Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008091.1 Hibiscus syriacus cultivar Beakdansim tig00110602_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: 2471235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2344471 original size:3 final size:3
Alignment explanation
Indices: 2344463--2344538 Score: 50
Period size: 3 Copynumber: 24.7 Consensus size: 3
2344453 CCCACTTCAA
* *
2344463 TTC TTC TTC TAT- TTC TTC TTTC TTC TTC TGT- ATC TTT TTC TTC TTC
1 TTC TTC TTC T-TC TTC TTC -TTC TTC TTC T-TC TTC TTC TTC TTC TTC
* *
2344509 TAAT- TTC TTC TTC TTC ATC TTT TTC TTC TT
1 T--TC TTC TTC TTC TTC TTC TTC TTC TTC TT
2344539 ACATTCTCTT
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
2 3 0.05
3 47 0.82
4 6 0.11
5 1 0.02
ACGTcount: A:0.07, C:0.25, G:0.01, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2344638 original size:3 final size:3
Alignment explanation
Indices: 2344632--2344660 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2344622 CTCCACGTGC
2344632 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2344661 ACCACATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:2345988 original size:21 final size:22
Alignment explanation
Indices: 2345957--2346002 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2345947 TTATTAAAAA
* * *
2345957 AAAATTAAAGATATGATACAAG
1 AAAATTAAAGAAATAAAACAAG
2345979 AAAA-TAAAGAAATAAAACAAG
1 AAAATTAAAGAAATAAAACAAG
2346000 AAA
1 AAA
2346003 TATTGATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAATTAAAGAAATAAAACAAG
Found at i:2346438 original size:17 final size:18
Alignment explanation
Indices: 2346400--2346445 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
2346390 GTTTATGATA
*
2346400 GAATTGAAATCTGTGAAG
1 GAATTGGAATCTGTGAAG
*
2346418 GAATTGGAATCTGT-CAG
1 GAATTGGAATCTGTGAAG
2346435 GAATTGGAATC
1 GAATTGGAATC
2346446 CAATTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GAATTGGAATCTGTGAAG
Found at i:2347265 original size:27 final size:27
Alignment explanation
Indices: 2347235--2347293 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
2347225 AAATTTCAAT
2347235 TCCATCCAAGAAGGGAATTGAATTCCA
1 TCCATCCAAGAAGGGAATTGAATTCCA
* ** * * *
2347262 TCCATTCTTGGATGGAATTGAATTCTA
1 TCCATCCAAGAAGGGAATTGAATTCCA
2347289 TCCAT
1 TCCAT
2347294 TTTTTGATGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (27 bp):
TCCATCCAAGAAGGGAATTGAATTCCA
Found at i:2347294 original size:27 final size:27
Alignment explanation
Indices: 2347248--2347307 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
2347238 ATCCAAGAAG
2347248 GGAATTGAATTCCATCCATTCTTGGAT
1 GGAATTGAATTCCATCCATTCTTGGAT
* * *
2347275 GGAATTGAATTCTATCCATTTTTTGAT
1 GGAATTGAATTCCATCCATTCTTGGAT
2347302 GGAATT
1 GGAATT
2347308 CACTTTCCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (27 bp):
GGAATTGAATTCCATCCATTCTTGGAT
Found at i:2347755 original size:15 final size:15
Alignment explanation
Indices: 2347737--2347768 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2347727 AATTATTGTC
*
2347737 AAAATTTAAAAATTT
1 AAAATTTAAAAAGTT
2347752 AAAATTTAAAAAGTT
1 AAAATTTAAAAAGTT
2347767 AA
1 AA
2347769 TAAAGATAAA
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:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATTTAAAAAGTT
Found at i:2353291 original size:17 final size:17
Alignment explanation
Indices: 2353269--2353319 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
2353259 TTGATTGAAG
2353269 TTTAAACTCAAATTCAA
1 TTTAAACTCAAATTCAA
* *
2353286 TTTAAACTTAAATTTAA
1 TTTAAACTCAAATTCAA
*
2353303 TTTAAGCTCAAATTCAA
1 TTTAAACTCAAATTCAA
2353320 ATTTTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (17 bp):
TTTAAACTCAAATTCAA
Found at i:2360118 original size:84 final size:84
Alignment explanation
Indices: 2359955--2360111 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 84
2359945 AGGGGACATC
* *
2359955 ATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGTACAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
2360020 CTCAGCTCCAAGGCATATT
66 CTCAGCTCCAAGGCATATT
* * * * *
2360039 ATTTGCAGTACAACTTAAGTCTAGAGGGGTTGTCTGCCAA-CAGAATACCTTCGAGTTCGATTAC
1 ATTTGCAGTACAACTTAAGTCGAGAAGGGTTATCTGCCAACCA-AAGACCTTCGAGTTCGACTAC
2360103 ACTCAGCTC
65 ACTCAGCTC
2360112 AGAGGCAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
83 2 0.03
84 63 0.97
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (84 bp):
ATTTGCAGTACAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
CTCAGCTCCAAGGCATATT
Found at i:2361917 original size:15 final size:14
Alignment explanation
Indices: 2361895--2361924 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2361885 TTTTCCTTTC
2361895 TGTTTTTTATTTAT
1 TGTTTTTTATTTAT
2361909 TGTTATTTTATTTAT
1 TGTT-TTTTATTTAT
2361924 T
1 T
2361925 TCATCTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (14 bp):
TGTTTTTTATTTAT
Found at i:2365754 original size:14 final size:14
Alignment explanation
Indices: 2365735--2365768 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2365725 ACAGATGATG
2365735 TTCGCTGCGTTCGC
1 TTCGCTGCGTTCGC
2365749 TTCGCTGCGTTCGC
1 TTCGCTGCGTTCGC
2365763 TTCGCT
1 TTCGCT
2365769 ACGCTCCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.26, T:0.38
Consensus pattern (14 bp):
TTCGCTGCGTTCGC
Found at i:2367569 original size:56 final size:54
Alignment explanation
Indices: 2367500--2367706 Score: 179
Period size: 56 Copynumber: 3.7 Consensus size: 54
2367490 TTAACTTATT
* *
2367500 AAATATATTTTATTATTAACTTAATTTGAGATTGTTTTATTATTTTTTTAATTTAAA
1 AAATATATTTTATTATTAACTTAATTTGA-AATATTTTATT-TTTTTTTAATTT-AA
* * * *
2367557 AATATATATTATTATTATTAGCTTAA-AT-ATATATTTTATTCTTATTTTAATTTAA
1 AA-ATATATT-TTATTATTAACTTAATTTGAAATATTTTATT-TTTTTTTAATTTAA
* ** *
2367612 ACAA-ATATTTTATTCTTATTTTAATTTGAAAATATTTTATTTTTATTTTAAATTTTA
1 A-AATATATTTTATTATTAACTTAATTTG-AAATATTTTATTTTT-TTTT-AATTTAA
* *
2367669 AAATATATTTTATT-TTATCTTAATTTACAAATATTTTA
1 AAATATATTTTATTATTAACTTAATTT-GAAATATTTTA
2367707 AAATTTTTAA
Statistics
Matches: 124, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
53 12 0.10
54 6 0.05
55 6 0.05
56 58 0.47
57 20 0.16
58 8 0.06
59 14 0.11
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (54 bp):
AAATATATTTTATTATTAACTTAATTTGAAATATTTTATTTTTTTTTAATTTAA
Found at i:2367571 original size:29 final size:28
Alignment explanation
Indices: 2367465--2367702 Score: 175
Period size: 27 Copynumber: 8.4 Consensus size: 28
2367455 TTTATATATC
* *
2367465 TTTAAAAGTATATTTTATTTTCATCTTAA
1 TTTAAAAATATATTTTATTTT-ATTTTAA
* * **
2367494 CTTATTAAATATATTTTATTATTAACTTAA
1 TTTA-AAAATATATTTTATT-TTATTTTAA
* * * *
2367524 TTT-GAGAT-TGTTTTATTATTTTTTTAA
1 TTTAAAAATATATTTTATT-TTATTTTAA
* *
2367551 TTTAAAAATATATATTA--TTATTATTAG
1 TTTAAAAATATATTTTATTTTATT-TTAA
* *
2367578 CTTAAATATATATTTTATTCTTATTTTAA
1 TTTAAAAATATATTTTATT-TTATTTTAA
2367607 TTTAAACAA-ATATTTTATTCTTATTTTAA
1 TTTAAA-AATATATTTTATT-TTATTTTAA
*
2367636 TTT-GAAA-ATATTTTATTTTTATTTTAAA
1 TTTAAAAATATATTTTA-TTTTATTTT-AA
* *
2367664 TTTTAAAATATATTTTATTTTATCTTAA
1 TTTAAAAATATATTTTATTTTATTTTAA
*
2367692 TTTACAAATAT
1 TTTAAAAATAT
2367703 TTTAAAATTT
Statistics
Matches: 168, Mismatches: 28, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
26 4 0.02
27 52 0.31
28 25 0.15
29 50 0.30
30 35 0.21
31 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTAAAAATATATTTTATTTTATTTTAA
Found at i:2367652 original size:27 final size:27
Alignment explanation
Indices: 2367498--2367706 Score: 179
Period size: 27 Copynumber: 7.5 Consensus size: 27
2367488 TCTTAACTTA
* **
2367498 TTAAATATATTTTATTATTAACTTAAT
1 TTAAAAATATTTTATTATTATTTTAAT
* * * * *
2367525 TTGAGATTGTTTTATTATTTTTTTAAT
1 TTAAAAATATTTTATTATTATTTTAAT
* **
2367552 TTAAAAATA-TATATTATTATTATTAGC
1 TTAAAAATATTTTATTATTATT-TTAAT
*
2367579 TTAAATATATATTTTATTCTTATTTTAAT
1 TTAAA-A-ATATTTTATTATTATTTTAAT
*
2367608 TTAAACAAATATTTTATTCTTATTTTAAT
1 TT-AA-AAATATTTTATTATTATTTTAAT
* *
2367637 TTGAAAATATTTTATTTTTATTTTAAATT
1 TTAAAAATATTTTATTATTATTTT-AA-T
*
2367666 TTAAAATATATTTTATT-TTATCTTAAT
1 TTAAAA-ATATTTTATTATTATTTTAAT
*
2367693 TTACAAATATTTTA
1 TTAAAAATATTTTA
2367707 AAATTTTTAA
Statistics
Matches: 148, Mismatches: 25, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
26 18 0.12
27 57 0.39
28 6 0.04
29 43 0.29
30 23 0.16
31 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.58
Consensus pattern (27 bp):
TTAAAAATATTTTATTATTATTTTAAT
Found at i:2367710 original size:10 final size:10
Alignment explanation
Indices: 2367692--2367737 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
2367682 TTTATCTTAA
2367692 TTTACAAATAT
1 TTTA-AAATAT
2367703 TTTAAAAT-T
1 TTTAAAATAT
*
2367712 TTT--AATTT
1 TTTAAAATAT
2367720 TTTAAAATAT
1 TTTAAAATAT
2367730 TTTAAAAT
1 TTTAAAAT
2367738 TTTACCCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
