Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 84 of 313
Found at i:28193994 original size:40 final size:40
Alignment explanation
Indices: 28193950--28194056 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 40
28193940 TTGACAACAA
* *
28193950 TTCGGTTATGTATGGCACTTAGTGTGC-GATTCAAGATAGC
1 TTCGGCTATATATGGCACTTAGTGTGCAGATT-AAGATAGC
*
28193990 TTCGGCTATATATGGCACTTAGTGTGCAAGATTGAGATAGC
1 TTCGGCTATATATGGCACTTAGTGTGC-AGATTAAGATAGC
* * *
28194031 TTCAGCTATTTAAGGCACTTAGTGTG
1 TTCGGCTATATATGGCACTTAGTGTG
28194057 TGTGATATTG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 25 0.42
41 30 0.51
42 4 0.07
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (40 bp):
TTCGGCTATATATGGCACTTAGTGTGCAGATTAAGATAGC
Found at i:28199389 original size:23 final size:23
Alignment explanation
Indices: 28199359--28199425 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
28199349 AGCTTTGCCA
*
28199359 ATCAGGCACTTTATGTGTCATAT
1 ATCAGGCACTTTATGTGTCGTAT
**
28199382 ATCAGGCACTTCGTGTGTCGT-T
1 ATCAGGCACTTTATGTGTCGTAT
28199404 -TCAGGCAC-TTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
28199425 A
1 A
28199426 CTGATTAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.24
21 9 0.24
22 1 0.03
23 18 0.49
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:28199622 original size:18 final size:19
Alignment explanation
Indices: 28199599--28199637 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28199589 TGGAATTATG
*
28199599 AATTGAAATGTGA-ATTGA
1 AATTGAAATATGAGATTGA
*
28199617 AATTGAGATATGAGATTGA
1 AATTGAAATATGAGATTGA
28199636 AA
1 AA
28199638 GCTTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (19 bp):
AATTGAAATATGAGATTGA
Found at i:28210263 original size:42 final size:43
Alignment explanation
Indices: 28210197--28210419 Score: 182
Period size: 43 Copynumber: 5.0 Consensus size: 43
28210187 TTATTAAAAT
* * **
28210197 AAAATAAAATTCTAGCCTATTTGAATGTTAAGATCTAAATTAG
1 AAAATAAAATTCTAACCTAATTGAATCCTAAGATCTAAATTAG
* * * *
28210240 AAAAT-AAATTTTAACCTAATTGAATCCTAAGTTCTAAATGAA
1 AAAATAAAATTCTAACCTAATTGAATCCTAAGATCTAAATTAG
* *
28210282 AAAATTAAAATTCTAACAT-ATCTAAATCCTAAGATCTAAATTAG
1 AAAA-TAAAATTCTAACCTAAT-TGAATCCTAAGATCTAAATTAG
* * ** *
28210326 AAAAATAAAATAAAATTCTATCTTTTTTGAATCCTAAAAT-TAAATTAG
1 ------AAAATAAAATTCTAACCTAATTGAATCCTAAGATCTAAATTAG
* * *
28210374 AAAAATAAAATTCCAACCTATTTGAATCCTTAGATCTAAATTAG
1 -AAAATAAAATTCTAACCTAATTGAATCCTAAGATCTAAATTAG
28210418 AA
1 AA
28210420 GGAAAAAAAA
Statistics
Matches: 143, Mismatches: 26, Indels: 22
0.75 0.14 0.12
Matches are distributed among these distances:
42 33 0.23
43 38 0.27
44 36 0.25
48 8 0.06
49 23 0.16
50 5 0.03
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.34
Consensus pattern (43 bp):
AAAATAAAATTCTAACCTAATTGAATCCTAAGATCTAAATTAG
Found at i:28217189 original size:180 final size:179
Alignment explanation
Indices: 28216887--28217344 Score: 812
Period size: 180 Copynumber: 2.6 Consensus size: 179
28216877 CGAGGAGCAG
28216887 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATAACA
1 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATAACA
* *
28216952 ATTCAACACAAAATTGTTGCTTTTAGTTATGCAACATCATACTGGGGGGGACACCACTAATTTTT
66 ATTCAACACAAAATTGTTGTTTTTAGTTATACAACATCATACTGGGGGGGACACCACTAATTTTT
28217017 AGATGTCACGGCTCTCTACTTTTCCACTAGAAAAAAAACAGAAGACTATT
131 AGATGTCACGGCTCTCTACTTTTCCACTAG-AAAAAAACAGAAGACTATT
28217067 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATAACA
1 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATAACA
*
28217132 ATTCAACACAAAATTGTTGTTTTTAGTTATACAACATCATATTGGGGGGGACACCACTAATTTTT
66 ATTCAACACAAAATTGTTGTTTTTAGTTATACAACATCATACTGGGGGGGACACCACTAATTTTT
* *
28217197 AGATGTCACTGCTCTCTACTTTTCCACTTGAAAAAAACAGAAGACTATT
131 AGATGTCACGGCTCTCTACTTTTCCACTAGAAAAAAACAGAAGACTATT
28217246 AGAACGAAATGAC--ATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATGATA
1 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACAT-A-A
* *
28217309 TAATTCAATACAAAATTGTTGTTTTTAGTTATACAA
64 CAATTCAACACAAAATTGTTGTTTTTAGTTATACAA
28217345 TGTCAGATGA
Statistics
Matches: 269, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
177 46 0.17
178 1 0.00
179 67 0.25
180 155 0.58
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (179 bp):
AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATAACA
ATTCAACACAAAATTGTTGTTTTTAGTTATACAACATCATACTGGGGGGGACACCACTAATTTTT
AGATGTCACGGCTCTCTACTTTTCCACTAGAAAAAAACAGAAGACTATT
Found at i:28222489 original size:30 final size:28
Alignment explanation
Indices: 28222445--28222508 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
28222435 TATTTTATAG
* *
28222445 TTATT-TAATTAGATAATTGTTATTTATT
1 TTATTATAATAAGATAATTATTA-TTATT
*
28222473 TATATTATAATAAGATATTTATTATTATT
1 T-TATTATAATAAGATAATTATTATTATT
28222502 TTATTAT
1 TTATTAT
28222509 TTTATTTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 7 0.23
29 10 0.32
30 14 0.45
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (28 bp):
TTATTATAATAAGATAATTATTATTATT
Found at i:28226105 original size:13 final size:13
Alignment explanation
Indices: 28226083--28226116 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
28226073 ACATTGTAAA
*
28226083 AATTACTTTTAAG
1 AATTATTTTTAAG
28226096 AATTATTTTTAAG
1 AATTATTTTTAAG
28226109 AATT-TTTT
1 AATTATTTT
28226117 AAAATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (13 bp):
AATTATTTTTAAG
Found at i:28231385 original size:16 final size:16
Alignment explanation
Indices: 28231364--28231395 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28231354 TGATTTAAAG
28231364 TGCCACGTCAGTTTAT
1 TGCCACGTCAGTTTAT
28231380 TGCCACGTCAGTTTAT
1 TGCCACGTCAGTTTAT
28231396 AGTGACATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (16 bp):
TGCCACGTCAGTTTAT
Found at i:28238895 original size:22 final size:22
Alignment explanation
Indices: 28238870--28238933 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
28238860 TTTTTATAGT
28238870 TTATATCTATCAAATAATTTAA
1 TTATATCTATCAAATAATTTAA
* *
28238892 TTATATTCTGT-AATTAATTTTAA
1 TTATA-TCTATCAAATAA-TTTAA
* *
28238915 GTA-ATATATCAAATAATTT
1 TTATATCTATCAAATAATTT
28238934 TATAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
21 6 0.18
22 16 0.48
23 11 0.33
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (22 bp):
TTATATCTATCAAATAATTTAA
Found at i:28239516 original size:16 final size:16
Alignment explanation
Indices: 28239495--28239544 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
28239485 ATATAGTGAT
* *
28239495 ATAATATATTAATTTA
1 ATAATATAATAAATTA
*
28239511 ATAATATAATAACTT-
1 ATAATATAATAAATTA
*
28239526 A-AATATAGTAAATTA
1 ATAATATAATAAATTA
28239541 ATAA
1 ATAA
28239545 ATCAAAATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 11 0.39
15 2 0.07
16 15 0.54
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATAATATAATAAATTA
Found at i:28243568 original size:2 final size:2
Alignment explanation
Indices: 28243520--28243553 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28243510 GTTGGGGAAA
