Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:3298233 original size:21 final size:24
Alignment explanation
Indices: 3298200--3298243 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 24
3298190 AAAATTAGTA
3298200 TATTTATTCATCTAATTT-CAATG
1 TATTTATTCATCTAATTTACAATG
*
3298223 TATTT-TT-ATCTATTTTACAAT
1 TATTTATTCATCTAATTTACAAT
3298244 TTAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTATTCATCTAATTTACAATG
Found at i:3298802 original size:29 final size:29
Alignment explanation
Indices: 3298767--3298848 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3298757 AAACTAAATT
*
3298767 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3298796 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3298825 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3298849 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3303568 original size:29 final size:29
Alignment explanation
Indices: 3303533--3303614 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3303523 AAACTAAATT
*
3303533 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3303562 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3303591 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3303615 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3315282 original size:18 final size:18
Alignment explanation
Indices: 3315244--3315282 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3315234 CAGTTGTCTC
*
3315244 TTTATAATTTTCAAATTT
1 TTTATAATTTTCAAATGT
* *
3315262 TTTATAATTTTTAGATGT
1 TTTATAATTTTCAAATGT
3315280 TTT
1 TTT
3315283 TTTTGTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTATAATTTTCAAATGT
Found at i:3324958 original size:43 final size:42
Alignment explanation
Indices: 3324854--3325013 Score: 178
Period size: 43 Copynumber: 3.8 Consensus size: 42
3324844 ATTGGGTTTG
* ** * *
3324854 TGTTAGAACCATTTTGATAGTTTCGAATTTCGGATTAGG-CA
1 TGTTAGAACGATTTCAATGGTTTCGAATTTCGGATTAGGATA
* *
3324895 TGTTAGAACGGTTTCAATGGTTTCGAATTTTGGATTAGGTATA
1 TGTTAGAACGATTTCAATGGTTTCGAATTTCGGATTAGG-ATA
* * * *
3324938 TGTTAGAACGATTTCGATGGTTTTGGATTTCGGGTTAGGCATA
1 TGTTAGAACGATTTCAATGGTTTCGAATTTCGGATTAGG-ATA
* *
3324981 TCTTAGAACGGTTTCAATGGTTTCGAATTTCGG
1 TGTTAGAACGATTTCAATGGTTTCGAATTTCGG
3325014 CTTCGATTAC
Statistics
Matches: 98, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 33 0.34
43 65 0.66
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.40
Consensus pattern (42 bp):
TGTTAGAACGATTTCAATGGTTTCGAATTTCGGATTAGGATA
Found at i:3325006 original size:86 final size:84
Alignment explanation
Indices: 3324854--3325010 Score: 233
Period size: 84 Copynumber: 1.8 Consensus size: 84
3324844 ATTGGGTTTG
* *
3324854 TGTTAGAACCATTTTGATAGTTTCGAATTTCGGATTAGGCATGTTAGAACGGTTTCAATGGTTTC
1 TGTTAGAACCATTTCGATAGTTTCGAATTTCGGATTAGGCATCTTAGAACGGTTTCAATGGTTTC
3324919 GAATTTTGGATTAGGTATA
66 GAATTTTGGATTAGGTATA
* * * * *
3324938 TGTTAGAACGATTTCGATGGTTTTGGATTTCGGGTTAGGCATATCTTAGAACGGTTTCAATGGTT
1 TGTTAGAACCATTTCGATAGTTTCGAATTTCGGATTAGGC--ATCTTAGAACGGTTTCAATGGTT
3325003 TCGAATTT
64 TCGAATTT
3325011 CGGCTTCGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
84 34 0.53
86 30 0.47
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (84 bp):
TGTTAGAACCATTTCGATAGTTTCGAATTTCGGATTAGGCATCTTAGAACGGTTTCAATGGTTTC
GAATTTTGGATTAGGTATA
Found at i:3329084 original size:21 final size:20
Alignment explanation
Indices: 3328998--3329155 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
3328988 AAATGACCAA
**
3328998 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3329017 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3329037 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3329057 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3329078 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3329099 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3329119 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3329140 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3329156 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3329184 original size:20 final size:20
Alignment explanation
Indices: 3329122--3329351 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
3329112 CGATTTTCCA
* ** *
3329122 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3329142 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3329162 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3329182 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3329202 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3329222 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3329242 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3329262 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
3329282 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
3329302 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
3329322 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
3329342 AAATCACAAC
1 AAATCGCAAC
3329352 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3330259 original size:12 final size:12
Alignment explanation
Indices: 3330242--3330266 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3330232 ATATAATCCT
3330242 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3330254 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3330266 G
1 G
3330267 TCCCGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3332594 original size:34 final size:33
Alignment explanation
Indices: 3332526--3332707 Score: 147
Period size: 33 Copynumber: 5.3 Consensus size: 33
3332516 CGGAAATTAC
* *
3332526 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
3332559 AATCCCAAC-ATGAAAATCGCAATGCAGAAATGAA
1 AATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
3332593 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
* * * * *
3332626 AATCGCAATGCG-AAAT-GACAAT-CGCAACGATA
1 AATCCCAACGAGAAAATCG-CAATGCGAAATGA-A
*
3332658 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCCCAA--CG--A-GAAAATCGCAATGCGAAATGAA
*
3332697 AATCGCAACGA
1 AATCCCAACGA
3332708 CACTTGTCAC
Statistics
Matches: 122, Mismatches: 13, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
31 7 0.06
32 9 0.07
33 47 0.39
34 30 0.25
35 2 0.02
36 2 0.02
38 9 0.07
39 9 0.07
40 7 0.06
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:3332631 original size:19 final size:19
Alignment explanation
Indices: 3332540--3332704 Score: 180
Period size: 19 Copynumber: 9.4 Consensus size: 19
3332530 GCAACGAGAG
3332540 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3332559 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3332573 AATCGCAATGCAGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3332593 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3332607 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3332626 AATCGCAATGCGAAATGAC
1 AATCGCAATGCGAAATGAA
*
3332645 AATCGCAA--CG--AT-AG
1 AATCGCAATGCGAAATGAA
3332659 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3332678 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3332697 AATCGCAA
1 AATCGCAA
3332705 CGACACTTGT
Statistics
Matches: 123, Mismatches: 7, Indels: 32
0.76 0.04 0.20
Matches are distributed among these distances:
14 31 0.25
15 3 0.02
16 5 0.04
17 4 0.03
18 4 0.03
19 63 0.51
20 13 0.11
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3332653 original size:52 final size:52
Alignment explanation
Indices: 3332568--3332707 Score: 253
Period size: 52 Copynumber: 2.7 Consensus size: 52
3332558 AAATCCCAAC
3332568 ATGAAAATCGCAATGCAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
3332621 ATGAAAATCGCAATGCGAAATGACAATCGCAACGATAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3332673 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
3332708 CACTTGTCAC
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
52 68 0.81
53 16 0.19
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3334473 original size:33 final size:33
Alignment explanation
Indices: 3334444--3334653 Score: 230
Period size: 33 Copynumber: 6.2 Consensus size: 33
3334434 CGGAAATTAC
3334444 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
3334477 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
3334511 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * * *
3334544 AATCGCAATGCGA-AAT-GACAAT-CGCAACGATA
1 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A
*
3334576 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
*
3334615 AATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
3334648 AATCGC
1 AATCGC
3334654 GTTGCGATTC
Statistics