7 3 0.10
8 4 0.13
9 4 0.13
10 16 0.52
11 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTAAAATAT
Found at i:2368733 original size:12 final size:12
Alignment explanation
Indices: 2368716--2368744 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2368706 TCAAAGAAAA
2368716 GCTTTCTATTAT
1 GCTTTCTATTAT
2368728 GCTTTCTATTAT
1 GCTTTCTATTAT
2368740 GCTTT
1 GCTTT
2368745 AGAAGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.59
Consensus pattern (12 bp):
GCTTTCTATTAT
Found at i:2371991 original size:2 final size:2
Alignment explanation
Indices: 2371984--2372013 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2371974 AAGAGACCTA
2371984 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
2372014 GGAAATAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2373280 original size:21 final size:21
Alignment explanation
Indices: 2373251--2373293 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2373241 ATATAAATTG
*
2373251 TGTATCGATGCACTGCTACAA
1 TGTACCGATGCACTGCTACAA
2373272 TGTACCGATGCACTGCTACAA
1 TGTACCGATGCACTGCTACAA
2373293 T
1 T
2373294 AACTTCAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
TGTACCGATGCACTGCTACAA
Found at i:2378776 original size:24 final size:24
Alignment explanation
Indices: 2378744--2378822 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
2378734 CAGAGCACGT
2378744 TATTATTATGGATATGCTTAGGTG
1 TATTATTATGGATATGCTTAGGTG
2378768 ---TATTAT---TATGCTTAGGTG
1 TATTATTATGGATATGCTTAGGTG
2378786 TATTATTATGGATATGCTTAGGTG
1 TATTATTATGGATATGCTTAGGTG
2378810 TATTATTATGGAT
1 TATTATTATGGAT
2378823 CTTGAGGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
18 12 0.24
21 12 0.24
24 25 0.51
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (24 bp):
TATTATTATGGATATGCTTAGGTG
Found at i:2378779 original size:18 final size:18
Alignment explanation
Indices: 2378756--2378795 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2378746 TTATTATGGA
2378756 TATGCTTAGGTGTATTAT
1 TATGCTTAGGTGTATTAT
2378774 TATGCTTAGGTGTATTAT
1 TATGCTTAGGTGTATTAT
2378792 TATG
1 TATG
2378796 GATATGCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.50
Consensus pattern (18 bp):
TATGCTTAGGTGTATTAT
Found at i:2393059 original size:60 final size:59
Alignment explanation
Indices: 2392985--2393118 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 59
2392975 ATTATCTCAT
** * *
2392985 TTTCATCCTTAAACTATGATTCTTATTC-TAATGTAATCCTTAAACTTTT-GAATATTTGAAA
1 TTTCATCCCCAAACTATGAATCTCATTCTTAAT-TAATCCTTAAACTTTTAG-AT-TTT-AAA
* * *
2393046 TTT-ATCCCCAAACTATTAATCTCATTCTTAATTGATCCTTAAACTTTTAGATTTTCAA
1 TTTCATCCCCAAACTATGAATCTCATTCTTAATTAATCCTTAAACTTTTAGATTTTAAA
2393104 TTTCATCCCCAAACT
1 TTTCATCCCCAAACT
2393119 CCTCCAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 5 0.08
59 14 0.22
60 36 0.57
61 8 0.13
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.44
Consensus pattern (59 bp):
TTTCATCCCCAAACTATGAATCTCATTCTTAATTAATCCTTAAACTTTTAGATTTTAAA
Found at i:2396192 original size:32 final size:32
Alignment explanation
Indices: 2396138--2396235 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
2396128 TTACCTTCAC
*
2396138 CCAAATCCCCTAAATCTCTAAAATCTCTAATAT
1 CCAAAT-CCCTAAATCTTTAAAATCTCTAATAT
* *
2396171 CCAAATCCCTATATCTTTAAAATCTCCAATAT
1 CCAAATCCCTAAATCTTTAAAATCTCTAATAT
* * *
2396203 AC-AATCCCTAAACCTTTAAAATCT-TAATCT
1 CCAAATCCCTAAATCTTTAAAATCTCTAATAT
2396233 CCA
1 CCA
2396236 CGATTAACGC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 5 0.09
31 20 0.36
32 24 0.44
33 6 0.11
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.32
Consensus pattern (32 bp):
CCAAATCCCTAAATCTTTAAAATCTCTAATAT
Found at i:2397617 original size:20 final size:18
Alignment explanation
Indices: 2397571--2397623 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
2397561 TGGACTAAAT
*
2397571 TTTTTAAATTCTTTTATA
1 TTTTTAAATTATTTTATA
*
2397589 TTTTTAAATTATTTTTTA
1 TTTTTAAATTATTTTATA
2397607 TTGTTTAAA--ATTTTATA
1 TT-TTTAAATTATTTTATA
2397624 ATTGTGTGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.23
18 18 0.58
19 6 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTAAATTATTTTATA
Found at i:2401451 original size:19 final size:19
Alignment explanation
Indices: 2401424--2401476 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
2401414 TTGTTAAAGT
2401424 AAAATTAAAAAAATAAAATC
1 AAAA-TAAAAAAATAAAATC