28243520 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28243554 TAACCTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28245449 original size:17 final size:18
Alignment explanation
Indices: 28245419--28245452 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28245409 AGCGAATATA
28245419 TTTTTAAAATTTTAACAG
1 TTTTTAAAATTTTAACAG
28245437 TTTTTAAAA-TTTAACA
1 TTTTTAAAATTTTAACA
28245453 CCTAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTTAAAATTTTAACAG
Found at i:28249634 original size:9 final size:9
Alignment explanation
Indices: 28249585--28249669 Score: 98
Period size: 9 Copynumber: 9.4 Consensus size: 9
28249575 TTTGGTTAAA
28249585 AATTAACCG
1 AATTAACCG
*
28249594 AATTACCCG
1 AATTAACCG
* *
28249603 GATTATCCG
1 AATTAACCG
* *
28249612 GATTACCCG
1 AATTAACCG
*
28249621 GATTAACCG
1 AATTAACCG
28249630 AATTAACCG
1 AATTAACCG
28249639 AATTAACCG
1 AATTAACCG
*
28249648 AATTGACCG
1 AATTAACCG
*
28249657 AATTGACCG
1 AATTAACCG
28249666 AATT
1 AATT
28249670 GAATCACTAC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:28249704 original size:17 final size:17
Alignment explanation
Indices: 28249682--28249742 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
28249672 ATCACTACAC
28249682 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
** * *
28249699 TACATAAGTCTTTGAATTAC
1 TACATAA---TTAAAAATAT
*
28249719 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
28249736 TACATAA
1 TACATAA
28249743 GTCTTTGAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 19 0.59
20 13 0.41
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:28249730 original size:37 final size:37
Alignment explanation
Indices: 28249680--28249801 Score: 185
Period size: 37 Copynumber: 3.3 Consensus size: 37
28249670 GAATCACTAC
*
28249680 ACTACATAATTAAAAATATTACATAAGTCTTTGAATT
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATT
*
28249717 ACTACATAATTAAAAACATTACATAAGTCTTTGAATC
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATT
*
28249754 ACTAAATAATTAAAAACATTACATAAGTC-TTGAAATT
1 ACTACATAATTAAAAACATTACATAAGTCTTTG-AATT
28249791 AAC-ACATAATT
1 -ACTACATAATT
28249802 GAAATGTCAG
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
36 3 0.04
37 73 0.94
38 2 0.03
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (37 bp):
ACTACATAATTAAAAACATTACATAAGTCTTTGAATT
Found at i:28251869 original size:18 final size:20
Alignment explanation
Indices: 28251839--28251883 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
28251829 TGCAAGAAAA
28251839 AAAAT-TATATAATAA-ATT
1 AAAATATATATAATAATATT
28251857 AAAATATAT-TAATAATATT
1 AAAATATATATAATAATATT
28251876 AAACATAT
1 AAA-ATAT
28251884 TTTTATACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.46
19 9 0.38
20 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATATATATAATAATATT
Found at i:28253516 original size:19 final size:19
Alignment explanation
Indices: 28253492--28253532 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
28253482 ACTATGATAC
*
28253492 TTTTGAAGGTTTTGGGAGA
1 TTTTGAAGGTTTTGAGAGA
28253511 TTTTGAAGGTTTTGAGAGA
1 TTTTGAAGGTTTTGAGAGA
28253530 TTT
1 TTT
28253533 GAAAATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (19 bp):
TTTTGAAGGTTTTGAGAGA
Found at i:28253953 original size:18 final size:19
Alignment explanation
Indices: 28253918--28253967 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
28253908 AACCAACCAA
28253918 TTAACCGAATTGGGTCGG-
1 TTAACCGAATTGGGTCGGT