Matches: 149, Mismatches: 14, Indels: 28
0.78 0.07 0.15
Matches are distributed among these distances:
31 7 0.05
32 9 0.06
33 74 0.50
34 30 0.20
35 2 0.01
36 2 0.01
38 10 0.07
39 8 0.05
40 7 0.05
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:3334549 original size:19 final size:19
Alignment explanation
Indices: 3334458--3334653 Score: 189
Period size: 19 Copynumber: 11.3 Consensus size: 19
3334448 GCAACGAGAG
3334458 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3334477 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3334491 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3334511 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3334525 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3334544 AATCGCAATGCGAAATGAC
1 AATCGCAATGCGAAATGAA
*
3334563 AATCGCAA--CG--AT-AG
1 AATCGCAATGCGAAATGAA
3334577 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3334596 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3334615 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
3334629 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
3334648 AATCGC
1 AATCGC
3334654 GTTGCGATTC
Statistics
Matches: 146, Mismatches: 10, Indels: 42
0.74 0.05 0.21
Matches are distributed among these distances:
14 41 0.28
15 4 0.03
16 7 0.05
17 6 0.04
18 5 0.03
19 70 0.48
20 13 0.09
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3334660 original size:52 final size:52
Alignment explanation
Indices: 3334486--3334653 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
3334476 AAATCCCAAC
3334486 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
3334539 ATGAAAATCGCAATGCGAAATGACAATCGCAACGATAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3334591 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3334643 ATTAAAATCGC
1 ATGAAAATCGC
3334654 GTTGCGATTC
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 94 0.85
53 16 0.15
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3334693 original size:52 final size:52
Alignment explanation
Indices: 3334632--3334745 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 52
3334622 ACGAGAGAAT
* *
3334632 CGCAATGCGAAATTAAAATCGCGTTGCGATTCTCTCGTTGCGATTTTCATTC
1 CGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTC
** * ** *
3334684 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTC
3334736 CGCATTGCGA
1 CGCATTGCGA
3334746 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (52 bp):
CGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTC
Found at i:3334746 original size:52 final size:52
Alignment explanation
Indices: 3334650--3334765 Score: 214
Period size: 52 Copynumber: 2.2 Consensus size: 52
3334640 GAAATTAAAA
*
3334650 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
*
3334702 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
3334754 TCGCATTGCGAT
1 TCGCATTGCGAT
3334766 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
Found at i:3334773 original size:19 final size:19
Alignment explanation
Indices: 3334669--3334765 Score: 141
Period size: 19 Copynumber: 5.4 Consensus size: 19
3334659 GATTCTCTCG
*
3334669 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTTCGCA
3334688 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3334707 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3334721 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3334740 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3334759 TTGCGAT
1 TTGCGAT
3334766 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 50 0.71
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3334889 original size:14 final size:14
Alignment explanation
Indices: 3334870--3334906 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3334860 CATCAATTAC
3334870 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3334884 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3334898 ACAAATCAA
1 ACAAATCAA
3334907 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3336866 original size:19 final size:19
Alignment explanation
Indices: 3336824--3336927 Score: 118
Period size: 19 Copynumber: 5.4 Consensus size: 19
3336814 TAGTTTACTT
* *
3336824 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
** *
3336844 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAACCAAAA
*
3336863 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3336882 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3336901 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3336920 TCGTAACG
1 TCGCAACG
3336928 ACAGAAGCGA
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 60 0.83
20 12 0.17
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3336994 original size:33 final size:33
Alignment explanation
Indices: 3336952--3337043 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3336942 AAAATCGCAA
*
3336952 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCAT
3336985 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCAT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCAT
*
3337018 TGCGATTTTGGTTTCTCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3337044 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCAT
Found at i:3337072 original size:20 final size:19
Alignment explanation
Indices: 3336952--3337080 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3336942 AAAATCGCAA
3336952 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3336971 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3336985 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3337004 TGCGATTCT-G--T--CAT
1 TGCGATTTTGGTTTCGCGT
*
3337018 TGCGATTTTGGTTTCTCGT
1 TGCGATTTTGGTTTCGCGT
3337037 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3337056 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3337076 TGCGA
1 TGCGA
3337081 AATTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.23
15 2 0.02
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3337086 original size:20 final size:20
Alignment explanation
Indices: 3337047--3337086 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3337037 TGCGATTTTG
**
3337047 GTTTCGCGTTGCGATTTTAA
1 GTTTCGCGTTGCGAAATTAA
*
3337067 GTTTCGTGTTGCGAAATTAA
1 GTTTCGCGTTGCGAAATTAA
3337087 ACTATTTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTTCGCGTTGCGAAATTAA
Found at i:3337241 original size:93 final size:93
Alignment explanation
Indices: 3337128--3337410 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
3337118 ATGGATTGCA
3337128 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3337192 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
3337220 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACCATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3337285 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3337313 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3337378 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3337406 TTACT
1 TTACT
3337411 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 184 0.98
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3339137 original size:20 final size:20
Alignment explanation
Indices: 3339106--3339202 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
3339096 TTTTGGTTGA
3339106 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
3339126 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3339146 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
3339165 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
3339180 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3339200 AAT
1 AAT
3339203 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3339158 original size:21 final size:21
Alignment explanation
Indices: 3339104--3339168 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3339094 TCTTTTGGTT
3339104 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
3339125 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3339145 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3339166 GAA
1 GAA
3339169 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:3339172 original size:14 final size:14
Alignment explanation
Indices: 3339153--3339209 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3339143 GAGAAATGAA
3339153 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3339167 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3339186 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3339200 AATCGCAACG
1 AATCGCAACG
3339210 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3339185 original size:33 final size:33
Alignment explanation