* * * *
2401444 TAAATAAAAATAGAAAATG
1 AAAATAAAAAAATAAAATC
2401463 AAAATAAATAAAAT
1 AAAATAAA-AAAAT
2401477 TAATCAAACT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAATAAAAAAATAAAATC
Found at i:2410708 original size:46 final size:48
Alignment explanation
Indices: 2410655--2410751 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 48
2410645 GGAACAATGT
2410655 AATTTATGATT-A-AATAATAATAATAATAAAAATGACATGTCATCAC
1 AATTTATGATTAATAATAATAATAATAATAAAAATGACATGTCATCAC
2410701 AATTTATGATTAAATAATAATAATAATAATAAAAATGACATGTCATCAC
1 AATTTATGATT-AATAATAATAATAATAATAAAAATGACATGTCATCAC
2410750 AA
1 AA
2410752 CGTTAGAGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
46 11 0.23
48 1 0.02
49 36 0.75
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (48 bp):
AATTTATGATTAATAATAATAATAATAATAAAAATGACATGTCATCAC
Found at i:2420964 original size:10 final size:10
Alignment explanation
Indices: 2420949--2420984 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
2420939 TTTCTCTCAT
2420949 TTCTTCTTCC
1 TTCTTCTTCC
2420959 TTCTTCTTCC
1 TTCTTCTTCC
*
2420969 TTCATCTT-C
1 TTCTTCTTCC
2420978 TTCTTCT
1 TTCTTCT
2420985 CTCAAACGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.61
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:2422210 original size:22 final size:22
Alignment explanation
Indices: 2422182--2422265 Score: 104
Period size: 22 Copynumber: 4.0 Consensus size: 22
2422172 GTTCTTAAGG
*
2422182 AGTGGTCATTCGGGAAATATAT
1 AGTGGTCATTCGGGACATATAT
*
2422204 AGTGGTCTTTCGGGACATATAT
1 AGTGGTCATTCGGGACATATAT
*
2422226 AGTGGTCCTTCGGGACATA-AT
1 AGTGGTCATTCGGGACATATAT
*
2422247 A---GTCATTCGGGACAAATAT
1 AGTGGTCATTCGGGACATATAT
2422266 TCAGTGCCCC
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.23
19 2 0.04
21 3 0.05
22 38 0.68
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (22 bp):
AGTGGTCATTCGGGACATATAT
Found at i:2438762 original size:25 final size:25
Alignment explanation
Indices: 2438734--2438798 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
2438724 TTTGTTCACA
2438734 ACAATTTTATAAGTTT-ACTCATCCT
1 ACAATTTTATAA-TTTCACTCATCCT
* *
2438759 ACAATTTTATAATTTCGCTCATCTT
1 ACAATTTTATAATTTCACTCATCCT
*
2438784 ACAATTTTACAATTT
1 ACAATTTTATAATTT
2438799 ATGTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 3 0.08
25 33 0.92
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.46
Consensus pattern (25 bp):
ACAATTTTATAATTTCACTCATCCT
Found at i:2440828 original size:16 final size:16
Alignment explanation
Indices: 2440803--2440900 Score: 70
Period size: 16 Copynumber: 5.9 Consensus size: 16
2440793 AGAGTATGAG
* *
2440803 ATTTTTTATATACAAA
1 ATTTTATATATATAAA
* *
2440819 ATTTTATATAAATTAA
1 ATTTTATATATATAAA
* *
2440835 ATTTAATAAATAATAAA
1 ATTTTATATAT-ATAAA
* *
2440852 ATTTTATATAAATTAA
1 ATTTTATATATATAAA
* * *
2440868 ATTTAATAAATAATTAA
1 ATTTTATATAT-ATAAA
2440885 ATTTTATATTATATAA
1 ATTTTATA-TATATAA
2440901 TGATAAATTC
Statistics
Matches: 61, Mismatches: 18, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
16 32 0.52
17 27 0.44
18 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTTATATATATAAA
Found at i:2440853 original size:33 final size:33
Alignment explanation
Indices: 2440816--2440893 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
2440806 TTTTATATAC
2440816 AAAATTTTATATAAATTAAATTTAATAAATAAT
1 AAAATTTTATATAAATTAAATTTAATAAATAAT
2440849 AAAATTTTATATAAATTAAATTTAATAAATAAT
1 AAAATTTTATATAAATTAAATTTAATAAATAAT
*
2440882 TAAATTTTATAT
1 AAAATTTTATAT
2440894 TATATAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AAAATTTTATATAAATTAAATTTAATAAATAAT
Found at i:2440855 original size:17 final size:17
Alignment explanation
Indices: 2440829--2440888 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
2440819 ATTTTATATA
2440829 AATTAAATTTAATAAAT
1 AATTAAATTTAATAAAT
* * *
2440846 AATAAAATTTTATATA-
1 AATTAAATTTAATAAAT
2440862 AATTAAATTTAATAAAT
1 AATTAAATTTAATAAAT
2440879 AATTAAATTT
1 AATTAAATTT
2440889 TATATTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.36
17 23 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTAAATTTAATAAAT
Found at i:2441203 original size:44 final size:43
Alignment explanation
Indices: 2441141--2441336 Score: 225
Period size: 43 Copynumber: 4.5 Consensus size: 43
2441131 TATATATATA
*
2441141 AAAAAGAGAGATTTAAAAAATTTAGGGAA-CTCAATTATAAAGGT
