Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 8 of 167
Found at i:2453499 original size:20 final size:20
Alignment explanation
Indices: 2453474--2453511 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2453464 TTGTTATGGA
2453474 CCAACTGTATTAAAATGGGC
1 CCAACTGTATTAAAATGGGC
* *
2453494 CCAACTGTGTTAATATGG
1 CCAACTGTATTAAAATGG
2453512 CCAAGGCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (20 bp):
CCAACTGTATTAAAATGGGC
Found at i:2453582 original size:60 final size:59
Alignment explanation
Indices: 2453506--2453642 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
2453496 AACTGTGTTA
* * *
2453506 ATATGGCCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATACTG
* * *
2453566 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATACTG
2453626 ATATGGGCTAAGGCCCA
1 ATATGGGCT-AGGCCCA
2453643 GTTAACACTA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
59 1 0.01
60 51 0.76
61 15 0.22
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:2455850 original size:19 final size:19
Alignment explanation
Indices: 2455826--2455894 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
2455816 CGTGTTTGCT
2455826 TTCCGTTTAGCCTTCGGGC
1 TTCCGTTTAGCCTTCGGGC
2455845 TTCCGTTTAGCACTT-GTGTGC
1 TTCCGTTTAGC-CTTCG-G-GC
*
2455866 TTCAG-TTAGCCTTCGGGC
1 TTCCGTTTAGCCTTCGGGC
2455884 TTCCGTTTAGC
1 TTCCGTTTAGC
2455895 ACTTATGTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
18 6 0.14
19 21 0.49
20 10 0.23
21 6 0.14
ACGTcount: A:0.09, C:0.28, G:0.25, T:0.39
Consensus pattern (19 bp):
TTCCGTTTAGCCTTCGGGC
Found at i:2455878 original size:39 final size:39
Alignment explanation
Indices: 2455832--2455925 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 39
2455822 TGCTTTCCGT
*
2455832 TTAGCCTTCGGGCTTCCGTTTAGCACTTGTGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
2455871 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
* *
2455910 CTAGACTTCGGGCTTC
1 TTAGCCTTCGGGCTTC
2455926 AGATCACGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.37
Consensus pattern (39 bp):
TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
Found at i:2457050 original size:19 final size:19
Alignment explanation
Indices: 2457026--2457094 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
2457016 CGTGTTTGCT
2457026 TTCCGTTTAGCCTTCGGGC
1 TTCCGTTTAGCCTTCGGGC
2457045 TTCCGTTTAGCACTT-GTGTGC
1 TTCCGTTTAGC-CTTCG-G-GC
*
2457066 TTCAG-TTAGCCTTCGGGC
1 TTCCGTTTAGCCTTCGGGC
2457084 TTCCGTTTAGC
1 TTCCGTTTAGC
2457095 ACTTATGTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
18 6 0.14
19 21 0.49
20 10 0.23
21 6 0.14
ACGTcount: A:0.09, C:0.28, G:0.25, T:0.39
Consensus pattern (19 bp):
TTCCGTTTAGCCTTCGGGC
Found at i:2457078 original size:39 final size:39
Alignment explanation
Indices: 2457032--2457125 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 39
2457022 TGCTTTCCGT
*
2457032 TTAGCCTTCGGGCTTCCGTTTAGCACTTGTGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
2457071 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
* *
2457110 CTAGACTTCGGGCTTC
1 TTAGCCTTCGGGCTTC
2457126 AGATCACGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.37
Consensus pattern (39 bp):
TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
Found at i:2465827 original size:50 final size:50
Alignment explanation
Indices: 2465742--2465907 Score: 219
Period size: 50 Copynumber: 3.3 Consensus size: 50
2465732 GCTAAATGAC
* *
2465742 CTTGTATATTCGGCCATA-AAGGTATGCACAAATGTGATATTATATTTGAAT
1 CTTGTATATTCGGCCATATAA-GTAAGCACATATGTGATATTATATTTG-AT
* *
2465793 -TTGTATATTCGGCCATATAAGTAAGTACATATGTGATATTAAATTTGAT
1 CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTATATTTGAT
* * * *
2465842 CTTGCATATTCGACCATATAGGTAAGCACATATGTGATATTGTATTTGAT
1 CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTATATTTGAT
*
2465892 CTTGTATATTTGGCCA
1 CTTGTATATTCGGCCA
2465908 AATGAGTGGT
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.02
50 96 0.96
51 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (50 bp):
CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTATATTTGAT
Found at i:2466061 original size:26 final size:26
Alignment explanation
Indices: 2466031--2466082 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2466021 TTATTGAAAT
2466031 GTTTATTTGCTTATGACTTACTAAGC
1 GTTTATTTGCTTATGACTTACTAAGC
2466057 GTTTATTTGCTTATGACTTACTAAGC
1 GTTTATTTGCTTATGACTTACTAAGC
2466083 TAAGTTAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (26 bp):
GTTTATTTGCTTATGACTTACTAAGC
Found at i:2466500 original size:21 final size:21
Alignment explanation
Indices: 2466476--2466518 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2466466 AATGGTAGTG
*
2466476 TAAATATGTTTGTATGTTTGC
1 TAAATATGTTTGTATCTTTGC
2466497 TAAATATGTTTGTATCTTTGC
1 TAAATATGTTTGTATCTTTGC
2466518 T
1 T
2466519 TGTAGATTGA
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:0.23, C:0.07, G:0.16, T:0.53
Consensus pattern (21 bp):
TAAATATGTTTGTATCTTTGC
Found at i:2470587 original size:16 final size:16
Alignment explanation
Indices: 2470563--2470593 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2470553 TAAAAAAATA
2470563 AATACATCAATCTATC
1 AATACATCAATCTATC
*
2470579 AATATATCAATCTAT
1 AATACATCAATCTAT
2470594 ACAAGTCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
AATACATCAATCTATC
Found at i:2475203 original size:18 final size:18
Alignment explanation
Indices: 2475177--2475219 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2475167 AAAAGTTATT
*
2475177 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
2475195 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
2475213 TTTATAT
1 TTTATAT
2475220 TTTAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:2475224 original size:16 final size:16
Alignment explanation
Indices: 2475182--2475225 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
2475172 TTATTTTTAC
*
2475182 ATATATTAATAAATTT
1 ATATTTTAATAAATTT
2475198 ATATATATTAATAAATTT
1 ATAT-T-TTAATAAATTT
2475216 ATATTTTAAT
1 ATATTTTAAT
2475226 TTTTTTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 1 0.04
18 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTTTAATAAATTT
Found at i:2493196 original size:14 final size:14
Alignment explanation
Indices: 2493172--2493204 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2493162 AATGACCAAA
*
2493172 AAATT-AATTAATT
1 AAATTAAATTAACT
2493185 AAATTAAATTAACT
1 AAATTAAATTAACT
2493199 AAATTA
1 AAATTA
2493205 TTTTCTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTAAATTAACT
Found at i:2494260 original size:7 final size:7
Alignment explanation
Indices: 2494250--2494294 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
2494240 ATACAAAAGC
2494250 AAAAATA
1 AAAAATA
2494257 AAAAATA
1 AAAAATA
2494264 AAAAAT-
1 AAAAATA
2494270 AAAAAT-
1 AAAAATA
2494276 AAAAATA
1 AAAAATA
2494283 GTAAAAATA
1 --AAAAATA
2494292 AAA
1 AAA
2494295 TAAGGTCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.34
7 16 0.46
9 7 0.20
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (7 bp):
AAAAATA
Found at i:2494267 original size:14 final size:14
Alignment explanation
Indices: 2494250--2494294 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 14
2494240 ATACAAAAGC
2494250 AAAAATAAAAAATA
1 AAAAATAAAAAATA
2494264 AAAAAT-AAAAAT-
1 AAAAATAAAAAATA
2494276 AAAAATAGTAAAAATA
1 AAAAATA--AAAAATA
2494292 AAA
1 AAA
2494295 TAAGGTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.22
13 6 0.22
14 6 0.22
15 6 0.22
16 3 0.11
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:2494297 original size:20 final size:20
Alignment explanation
Indices: 2494250--2494294 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
2494240 ATACAAAAGC
2494250 AAAAATAAAAAATAAAAAAT
1 AAAAATAAAAAATAAAAAAT
2494270 AAAAAT-AAAAATAGTAAAAAT
1 AAAAATAAAAAATA--AAAAAT
2494291 AAAA
1 AAAA
2494295 TAAGGTCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 6 0.26
21 10 0.43
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAATAAAAAATAAAAAAT
Found at i:2494854 original size:21 final size:21
Alignment explanation
Indices: 2494828--2494870 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2494818 GGTTCGCTGT
*
2494828 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
2494849 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
2494870 A
1 A
2494871 ATAGAGGTGT
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:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:2494870 original size:16 final size:16
Alignment explanation