Indices: 3339104--3339226 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
3339094 TCTTTTGGTT
*
3339104 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
3339145 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3339178 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3339211 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3339227 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3339262 original size:14 final size:14
Alignment explanation
Indices: 3339243--3339299 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3339233 TTTGGTTTCG
3339243 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3339257 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3339276 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3339290 CGTTGCGATT
1 CGTTGCGATT
3339300 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3339275 original size:33 final size:33
Alignment explanation
Indices: 3339227--3339307 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
3339217 AAAATCGCAA
**
3339227 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3339260 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3339293 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
3339308 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3339310 original size:21 final size:21
Alignment explanation
Indices: 3339284--3339359 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3339274 CGCGTTGCGA
3339284 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3339305 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3339325 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
3339346 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
3339360 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3339340 original size:41 final size:41
Alignment explanation
Indices: 3339283--3339360 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
3339273 TCGCGTTGCG
*
3339283 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
3339324 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
3339361 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:3339481 original size:33 final size:33
Alignment explanation
Indices: 3339439--3339509 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3339429 AATACTAACT
*
3339439 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3339472 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3339505 TGAAA
1 TGAAA
3339510 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3339742 original size:22 final size:22
Alignment explanation
Indices: 3339690--3339744 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3339680 TGGTTGTGAG
**
3339690 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3339712 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3339734 GGATTTCTTCG
1 GGATTTCTTCG
3339745 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3339916 original size:20 final size:20
Alignment explanation
Indices: 3339891--3340084 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
3339881 CTTTATATAT
3339891 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3339911 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3339933 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3339952 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3339972 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
*
3339992 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3340012 CACGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3340032 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3340052 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3340072 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3340085 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3340056 original size:60 final size:60
Alignment explanation
Indices: 3339893--3340064 Score: 227
Period size: 60 Copynumber: 2.9 Consensus size: 60
3339883 TTATATATCG
** *
3339893 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** * *
3339954 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGTGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
* *
3340014 CGTTGTGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
3340065 TCATATTCGC
Statistics
Matches: 92, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 66 0.72
61 26 0.28
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:3340078 original size:60 final size:60
Alignment explanation
Indices: 3339891--3340084 Score: 226
Period size: 60 Copynumber: 3.2 Consensus size: 60
3339881 CTTTATATAT
** *
3339891 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* * *** * * *
3339952 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * * *
3340012 CACGTTGTGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
3340072 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3340085 TGGAAAATCG
Statistics
Matches: 108, Mismatches: 25, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
60 80 0.74
61 28 0.26
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:3340101 original size:21 final size:21
Alignment explanation
Indices: 3340071--3340153 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3340061 ATTTTCATAT
*
3340071 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3340092 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3340113 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3340134 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3340154 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3340144 original size:42 final size:43
Alignment explanation
Indices: 3340051--3340149 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3340041 ATTTATGTGT
* *
3340051 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3340092 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3340134 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3340150 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:3341123 original size:20 final size:20
Alignment explanation
Indices: 3341016--3341122 Score: 124
Period size: 20 Copynumber: 5.3 Consensus size: 20
3341006 ATTCGCGTTG
3341016 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTT
* *
3341036 CATTTTGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTT
* * *
3341056 CAGTTCGCGTTGCGATAGTTA
1 CATTTCGCGTTGCGAT-TTTT
* **
3341077 AAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTT
*
3341097 CATTTCTCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTT
3341117 CATTTC
1 CATTTC
3341123 TTGTGATAGT
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 56 0.79
21 15 0.21
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTT
Found at i:3341204 original size:6 final size:6
Alignment explanation
Indices: 3341193--3341222 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3341183 GAAGACACGT
3341193 ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC
3341223 CGAGACGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:3341233 original size:5 final size:5
Alignment explanation
Indices: 3341223--3341258 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
3341213 GACCACGACC
3341223 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
3341259 GCGGCGGCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.36, C:0.22, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:3341756 original size:6 final size:6
Alignment explanation
Indices: 3341740--3341771 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3341730 GACCGTCTCG
3341740 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
3341772 AATACGCGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:3341881 original size:22 final size:22
Alignment explanation
Indices: 3341856--3341908 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
3341846 AATCTAGAAA
*
3341856 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACAGTAGACT
*
3341878 ATCGCAACAACAACAGTAGACT
1 ATCGCAACGACAACAGTAGACT
3341900 ATCGCAACG
1 ATCGCAACG
3341909 CAAAATGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.15
Consensus pattern (22 bp):
ATCGCAACGACAACAGTAGACT
Found at i:3342541 original size:40 final size:40
Alignment explanation
Indices: 3342486--3342565 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
3342476 TATATATATA
3342486 TATATATAAAATGATGATTAACAAGTTGGAGGTAAAAAAG
1 TATATATAAAATGATGATTAACAAGTTGGAGGTAAAAAAG
3342526 TATATATAAAATGATGATTAACAAGTTGGAGGTAAAAAAG
1 TATATATAAAATGATGATTAACAAGTTGGAGGTAAAAAAG
3342566 AGTGGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.28
Consensus pattern (40 bp):
TATATATAAAATGATGATTAACAAGTTGGAGGTAAAAAAG
