4 0.01
108 33 0.07
109 1 0.00
110 2 0.00
111 3 0.01
112 51 0.11
113 201 0.42
114 2 0.00
115 77 0.16
116 19 0.04
117 3 0.01
118 1 0.00
119 10 0.02
120 32 0.07
121 2 0.00
123 2 0.00
124 33 0.07
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
AAATTCATCATTTGATGGATCAACATTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
Found at i:3582278 original size:124 final size:120
Alignment explanation
Indices: 3582044--3582321 Score: 366
Period size: 124 Copynumber: 2.3 Consensus size: 120
3582034 CAGTTTTTTT
*
3582044 AGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGCTTAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATAAGAAGAGCTTAT
* * * * * * * *
3582108 TCAACCTTTTGCATAATTCTATCACAGAAGTAGATAGATTAGCATCAACCTTTCC
66 TCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACCCTACC
*
3582163 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAATGAAGAAGTTCATAATAAGAAGAGC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-A--AA-AAGTTCACAATAAGAAGAGC
* * *
3582228 TTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATA-AGTCAACATCATCCCTAGC
62 TTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGA-TCAACATCAACCCTACC
3582287 -G-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
3582322 AGAGAAGAAT
Statistics
Matches: 140, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
119 4 0.03
120 33 0.24
121 1 0.01
122 34 0.24
123 4 0.03
124 64 0.46
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (120 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATAAGAAGAGCTTAT
TCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACCCTACC
Found at i:3582521 original size:3 final size:3
Alignment explanation
Indices: 3582469--3582508 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3582459 TTCATTTAAA
3582469 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3582509 ATAAATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 3 0.09
3 30 0.88
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3586154 original size:20 final size:20
Alignment explanation
Indices: 3586129--3586166 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3586119 GAAAATCTAT
3586129 TTCGTCCCCTAAAATTTTAG
1 TTCGTCCCCTAAAATTTTAG
* *
3586149 TTCGTCCTCTAGAATTTT
1 TTCGTCCCCTAAAATTTT
3586167 GGTTTGCCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
TTCGTCCCCTAAAATTTTAG
Found at i:3587334 original size:7 final size:7
Alignment explanation
Indices: 3587315--3587346 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
3587305 TACATTTTGA
3587315 AAAATCT
1 AAAATCT
3587322 -AAATCT
1 AAAATCT
3587328 AAAATCT
1 AAAATCT
3587335 AAAATCT
1 AAAATCT
3587342 AAAAT
1 AAAAT
3587347 TTTTAGTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATCT
Found at i:3587863 original size:24 final size:24
Alignment explanation
Indices: 3587813--3587862 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
3587803 GAACTTAATA
*
3587813 TTAATAAAATATTTTAATATCATT
1 TTAATAAAATATTTAAATATCATT
3587837 TTAATAAAAATATTTAAAATAT-ATT
1 TTAAT-AAAATATTT-AAATATCATT
3587862 T
1 T
3587863 ATTAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 13 0.57
26 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAATAAAATATTTAAATATCATT
Found at i:3587892 original size:21 final size:21
Alignment explanation
Indices: 3587868--3587908 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3587858 TATTTATTAA
3587868 TATTTATTAATAATATAATAT
1 TATTTATTAATAATATAATAT
* *
3587889 TATTTTTTAATATTATAATA
1 TATTTATTAATAATATAATA
3587909 AAATACTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTATTAATAATATAATAT
Found at i:3588653 original size:22 final size:22
Alignment explanation
Indices: 3588623--3588673 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3588613 TTTCTATCAA
*
3588623 AATAATAAATAA-ATAAATAAAT
1 AATATTAAATAATAT-AATAAAT
**
3588645 AATATTAAATTTTATAATAAAT
1 AATATTAAATAATATAATAAAT
3588667 AATATTA
1 AATATTA
3588674 TTTATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATTAAATAATATAATAAAT
Found at i:3588677 original size:19 final size:21
Alignment explanation
Indices: 3588638--3588682 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
3588628 TAAATAAATA
3588638 AATAAATAATATTAAATTTTAT
1 AATAAATAATATT-AATTTTAT
*
3588660 AATAAATAATATTATTTATTAT
1 AATAAATAATATTAATT-TTAT
3588682 A
1 A
3588683 TTTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAAATAATATTAATTTTAT
Found at i:3589164 original size:20 final size:20
Alignment explanation
Indices: 3589139--3589185 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
3589129 GCAAAGGTTG
3589139 GGCCATATTATTGTAATTGA
1 GGCCATATTATTGTAATTGA
3589159 GGCCATATTATTGTAATTGA
1 GGCCATATTATTGTAATTGA
3589179 GGCCATA
1 GGCCATA
3589186 AGCCTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
GGCCATATTATTGTAATTGA
Found at i:3591494 original size:255 final size:244
Alignment explanation
Indices: 3590992--3591522 Score: 631
Period size: 255 Copynumber: 2.1 Consensus size: 244
3590982 ACACGGCACA
* *
3590992 AAATAA-AAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTGAAAAAAAATATATATAGG
1 AAATAATAAAAAA-TATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAAATATATAGAGG
* * * *
3591056 GGTATTATTGTAATTATTCCTGAATATATAAGGTAAAATTATATATATTTTTCGGGTCGGGTATG
65 GGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATACATATCTTTCGGGTCGGGTA--
* *
3591121 GTTTTTTACCCTAAACCCGAACCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAATA
128 GTTTTTCACCCTAAACCCGAACCGACCCGAATATCACACTTAAAAAAACCGACCCGAACAAAATA
* * * * *
3591186 AAGTTTCACCCGACCCGAAATATATGAATTAGAAGTCCGACCGACCCGACCCG
193 AAGTTTCACCCGACCCGAAAGACACGAATTAGAAGTCAGA-CAACCCGACCCG
*
3591239 AAATAATAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAATTATATATAGAGG
1 AAATAATAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAA-AATATATAGAGG
*
3591304 GGTATTATTGTAATTATTCCTAAATTTATAAGATAAAATTATACATA-CTTTCGGGTCGGGTA-T
65 GGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATACATATCTTTCGGGTCGGGTAGT
* *
3591367 TTTTCACCCTAAACCCGAACTCGACCCGACCCGACCCGAATATCACATTTAAAAAAATCGACCCG
130 TTTTCACCCTAAA--C---C-CGA----A-CCGACCCGAATATCACACTTAAAAAAACCGACCCG
* ** * * * *
3591432 ACCAAAATAAAGTTTCACCCGACCCGACCCGACCCGAATATATGAA-TTAGA-AATCTGACCCG
184 AACAAAATAAAGTTTCACCCGACCCGA-AAGACACGAAT-TA-GAAGTCAGACAACCCGACCCG
3591494 AAATAATAAAAAAATATTTTTATTCAATA
1 AAATAAT-AAAAAATATTTTTATTCAATA
3591523 TATGAATAAG
Statistics
Matches: 243, Mismatches: 24, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
244 13 0.05
246 1 0.00
247 58 0.24
248 59 0.24
249 1 0.00
250 3 0.01
254 1 0.00
255 73 0.30
256 26 0.11
257 5 0.02
258 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.28
Consensus pattern (244 bp):
AAATAATAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAAATATATAGAGGG
GTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATACATATCTTTCGGGTCGGGTAGTT
TTTCACCCTAAACCCGAACCGACCCGAATATCACACTTAAAAAAACCGACCCGAACAAAATAAAG
TTTCACCCGACCCGAAAGACACGAATTAGAAGTCAGACAACCCGACCCG
Found at i:3592591 original size:21 final size:18
Alignment explanation
Indices: 3592560--3592611 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
3592550 CAGAAAGCAA
* *
3592560 AAAAAAAAAAATAGAAAT
1 AAAATAAAAAATAAAAAT
*
3592578 ACAATATAAGAAAAGAAAAAT
1 A-AA-ATAA-AAAATAAAAAT
3592599 AAAATAAAAAATA
1 AAAATAAAAAATA
3592612 CGCGTCGACA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 6 0.22
19 6 0.22
20 5 0.19
21 10 0.37
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (18 bp):
AAAATAAAAAATAAAAAT
Found at i:3593522 original size:15 final size:15
Alignment explanation
Indices: 3593502--3593538 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3593492 TTGAGACTTA
**
3593502 CCCGCCCCGTATCCG
1 CCCGCCCCACATCCG
3593517 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
3593532 CCCGCCC
1 CCCGCCC
3593539 AACTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.68, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Done.