Indices: 2494851--2494883 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2494841 TGTATTGGAT
*
2494851 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
2494867 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
2494883 T
1 T
2494884 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:2495095 original size:18 final size:17
Alignment explanation
Indices: 2495074--2495108 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2495064 TTATTATTTA
*
2495074 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2495092 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2495109 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2495102 original size:28 final size:27
Alignment explanation
Indices: 2495032--2495104 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
2495022 TTTATTATCA
*
2495032 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
2495060 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
2495087 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
2495105 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:2495219 original size:71 final size:71
Alignment explanation
Indices: 2495135--2495394 Score: 520
Period size: 71 Copynumber: 3.7 Consensus size: 71
2495125 TCTTATATGA
2495135 ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAATACCGTAAATCACTCCAAT
1 ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAATACCGTAAATCACTCCAAT
2495200 TTTCCT
66 TTTCCT
2495206 ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAATACCGTAAATCACTCCAAT
1 ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAATACCGTAAATCACTCCAAT
2495271 TTTCCT
66 TTTCCT
2495277 ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAATACCGTAAATCACTCCAAT
1 ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAATACCGTAAATCACTCCAAT
2495342 TTTCCT
66 TTTCCT
2495348 ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAAT
1 ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAAT
2495395 GGAAGCAAAC
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 189 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (71 bp):
ATTTAAACTCTATAACTATATTTGCTGCAACATCATAGAAATTCAATACCGTAAATCACTCCAAT
TTTCCT
Found at i:2502624 original size:10 final size:10
Alignment explanation
Indices: 2502609--2502634 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2502599 CGGCGTTTCC
2502609 TTTTTTTTAT
1 TTTTTTTTAT
2502619 TTTTTTTTAT
1 TTTTTTTTAT
2502629 TTTTTT
1 TTTTTT
2502635 GTTACACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:2518691 original size:18 final size:18
Alignment explanation
Indices: 2518668--2518713 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2518658 AATGTTAGCA
2518668 TATTTAATCTACTTTTAT
1 TATTTAATCTACTTTTAT
**
2518686 TATTTAATCTGGTTTTAT
1 TATTTAATCTACTTTTAT
*
2518704 TTTTTAATCT
1 TATTTAATCT
2518714 TAGGGTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (18 bp):
TATTTAATCTACTTTTAT
Found at i:2520361 original size:38 final size:38
Alignment explanation
Indices: 2520310--2520386 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
2520300 GAGTTGGGTG
* ** *
2520310 TTCTTGGAGATTTTGTTCTCAATTCTGAAGGTGTCCTT
1 TTCTTGGAGATTTTGGTCTCAATGATGAAAGTGTCCTT
2520348 TTCTTGGAGATTTTGGTCTCAATGATGAAAGTGTCCTT
1 TTCTTGGAGATTTTGGTCTCAATGATGAAAGTGTCCTT
2520386 T
1 T
2520387 GTTTCAAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.45
Consensus pattern (38 bp):
TTCTTGGAGATTTTGGTCTCAATGATGAAAGTGTCCTT
Found at i:2532371 original size:172 final size:172
Alignment explanation
Indices: 2532085--2532429 Score: 636
Period size: 172 Copynumber: 2.0 Consensus size: 172
2532075 GGATTAGAAG
* *
2532085 TTAAATTGATGTTTACTAAGTGAATTCGTGAAACATAGAAATGTGTTATTAATTATAAGTTAAAA
1 TTAAATTGATGTTTACTAAGTGAATTCGAGAAACATAGAAATGTATTATTAATTATAAGTTAAAA
2532150 AGGATTTCAGCATAAATTGATTTCTGATTCAAAACTTCAGATGTGAAATTGATGATTGCTTGTTG
66 AGGATTTCAGCATAAATTGATTTCTGATTCAAAACTTCAGATGTGAAATTGATGATTGCTTGTTG
*
2532215 CTTTGAAATAAAGTGTGTATACCAAGAAGCTCTGAGATTGTA
131 CTTTGAAATAAAGTGTGTACACCAAGAAGCTCTGAGATTGTA
2532257 TTAAATTGATGTTTACTAAGTGAATTCGAGAAACATAGAAATGTATTATTAATTATAAGTTAAAA
1 TTAAATTGATGTTTACTAAGTGAATTCGAGAAACATAGAAATGTATTATTAATTATAAGTTAAAA
* *
2532322 AGGATTTCAGTATAAATTGATTTCTGATTCAGAACTTCAGATGTGAAATTGATGATTGCTTGTTG
66 AGGATTTCAGCATAAATTGATTTCTGATTCAAAACTTCAGATGTGAAATTGATGATTGCTTGTTG
*
2532387 CTTTGAAATAAAGTGTGTACACCAATAAGCTCTGAGATTGTA
131 CTTTGAAATAAAGTGTGTACACCAAGAAGCTCTGAGATTGTA
2532429 T
1 T
2532430 AACCATTGTT
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
172 167 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (172 bp):
TTAAATTGATGTTTACTAAGTGAATTCGAGAAACATAGAAATGTATTATTAATTATAAGTTAAAA
AGGATTTCAGCATAAATTGATTTCTGATTCAAAACTTCAGATGTGAAATTGATGATTGCTTGTTG
CTTTGAAATAAAGTGTGTACACCAAGAAGCTCTGAGATTGTA
Found at i:2534545 original size:30 final size:30
Alignment explanation
Indices: 2534489--2534546 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2534479 TATGATTTCA
**
2534489 TGTAAGACCACGTCTGGGACGTTGGCATAG
1 TGTAAGACCACGTCTGGGACACTGGCATAG
**
2534519 TGTAAGACCGTGTCTGGGACACTGGCAT
1 TGTAAGACCACGTCTGGGACACTGGCAT
2534547 TGATTAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (30 bp):
TGTAAGACCACGTCTGGGACACTGGCATAG
Found at i:2539018 original size:42 final size:43
Alignment explanation
Indices: 2538943--2539052 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 43
2538933 GACTTTTATT
*
2538943 TTACGTGTAATACCATGTCTGGGACATCAGCATC-ATATTTGA
1 TTACGTGTAAGACCATGTCTGGGACATCAGCATCGATATTTGA
* * * * *
2538985 TTTCGTGTAAGACCCTGTCTGGGATAGT-GGCATCGATGTTTGA
1 TTACGTGTAAGACCATGTCTGGGACA-TCAGCATCGATATTTGA
* * *
2539028 TTACATGTAAGACCACGTCTAGGAC
1 TTACGTGTAAGACCATGTCTGGGAC
2539053 GTTGGCATTG
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
42 27 0.50
43 27 0.50
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACATCAGCATCGATATTTGA
Found at i:2539059 original size:43 final size:42
Alignment explanation
Indices: 2538903--2539060 Score: 126
Period size: 43 Copynumber: 3.7 Consensus size: 42
2538893 ATGTGATTTT
*
2538903 GTGTAAGACCACATCTAGGACGTTGGCATCGACTTTT-ATTTTAC
1 GTGTAAGACCACGTCTAGGACGTTGGCATCGA-TTTTGA--TTAC
* * * * ** *
2538947 GTGTAATACCATGTCTGGGACATCAGCATC-ATATTTGATTTC
1 GTGTAAGACCACGTCTAGGACGTTGGCATCGAT-TTTGATTAC
* *
2538989 GTGTAAGACC-CTGTCTGGGATAG-TGGCATCGATGTTTGATTAC
1 GTGTAAGACCAC-GTCTAGGA-CGTTGGCATCGAT-TTTGATTAC
*
2539032 ATGTAAGACCACGTCTAGGACGTTGGCAT
1 GTGTAAGACCACGTCTAGGACGTTGGCAT
2539061 TGTATATGGT
Statistics
Matches: 88, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
42 27 0.31
43 36 0.41
44 25 0.28
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (42 bp):
GTGTAAGACCACGTCTAGGACGTTGGCATCGATTTTGATTAC
Found at i:2540807 original size:19 final size:19
Alignment explanation
Indices: 2540783--2540820 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2540773 CATACATCGG
2540783 ATAAACGGATCTCCGGACT
1 ATAAACGGATCTCCGGACT
*
2540802 ATAAACGGATCTCTGGACT
1 ATAAACGGATCTCCGGACT
2540821 CCCACAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (19 bp):
ATAAACGGATCTCCGGACT
Found at i:2542213 original size:43 final size:42
Alignment explanation
Indices: 2542080--2542235 Score: 188
Period size: 42 Copynumber: 3.7 Consensus size: 42
2542070 ACTAATACTA
*
2542080 CGTGTAAAACCATATCTAGGATATGGCATCAATATGAGACTT
1 CGTGTAAAACCATATCTAGGATATGGCATCGATATGAGACTT
2542122 CGTGTAAAACCATATCTAGGATATGGCATCGATATGAGACTT
1 CGTGTAAAACCATATCTAGGATATGGCATCGATATGAGACTT
* * * * * *
2542164 CATGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGA-TT
1 CGTGTAAAACCATATCTAGGATA-TGGCATCGATATGAGACTT
* * * *
2542206 ACGTGTAAGACCAGATTTGGGATATGGCAT
1 -CGTGTAAAACCATATCTAGGATATGGCAT
2542236 TGGTACGGTA
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
42 67 0.67
43 33 0.33
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (42 bp):
CGTGTAAAACCATATCTAGGATATGGCATCGATATGAGACTT
Found at i:2549000 original size:49 final size:50
Alignment explanation
Indices: 2548937--2549172 Score: 296
Period size: 49 Copynumber: 4.7 Consensus size: 50
2548927 AGGTCAGGTC
* *
2548937 TGTAGTACTAAGTGCAGGCTATTATGTGTACCGGATAATT-GGTCACATG
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCACATG
* * * * *
2548986 TGTAGTACTAAGTGCAGGTTACTATGCGTACCCGATAACTTCGATCACATG
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TTAGGTCACATG
* * ** **
2549037 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATGTG
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCACATG
* *
2549087 TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCACATG
* *