Found at i:3345482 original size:23 final size:23
Alignment explanation
Indices: 3345455--3345498 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3345445 ATGCCTAAAC
*
3345455 CAGTTATATGTCTAAAACAAAAA
1 CAGTTAAATGTCTAAAACAAAAA
*
3345478 CAGTTAAATGTCTAGAACAAA
1 CAGTTAAATGTCTAAAACAAA
3345499 TTGTACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (23 bp):
CAGTTAAATGTCTAAAACAAAAA
Found at i:3346922 original size:64 final size:63
Alignment explanation
Indices: 3346805--3346925 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 63
3346795 AATTTTTTTA
*
3346805 TTATTTCTGGTCGGGTTGGGTCGGGTTTCTAATTGATATATTCGGGTCGGGTCGGGTGAAACT
1 TTATTTCTGGTCGGGTTGGGTCGGGTTTCTAAGTGATATATTCGGGTCGGGTCGGGTGAAACT
* *
3346868 TTATTT-TGGTCGGGTTGGGTCGGTTTTTTTTAAGTG-TGATATTCGGGTCGGGTCGGGT
1 TTATTTCTGGTCGGGTTGGGTCGG--GTTTCTAAGTGAT-ATATTCGGGTCGGGTCGGGT
3346926 TAGGATTTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
62 17 0.33
63 7 0.13
64 28 0.54
ACGTcount: A:0.12, C:0.11, G:0.36, T:0.41
Consensus pattern (63 bp):
TTATTTCTGGTCGGGTTGGGTCGGGTTTCTAAGTGATATATTCGGGTCGGGTCGGGTGAAACT
Found at i:3347152 original size:270 final size:270
Alignment explanation
Indices: 3346635--3347120 Score: 664
Period size: 270 Copynumber: 1.8 Consensus size: 270
3346625 TTTATTTTGG
* * *
3346635 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTAAAAAATACTCGACCCGACCCCACCTGAAAATATAT
1 TCGGGTCGGGTCGAGTTAGGATTTAGGGTAAAAAATACCCGACCCGACCCCA-C--AAAATATAT
3346700 ATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCA
63 ATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCA
* * * ****
3346765 ATTAAGTCATTATTTTTATTGAATAAAAATAATTTTTTTATTATTTCTGGTCGGGTTGGGTCGGG
128 ATTAAGTCA-CATTTTTATTGAATAAAAATAATTTTTTTATTATTTCAGGTCGGGTCGGGTAAAA
* * * *
3346830 TTTCTAATTGATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTTGGGTCGGTTTT
192 CTTCTAATT-ATATAGTCGGGTCGGGTCGGGTGAAACCTTATTTTGGTCGGGTCGGGTCGGTTTT
3346895 TTTTAAGTGTGATAT
256 TTTTAAGTGTGATAT
* * *
3346910 TCGGGTCGGGTCGGGTTAGGATTTAGGGTGAAAAATACCCGACCCGA-TCCA-AAAATATATATA
1 TCGGGTCGGGTCGAGTTAGGATTTAGGGTAAAAAATACCCGACCCGACCCCACAAAATATATATA
* *
3346973 TTTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAA-TTTTTTTCAATT
66 ATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATT
* *
3347037 ACGTC-CGTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCAGGTCGGGTCGGGTAAAACTT
131 AAGTCACATTTTTATTGAATAAAAATAA-TTTTTTTATTATTTCAGGTCGGGTCGGGTAAAACTT
*
3347101 -T-ATT-T-TGGTCGGGTCGGGTC
195 CTAATTATATAGTCGGGTCGGGTC
3347121 TCGGATGGAT
Statistics
Matches: 190, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
263 13 0.07
264 1 0.01
266 3 0.02
267 21 0.11
268 29 0.15
269 16 0.08
270 62 0.33
274 3 0.02
275 42 0.22
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (270 bp):
TCGGGTCGGGTCGAGTTAGGATTTAGGGTAAAAAATACCCGACCCGACCCCACAAAATATATATA
ATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATT
AAGTCACATTTTTATTGAATAAAAATAATTTTTTTATTATTTCAGGTCGGGTCGGGTAAAACTTC
TAATTATATAGTCGGGTCGGGTCGGGTGAAACCTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTA
AGTGTGATAT
Found at i:3347679 original size:73 final size:72
Alignment explanation
Indices: 3347596--3347742 Score: 197
Period size: 72 Copynumber: 2.0 Consensus size: 72
3347586 AAATTATTTT
* * * *
3347596 CTTAAGTCTTAACCATAATGTCTTTAAATTTTA-ACTTATTTTATTATCGGTAGGAATGATTTGA
1 CTTAAATCTTAACCATAATGTCTTTAAATTTTAGA-TT-TTTTATCATCCGTAAGAATGATTTGA
* *
3347660 GTGGAATGA
64 GTAGAACGA
**
3347669 CTTAAATCTTAATTATAATGTCTTTAAATTTTAGATTTTTTATCATCCGTAAGAATGATTTGAGT
1 CTTAAATCTTAACCATAATGTCTTTAAATTTTAGATTTTTTATCATCCGTAAGAATGATTTGAGT
3347734 AGAACGA
66 AGAACGA
3347741 CT
1 CT
3347743 AAAAATTATC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
72 32 0.49
73 32 0.49
74 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (72 bp):
CTTAAATCTTAACCATAATGTCTTTAAATTTTAGATTTTTTATCATCCGTAAGAATGATTTGAGT
AGAACGA
Found at i:3354022 original size:24 final size:22
Alignment explanation
Indices: 3353989--3354033 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
3353979 ACACTTATCA
3353989 TTTTCTTTAAATAATTATTTTTTCC
1 TTTTCTTT-AATAA--ATTTTTTCC
3354014 TTTT-TTTAATAAATTTTTTC
1 TTTTCTTTAATAAATTTTTTC
3354034 ATTAAATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.40
23 5 0.25
24 3 0.15
25 4 0.20
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCTTTAATAAATTTTTTCC
Found at i:3354486 original size:15 final size:16
Alignment explanation
Indices: 3354453--3354490 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3354443 CTCAATTATC
* *
3354453 AAAATAAAATGAATTA
1 AAAATATAATGAATAA
3354469 AAAATATAAT-AATAA
1 AAAATATAATGAATAA
3354484 AAAATAT
1 AAAATAT
3354491 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAATATAATGAATAA
Found at i:3356005 original size:21 final size:21
Alignment explanation
Indices: 3355974--3356035 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3355964 CGATTTACAT
* *
3355974 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAATCCAA
* **
3355995 GTTCGCGTTGCGATTTTCCAA
1 ATTCGCGTTGCGATAATCCAA
3356016 ATT--CGTTGCGATAATCCAA
1 ATTCGCGTTGCGATAATCCAA
3356035 A
1 A
3356036 ATCATGCACC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTCGCGTTGCGATAATCCAA
Found at i:3356033 original size:19 final size:20
Alignment explanation
Indices: 3355981--3356035 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
3355971 CATATTCGCA
* *
3355981 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAATCCAAATTC-CG
**
3356002 TTGCGATTTTCCAAATT-CG
1 TTGCGATAATCCAAATTCCG
3356021 TTGCGATAATCCAAA
1 TTGCGATAATCCAAA
3356036 ATCATGCACC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
21 14 0.48
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGCGATAATCCAAATTCCG
Found at i:3356634 original size:21 final size:19
Alignment explanation
Indices: 3356600--3356735 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
3356590 TCGTTGCGAT
*
3356600 TTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
3356619 TTTTGAATAAATCGCAATGCG-A
1 TTTGGAAT--ATCGCAA--CGAA
* *
3356641 TCTTCGACTATCGCAACGAA
1 T-TTGGAATATCGCAACGAA
* *
3356661 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
3356680 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* * *
3356703 CTTGGACTACCGCAACGAA
1 TTTGGAATATCGCAACGAA
* *
3356722 TTTAGAAAATCGCA
1 TTTGGAATATCGCA
3356736 TTGCGATAGT
Statistics
Matches: 91, Mismatches: 16, Indels: 20
0.72 0.13 0.16
Matches are distributed among these distances:
19 44 0.48
20 1 0.01
21 27 0.30
22 2 0.02
23 17 0.19
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:3356670 original size:19 final size:19
Alignment explanation
Indices: 3356601--3356721 Score: 98
Period size: 19 Copynumber: 5.9 Consensus size: 19
3356591 CGTTGCGATT
*
3356601 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
* * *
3356620 TTTGAATAAATCGCAATGCGATC
1 TTGGACT--ATCGCAA--CGAAC
*
3356643 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
3356662 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
3356681 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
3356704 TTGGACTACCGCAACGAA
1 TTGGACTATCGCAACGAA
3356722 TTTAGAAAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
19 36 0.44
21 27 0.33
23 18 0.22
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:3356670 original size:61 final size:61
Alignment explanation
Indices: 3356601--3356721 Score: 197
Period size: 61 Copynumber: 2.0 Consensus size: 61
3356591 CGTTGCGATT
* * * *
3356601 TTGGACTATCGCAACGAATTTTGAATAAATCGCAATGCGATCTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAAC
*
3356662 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTACCGCAACGAA
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAA
3356722 TTTAGAAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (61 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAAC
Found at i:3356734 original size:61 final size:61
Alignment explanation
Indices: 3356608--3356735 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
3356598 ATTTTGGACT
* * * * * **
3356608 ATCGCAACGAATTTTGAATAAATCGCAATGCGATCTTCGACTATCGCAACGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTAGAAA
* *
3356669 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTACCGCAACGAATTTAGAAA
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTAGAAA
3356730 ATCGCA
1 ATCGCA
3356736 TTGCGATAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (61 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTAGAAA
Found at i:3360413 original size:20 final size:20
Alignment explanation