1 AAAAAGTGAGA-TTAAAAAATTTA-GGAACCTCAATTATAAAGGT
* ** * *
2441185 AAAAAGTGAGATTGAAAAATTTTAGGGGCATCAATTATAAAGAT
1 AAAAAGTGAGATT-AAAAAATTTAGGAACCTCAATTATAAAGGT
* * * *
2441229 AGAAAGTGAGATTAAAAAAATTAGAAACCTCAATTATAAATGT
1 AAAAAGTGAGATTAAAAAATTTAGGAACCTCAATTATAAAGGT
*
2441272 AAAAAGTGAGACTGAAAAAA-TTAGGAACCTCAATTATAAAGGT
1 AAAAAGTGAGA-TTAAAAAATTTAGGAACCTCAATTATAAAGGT
*
2441315 AAAAAATGAGATTACAAAAATT
1 AAAAAGTGAGATTA-AAAAATT
2441337 AAGAGTTTTA
Statistics
Matches: 126, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
42 2 0.02
43 72 0.57
44 52 0.41
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (43 bp):
AAAAAGTGAGATTAAAAAATTTAGGAACCTCAATTATAAAGGT
Found at i:2441263 original size:87 final size:86
Alignment explanation
Indices: 2441141--2441337 Score: 243
Period size: 87 Copynumber: 2.3 Consensus size: 86
2441131 TATATATATA
* * * * *
2441141 AAAAAGAGAGATTTAAAAAATTTAGGGAACTCAATTATAAAGGTAAAAAGTGAGATTGAAAAATT
1 AAAAAGTGAGA-TTAAAAAAATTAGGAAACTCAATTATAAAGGTAAAAAGTGAGACTGAAAAA-A
**
2441206 TTAGGGGCATCAATTATAAAGAT
64 TTAGGAACATCAATTATAAAGAT
* *
2441229 AGAAAGTGAGATTAAAAAAATTA-GAAACCTCAATTATAAATGTAAAAAGTGAGACTGAAAAAAT
1 AAAAAGTGAGATTAAAAAAATTAGGAAA-CTCAATTATAAAGGTAAAAAGTGAGACTGAAAAAAT
* *
2441293 TAGGAACCTCAATTATAAAGGT
65 TAGGAACATCAATTATAAAGAT
* *
2441315 AAAAAATGAGATTACAAAAATTA
1 AAAAAGTGAGATTAAAAAAATTA
2441338 AGAGTTTTAA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
86 42 0.45
87 43 0.46
88 9 0.10
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (86 bp):
AAAAAGTGAGATTAAAAAAATTAGGAAACTCAATTATAAAGGTAAAAAGTGAGACTGAAAAAATT
AGGAACATCAATTATAAAGAT
Found at i:2451514 original size:20 final size:21
Alignment explanation
Indices: 2451477--2451516 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2451467 AAATTAAGTT
2451477 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
2451498 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
2451517 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:2451801 original size:64 final size:64
Alignment explanation
Indices: 2451733--2451890 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 64
2451723 GATTTAATTG
* ** * *
2451733 AACATCGAATGCATTTCATGCACCGATGCACTATCCATGCATCGATGCACTC-GGA-ATATTTTC
1 AACATCGAATGCATTTCATGCATCGATGCAAAAGCAATGCATCGATGCAC-CAGGATAT-TTTTC
2451796 A
64 A
* * * *
2451797 AACATTGAATGCATTTGATGCATCGATGCAAAAGCAATGCATTGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCAAAAGCAATGCATCGATGCACCAGGATATTTTTCA
*
2451861 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
2451891 TCCTTAGTGC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 78 0.96
65 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCAAAAGCAATGCATCGATGCACCAGGATATTTTTCA
Found at i:2453196 original size:20 final size:21
Alignment explanation
Indices: 2453159--2453198 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2453149 AAATTAAGTT
2453159 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
2453180 AAATG-ATTTTATA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
2453199 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:2453478 original size:64 final size:64
Alignment explanation
Indices: 2453410--2453567 Score: 219
Period size: 64 Copynumber: 2.5 Consensus size: 64
2453400 GATTTAATTG
* * * *
2453410 AACATCGAATGCATTTCATGCACCGATGCACTATCCATGCATCGATGCACTCAGAATA-TTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCATCGATGCAC-CAGAATATTTTTCA
* * **
2453474 AACATTGAATGCATTTGATGCATCGATGCACAAGCAATGCATCGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCATCGATGCACCAGAATATTTTTCA
*
2453538 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
2453568 TCCTTAGTGC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 5 0.06
64 78 0.94
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCATCGATGCACCAGAATATTTTTCA
Found at i:2453584 original size:64 final size:62
Alignment explanation
Indices: 2453410--2453588 Score: 184
Period size: 64 Copynumber: 2.8 Consensus size: 62
2453400 GATTTAATTG
*
2453410 AACATCGAATGCATTTCATGCACCGATGCA-CTATCCATGCATCGATGCACTCAGAATATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACCT-T--ATGCATCGATGCACTCAGAATATTTTCA
* * * **
2453474 AACATTGAATGCATTTGATGCATCGATGCACAAGC-AATGCATCGATGCAC-CAGGCTATTTTTC
1 AACATCGAATGCATTTCATGCATCGATGCAC---CTTATGCATCGATGCACTCAGAATA-TTTTC
2453537 A
62 A
* *