2549136 TGTAGTACTAAGTGCAAGCTACTATGCGTACCAGATA
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
2549173 GCTTTGGTTA
Statistics
Matches: 160, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
49 74 0.46
50 47 0.29
51 39 0.24
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (50 bp):
TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCACATG
Found at i:2556422 original size:47 final size:47
Alignment explanation
Indices: 2556358--2556468 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
2556348 GACCTTGAGT
* *
2556358 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTCCCGGATTTGTTC
* * *
2556405 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTCCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTCCCGGATTTGTTC
2556452 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
2556469 CTTATCCCGA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTCCCGGATTTGTTC
Found at i:2557831 original size:3 final size:3
Alignment explanation
Indices: 2557823--2557986 Score: 106
Period size: 3 Copynumber: 54.7 Consensus size: 3
2557813 AGTCTTATAT
*
2557823 TTA TTA TTA TTA TGT- TTA TTA TTA TT- TTGA GTA TTA TTA TT- TCTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA
* * * * * * * *
2557868 TTA TTG TTG TTA CTA TTG TTT TTA TT- TGTA TTA TTA CTG TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* *
2557913 TTA TTA TTA TTA TTA TTA CTA TTA TTA -TA TTTA TTA -TA TTTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA
* * *
2557958 TTA TTA TTT TTG TTA CTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2557987 GTCATACTAT
Statistics
Matches: 125, Mismatches: 24, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
2 9 0.07
3 109 0.87
4 7 0.06
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2559546 original size:2 final size:2
Alignment explanation
Indices: 2559541--2559572 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2559531 TCTATATATA
2559541 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2559573 GAAAAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2561121 original size:21 final size:21
Alignment explanation
Indices: 2561082--2561121 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2561072 GTAATTTTGT
* *
2561082 TTAGAACATTAATTGAATGTA
1 TTAGAACATTAAATAAATGTA
2561103 TTAGAACATTAAATAAATG
1 TTAGAACATTAAATAAATG
2561122 AAAACGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.35
Consensus pattern (21 bp):
TTAGAACATTAAATAAATGTA
Found at i:2562420 original size:17 final size:18
Alignment explanation
Indices: 2562398--2562431 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2562388 TAGGAAACCG
*
2562398 TGTGTTTAA-ATTGTGGT
1 TGTGTTGAATATTGTGGT
2562415 TGTGTTGAATATTGTGG
1 TGTGTTGAATATTGTGG
2562432 AATTATTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (18 bp):
TGTGTTGAATATTGTGGT
Found at i:2570306 original size:5 final size:5
Alignment explanation
Indices: 2570298--2570324 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2570288 TTATTATTAT
2570298 TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TA
2570325 ATTACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:2578698 original size:31 final size:31
Alignment explanation
Indices: 2578629--2578698 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
2578619 CTTAACAACC
*
2578629 TAGTAACTTAAATAAAAACTTCCAAATAGTT
1 TAGTGACTTAAATAAAAACTTCCAAATAGTT
* * * ***
2578660 CAATGACTTAAATGAAAACTTTTGAATAGTT
1 TAGTGACTTAAATAAAAACTTCCAAATAGTT
2578691 TAGTGACT
1 TAGTGACT
2578699 ATTCTGTAAC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTCCAAATAGTT
Found at i:2580714 original size:19 final size:19
Alignment explanation
Indices: 2580649--2580715 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
2580639 ATAAGAGTAC
*
2580649 GAAAGAAAGAAATATGAGA
1 GAAAGAAAGAGATATGAGA
* *
2580668 GAAA-AATATA-AGGATGAGA
1 GAAAGAA-AGAGA-TATGAGA
2580687 -AAA-AAAGAGATATGAGA
1 GAAAGAAAGAGATATGAGA
*
2580704 GAAAGATAGAGA
1 GAAAGAAAGAGA
2580716 CGAGAGAGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 8 0.21
18 12 0.32
19 18 0.47
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (19 bp):
GAAAGAAAGAGATATGAGA
Found at i:2580828 original size:84 final size:82
Alignment explanation
Indices: 2580734--2580923 Score: 195
Period size: 82 Copynumber: 2.3 Consensus size: 82
2580724 AGAGAAAGTT
* * * * * * * *
2580734 AAATATGGGAAAAGAGAGAGAATAA-CAGTTATGTAAAATAGATATATGAAATAGAATTGAATAT
1 AAATATGGGAAAAGAAAAAAAATAATC-GATATG-AAAATAAACATATAAAAGAGAATTGAATA-
*
2580798 TTTATGGAAAATAGAGAATC
63 CTTATGGAAAATAGAGAATC
* * *
2580818 AAATATGGGAAAATAAAAAAAATAATCGATATGAAAATAAACATATAAAAGGGAATTTAATACTT
1 AAATATGGGAAAAGAAAAAAAATAATCGATATGAAAATAAACATATAAAAGAGAATTGAATACTT
*
2580883 ATGGGAAATAGAGAATC
66 ATGGAAAATAGAGAATC
* *
2580900 AAATAT-AGAAAAGGAAAGAAAATA
1 AAATATGGGAAAA-GAAAAAAAATA
2580924 GAATATATAA
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
81 5 0.06
82 33 0.38
83 23 0.26
84 26 0.30
85 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.18, T:0.23
Consensus pattern (82 bp):
AAATATGGGAAAAGAAAAAAAATAATCGATATGAAAATAAACATATAAAAGAGAATTGAATACTT
ATGGAAAATAGAGAATC
Found at i:2580940 original size:47 final size:47
Alignment explanation
Indices: 2580888--2580988 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 47
2580878 TACTTATGGG
* *
2580888 AAATAGAGAATCAAATAT-AGAAAAGGAAAGAAAATAGA-ATATATAAA
1 AAATAGAGAATAAAAAATGAG-AAAGGAAAGAAAATA-ACATATATAAA
* * **
2580935 AAATAGAGAATAAAAAATGAGAGAGGAAAGAGAATAACATATATGGA
1 AAATAGAGAATAAAAAATGAGAAAGGAAAGAAAATAACATATATAAA
2580982 AAATAGA
1 AAATAGA
2580989 TCATATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 1 0.02
47 43 0.93
48 2 0.04
ACGTcount: A:0.63, C:0.02, G:0.19, T:0.16
Consensus pattern (47 bp):
AAATAGAGAATAAAAAATGAGAAAGGAAAGAAAATAACATATATAAA
Found at i:2580947 original size:14 final size:15
Alignment explanation
Indices: 2580930--2580958 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2580920 AATAGAATAT
2580930 ATAAAAAAT-AGAGA
1 ATAAAAAATGAGAGA
2580944 ATAAAAAATGAGAGA
1 ATAAAAAATGAGAGA
2580959 GGAAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (15 bp):
ATAAAAAATGAGAGA
Found at i:2592308 original size:22 final size:22
Alignment explanation
Indices: 2592283--2592325 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2592273 AAGTAAAATT
2592283 TTAAATTC-AAAAAATAGAAAGA
1 TTAAATTCTAAAAAATA-AAAGA
*
2592305 TTAAATTCTTAAAAATAAAAG
1 TTAAATTCTAAAAAATAAAAG
2592326 TAGGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (22 bp):
TTAAATTCTAAAAAATAAAAGA
Found at i:2594013 original size:21 final size:22
Alignment explanation
Indices: 2593978--2594018 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2593968 GGTAGAATAT
*
2593978 GTTAAACATATTTTAATTATTA
1 GTTAAACAAATTTTAATTATTA
*
2594000 GTTAAA-AAATTTTAGTTAT
1 GTTAAACAAATTTTAATTAT
2594019 AATATATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (22 bp):
GTTAAACAAATTTTAATTATTA
Found at i:2597123 original size:62 final size:62
Alignment explanation
Indices: 2597042--2597211 Score: 286
Period size: 62 Copynumber: 2.7 Consensus size: 62
2597032 TAATCACATT
* * *
2597042 AATATTAAATTAAATTTAATATCTCATATTAATATCTAAATAAATAAAATATTGTCTAGATA
1 AATATTAAATTTAATTTAATATCTCATATTAATATCTAAATAAATAAAATACTATCTAGATA
*
2597104 AATATTTAATTTAATTTAATATCTCATATTAATATCTAAATAAATAAAATACTATCTAGATA
1 AATATTAAATTTAATTTAATATCTCATATTAATATCTAAATAAATAAAATACTATCTAGATA
* *
2597166 AATATTAAATTTAATTTAATATCTCATATTAAAATCTAGATAAATA
1 AATATTAAATTTAATTTAATATCTCATATTAATATCTAAATAAATA
2597212 TTAAATTTAA
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 101 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (62 bp):
AATATTAAATTTAATTTAATATCTCATATTAATATCTAAATAAATAAAATACTATCTAGATA
Found at i:2597245 original size:17 final size:17
Alignment explanation
Indices: 2597206--2597242 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2597196 AAAATCTAGA
2597206 TAAATATTAAATTTAAT
1 TAAATATTAAATTTAAT
*
2597223 TTAATATTAAATTT-AT
1 TAAATATTAAATTTAAT
2597239 TAAA
1 TAAA
2597243 ATAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATATTAAATTTAAT
Found at i:2608508 original size:23 final size:24
Alignment explanation
Indices: 2608464--2608508 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2608454 TTACAAAATT
*
2608464 TAAAATAATTTTTTAATAAATAAA
1 TAAAATAATATTTTAATAAATAAA
*
2608488 TAAAAT-ATATTTTAATTAATA
1 TAAAATAATATTTTAATAAATA
2608509 TATACAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATAATATTTTAATAAATAAA
Found at i:2612044 original size:15 final size:15