Indices: 3360390--3360441 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3360380 AACGCGATCC
3360390 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
3360410 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
3360430 CCAAAATCGCAA
1 CCAGAATCGCAA
3360442 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:3360458 original size:21 final size:20
Alignment explanation
Indices: 3360431--3360529 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
3360421 AATCAGTTTC
3360431 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3360452 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3360473 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3360493 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3360514 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3360530 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3360558 original size:20 final size:20
Alignment explanation
Indices: 3360496--3360689 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3360486 CGATTTTCCA
* ** *
3360496 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3360516 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3360536 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3360556 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3360576 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3360596 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3360616 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
3360636 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
3360656 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
3360677 AAATCGCAACGCG
1 AAATCGCAACGCG
3360690 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3360580 original size:60 final size:60
Alignment explanation
Indices: 3360496--3360689 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3360486 CGATTTTCCA
* ** * *
3360496 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
3360556 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
3360616 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
3360677 AAATCGCAACGCG
1 AAATCGCAACGCG
3360690 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:3361110 original size:33 final size:33
Alignment explanation
Indices: 3361071--3361141 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3361061 TTCACTTAGA
*
3361071 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3361104 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3361137 TTTCA
1 TTTCA
3361142 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3361280 original size:14 final size:14
Alignment explanation
Indices: 3361261--3361315 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3361251 AGAATGACTG
3361261 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
3361275 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
3361294 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3361308 TCGCAACG
1 TCGCAACG
3361316 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:3361328 original size:33 final size:33
Alignment explanation
Indices: 3361261--3361331 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3361251 AGAATGACTG
***
3361261 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3361294 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3361327 TCGCA
1 TCGCA
3361332 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:3361349 original size:19 final size:18
Alignment explanation
Indices: 3361327--3361444 Score: 89
Period size: 14 Copynumber: 7.1 Consensus size: 18
3361317 GAAACCAAAA
*
3361327 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
3361346 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
3361360 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
3361378 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
* *
3361392 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATT
3361411 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
3361425 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
3361443 TC
1 TC
3361445 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
14 30 0.38
15 7 0.09
16 2 0.03
17 8 0.10
18 13 0.16
19 20 0.25
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:3361420 original size:33 final size:32
Alignment explanation
Indices: 3361332--3361444 Score: 199
Period size: 32 Copynumber: 3.5 Consensus size: 32
3361322 CAAAATCGCA
3361332 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
3361365 TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
*
3361397 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATT-TCATTTCGCGTTGCGATTCTCTCG
3361430 TTGCGATTTCATTTC
1 TTGCGATTTCATTTC
3361445 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
32 40 0.52
33 37 0.48
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3363297 original size:91 final size:93
Alignment explanation
Indices: 3363128--3363500 Score: 681
Period size: 91 Copynumber: 4.1 Consensus size: 93
3363118 TAGATTGCTT
*
3363128 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3363193 -TT-TCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3363219 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3363283 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3363310 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3363375 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3363403 AGTAAATTTGTTCGGTTGCTGCCAATT-TGCTAAAC--TGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3363465 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3363492 AGTAAATTT
1 AGTAAATTT
3363501 ATCCATTCAA
Statistics
Matches: 277, Mismatches: 1, Indels: 10
0.96 0.00 0.03
Matches are distributed among these distances:
89 26 0.09
90 39 0.14
91 142 0.51
92 26 0.09
93 44 0.16
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3363583 original size:19 final size:19
Alignment explanation
Indices: 3363543--3363670 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
3363533 TAGTTTACTT
* *
3363543 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3363563 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3363582 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3363601 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3363615 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3363634 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3363648 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
3363666 TCGCA
1 TCGCA
3363671 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 9 0.10
19 38 0.43
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3363622 original size:33 final size:32
Alignment explanation
Indices: 3363579--3363670 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
3363569 CGCGAAACCA
**
3363579 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3363611 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3363644 AAGATCGCAACGCGAAACC-AAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3363671 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 10 0.18
33 46 0.82
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3363693 original size:19 final size:19
Alignment explanation
Indices: 3363666--3363800 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
3363656 CGAAACCAAA
*
3363666 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3363685 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3363701 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3363718 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3363734 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3363751 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3363770 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3363790 TCGTGTTGCGA
1 TCGCGTTGCGA
3363801 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3363707 original size:14 final size:14
Alignment explanation
Indices: 3363688--3363744 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3363678 TTTCATTTCG
3363688 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3363702 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3363719 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
3363735 CGTTGCGATT
1 CGTTGCGATT
3363745 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3363713 original size:33 final size:33
Alignment explanation
Indices: 3363671--3363763 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
3363661 CCAAATCGCA
*
3363671 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3363704 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3363737 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3363764 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3364791 original size:34 final size:36