2453538 AACATCGAATGCATTTTATGCATCGATGCATCCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCA-CCTTA-TGCATCGATGCACT
2453589 AAGTGTCCCA
Statistics
Matches: 96, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 6 0.06
64 87 0.91
65 1 0.01
68 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (62 bp):
AACATCGAATGCATTTCATGCATCGATGCACCTTATGCATCGATGCACTCAGAATATTTTCA
Found at i:2460932 original size:21 final size:21
Alignment explanation
Indices: 2460890--2460933 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2460880 ACCCCGGGAG
*
2460890 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
2460911 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
2460932 CT
1 CT
2460934 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:2461731 original size:20 final size:21
Alignment explanation
Indices: 2461694--2461733 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2461684 AAATTAAGTT
2461694 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
2461715 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
2461734 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:2462018 original size:64 final size:64
Alignment explanation
Indices: 2461902--2462107 Score: 213
Period size: 64 Copynumber: 3.2 Consensus size: 64
2461892 ATTCAAGGTG
* * * * * *
2461902 ATGCACCGATGCATCAAACCATGCATCGATGCACCTATGAT-TTAATT-GAACATCGAATGCATT
1 ATGCATCGATGCA-CAAGCAATGCATCGATGCACC-AGGATATT-TTTCAAACATCGAATGCATT
2461965 TC
63 TC
* * * * *
2461967 ATGCACCGATGCACTATCCATGCATCGATGCACTC-GGA-ATATTTTCAAACATTGAATGCATTT
1 ATGCATCGATGCACAAGCAATGCATCGATGCAC-CAGGATAT-TTTTCAAACATCGAATGCATTT
*
2462030 G
64 C
* *
2462031 ATGCATCGATGCACAAGCAATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTC
2462095 ATGCATCGATGCA
1 ATGCATCGATGCA
2462108 TCCTTAGTGC
Statistics
Matches: 121, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 6 0.05
64 99 0.82
65 16 0.13
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCAATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTC
Found at i:2462124 original size:64 final size:62
Alignment explanation
Indices: 2461950--2462128 Score: 177
Period size: 64 Copynumber: 2.8 Consensus size: 62
2461940 GATTTAATTG
*
2461950 AACATCGAATGCATTTCATGCACCGATGCA-CTATCCATGCATCGATGCACTCGGAATATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACCT-T--ATGCATCGATGCACTCGGAATATTTTCA
* * * *
2462014 AACATTGAATGCATTTGATGCATCGATGCACAAGC-AATGCATCGATGCAC-CAGG-CTATTTTT
1 AACATCGAATGCATTTCATGCATCGATGCAC---CTTATGCATCGATGCACTC-GGAATA-TTTT
2462076 CA
61 CA
* *
2462078 AACATCGAATGCATTTTATGCATCGATGCATCCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCA-CCTTA-TGCATCGATGCACT
2462129 AAGTGTCCCA
Statistics
Matches: 96, Mismatches: 9, Indels: 19
0.77 0.07 0.15
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 89 0.93
65 1 0.01
68 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (62 bp):
AACATCGAATGCATTTCATGCATCGATGCACCTTATGCATCGATGCACTCGGAATATTTTCA
Found at i:2463263 original size:16 final size:16
Alignment explanation
Indices: 2463213--2463263 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2463203 GTTTGATTCA
2463213 CGGAATGTAAGATTAC
1 CGGAATGTAAGATTAC
* *
2463229 CAGAGATAATAAGATTAC
1 CGGA-AT-GTAAGATTAC
*
2463247 CGGAATGTAACATTAC
1 CGGAATGTAAGATTAC
2463263 C
1 C
2463264 TAACACATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 12 0.43
17 4 0.14
18 12 0.43
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (16 bp):
CGGAATGTAAGATTAC
Found at i:2464062 original size:3 final size:3
Alignment explanation
Indices: 2464054--2464188 Score: 87
Period size: 3 Copynumber: 42.0 Consensus size: 3
2464044 TAATCAAATG
*
2464054 ATA ATA ATA ATA ATA AT- ATAA ATA ATA ATA GTGGA ATA GA-A ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA AT--A ATA -ATA ATA ATA
* *
2464101 GATA ATA ATA GATA ATA ATA ATA ATAA ATA GTA GATA ATA TAGA ATA
1 -ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA -ATA ATA -ATA ATA
* * *
2464148 ATA CTA TAGA ATA ATA AT- ATAA ATA ACA ATA TATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA
2464189 TGGACTAATT
Statistics
Matches: 105, Mismatches: 12, Indels: 30
0.71 0.08 0.20
Matches are distributed among these distances:
2 5 0.05
3 76 0.72
4 22 0.21
5 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2464091 original size:23 final size:23
Alignment explanation
Indices: 2464065--2464189 Score: 89
Period size: 23 Copynumber: 5.3 Consensus size: 23