Alignment explanation
Indices: 2612020--2612097 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
2612010 AGAAAACCGA
2612020 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
2612035 ATAGAGAAATCC-AG
1 ATAAAGAAATCCAAG
2612049 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
2612064 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
2612080 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
2612095 ATA
1 ATA
2612098 TGATACTATG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
14 2 0.04
15 51 0.94
16 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:2612053 original size:30 final size:30
Alignment explanation
Indices: 2612009--2612097 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
2611999 CAAAGATAAC
*
2612009 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAATCCAGAATAAAGAAATCCAAGATA
*
2612038 GAGAAATCCAGAATAAAGAAATCC-AGAATA
1 AAGAAATCCAGAATAAAGAAATCCAAG-ATA
* * *
2612068 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAATCCAGAATAAAGAAATCCAAGATA
2612098 TGATACTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.18
30 40 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGAAATCCAGAATAAAGAAATCCAAGATA
Found at i:2620556 original size:26 final size:26
Alignment explanation
Indices: 2620525--2620632 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
2620515 TGAAATGCCC
*
2620525 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2620551 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2620577 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2620603 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2620629 ATCA
1 ATCA
2620633 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2627656 original size:26 final size:26
Alignment explanation
Indices: 2627625--2627676 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2627615 TGAAATGCCC
2627625 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
2627651 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
2627677 GTCAATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:2634284 original size:21 final size:21
Alignment explanation
Indices: 2634254--2634298 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2634244 GAAGGATCAA
*
2634254 ATGCTAGAGTCCCAGAAAAAC
1 ATGCTAGAGTCACAGAAAAAC
* *
2634275 ATGCTGGAGTCACAGAACAAC
1 ATGCTAGAGTCACAGAAAAAC
2634296 ATG
1 ATG
2634299 ATGAGCTAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (21 bp):
ATGCTAGAGTCACAGAAAAAC
Found at i:2642141 original size:44 final size:44
Alignment explanation
Indices: 2642075--2642194 Score: 195
Period size: 44 Copynumber: 2.7 Consensus size: 44
2642065 ATTTTGGCGA
*
2642075 AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGCTTTCAGCCACC
1 AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATTTCAGCCACC
*
2642119 AGTCTTATCTTCACTGAATAGGAGTGGAGCAGATTTCAGCCACC
1 AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATTTCAGCCACC
* * *
2642163 AGCCTTATCTTCACTGAGCAGAAGTGGAGCAG
1 AGTCTTATCTTCACTGAGTAGGAGTGGAGCAG
2642195 GCTAAACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATTTCAGCCACC
Found at i:2642329 original size:44 final size:43
Alignment explanation
Indices: 2642022--2642464 Score: 144
Period size: 44 Copynumber: 9.9 Consensus size: 43
2642012 AAAGACAGAT
* * * * *
2642022 ATCATCAGCCTTATCTTTACTGAGCAGGAGTGAAGCAGATCAA
1 ATCATCAGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATCTA
** * *
2642065 ATTTTGGCGAAGTCTTATCTTCACTGAGTAGGAGTGGAGCAGCTTTCA
1 ATCAT--C--AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATCT-A
** * * *
2642113 GCCACCAGTCTTATCTTCACTGAATAGGAGTGGAGCAGATTTCA
1 ATCATCAGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATCT-A
** * * * * *
2642157 GCCACCAGCCTTATCTTCACTGAGCAGAAGTGGAGCAG-GCTA
1 ATCATCAGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATCTA
* * * * * * *
2642199 AACATACCTGATCTTTTCTTCACTGAGCAAGAGTGAAGCAGATCAA
1 ATCAT--CAG-TCTTATCTTCACTGAGTAGGAGTGGAGCAGATCTA
** * * * * *
2642245 ATTTTGGCGAGTTTTATCTCCA-TGTA-TCGACAATGGAGCAGATTCTA
1 ATCAT--C-AGTCTTATCTTCACTG-AGTAG-GAGTGGAGCAGA-TCTA
* * *
2642292 ATCATCAGCCTTATCTTCACTGAGTAGGAGTGAAGCAG-GCTA
1 ATCATCAGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATCTA
* * * *
2642334 AGT-ATAGCAGATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCGA
1 A-TCAT--CAG-TCTTATCTTCACTGAGTAGGAGTGGAGCAGATCTA
** * * * * *
2642380 ATTTTGGTGAATCTTATC-TCCCTGTACTAGCGA-TGGAGCAGATTCCA
1 A---TCATCAGTCTTATCTTCACTG-AGTAG-GAGTGGAGCAGA-TCTA
* * *
2642427 ATCATCAGACTTATCTTCACTGAGCAGGAGTGAAGCAG
1 ATCATCAGTCTTATCTTCACTGAGTAGGAGTGGAGCAG
2642465 GCTAAATATA
Statistics
Matches: 288, Mismatches: 84, Indels: 55
0.67 0.20 0.13
Matches are distributed among these distances:
42 9 0.03
43 7 0.02
44 113 0.39
45 68 0.24
46 45 0.16
47 43 0.15
48 2 0.01
49 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
ATCATCAGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATCTA
Found at i:2642493 original size:135 final size:135
Alignment explanation
Indices: 2642143--2642509 Score: 439
Period size: 135 Copynumber: 2.7 Consensus size: 135
2642133 TGAATAGGAG
* ** * * * * *
2642143 TGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGAAGTGGAGCAGGCTAAACATACCT
1 TGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATACCA
* * * * * *
2642208 GATCTTTTCTTCACTGAGCAAGAGTGAAGCAGATCAAATTTTGGCGAGTTTTATCTCCATGTATC
66 GATCTTATCTTCGCTGAGCAAGAGTGGAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTATA
2642273 GACAA
131 GACAA
* * * *
2642278 TGGAGCAGATTCTAATCATCAGCCTTATCTTCACTGAGTAGGAGTGAAGCAGGCTAAGTATAGCA
1 TGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATACCA
* * * * *
2642343 GATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCGAATTTTGGTGAATCTTATCTCCCTGTACT
66 GATCTTATCTTCGCTGAGCAAGAGTGGAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTA-T
*
2642408 AG-CGA
130 AGACAA
* *
2642413 TGGAGCAGATTCCAATCATCAGACTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATATCA
1 TGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATACCA
* * * * *
2642478 AATATTGTCTCCGCTGAACAAGAGTGGAGCAG
66 GATCTTATCTTCGCTGAGCAAGAGTGGAGCAG
2642510 GTCAGATACA
Statistics
Matches: 195, Mismatches: 36, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
135 193 0.99
136 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (135 bp):
TGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATACCA
GATCTTATCTTCGCTGAGCAAGAGTGGAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTATA
GACAA
Found at i:2659322 original size:17 final size:18
Alignment explanation
Indices: 2659297--2659330 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2659287 AAAAAGTAAA
2659297 AAATCATTAAAAAAACAG
1 AAATCATTAAAAAAACAG
2659315 AAAT-ATTAAAAAAACA
1 AAATCATTAAAAAAACA
2659331 TTAATTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATCATTAAAAAAACAG
Found at i:2659474 original size:7 final size:7
Alignment explanation
Indices: 2659459--2659489 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2659449 GAATAATAGA
2659459 AAATTAT
1 AAATTAT
*
2659466 AAATGAT
1 AAATTAT
2659473 AAATTAT
1 AAATTAT
2659480 AAATTAT
1 AAATTAT
2659487 AAA
1 AAA
2659490 AAAAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (7 bp):
AAATTAT
Found at i:2659504 original size:21 final size:21
Alignment explanation
Indices: 2659458--2659505 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2659448 AGAATAATAG
*
2659458 AAAATTATAAATGATAAATTAT
1 AAAATTATAAA-GAAAAATTAT
2659480 -AAATTATAAA-AAAAATTCAT
1 AAAATTATAAAGAAAAATT-AT
2659500 AAAATT
1 AAAATT
2659506 TTAACATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 6 0.26
20 2 0.09
21 15 0.65
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATTATAAAGAAAAATTAT
Found at i:2662068 original size:28 final size:28
Alignment explanation
Indices: 2661997--2662084 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
2661987 CTTTATACAT
* *
2661997 ATATACATTATTT-GTTTTAAAT-TTTT
1 ATATACATTATTTATTTTTAAATCTTTC
* *
2662023 ATATA-TTTACTGTCATTTTTAAATCTTTC
1 ATATACATTA-T-TTATTTTTAAATCTTTC
*
2662052 ATATACATTATTTATTTTTTAAGTCTTTAC
1 ATATACATTATTTA-TTTTTAAATCTTT-C
2662082 ATA
1 ATA
2662085 CTGTTATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.06
26 6 0.12
27 1 0.02
28 10 0.21
29 21 0.44
30 7 0.15
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (28 bp):
ATATACATTATTTATTTTTAAATCTTTC
Found at i:2662370 original size:24 final size:23
Alignment explanation
Indices: 2662284--2662385 Score: 86
Period size: 24 Copynumber: 4.4 Consensus size: 23