Alignment explanation
Indices: 3364736--3364802 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
3364726 ATTGATTGTT
3364736 TTTTGATTGTTAATTGATTTGTAAAAG-TGATTCAA
1 TTTTGATTGTTAATTGATTTGTAAAAGATGATTCAA
3364771 TTTTGATTGTT-ATTGATTTGTAAAAGATGATT
1 TTTTGATTGTTAATTGATTTGTAAAAGATGATT
3364803 TGTAAAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 15 0.48
35 16 0.52
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (36 bp):
TTTTGATTGTTAATTGATTTGTAAAAGATGATTCAA
Found at i:3364803 original size:14 final size:14
Alignment explanation
Indices: 3364784--3364819 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3364774 TGATTGTTAT
3364784 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3364798 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3364812 TGATTTGT
1 TGATTTGT
3364820 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3364942 original size:19 final size:19
Alignment explanation
Indices: 3364926--3365027 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3364916 AAAAATGACT
3364926 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3364945 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3364964 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3364978 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3364997 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3365017 ATCGCAATGCG
1 ATCGCAATGCG
3365028 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3365076 original size:33 final size:36
Alignment explanation
Indices: 3365034--3365350 Score: 318
Period size: 33 Copynumber: 9.1 Consensus size: 36
3365024 TGCGTTTATA
*
3365034 ATTTCGCATTGCGA-TT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
3365067 ATTTCGCATTGCGATTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTCATTTCG-ATTGCGATTTTC
3365102 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
3365136 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
3365174 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
3365210 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
3365245 ATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
3365278 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
3365314 -TCTCG--TTGCGATTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTT-CG-ATTGCGATTTTC
3365349 AT
1 AT
3365351 GTTGGGATTT
Statistics
Matches: 250, Mismatches: 10, Indels: 45
0.82 0.03 0.15
Matches are distributed among these distances:
32 14 0.06
33 98 0.39
34 10 0.04
35 34 0.14
36 17 0.07
37 30 0.12
38 47 0.19
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (36 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
Found at i:3365080 original size:19 final size:19
Alignment explanation
Indices: 3365056--3365350 Score: 375
Period size: 19 Copynumber: 16.7 Consensus size: 19
3365046 GATTATCTCG
3365056 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3365075 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3365093 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3365107 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3365126 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3365144 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
3365163 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
3365182 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3365201 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3365215 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3365234 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3365253 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3365267 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3365286 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3365305 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3365319 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3365338 TTGCGATTTTCAT
1 TTGCGATTTTCAT
3365351 GTTGGGATTT
Statistics
Matches: 244, Mismatches: 10, Indels: 43
0.82 0.03 0.14
Matches are distributed among these distances:
14 24 0.10
15 3 0.01
16 28 0.11
17 27 0.11
18 36 0.15
19 120 0.49
20 6 0.02
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3365235 original size:52 final size:52
Alignment explanation
Indices: 3365034--3365350 Score: 523
Period size: 52 Copynumber: 6.0 Consensus size: 52
3365024 TGCGTTTATA
*
3365034 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3365085 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
3365136 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
3365193 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
3365245 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
3365297 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
3365349 AT
1 AT
3365351 GTTGGGATTT
Statistics
Matches: 254, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
51 71 0.28
52 126 0.50
53 3 0.01
54 9 0.04
55 3 0.01
56 24 0.09
57 18 0.07
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3367689 original size:12 final size:12
Alignment explanation
Indices: 3367672--3367696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3367662 TCTTCGGGGA
3367672 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3367684 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3367696 C
1 C
3367697 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3367904 original size:24 final size:24
Alignment explanation
Indices: 3367870--3367916 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3367860 CTGAAACATC
3367870 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3367894 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3367917 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3368614 original size:20 final size:20
Alignment explanation
Indices: 3368586--3368954 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
3368576 AAATTTCAGT
* * * *
3368586 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3368606 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3368626 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3368646 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3368666 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3368686 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3368706 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3368726 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3368746 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3368766 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
3368786 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3368806 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3368826 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
3368846 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
3368866 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3368886 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3368906 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
3368926 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
3368946 GTTGCGATT
1 GTTGCGATT
3368955 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3377251 original size:113 final size:115
Alignment explanation
Indices: 3377046--3377267 Score: 315
Period size: 113 Copynumber: 1.9 Consensus size: 115
3377036 GGGTCAGGTA
* * *
3377046 CGAGTTTCAACCTAAAAATCCAAGTCGAATTTCGAACCTATAGAGACCTTCTTAAACCCTAAGTA
1 CGAGTTTCAACCTAAAAATCCAAGTCGAATTTCAAACCGAAAGAGACC-TCTTAAACCCTAAGTA
*
3377111 GGATCAAATACAAATAGAAAAATTTATTCTTT-GGATCAAATTCGAACTATC
65 GGATCAAATACAAATAGAAAAAATTATT-TTTCGGATCAAATTCGAACTATC
* * * * *
3377162 CGAGTTTCAACCTAAAAATTCAAGTCGGATTTTAAACCGAAAGATA-C-CTTAAACCCTAAGTCG
1 CGAGTTTCAACCTAAAAATCCAAGTCGAATTTCAAACCGAAAGAGACCTCTTAAACCCTAAGTAG
*
3377225 GATGAAATACAAATAGAAAAAATTATTTTTCGGATCAAATTCG
66 GATCAAATACAAATAGAAAAAATTATTTTTCGGATCAAATTCG
3377268 GAATGACAGA
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
112 3 0.03
113 52 0.55
115 1 0.01
116 39 0.41
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (115 bp):
CGAGTTTCAACCTAAAAATCCAAGTCGAATTTCAAACCGAAAGAGACCTCTTAAACCCTAAGTAG
GATCAAATACAAATAGAAAAAATTATTTTTCGGATCAAATTCGAACTATC
Found at i:3384289 original size:21 final size:21
Alignment explanation
Indices: 3384263--3384302 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3384253 AAGCACAAGC
3384263 TGAGGTGAGGCGAATCTATGA
1 TGAGGTGAGGCGAATCTATGA
3384284 TGAGGTGAGGCGAATCTAT
1 TGAGGTGAGGCGAATCTAT
3384303 CTAAAGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.38, T:0.25