2464055 TAATAATAAT
*
2464065 AATAATATAAATAATAATAGTGG
1 AATAATATAAATAATAATAGTAG
* *
2464088 AATAGAAAT-AATAGATAATAATAG
1 AATA-ATATAAATA-ATAATAGTAG
2464112 -ATAATA-ATAATAATAAATAGTAG
1 AATAATATA-AATAAT-AATAGTAG
* *
2464135 -ATAATATAGAATAATACTATAGAAT
1 AATAATATA-AATAATA--ATAGTAG
* *
2464160 AATAATATAAATAACAATA-TAT
1 AATAATATAAATAATAATAGTAG
2464182 AATAATAT
1 AATAATAT
2464190 GGACTAATTT
Statistics
Matches: 83, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
22 14 0.17
23 32 0.39
24 18 0.22
25 11 0.13
26 8 0.10
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (23 bp):
AATAATATAAATAATAATAGTAG
Found at i:2464109 original size:10 final size:9
Alignment explanation
Indices: 2464094--2464188 Score: 66
Period size: 10 Copynumber: 9.8 Consensus size: 9
2464084 GTGGAATAGA
2464094 AATAATAGAT
1 AATAATA-AT
2464104 AATAATAGAT
1 AATAATA-AT
2464114 AATAATAAT
1 AATAATAAT
*
2464123 AATAAATAGT
1 AAT-AATAAT
*
2464133 AGATAATATAG
1 A-ATAATA-AT
*
2464144 AATAATACT
1 AATAATAAT
*
2464153 ATAGAATAAT
1 A-ATAATAAT
2464163 AAT-ATAAAT
1 AATAAT-AAT
*
2464172 AACAATATAT
1 AATAATA-AT
2464182 AATAATA
1 AATAATA
2464189 TGGACTAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
8 2 0.03
9 13 0.19
10 50 0.74
11 3 0.04
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (9 bp):
AATAATAAT
Found at i:2464149 original size:43 final size:41
Alignment explanation
Indices: 2464024--2464172 Score: 123
Period size: 39 Copynumber: 3.7 Consensus size: 41
2464014 ATTAATAAAT
* * * *
2464024 ATAATAGTATAAATAAATATTAATCAA-AT-GATAATA-ATA
1 ATAATAATATAAAT-AATAATAATAAATATAGATAATATAGA
* **
2464063 ATAATAATATAAATAATAATAGTGGA-ATAGA-AATAATAG-
1 ATAATAATATAAATAATAATAATAAATATAGATAAT-ATAGA
*
2464102 ATAATAATAGATAATAATAATAATAAATAGTAGATAATATAGA
1 ATAATAATATA-AATAATAATAATAAATA-TAGATAATATAGA
*
2464145 ATAATACTATAGAATAATAAT-ATAAATA
1 ATAATAATATA-AATAATAATAATAAATA
2464173 ACAATATATA
Statistics
Matches: 89, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
38 13 0.15
39 26 0.29
40 13 0.15
41 1 0.01
42 15 0.17
43 21 0.24
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (41 bp):
ATAATAATATAAATAATAATAATAAATATAGATAATATAGA
Found at i:2464182 original size:40 final size:38
Alignment explanation
Indices: 2464062--2464182 Score: 102
Period size: 40 Copynumber: 3.0 Consensus size: 38
2464052 TGATAATAAT
*
2464062 AATAATAATATAAATAATAATAGTGGAATAGAAATA-ATAG
1 AATAATAATATAAATAATAATA-T-AAATA-AAATATATAG
* *
2464102 -ATAATAATAGATAATAATAATAATAAATAGTAGATAATATAG
1 AATAATAATATA-AATAATAAT-ATAAATA--AAAT-ATATAG
*
2464144 AATAATACTATAGAATAATAATATAAATAACAATATATA
1 AATAATAATATA-AATAATAATATAAATAA-AATATATA
2464183 ATAATATGGA
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
39 14 0.21
40 19 0.29
41 4 0.06
42 11 0.17
43 18 0.27
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (38 bp):
AATAATAATATAAATAATAATATAAATAAAATATATAG
Found at i:2465611 original size:201 final size:199
Alignment explanation
Indices: 2465261--2465882 Score: 683
Period size: 200 Copynumber: 3.1 Consensus size: 199
2465251 AGTAGATAAT
* * * ** * * * * *
2465261 TCTTATCGCCTTAAGTTATGTCAAAATTTGAATGGGAAGTGGTTCCTTATTTCCAAATCGCAATC
1 TCTTCTCGCCTTAAGCTATGTCGAAATTTGAATGAAAAGTGGTTTCTTATTGCCAAATCACAGTA
* * * * * * *
2465326 AACCTAGGTCTTTTTCTCGGTTTAAAGACCTCGGTTTGAATTTTGATTGAAAGGTAGTTTCTCGT
66 AAACTAGGTCTTCTTCTTGGTTTAAAGACCTCGATTTGAATTTTGATCGAAAGGTAGTTCCTCGC
* ** * *
2465391 TGTTACCATGCATTCGATGCGTCCTCCAGCTGAGTGGAATCAAACTCGAAAAGCTTTGGTCGACA
131 TGATACCATGCGGTCGATGC-TCCTCGAGCTGAGTGGAATCGAACTCG-AAAGCTTTGGTCGACA
2465456 GATAGC
194 GATAGC
* *
2465462 TCTTCTCGCCTTAAGCTATGTCGAAATTTGAATGAAAAGTGGTTTCTTGTTGCCAAATCATAGT-
1 TCTTCTCGCCTTAAGCTATGTCGAAATTTGAATGAAAAGTGGTTTCTTATTGCCAAATCACAGTA
* * * * *
2465526 TAGCTGGGGTCTTCTTCTTGGTTTAAAGACCTCAATTTGAATTTTGATCGGAAGGTAGTTCCTCG
66 AAACT-AGGTCTTCTTCTTGGTTTAAAGACCTCGATTTGAATTTTGATCGAAAGGTAGTTCCTCG
* * * * * *
2465591 CTGATACCATGCGGTCGATGCACTCTTGAGTTGAGTGGGATCGAACTTGAAAGCTTTGGTCGATA
130 CTGATACCATGCGGTCGATGCTC-CTCGAGCTGAGTGGAATCGAACTCGAAAGCTTTGGTCGACA
*
2465656 TATAGC
194 GATAGC
* * * *
2465662 TCTTGTCACCTTAAGCTATGTCGAAATTTGATTGAAAAATGGTTTCTTATTGCCAAATCACAGTA
1 TCTTCTCGCCTTAAGCTATGTCGAAATTTGAATGAAAAGTGGTTTCTTATTGCCAAATCACAGTA
** * * * * *
2465727 AAACTATCTCTTCTTCTTAGCTTAAAGACCCCGTTTTGAATTTTGA-CTGAAAGATAGTTCCTCG
66 AAACTAGGTCTTCTTCTTGGTTTAAAGACCTCGATTTGAATTTTGATC-GAAAGGTAGTTCCTCG