2662274 CTACATGTTG
2662284 TTTTAAATTGTTATATA-TATTA
1 TTTTAAATTGTTATATATTATTA
* * * *
2662306 -TTT-ATTTTTTCTTTATT-TTA
1 TTTTAAATTGTTATATATTATTA
2662326 TTTTAAATTATGTTATATATTAATTA
1 TTTTAAA-T-TGTTATATATT-ATTA
*
2662352 TTTTAAATTGTTTTATATTATCTA
1 TTTTAAATTGTTATATATTAT-TA
*
2662376 CTTTAAATTG
1 TTTTAAATTG
2662386 CTTCGTAACT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
20 11 0.18
21 7 0.11
22 1 0.02
23 3 0.05
24 29 0.47
25 1 0.02
26 10 0.16
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTAAATTGTTATATATTATTA
Found at i:2668172 original size:4 final size:4
Alignment explanation
Indices: 2668163--2668196 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
2668153 AAGTTTTATT
2668163 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
2668197 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:2668204 original size:22 final size:22
Alignment explanation
Indices: 2668146--2668205 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
2668136 AAGTGGCCCA
*
2668146 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
2668170 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
2668191 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
2668206 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:2679097 original size:15 final size:15
Alignment explanation
Indices: 2679077--2679105 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2679067 AATGGGTATC
2679077 CTAAATTTTTTTGAG
1 CTAAATTTTTTTGAG
2679092 CTAAATTTTTTTGA
1 CTAAATTTTTTTGA
2679106 CTGTCACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (15 bp):
CTAAATTTTTTTGAG
Found at i:2680148 original size:16 final size:16
Alignment explanation
Indices: 2680127--2680179 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2680117 GTAAATTATG
2680127 TTTTCCATCTTTTCAT
1 TTTTCCATCTTTTCAT
* * *
2680143 TTTTCCAGCCATTTAAT
1 TTTTCCA-TCTTTTCAT
2680160 TTTT-CATCTTTTCAAT
1 TTTTCCATCTTTTC-AT
2680176 TTTT
1 TTTT
2680180 TTTCACTCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 4 0.14
16 15 0.52
17 10 0.34
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTCCATCTTTTCAT
Found at i:2703658 original size:11 final size:11
Alignment explanation
Indices: 2703642--2703666 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2703632 AAATCCAAAC
2703642 AAAAATAAAAT
1 AAAAATAAAAT
2703653 AAAAATAAAAT
1 AAAAATAAAAT
2703664 AAA
1 AAA
2703667 TAAAACCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2705896 original size:11 final size:10
Alignment explanation
Indices: 2705871--2705900 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2705861 CAAATCGGGG
2705871 TTAAAAAGGT
1 TTAAAAAGGT
2705881 TTAAAAAGGT
1 TTAAAAAGGT
2705891 TCTAAAAAGG
1 T-TAAAAAGG
2705901 GTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (10 bp):
TTAAAAAGGT
Found at i:2708645 original size:20 final size:20
Alignment explanation
Indices: 2708617--2708654 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2708607 AAGTATATAA
2708617 AAATATTAACTAA-AAAATGT
1 AAATATTAA-TAAGAAAATGT
*
2708637 AAATTTTAATAAGAAAAT
1 AAATATTAATAAGAAAAT
2708655 ATATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATATTAATAAGAAAATGT
Found at i:2711437 original size:22 final size:21
Alignment explanation
Indices: 2711412--2711452 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2711402 TACAATATTC
*
2711412 AAATCATAACAATAAAATAATA
1 AAATCACAACAA-AAAATAATA
*
2711434 AAATGACAACAAAAAATAA
1 AAATCACAACAAAAAATAA
2711453 CAGAAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.17
Consensus pattern (21 bp):
AAATCACAACAAAAAATAATA
Found at i:2711834 original size:24 final size:24
Alignment explanation
Indices: 2711800--2711848 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2711790 AAAAGTAAAT
*
2711800 TAAAATTAAAAT-TAAATGTTTATA
1 TAAAATCAAAATGTAAATG-TTATA
*
2711824 TAAAATCAAAATGTATATGTTATA
1 TAAAATCAAAATGTAAATGTTATA
2711848 T
1 T
2711849 TATGAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (24 bp):
TAAAATCAAAATGTAAATGTTATA
Found at i:2712460 original size:20 final size:20
Alignment explanation
Indices: 2712435--2712472 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2712425 GTTTTTAGTA
*
2712435 TTTTTAATATATTATATAAT
1 TTTTTAAAATATTATATAAT
*
2712455 TTTTTAAAATTTTATATA
1 TTTTTAAAATATTATATA
2712473 TAAAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTAAAATATTATATAAT
Found at i:2719920 original size:13 final size:12
Alignment explanation
Indices: 2719897--2719924 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2719887 TTCATTCTCC
2719897 TTTTCTTTTTTT
1 TTTTCTTTTTTT
2719909 TTTTCTTTTTTT
1 TTTTCTTTTTTT
2719921 TTTT
1 TTTT
2719925 AATTTTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:2724397 original size:31 final size:31
Alignment explanation
Indices: 2724362--2724421 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2724352 GGACCTTAAC
2724362 AGTTTAATAACTTAAATAAAAATTTTCGAAT
1 AGTTTAATAACTTAAATAAAAATTTTCGAAT
* * * *
2724393 AGTTTAGTGACTTGAATGAAAATTTTCGA
1 AGTTTAATAACTTAAATAAAAATTTTCGA
2724422 GTAAATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (31 bp):
AGTTTAATAACTTAAATAAAAATTTTCGAAT
Found at i:2729338 original size:14 final size:14
Alignment explanation
Indices: 2729319--2729346 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2729309 TTTTATAAGA
2729319 TTTTATAATATTAT
1 TTTTATAATATTAT
2729333 TTTTATAATATTAT
1 TTTTATAATATTAT
2729347 AAAAATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATAATATTAT
Found at i:2730052 original size:6 final size:6
Alignment explanation
Indices: 2730031--2730064 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
2730021 TTCATCATTA
2730031 TTTTATT TTGTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTA-T TT-TTAT TTTTAT TTTTAT TTTTAT TT
2730065 GAGTCCACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.69
7 5 0.19
8 3 0.12
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:2730959 original size:27 final size:26
Alignment explanation
Indices: 2730929--2730983 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
2730919 TCATAATATT
* * *
2730929 TTATGTAAATATTTTTTTCTAAATTTA
1 TTATATAAATATTTTCTT-TAAAATTA
*
2730956 TTATATATATATTTTCTTTAAAATTA
1 TTATATAAATATTTTCTTTAAAATTA
2730982 TT
1 TT
2730984 CATTTGAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (26 bp):
TTATATAAATATTTTCTTTAAAATTA
Found at i:2734163 original size:22 final size:22
Alignment explanation
Indices: 2734138--2734179 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2734128 AGGAGGGGCC
*
2734138 AAATTTGAATTATAAATTTTTG
1 AAATGTGAATTATAAATTTTTG
*
2734160 AAATGTGAATTATAGATTTT
1 AAATGTGAATTATAAATTTT
2734180 ATCATGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (22 bp):
AAATGTGAATTATAAATTTTTG
Found at i:2739700 original size:15 final size:15
Alignment explanation
Indices: 2739661--2739703 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
2739651 TGAAATATTT
2739661 TTTAA-TATTATAATA
1 TTTAATTATTA-AATA
*
2739676 TTAAAATTATTAAATA
1 TT-TAATTATTAAATA
2739692 TTTAATTATTAA
1 TTTAATTATTAA
2739704 GCTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 11 0.46
16 8 0.33
17 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAATTATTAAATA
Found at i:2742102 original size:60 final size:60
Alignment explanation
Indices: 2742006--2742127 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
2741996 TTTCATATTC
*
2742006 ATTCAAAATCCATTTTAAGGAATGTACTCCTCTTTCAGTAGCTTCTGCGAATAAAATGCA
1 ATTCAAAATCCATTTTAAGGAATGCACTCCTCTTTCAGTAGCTTCTGCGAATAAAATGCA
* *
2742066 ATTCAAAATCCGTTTTAAGGAATGCACTCCTTTTTCAGTAGCTTCTGCGAATAAAATGCA
1 ATTCAAAATCCATTTTAAGGAATGCACTCCTCTTTCAGTAGCTTCTGCGAATAAAATGCA
2742126 AT
1 AT
2742128 CATCTGCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (60 bp):
ATTCAAAATCCATTTTAAGGAATGCACTCCTCTTTCAGTAGCTTCTGCGAATAAAATGCA
Found at i:2743336 original size:24 final size:25
Alignment explanation
Indices: 2743315--2743367 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
2743305 CACCATAAGA
2743315 ATAAAA-AAAAAATCCAAAATAAAT
1 ATAAAACAAAAAATCCAAAATAAAT
* *
2743339 ATAAAACTAAAATTCCAAAA-ATAAT
1 ATAAAACAAAAAATCCAAAATA-AAT
2743364 ATAA
1 ATAA
2743368 TGCAATGACG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (25 bp):
ATAAAACAAAAAATCCAAAATAAAT
Found at i:2744210 original size:16 final size:18
Alignment explanation
Indices: 2744181--2744215 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2744171 GGACATAAAA
2744181 TTTTCCTCCATTTGTCTT
1 TTTTCCTCCATTTGTCTT
2744199 TTTTCCT-C-TTTGTCTT