Consensus pattern (21 bp):
TGAGGTGAGGCGAATCTATGA
Found at i:3384318 original size:14 final size:14
Alignment explanation
Indices: 3384299--3384325 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3384289 TGAGGCGAAT
3384299 CTATCTAAAGGTTC
1 CTATCTAAAGGTTC
3384313 CTATCTAAAGGTT
1 CTATCTAAAGGTT
3384326 GTCTAACAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
CTATCTAAAGGTTC
Found at i:3384608 original size:26 final size:26
Alignment explanation
Indices: 3384578--3384629 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3384568 TTTTTATGTT
* *
3384578 AGGGGGTAAACTTTTAAAATTTTAGG
1 AGGGGATAAACTTATAAAATTTTAGG
3384604 AGGGGATAAACTTATAAAATTTTAGG
1 AGGGGATAAACTTATAAAATTTTAGG
3384630 GGAACTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (26 bp):
AGGGGATAAACTTATAAAATTTTAGG
Found at i:3384637 original size:20 final size:20
Alignment explanation
Indices: 3384612--3384652 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3384602 GGAGGGGATA
3384612 AACTTATAAAATTTTAGGGG
1 AACTTATAAAATTTTAGGGG
3384632 AACTTATAAAATTTTAGGGG
1 AACTTATAAAATTTTAGGGG
3384652 A
1 A
3384653 CGAAAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (20 bp):
AACTTATAAAATTTTAGGGG
Found at i:3386888 original size:21 final size:20
Alignment explanation
Indices: 3386859--3386899 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3386849 TTATTTTTTT
3386859 TAATAAAAACAAATAAATTAA
1 TAATAAAAACAAAT-AATTAA
* *
3386880 TAATTAAAATAAATAATTAA
1 TAATAAAAACAAATAATTAA
3386900 AATCAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
TAATAAAAACAAATAATTAA
Found at i:3386911 original size:13 final size:13
Alignment explanation
Indices: 3386873--3386902 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3386863 AAAAACAAAT
*
3386873 AAATTAATAATTA
1 AAATAAATAATTA
3386886 AAATAAATAATTA
1 AAATAAATAATTA
3386899 AAAT
1 AAAT
3386903 CAGTAATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATAAATAATTA
Found at i:3387169 original size:17 final size:17
Alignment explanation
Indices: 3387149--3387206 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
3387139 ATTTTTTAAA
3387149 TATTAAAATAATTTATT
1 TATTAAAATAATTTATT
3387166 TATTAATAA-AATATTATT
1 TATTAA-AATAAT-TTATT
*
3387184 T-TTATAAT--TTTA-T
1 TATTAAAATAATTTATT
3387197 TATTAAAATA
1 TATTAAAATA
3387207 TTAATATTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 2 0.06
14 9 0.26
15 1 0.03
16 2 0.06
17 12 0.35
18 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTAAAATAATTTATT
Found at i:3387214 original size:14 final size:14
Alignment explanation
Indices: 3387165--3387214 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
3387155 AATAATTTAT
*
3387165 TTATTAATAAAATA
1 TTATTATTAAAATA
* * *
3387179 TTATTTTTATAATT
1 TTATTATTAAAATA
3387193 TTATTATTAAAATA
1 TTATTATTAAAATA
*
3387207 TTAATATT
1 TTATTATT
3387215 GGTATATTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATTATTAAAATA
Found at i:3387451 original size:29 final size:30
Alignment explanation
Indices: 3387419--3387500 Score: 73
Period size: 29 Copynumber: 2.8 Consensus size: 30
3387409 AATTTTATTA
3387419 ATAATTTATTATATTATTAAAATAAAAAT-
1 ATAATTTATTATATTATTAAAATAAAAATG
* * *
3387448 ATAATATCT-TTAT-TTATTATAAT-ATATTG
1 ATAAT-T-TATTATATTATTAAAATAAAAATG
* *
3387477 ATTATTTATTATAATATTAAAATA
1 ATAATTTATTATATTATTAAAATA
3387501 TAATTTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.02
28 8 0.20
29 26 0.63
30 5 0.12
31 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
ATAATTTATTATATTATTAAAATAAAAATG
Found at i:3387470 original size:18 final size:20
Alignment explanation
Indices: 3387447--3387493 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
3387437 AAAATAAAAA
3387447 TATAATAT-CT-TTATTTAT
1 TATAATATACTATTATTTAT
*
3387465 TATAATATATTGATTATTTAT
1 TATAATATACT-ATTATTTAT
3387486 TATAATAT
1 TATAATAT
3387494 TAAAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 1 0.04
21 16 0.64
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TATAATATACTATTATTTAT
Found at i:3388162 original size:119 final size:120
Alignment explanation
Indices: 3387988--3388232 Score: 438
Period size: 121 Copynumber: 2.0 Consensus size: 120
3387978 CTTTTAATCT
*
3387988 CACGCTAATTAATTAAATAAACATAGTTAAATCTATCAAATATGGAATTTTATACTA-TTTTTGT
1 CACGCTAATTAACTAAATAAACATAGTTAAATCTATCAAATATGGAATTTTATACTATTTTTTGT
*
3388052 TTTACTCCCGTTTACAAGATTTCATCTTGATTAATCTTGACCGACCCACATCGCA
66 TTTACTCCCGTTTACAAGATTTCATCTTGATTAATCTAGACCGACCCACATCGCA
3388107 CACGCTAATTAACTAAATAAACATAGTTAAATCTATCAAATATGGAATTTTATACTATTTTTTTG
1 CACGCTAATTAACTAAATAAACATAGTTAAATCTATCAAATATGGAATTTTATACTA-TTTTTTG
* *
3388172 TTTTACTCCCGTTTATAAGATTTCGTCTTGATTAATCTAGACCGACCCACATCGCA
65 TTTTACTCCCGTTTACAAGATTTCATCTTGATTAATCTAGACCGACCCACATCGCA
3388228 CACGC
1 CACGC
3388233 GAGACCTTAC
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
119 56 0.47
121 64 0.53
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (120 bp):
CACGCTAATTAACTAAATAAACATAGTTAAATCTATCAAATATGGAATTTTATACTATTTTTTGT
TTTACTCCCGTTTACAAGATTTCATCTTGATTAATCTAGACCGACCCACATCGCA
Found at i:3399560 original size:21 final size:21
Alignment explanation
Indices: 3399520--3399561 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3399510 AGAATAGGGC
* **
3399520 AGATGATGATATGGGTGATGA
1 AGATGATGACATGGCAGATGA
3399541 AGATGATGACATGGCAGATGA
1 AGATGATGACATGGCAGATGA
3399562 TGGGGATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.24
Consensus pattern (21 bp):
AGATGATGACATGGCAGATGA
Found at i:3408323 original size:2 final size:2
Alignment explanation
Indices: 3408318--3408359 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3408308 GAAGACAATT
3408318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3408360 CATGTGGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3410017 original size:35 final size:36
Alignment explanation
Indices: 3409945--3410017 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
3409935 TACTATAATT
**
3409945 AATTTATATATTTTCTTTAAAAATTTTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAA-TTTAAAAACATAA
*
3409982 AATTTATATATTTT-TTTACAAAA-TTAAAAAGATAA
1 AATTTATATATTTTCTTTA-AAAATTTAAAAACATAA
3410017 A
1 A
3410018 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 10 0.31
36 4 0.12
37 18 0.56
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
AATTTATATATTTTCTTTAAAAATTTAAAAACATAA
Found at i:3420309 original size:52 final size:52
Alignment explanation
Indices: 3420247--3420351 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
3420237 AAACTTCTTA
*
3420247 TTAAAGCTTTCACCAGTGGAAAGAGAAACATAAAAGCAAATAAGATACAACT
1 TTAAAGCTTTCACCAGGGGAAAGAGAAACATAAAAGCAAATAAGATACAACT
* *
3420299 TTAAAGCTTTCACCAGGGGAAAGAGAAACATAAAAGCAAATTAGATACGACT
1 TTAAAGCTTTCACCAGGGGAAAGAGAAACATAAAAGCAAATAAGATACAACT
3420351 T
1 T
3420352 ACCATCCTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (52 bp):
TTAAAGCTTTCACCAGGGGAAAGAGAAACATAAAAGCAAATAAGATACAACT
Found at i:3422142 original size:6 final size:6
Alignment explanation
Indices: 3422127--3422223 Score: 86
Period size: 6 Copynumber: 15.2 Consensus size: 6
3422117 TTCATCATTC
* * *
3422127 AAAATA AAAATG AAAATA AAAATG AAAATA AAAATA ATGAACTA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A--AAATA AAAATA
* * *
3422177 TAAAATG AAAATG AAAATA AAAATA ATGAACTA AAAATA TAAAATA A
1 -AAAATA AAAATA AAAATA AAAATA A--AAATA AAAATA -AAAATA A
3422224 TTGTATAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
6 54 0.72
7 11 0.15
8 10 0.13
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:3422174 original size:14 final size:14
Alignment explanation
Indices: 3422155--3422215 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
3422145 AAAATGAAAA
3422155 TAAAAATAATGAAC
1 TAAAAATAATGAAC
* *
3422169 TAAAAAT-ATAAAA
1 TAAAAATAATGAAC
*
3422182 TGAAAATGAA--AA-
1 TAAAAAT-AATGAAC
3422194 TAAAAATAATGAAC
1 TAAAAATAATGAAC
3422208 TAAAAATA
1 TAAAAATA
3422216 TAAAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 2 0.05
12 6 0.16
13 14 0.37
14 15 0.39
15 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (14 bp):
TAAAAATAATGAAC
Found at i:3422188 original size:39 final size:39
Alignment explanation
Indices: 3422131--3422223 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 39
3422121 TCATTCAAAA
*
3422131 TAAAAAT-GAAAATAAAAATGAAAATAAAAATAATGAAC
1 TAAAAATATAAAATAAAAATGAAAATAAAAATAATGAAC
*
3422169 TAAAAATATAAAATGAAAATGAAAATAAAAATAATGAAC
1 TAAAAATATAAAATAAAAATGAAAATAAAAATAATGAAC
3422208 TAAAAATATAAAATAA
1 TAAAAATATAAAATAA
3422224 TTGTATAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 7 0.14