* * * *
2465791 CTGCTATCATGCGGTCGATGAACT-CTCGAGCTGAGTGGAATTGAACTCGAAAGCTTTGGTTGAC
130 CTGATACCATGCGGTCGATG--CTCCTCGAGCTGAGTGGAATCGAACTCGAAAGCTTTGGTCGAC
2465855 AGATAGC
193 AGATAGC
**
2465862 TCTTCTCGATTTAAGCTATGT
1 TCTTCTCGCCTTAAGCTATGT
2465883 TATGGACGAT
Statistics
Matches: 348, Mismatches: 67, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
199 1 0.00
200 203 0.58
201 143 0.41
202 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (199 bp):
TCTTCTCGCCTTAAGCTATGTCGAAATTTGAATGAAAAGTGGTTTCTTATTGCCAAATCACAGTA
AAACTAGGTCTTCTTCTTGGTTTAAAGACCTCGATTTGAATTTTGATCGAAAGGTAGTTCCTCGC
TGATACCATGCGGTCGATGCTCCTCGAGCTGAGTGGAATCGAACTCGAAAGCTTTGGTCGACAGA
TAGC
Found at i:2466055 original size:72 final size:72
Alignment explanation
Indices: 2465952--2466132 Score: 179
Period size: 72 Copynumber: 2.5 Consensus size: 72
2465942 CAAACAAGAT
* * *** *
2465952 GACTCTCATTCACGGTTTAA-TCCA-GTCTTGATTCTTTGGGTGACTCTCCTTCA-TGGGAAAAC
1 GACTCACATTCACGGTTTAAGT--AGGTATTGATTCTTTCAATGACTCCCCTTCACT-GGAAAAC
* **
2466014 TAGTTGAGAC
63 CAAATGAGAC
* * *
2466024 GACTCACCTTCACGGTTTAAGTAGGTATTGATTCCTTCAATGACTCCCCTTCACTGGAAAGCCAA
1 GACTCACATTCACGGTTTAAGTAGGTATTGATTCTTTCAATGACTCCCCTTCACTGGAAAACCAA
*
2466089 ATGAGAT
66 ATGAGAC
* *
2466096 GACTCTCATTCACGGTTTAAGTAGGTTTTGATTCTTT
1 GACTCACATTCACGGTTTAAGTAGGTATTGATTCTTT
2466133 TTGGATGACT
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
71 1 0.01
72 86 0.97
73 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (72 bp):
GACTCACATTCACGGTTTAAGTAGGTATTGATTCTTTCAATGACTCCCCTTCACTGGAAAACCAA
ATGAGAC
Found at i:2466347 original size:43 final size:43
Alignment explanation
Indices: 2466208--2466353 Score: 125
Period size: 43 Copynumber: 3.3 Consensus size: 43
2466198 TTTTGGTTAT
* * * *
2466208 TTGGATGACTCCCCTTCACGGGTCTAAGTCAATTGAGACGACTTC
1 TTGGATGACTCCCCTTCACGAG--AAAGTCAAGTGAGACAACTTC
* * * * *
2466253 TTGGATGACTCTCCTTCACGGGAAA-ACTATGTGAGACATTCTT-
1 TTGGATGACTCCCCTTCACGAGAAAGTC-AAGTGAGACA-ACTTC
** **
2466296 TTAAATGACTCCCCTTTGCGAGAAAGTCAAGTGAGACAACTTC
1 TTGGATGACTCCCCTTCACGAGAAAGTCAAGTGAGACAACTTC
2466339 TTGGATGACTCCCCT
1 TTGGATGACTCCCCT
2466354 CTATGGGAAA
Statistics
Matches: 79, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
42 4 0.05
43 50 0.63
44 4 0.05
45 21 0.27
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (43 bp):
TTGGATGACTCCCCTTCACGAGAAAGTCAAGTGAGACAACTTC
Found at i:2466364 original size:43 final size:42
Alignment explanation
Indices: 2466208--2466374 Score: 115
Period size: 43 Copynumber: 3.8 Consensus size: 42
2466198 TTTTGGTTAT
* * * *
2466208 TTGGATGACTCCCCTTCACGGGTCTAAGTCAATTGAGACGACTTC
1 TTGGATGACTCCCCTT-ATGGG--AAAGTCAAGTGAGACAACTTC
* * * * *
2466253 TTGGATGACTCTCCTTCACGGGAAA-ACTATGTGAGACATTCTT-
1 TTGGATGACTCCCCTT-ATGGGAAAGTC-AAGTGAGACA-ACTTC
**
2466296 TTAAATGACTCCCCTT-TGCGAGAAAGTCAAGTGAGACAACTTC
1 TTGGATGACTCCCCTTATG-G-GAAAGTCAAGTGAGACAACTTC
* *
2466339 TTGGATGACTCCCCTCTATGGGAAAGCCATGTGAGA
1 TTGGATGACTCCCCT-TATGGGAAAGTCAAGTGAGA
2466375 TATTCTGTTA
Statistics
Matches: 96, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 61 0.64
44 6 0.06
45 23 0.24
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
TTGGATGACTCCCCTTATGGGAAAGTCAAGTGAGACAACTTC
Found at i:2467943 original size:20 final size:21
Alignment explanation
Indices: 2467906--2467944 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2467896 ATGTTCCCCT
* *
2467906 TTTGTATTCTTCACTTTTTGA
1 TTTGTATTCCTCAATTTTTGA
2467927 TTTG-ATTCCTCAATTTTT
1 TTTGTATTCCTCAATTTTT
2467945 TTAGTGCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (21 bp):
TTTGTATTCCTCAATTTTTGA
Found at i:2468541 original size:20 final size:20
Alignment explanation
Indices: 2468500--2468541 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2468490 ATCAGATTGT
*
2468500 CCAGGGGGTACAGATTTCCC
1 CCAGGGGGTACAGATTCCCC
2468520 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
2468540 CC
1 CC
2468542 TGTCTAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.36, G:0.29, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:2469946 original size:3 final size:3
Alignment explanation
Indices: 2469925--2469962 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2469915 TGAAGAAAGT
* *
2469925 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2469963 TGAGGATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Done.