1 TTTTCCTCCATTTGTCTT
2744215 T
1 T
2744216 AGTGTAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.03, C:0.26, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTCCTCCATTTGTCTT
Found at i:2748199 original size:40 final size:40
Alignment explanation
Indices: 2748101--2748363 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
2748091 TCCTCGTTCA
* * * * *
2748101 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
2748140 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2748180 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2748220 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2748260 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
2748300 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
2748340 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2748364 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2750861 original size:19 final size:19
Alignment explanation
Indices: 2750837--2750883 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2750827 TACCAAACTA
*
2750837 AAAAATATGATGAAGTACC
1 AAAAATATGAGGAAGTACC
*
2750856 AAAAATTATGAGGGAGTACC
1 AAAAA-TATGAGGAAGTACC
2750876 AAAAATAT
1 AAAAATAT
2750884 ACGAGGGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
AAAAATATGAGGAAGTACC
Found at i:2750889 original size:21 final size:20
Alignment explanation
Indices: 2750850--2750892 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2750840 AATATGATGA
*
2750850 AGTACCAAAAATTATGAGGG
1 AGTACCAAAAATTACGAGGG
2750870 AGTACCAAAAATATACGAGGG
1 AGTACCAAAAAT-TACGAGGG
2750891 AG
1 AG
2750893 AGGGAATACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.47, C:0.12, G:0.26, T:0.16
Consensus pattern (20 bp):
AGTACCAAAAATTACGAGGG
Found at i:2751119 original size:23 final size:23
Alignment explanation
Indices: 2751093--2751150 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2751083 AGTTACGAGG
*
2751093 AATACAAGAAAAAAA-GAAGAGAA
1 AATACAA-AAAAAAATCAAGAGAA
*
2751116 AATACCAAAAAAAAATCATGAGAA
1 AATA-CAAAAAAAAATCAAGAGAA
*
2751140 AATACCAAAAA
1 AATACAAAAAA
2751151 TTACGAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.09
Consensus pattern (23 bp):
AATACAAAAAAAAATCAAGAGAA
Found at i:2751128 original size:24 final size:24
Alignment explanation
Indices: 2751093--2751150 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
2751083 AGTTACGAGG
* *
2751093 AATA-CAAGAAAAAAAGAAGAGAA
1 AATACCAAAAAAAAAACAAGAGAA
* *
2751116 AATACCAAAAAAAAATCATGAGAA
1 AATACCAAAAAAAAAACAAGAGAA
2751140 AATACCAAAAA
1 AATACCAAAAA
2751151 TTACGAGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.09
Consensus pattern (24 bp):
AATACCAAAAAAAAAACAAGAGAA
Found at i:2751151 original size:20 final size:20
Alignment explanation
Indices: 2751126--2751210 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
2751116 AATACCAAAA
2751126 AAAAATCATGAGAAAATACC
1 AAAAATCATGAGAAAATACC
* * *
2751146 AAAAATTACGAGAGAGA-ACC
1 AAAAATCATGAGA-AAATACC
* * *
2751166 AAAAATCATGAGAGAGTACA
1 AAAAATCATGAGAAAATACC
* *
2751186 AAAAATTC-TTAGGAAATACC
1 AAAAA-TCATGAGAAAATACC
2751206 AAAAA
1 AAAAA
2751211 AGAAAAAAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
20 44 0.92
21 4 0.08
ACGTcount: A:0.58, C:0.13, G:0.14, T:0.15
Consensus pattern (20 bp):
AAAAATCATGAGAAAATACC
Found at i:2751643 original size:18 final size:18
Alignment explanation
Indices: 2751620--2751654 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2751610 AAAAATTATA
2751620 AAGG-AATACCAAAAAAAC
1 AAGGAAATA-CAAAAAAAC
2751638 AAGGAAATACAAAAAAA
1 AAGGAAATACAAAAAAA
2751655 AAATTTGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.71, C:0.11, G:0.11, T:0.06
Consensus pattern (18 bp):
AAGGAAATACAAAAAAAC
Found at i:2751655 original size:19 final size:18
Alignment explanation
Indices: 2751620--2751655 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2751610 AAAAATTATA
*
2751620 AAGGAATACCAAAAAAAC
1 AAGGAATACAAAAAAAAC
2751638 AAGGAAATACAAAAAAAA
1 AAGG-AATACAAAAAAAA
2751656 AATTTGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.11, G:0.11, T:0.06
Consensus pattern (18 bp):
AAGGAATACAAAAAAAAC
Found at i:2753868 original size:23 final size:23
Alignment explanation
Indices: 2753842--2753899 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
2753832 ATAAATTTAT
2753842 TTTTTTAATTTTTTAAAATTA-AA
1 TTTTTTAATTTTTTAAAA-TACAA
* * *
2753865 -TTTTTATACTTTTTCAAATACAT
1 TTTTTTA-ATTTTTTAAAATACAA
2753888 TTTTTTAATTTT
1 TTTTTTAATTTT
2753900 ATATGTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTTAATTTTTTAAAATACAA
Found at i:2753899 original size:22 final size:23
Alignment explanation
Indices: 2753840--2753899 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
2753830 TCATAAATTT
2753840 ATTTTTTTAATTTTTTAAAATTAA
1 ATTTTTTTAA-TTTTTAAAATTAA
* * * *
2753864 ATTTTTATACTTTTTCAAA-TAC
1 ATTTTTTTAATTTTTAAAATTAA
2753886 ATTTTTTTAATTTT
1 ATTTTTTTAATTTT
2753900 ATATGTTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 14 0.47
23 8 0.27
24 8 0.27
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTTTTAATTTTTAAAATTAA
Found at i:2754051 original size:26 final size:27
Alignment explanation
Indices: 2754020--2754071 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2754010 AAATGATGAG
*
2754020 ACTAAA-TTAAACCAAAA-AAATCAAAA
1 ACTAAATTTAAA-AAAAACAAATCAAAA
2754046 ACTAAATTTAAAAAAAACAAATCAAA
1 ACTAAATTTAAAAAAAACAAATCAAA
2754072 TAGAAACTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.17
Consensus pattern (27 bp):
ACTAAATTTAAAAAAAACAAATCAAAA
Found at i:2759040 original size:40 final size:40
Alignment explanation
Indices: 2758985--2759110 Score: 200
Period size: 40 Copynumber: 3.1 Consensus size: 40
2758975 TATTCGGATG
2758985 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
2759025 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
2759065 ATATCCGGGTTAAGTCCCGAAGGAAATTGAGCGAG-TAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
2759105 ATATCC
1 ATATCC
2759111 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
39 2 0.02
40 79 0.98
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:2772447 original size:46 final size:46
Alignment explanation
Indices: 2772390--2772694 Score: 477
Period size: 46 Copynumber: 6.6 Consensus size: 46
2772380 ATGAAATGTG
*
2772390 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
*
2772436 TAAGACCATGGTTGAAATATACCATGGCAACGTGACATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
* *
2772482 TAAGATCATGGTGGAAAGATACCATGGCAACGTGACATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
* *
2772528 TAAGATCATGGTTGAAAGATACCATGGCAACGTGATATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
*
2772574 TAAGACCATGGTTGAAATATACCATGGCAACGTGACATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
* * *
2772620 TAAGATCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA-GAA
* * *
2772666 TAAGACCATTGTTGAAAGACACTATGGCA
1 TAAGACCATGGTTGAAAGATACCATGGCA
2772695 TCATGTCGAA
Statistics
Matches: 240, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 5 0.02
46 235 0.98
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
Found at i:2772628 original size:138 final size:138
Alignment explanation
Indices: 2772390--2772694 Score: 531
Period size: 138 Copynumber: 2.2 Consensus size: 138
2772380 ATGAAATGTG
2772390 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAAGAATAAGACCATGGTTGAAATA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAAGAATAAGACCATGGTTGAAATA
*
2772455 TACCATGGCAACGTGACATGAAAAGAATAAGATCATGGTGGAAAGATACCATGGCAACGTGACAT
66 TACCATGGCAACGTGACATGAAAAGAATAAGATCATGGTGGAAAGATACCATGGCAACATGACA-
2772520 GAAAA-GAA
130 GAAAATGAA
*
2772528 TAAGATCATGGTTGAAAGATACCATGGCAACGTGATATGAAAAGAATAAGACCATGGTTGAAATA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAAGAATAAGACCATGGTTGAAATA
*
2772593 TACCATGGCAACGTGACATGAAAAGAATAAGATCATGGTTGAAAGATACCATGGCAACATGACAG
66 TACCATGGCAACGTGACATGAAAAGAATAAGATCATGGTGGAAAGATACCATGGCAACATGACAG
*
2772658 AAAATGAG
131 AAAATGAA
* * *
2772666 TAAGACCATTGTTGAAAGACACTATGGCA
1 TAAGACCATGGTTGAAAGATACCATGGCA
2772695 TCATGTCGAA
Statistics
Matches: 158, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
137 5 0.03
138 153 0.97
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (138 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAAGAATAAGACCATGGTTGAAATA
TACCATGGCAACGTGACATGAAAAGAATAAGATCATGGTGGAAAGATACCATGGCAACATGACAG
AAAATGAA
Found at i:2774830 original size:31 final size:32
Alignment explanation
Indices: 2774789--2774851 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