39 44 0.86
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (39 bp):
TAAAAATATAAAATAAAAATGAAAATAAAAATAATGAAC
Found at i:3423354 original size:18 final size:19
Alignment explanation
Indices: 3423331--3423377 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
3423321 GTTCTATTAA
*
3423331 CGGTTAA-AGAAAAAAAAT
1 CGGTTAATAAAAAAAAAAT
3423349 CGGTTAATTCAAAAAAAAAAT
1 CGGTTAA-T-AAAAAAAAAAT
3423370 CGGTTAAT
1 CGGTTAAT
3423378 TCGGTTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
20 1 0.04
21 17 0.68
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (19 bp):
CGGTTAATAAAAAAAAAAT
Found at i:3423366 original size:21 final size:21
Alignment explanation
Indices: 3423340--3423379 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3423330 ACGGTTAAAG
3423340 AAAAAAAATCGGTTAATTCAA
1 AAAAAAAATCGGTTAATTCAA
3423361 AAAAAAAATCGGTTAATTC
1 AAAAAAAATCGGTTAATTC
3423380 GGTTAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (21 bp):
AAAAAAAATCGGTTAATTCAA
Found at i:3429324 original size:22 final size:23
Alignment explanation
Indices: 3429298--3429346 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
3429288 TAAACAACCG
3429298 AAAACATATCATAAGA-ATAGA-A
1 AAAACATATCATAA-ATATAGAGA
* *
3429320 AAAACGTATTATAAATATAGAGA
1 AAAACATATCATAAATATAGAGA
3429343 AAAA
1 AAAA
3429347 TATACTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 17 0.74
23 5 0.22
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.20
Consensus pattern (23 bp):
AAAACATATCATAAATATAGAGA
Found at i:3439738 original size:19 final size:19
Alignment explanation
Indices: 3439714--3439753 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3439704 AGTCTTGTTT
3439714 CATACAGAATCTCATAAAG
1 CATACAGAATCTCATAAAG
3439733 CATACAGAATCTCATAAAG
1 CATACAGAATCTCATAAAG
3439752 CA
1 CA
3439754 AAAAGGCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.20
Consensus pattern (19 bp):
CATACAGAATCTCATAAAG
Found at i:3442672 original size:2 final size:2
Alignment explanation
Indices: 3442665--3442690 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3442655 GTTTCTATGC
3442665 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
3442691 TTTTTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3449161 original size:20 final size:20
Alignment explanation
Indices: 3449136--3449195 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
3449126 ATTTAAATGA
3449136 TAAACGAACATAAACGAACG
1 TAAACGAACATAAACGAACG
3449156 TAAACGAACATAAACGAACG
1 TAAACGAACATAAACGAACG
* *
3449176 TAAACAAACACAAACGAACG
1 TAAACGAACATAAACGAACG
3449196 AACACAAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.57, C:0.22, G:0.13, T:0.08
Consensus pattern (20 bp):
TAAACGAACATAAACGAACG
Found at i:3449199 original size:14 final size:14
Alignment explanation
Indices: 3449182--3449208 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3449172 AACGTAAACA
3449182 AACACAAACGAACG
1 AACACAAACGAACG
3449196 AACACAAACGAAC
1 AACACAAACGAAC
3449209 ATAATAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.30, G:0.11, T:0.00
Consensus pattern (14 bp):
AACACAAACGAACG
Found at i:3449202 original size:20 final size:20
Alignment explanation
Indices: 3449136--3449204 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
3449126 ATTTAAATGA
*
3449136 TAAACGAACATAAACGAACG
1 TAAACAAACATAAACGAACG
*
3449156 TAAACGAACATAAACGAACG
1 TAAACAAACATAAACGAACG
*
3449176 TAAACAAACACAAACGAACG
1 TAAACAAACATAAACGAACG
3449196 -AACACAAAC
1 TAA-ACAAAC
3449205 GAACATAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 2 0.04
20 44 0.96
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.07
Consensus pattern (20 bp):
TAAACAAACATAAACGAACG
Found at i:3449232 original size:10 final size:10
Alignment explanation
Indices: 3449135--3449194 Score: 84
Period size: 10 Copynumber: 6.0 Consensus size: 10
3449125 CATTTAAATG
3449135 ATAAACGAAC
1 ATAAACGAAC
3449145 ATAAACGAAC
1 ATAAACGAAC
*
3449155 GTAAACGAAC
1 ATAAACGAAC
3449165 ATAAACGAAC
1 ATAAACGAAC
* *
3449175 GTAAACAAAC
1 ATAAACGAAC
*
3449185 ACAAACGAAC
1 ATAAACGAAC
3449195 GAACACAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 43 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3468461 original size:18 final size:17
Alignment explanation
Indices: 3468429--3468463 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3468419 AAGAAGAGGG
*
3468429 GAAGAAGATTTGCAGTT
1 GAAGAAGAGTTGCAGTT
3468446 GAAGAAGCAGTTGCAGTT
1 GAAGAAG-AGTTGCAGTT
3468464 CAGCTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (17 bp):
GAAGAAGAGTTGCAGTT
Found at i:3468796 original size:4 final size:4
Alignment explanation
Indices: 3468787--3468813 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3468777 AACTACACCA
3468787 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
3468814 TTGTGCTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:3471084 original size:22 final size:22
Alignment explanation
Indices: 3471045--3471097 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
3471035 TACGGAGATT
*
3471045 TTATTTTATTACGAATTT-TCAA
1 TTATTTTATTACAAATTTGT-AA
3471067 TTATTTTATTA-AATATTTGTAA
1 TTATTTTATTACAA-ATTTGTAA
3471089 TTAATTTTA
1 TT-ATTTTA
3471098 GCTTTATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 19 0.70
23 7 0.26
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (22 bp):
TTATTTTATTACAAATTTGTAA
Found at i:3471159 original size:11 final size:11
Alignment explanation
Indices: 3471131--3471162 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3471121 TTAAAATAAA
3471131 TTAAGATTTTT
1 TTAAGATTTTT
3471142 TT-A-ATTTTT
1 TTAAGATTTTT
3471151 TTAAGATTTTT
1 TTAAGATTTTT
3471162 T
1 T
3471163 CTTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.42
10 2 0.11
11 9 0.47
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (11 bp):
TTAAGATTTTT
Found at i:3471807 original size:19 final size:17
Alignment explanation
Indices: 3471775--3471812 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
3471765 TCTAAATTAA
3471775 TTATTTTTCTTTTATTT
1 TTATTTTTCTTTTATTT
3471792 TTATTCTTTCCTTTTATTT
1 TTATT-TTT-CTTTTATTT
3471811 TT
1 TT
3471813 TTATTCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 3 0.16
19 11 0.58
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTTTCTTTTATTT
Found at i:3496349 original size:19 final size:19
Alignment explanation
Indices: 3496325--3496372 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3496315 AAGATATTCT
3496325 TTTTAATATTA-TACTTTTA
1 TTTTAATATTATTA-TTTTA
* *
3496344 TTTTAAAAATATTATTTTA
1 TTTTAATATTATTATTTTA
*
3496363 TTTAAATATT
1 TTTTAATATT
3496373 TTTAAAAATG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAATATTATTATTTTA
Found at i:3496378 original size:10 final size:10
Alignment explanation
Indices: 3496363--3496398 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3496353 TATTATTTTA
3496363 TTTAAATATT
1 TTTAAATATT
*
3496373 TTTAAAAATGT
1 TTTAAATAT-T
3496384 TTTAAATATT
1 TTTAAATATT
3496394 TTTAA
1 TTTAA
3496399 TTTGAGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
TTTAAATATT
Found at i:3498342 original size:17 final size:18
Alignment explanation
Indices: 3498309--3498342 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3498299 CCGCTACTAG
3498309 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
3498327 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
3498343 GACTGGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:3505246 original size:17 final size:16
Alignment explanation
Indices: 3505220--3505254 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3505210 TTTAAATAAT
3505220 AAAATCTAAAATATTTA
1 AAAATCTAAAAT-TTTA
*
3505237 AAAATTTAAAATTTTA
1 AAAATCTAAAATTTTA
3505253 AA
1 AA
3505255 GGAGACGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATCTAAAATTTTA
Found at i:3505931 original size:2 final size:2
Alignment explanation
Indices: 3505924--3505977 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3505914 TCTAACAATA
3505924 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
3505966 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3505978 TCTTTTCACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3506161 original size:21 final size:21
Alignment explanation
Indices: 3506137--3506178 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3506127 TCGTAAACAA
*
3506137 TTGTAGTTAAAAGACTAAATT
1 TTGTAGTCAAAAGACTAAATT
3506158 TTGTAGTCAAAAGACTAAATT
1 TTGTAGTCAAAAGACTAAATT
3506179 GAGTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (21 bp):
TTGTAGTCAAAAGACTAAATT
Done.