2774779 TTATTTATAA
*
2774789 AAGATATTTAT-TAATTAAATAT-TTATATTAT
1 AAGATATTTATGTAA-TAAATATATTAAATTAT
*
2774820 AAGATTTTTATGTAATAAATATATTAAATTAT
1 AAGATATTTATGTAATAAATATATTAAATTAT
2774852 GACAAGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
AAGATATTTATGTAATAAATATATTAAATTAT
Found at i:2775715 original size:47 final size:46
Alignment explanation
Indices: 2775646--2775762 Score: 153
Period size: 47 Copynumber: 2.5 Consensus size: 46
2775636 GATATTGTTA
* *
2775646 CTGTTACCGTTACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACT
1 CTGTTACCG-TACTGTTACTGTTCCAGATTTCTTCCGATGAGGTACT
*
2775693 CTGTATACCGTACTGTTACTGTTCCGGATTTCTTCCGATGAGGTACT
1 CTGT-TACCGTACTGTTACTGTTCCAGATTTCTTCCGATGAGGTACT
* * *
2775740 CTATGTACCGTATTGCTACTGTT
1 CTGT-TACCGTACTGTTACTGTT
2775763 ACTATTACTG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 57 0.92
48 5 0.08
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (46 bp):
CTGTTACCGTACTGTTACTGTTCCAGATTTCTTCCGATGAGGTACT
Found at i:2775960 original size:18 final size:18
Alignment explanation
Indices: 2775897--2775962 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
2775887 AGATCGACTG
* *
2775897 TTACTGAATAATTTAATTG
1 TTACTGAATAA-TTGATTA
*
2775916 TTACTGAATAACTGATTA
1 TTACTGAATAATTGATTA
**
2775934 TTGTTGAATAATTGATTA
1 TTACTGAATAATTGATTA
*
2775952 TTACCGAATAA
1 TTACTGAATAA
2775963 CTAGCTGTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 27 0.71
19 11 0.29
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (18 bp):
TTACTGAATAATTGATTA
Found at i:2780934 original size:12 final size:12
Alignment explanation
Indices: 2780917--2780941 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2780907 GCCGACTACT
2780917 GTTACTGTTACC
1 GTTACTGTTACC
2780929 GTTACTGTTACC
1 GTTACTGTTACC
2780941 G
1 G
2780942 ATTCGGCACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:2781041 original size:47 final size:46
Alignment explanation
Indices: 2780972--2781088 Score: 171
Period size: 47 Copynumber: 2.5 Consensus size: 46
2780962 GATATTGTTA
* *
2780972 CTGTTACCGTTACTGTTACTGTTTCGGATTTGTTCCGATGAGGTACT
1 CTGTTACCG-TACTGTTACTGTTCCAGATTTGTTCCGATGAGGTACT
2781019 CTGTATACCGTACTGTTACTGTTCCAGATTTGTTCCGATGAGGTACT
1 CTGT-TACCGTACTGTTACTGTTCCAGATTTGTTCCGATGAGGTACT
* *
2781066 CTGTGTACCGTATTGCTACTGTT
1 CTGT-TACCGTACTGTTACTGTT
2781089 ATTGTTACTG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 59 0.92
48 5 0.08
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (46 bp):
CTGTTACCGTACTGTTACTGTTCCAGATTTGTTCCGATGAGGTACT
Found at i:2781270 original size:18 final size:18
Alignment explanation
Indices: 2781222--2781307 Score: 100
Period size: 18 Copynumber: 4.7 Consensus size: 18
2781212 AAAGATCGAC
* *
2781222 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAA-CTGAT
2781241 TGTTACTGAATAACTGAT
1 TGTTACTGAATAACTGAT
* * *
2781259 TATTATTGAATAATTGAT
1 TGTTACTGAATAACTGAT
* *
2781277 TGTTACCGAATAACTGAC
1 TGTTACTGAATAACTGAT
2781295 TGTTACTGAATAA
1 TGTTACTGAATAA
2781308 ATAATCATTC
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
18 43 0.77
19 13 0.23
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (18 bp):
TGTTACTGAATAACTGAT
Found at i:2781288 original size:36 final size:37
Alignment explanation
Indices: 2781219--2781307 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 37
2781209 TGGAAAGATC
* *
2781219 GACTGTTACTGAATAATTTAATTGTTACTGAATAACT
1 GACTATTACTGAATAATTTAATTGTTACCGAATAACT
* * *
2781256 GATTATTATTGAATAA-TTGATTGTTACCGAATAACT
1 GACTATTACTGAATAATTTAATTGTTACCGAATAACT
*
2781292 GACTGTTACTGAATAA
1 GACTATTACTGAATAA
2781308 ATAATCATTC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 31 0.70
37 13 0.30
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (37 bp):
GACTATTACTGAATAATTTAATTGTTACCGAATAACT
Found at i:2786092 original size:29 final size:30
Alignment explanation
Indices: 2786033--2786090 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2786023 TCCGAGCCTT
*
2786033 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
2786063 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
2786091 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:2786320 original size:13 final size:13
Alignment explanation
Indices: 2786302--2786333 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2786292 TTTCCAGCAA
2786302 TTATGAATTTATT
1 TTATGAATTTATT
2786315 TTATGAATTTATT
1 TTATGAATTTATT
*
2786328 TGATGA
1 TTATGA
2786334 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:2786508 original size:50 final size:50
Alignment explanation
Indices: 2786428--2786612 Score: 361
Period size: 50 Copynumber: 3.7 Consensus size: 50
2786418 ATTTGGGTAA
*
2786428 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
2786478 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
2786528 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
2786578 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
2786613 TTTGGCATGT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:2789729 original size:45 final size:44
Alignment explanation
Indices: 2789442--2790207 Score: 409
Period size: 45 Copynumber: 16.7 Consensus size: 44
2789432 TGTAGCTTGA
* ** * *
2789442 TCTGCTCCATTGCAACTTCAATGAGATAAGATTTATTATCTTGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-GTATCTTCAG
* * * * * *
2789487 TTTGCTCCACCGCGACTTCAGAGAGATAAGACTTGTAACTTCA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAG
* * * * ** *
2789530 ACTTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGTGGCTTCAA
1 TC-TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAG
* * * *
2789575 TCTACTCCACTACAACTTCAGGGAGATAAGATTCACCATGGTAGT-TTGAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-----T-GTA-TCTTCAG
* * * * * * * *
2789625 TC-GAC-CTACTGCAACTTTAGAGG-TATAGGATTTATAGCTTTAA
1 TCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTATCTTCAG
* * *
2789668 TCTGCTCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAG
* *
2789713 TCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGATTTGTAGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAA-------GATTTGTATCTTCAG
* **
2789764 TCTGCCCCACTGCAACTTCAGGGAGATAAGATCCGTTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAG
* * * *
2789809 TCTGCTCCACTGCAACTTTAGAGAGATAAGGTTTGTGATTTGTAGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAA-------GATTTGTATCTTCAG
* *
2789860 TCTGC-CCAACTGCAACTTCAAGGAGATAAGATTCGCTATCTTCAG
1 TCTGCTCC-ACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAG
* * * *
2789905 TCTACTCCACTGCAACTTTAGGGAGATAAGACTTGTAAT-TTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ATCTTCAG
* * * * *
2789949 CCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGTTTGTAGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAA-------GATTTGTATCTTCAG
* * *
2790000 TCTGCCCCACTGCAACTTTAGGGAGATAAGATTCGCTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAG
* ** * *
2790045 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGGCTTAAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAG
* * * * * * *
2790089 TCTGCTCCCCTACTACCTC-GGGAAGATAATATTCGCCATCTTC-G
1 TCTGCTCCACTGCAACTTCAGGG-AGATAAGATTTG-TATCTTCAG
* ** * * * *
2790133 ATCTGCTCCACTACTGCTT-AGGGAGATAATATCTGAAATTTTCAG
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAG
2790178 TCTGCTCCACTGCAACTTCAGGGAGATAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG
2790208 GCTGGTGGCT
Statistics
Matches: 545, Mismatches: 126, Indels: 100
0.71 0.16 0.13
Matches are distributed among these distances:
43 12 0.02
44 190 0.35
45 198 0.36
46 2 0.00
49 20 0.04
50 13 0.02
51 100 0.18
52 10 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAG
Found at i:2789781 original size:96 final size:96
Alignment explanation
Indices: 2789653--2789934 Score: 431
Period size: 96 Copynumber: 2.9 Consensus size: 96
2789643 AGAGGTATAG
* * * * * *
2789653 GATTTATAGCTTTAATCTGCTCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGC
1 GATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCAGTCTGC
*
2789718 TCCACTGCAACTTCAGGGAGATAAGGTTTGT
66 TCCACTGCAACTTTAGGGAGATAAGGTTTGT
* * * *
2789749 GATTTGTAGCTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATCCGTTATCTTCAGTCTGC
1 GATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCAGTCTGC
*
2789814 TCCACTGCAACTTTAGAGAGATAAGGTTTGT
66 TCCACTGCAACTTTAGGGAGATAAGGTTTGT
*
2789845 GATTTGTAGCTTCAATCTGCCCAACTGCAACTTCA-AGGAGATAAGATTCGCTATCTTCAGTCTA
1 GATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAGA-GAGATAAGATTCGCTATCTTCAGTCTG
2789909 CTCCACTGCAACTTTAGGGAGATAAG
65 CTCCACTGCAACTTTAGGGAGATAAG
2789935 ACTTGTAATT
Statistics
Matches: 168, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
96 168 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (96 bp):
GATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCAGTCTGC
TCCACTGCAACTTTAGGGAGATAAGGTTTGT
Found at i:2789991 original size:140 final size:141
Alignment explanation
Indices: 2789770--2790080 Score: 482
Period size: 140 Copynumber: 2.2 Consensus size: 141
2789760 TCAATCTGCC
* * ** *
2789770 CCACTGCAACTTCAGGGAGATAAGA-TCCGTTATCTTCAGTCTGCTCCACTGCAACTTTAGAGAG
1 CCACTGCAACTTCAGGGAGATAAGACT-TGTAATCTTCAACCTGCTCCACTGCAACTTCAGAGAG
2789834 ATAAGGTTTGTGATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAAGGAGATAAGATTCGCTAT
65 ATAAGGTTTGTGATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAAGGAGATAAGATTCGCTAT
2789899 CTTCAGTCTACT
130 CTTCAGTCTACT
* *
2789911 CCACTGCAACTTTAGGGAGATAAGACTTGTAAT-TTCAACCTGCTCCACTGCAACTTCAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAATCTTCAACCTGCTCCACTGCAACTTCAGAGAGA
* * * * *
2789975 TAAGGTTTGTGGTTTGTAGCTTTAATCTGCCCCACTGCAACTTTAGGGAGATAAGATTCGCTATC
66 TAAGGTTTGTGATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAAGGAGATAAGATTCGCTATC
*
2790040 TTCAGTCTGCT
131 TTCAGTCTACT
2790051 CCACTGCAACTTCAGGGAGATAAGACTTGT
1 CCACTGCAACTTCAGGGAGATAAGACTTGT
2790081 GGCTTAAATC
Statistics
Matches: 155, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
140 126 0.81
141 28 0.18
142 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (141 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGTAATCTTCAACCTGCTCCACTGCAACTTCAGAGAGA
TAAGGTTTGTGATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAAGGAGATAAGATTCGCTATC
TTCAGTCTACT
Found at i:2790116 original size:140 final size:140
Alignment explanation
Indices: 2789770--2790117 Score: 430
Period size: 140 Copynumber: 2.5 Consensus size: 140
2789760 TCAATCTGCC
* * * ** * * * *
2789770 CCACTGCAACTTCAGGGAGATAAGA-TCCGTTATCTTCAGTCTGCTCCACTGCAACTTTAGAGAG
1 CCACTGCAACTTCAGGGAGATAAGACT-TG-TAACTTAAACCTGCTCCACTACAACCTCAGGGAG
2789834 ATAAGGTTTGTGATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAAGGAGATAAGATTCGCTAT
64 ATAAGGTTTGTGATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAAGGAGATAAGATTCGCTAT
2789899 CTTCAGTCTACT
129 CTTCAGTCTACT
* * * * *
2789911 CCACTGCAACTTTAGGGAGATAAGACTTGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGAT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTAAACCTGCTCCACTACAACCTCAGGGAGAT
* * * * *
2789976 AAGGTTTGTGGTTTGTAGCTTTAATCTGCCCCACTGCAACTTTAGGGAGATAAGATTCGCTATCT
66 AAGGTTTGTGATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAAGGAGATAAGATTCGCTATCT
*
2790041 TCAGTCTGCT
131 TCAGTCTACT
** * * *
2790051 CCACTGCAACTTCAGGGAGATAAGACTTGTGGCTTAAATCTGCTCCCCTACTACCTC-GGGAAGA
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTAAACCTGCTCCACTACAACCTCAGGG-AGA
2790115 TAA
65 TAA
2790118 TATTCGCCAT
Statistics
Matches: 181, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
139 3 0.02
140 152 0.84
141 25 0.14
142 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (140 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTAAACCTGCTCCACTACAACCTCAGGGAGAT
AAGGTTTGTGATTTGTAGCTTCAATCTGCCCAACTGCAACTTCAAGGAGATAAGATTCGCTATCT
TCAGTCTACT
Found at i:2790556 original size:19 final size:17
Alignment explanation
Indices: 2790528--2790562 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
2790518 ATGTTACAAT
2790528 TAATTGGTTTTTGATAAC
1 TAATTGGTTTTT-ATAAC
2790546 TAATATGGTTTTTATAA
1 TAAT-TGGTTTTTATAA
2790563 AAATAGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.51
Consensus pattern (17 bp):
TAATTGGTTTTTATAAC
Found at i:2790905 original size:16 final size:16
Alignment explanation
Indices: 2790884--2790951 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
2790874 TTTGGTTCGC
2790884 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2790900 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
2790916 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
2790932 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2790948 TGTA
1 TGTA
2790952 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:2791205 original size:16 final size:16
Alignment explanation
Indices: 2791168--2791209 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2791158 TTAATCATAT
*
2791168 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
2791184 TT-AAATATATTATAA
1 TTAAAATATATTATAA
2791199 TTAAAATATAT
1 TTAAAATATAT
2791210 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:2791216 original size:14 final size:15
Alignment explanation
Indices: 2791177--2791218 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2791167 TTTAAACATA
*
2791177 ATTATTATTAAATAT
1 ATTATAATTAAATAT
2791192 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
2791206 A-TATAATTTAATA
1 ATTATAATTAAATA
2791219 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:2791329 original size:18 final size:18
Alignment explanation
Indices: 2791308--2791355 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2791298 TTATTATTAA
2791308 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
2791326 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
2791343 -TAT-TAATAATTAA
1 ATATATTATAATTAA
2791356 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:2791336 original size:14 final size:15
Alignment explanation
Indices: 2791287--2791338 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2791277 ATAAAATATA
2791287 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
2791302 TATTAAATATATTAT
1 AATTAAATATATTAT
2791317 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
2791330 AATTTAATA
1 AATTAAATA
2791339 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:2791344 original size:44 final size:43
Alignment explanation
Indices: 2791264--2791347 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
2791254 CTCAAATCAT
* *
2791264 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATATAAAATATAAATTAACAAAATTATTATTA
* *
2791307 AATATATTATAAT-TAAAATATATAATTTAATAAAATTATTA
1 AATATATGATAATATAAAATATA-AA-TTAACAAAATTATTA
2791348 ATAATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 9 0.26
43 13 0.37
44 13 0.37
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
AATATATGATAATATAAAATATAAATTAACAAAATTATTATTA
Found at i:2793679 original size:12 final size:13
Alignment explanation
Indices: 2793651--2793684 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
2793641 TGGAGAAAGC
2793651 AAAGCAAAGGAAG
1 AAAGCAAAGGAAG
2793664 AAAGCAAAGG-AG
1 AAAGCAAAGGAAG
2793676 AAAGCAAAG
1 AAAGCAAAG
2793685 CAAAGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.62, C:0.09, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAGCAAAGGAAG
Found at i:2793753 original size:19 final size:19
Alignment explanation
Indices: 2793729--2793765 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2793719 AATCGGGCGA
2793729 AACAGAAGAGGCAAAGGGG
1 AACAGAAGAGGCAAAGGGG
*
2793748 AACAGAAGAGGCAGAGGG
1 AACAGAAGAGGCAAAGGG
2793766 TAAAACAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.43, T:0.00
Consensus pattern (19 bp):
AACAGAAGAGGCAAAGGGG
Found at i:2797562 original size:23 final size:21
Alignment explanation
Indices: 2797529--2797572 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
2797519 GAAATATAAA
2797529 TATTTGCTTATATTAATTTATTT
1 TATTTGCTTATA-TAA-TTATTT
*
2797552 TATTTGTTTATATAATTATTT
1 TATTTGCTTATATAATTATTT
2797573 GTCGAAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
23 11 0.55
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
TATTTGCTTATATAATTATTT
Found at i:2798367 original size:3 final size:3
Alignment explanation
Indices: 2798346--2798411 Score: 98
Period size: 3 Copynumber: 21.7 Consensus size: 3
2798336 AGTAACTAAC
2798346 ATA A-A ATA ATGA CATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA AT-A -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
2798392 ATA ATA AAA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
2798412 GAAGAATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 2 0.03
3 52 0.90
4 2 0.03
5 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2803635 original size:3 final size:3
Alignment explanation
Indices: 2803627--2803653 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2803617 CCTAACACAA
2803627 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
2803654 CAACTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Done.