***
28253936 TTAACCGAATTTTTTCGGTT
1 TTAACCGAATTGGGTCGG-T
28253956 TTAACCGAATTG
1 TTAACCGAATTG
28253968 TGCACACCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (19 bp):
TTAACCGAATTGGGTCGGT
Found at i:28254864 original size:13 final size:13
Alignment explanation
Indices: 28254842--28254881 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
28254832 TGCCAAATGA
*
28254842 ACACGACCGTGTG
1 ACACGCCCGTGTG
28254855 ACACGCCCGTGTG
1 ACACGCCCGTGTG
28254868 ACACGCCCGTGTG
1 ACACGCCCGTGTG
28254881 A
1 A
28254882 GGAAGTCCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (13 bp):
ACACGCCCGTGTG
Found at i:28257549 original size:429 final size:429
Alignment explanation
Indices: 28256746--28257601 Score: 1216
Period size: 429 Copynumber: 2.0 Consensus size: 429
28256736 CTCGATCAAT
* * * * *
28256746 GCTGAATAGTTTATTGCTTAAGTGTACACTTTCAAGTGCATATTGTGTGTCTGGAAAAATGAATT
1 GCTGAATAGTTTATTGCTTAAGTGTACACTCTCAAGCGAACATTGCGTGTCTGGAAAAATGAATT
* * * * * * *
28256811 CCCTGTCCTGCGTGATCTGCCTACATTAGATGTGTCTCCGATAACTTTCAAGTTTGTCCTGGACT
66 CCCCGTCCTACGTGATCTACCTACATGAGAGGTGTCTCCGATAACTTTCAAGCTTGTCCTGGACA
* * * *
28256876 AAAGGTTGCGTAGGAATCTGAAAGGTCATCCGCAAGTAACTAGAATCCATAATGAAATGGATATT
131 AAAGGTTGCGTAGGAATCCGAAAGGTCATCCGCAAGTAACCAGAATCCATAATGAAATAGACATT
** * * *
28256941 AGGGAGAAAACCAACGGGAAGCTTTGTGGCTTGTGCAGATTAGCTAGGCATAGTCGGAGTAAATA
196 AGGGAGAAAACCAACGAAAAGCTTTGTGGCGTGTGCAGATTAGCTAGGCATAATCAGAGTAAATA
*
28257006 CCCGCAACGAACCTACCATATTGGACAATTGTCGTGATCGGGTGAGAATTGTGCTAATGTACTCC
261 CCCGCAACGAACCTACCATATTGGACAATTGTCGTGATCGGGTGAGAATTATGCTAATGTACTCC
* * *
28257071 ATGTGGAATTTGGATATGTATTTTACAGATTTTGTTCCAATGCATCTAATTTAAATTACAAAATT
326 ATGTGAAATATGGATATGTATTTTACAGAGTTTGTTCCAATGCATCTAATTTAAATTACAAAATT
*
28257136 TGTTTCAAGTTTAGTGCAATGCATCTCATTTAAATTACA
391 TGTTCCAAGTTTAGTGCAATGCATCTCATTTAAATTACA
*
28257175 GCTGAATAGTTTATTGCTTAAGTGTACACTCTCAAGCGAACATTGCGTGTCTAGG-AAAATGAGT
1 GCTGAATAGTTTATTGCTTAAGTGTACACTCTCAAGCGAACATTGCGTGTCT-GGAAAAATGAAT
* * * * * *
28257239 TCCCCGTCCTACGTGATTTATCTATATGGGAGGTGTCTCCGATGACTTTCGAA-CTTGTCTTGGA
65 TCCCCGTCCTACGTGATCTACCTACATGAGAGGTGTCTCCGATAACTTTC-AAGCTTGTCCTGGA
* * **
28257303 -AAAAGGGTTG-TTGAGGAATCCGAAAGGTCATTCGCAAGTGGCCAGAATCCATAATGAAATAGA
129 CAAAA-GGTTGCGT-AGGAATCCGAAAGGTCATCCGCAAGTAACCAGAATCCATAATGAAATAGA
* * *
28257366 CATTAGGGAGAAAACCGACGAAAAGCTTTGTGGCGTGTGCAGATTAGCTGGGTATAATCAGAGTA
192 CATTAGGGAGAAAACCAACGAAAAGCTTTGTGGCGTGTGCAGATTAGCTAGGCATAATCAGAGTA
* *
28257431 AATGCCCGCAACGAACCTACCATATTGGACAATTGTCGTGATCGGGTGGGAATTATGCTAATGTA
257 AATACCCGCAACGAACCTACCATATTGGACAATTGTCGTGATCGGGTGAGAATTATGCTAATGTA
* * *
28257496 CTCCATGTTAAATATGGATATGTATTTTACAGAGTTTGTTTCAATGTATCTAATTTAAATTACAA
322 CTCCATGTGAAATATGGATATGTATTTTACAGAGTTTGTTCCAATGCATCTAATTTAAATTACAA
* * *
28257561 AGTTTGTTCCAAGTTTGGTGCAATGCATCTTATTTAAATTA
387 AATTTGTTCCAAGTTTAGTGCAATGCATCTCATTTAAATTA
28257602 TAAAGTTTGT
Statistics
Matches: 375, Mismatches: 48, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
428 4 0.01
429 367 0.98
430 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (429 bp):
GCTGAATAGTTTATTGCTTAAGTGTACACTCTCAAGCGAACATTGCGTGTCTGGAAAAATGAATT
CCCCGTCCTACGTGATCTACCTACATGAGAGGTGTCTCCGATAACTTTCAAGCTTGTCCTGGACA
AAAGGTTGCGTAGGAATCCGAAAGGTCATCCGCAAGTAACCAGAATCCATAATGAAATAGACATT
AGGGAGAAAACCAACGAAAAGCTTTGTGGCGTGTGCAGATTAGCTAGGCATAATCAGAGTAAATA
CCCGCAACGAACCTACCATATTGGACAATTGTCGTGATCGGGTGAGAATTATGCTAATGTACTCC
ATGTGAAATATGGATATGTATTTTACAGAGTTTGTTCCAATGCATCTAATTTAAATTACAAAATT
TGTTCCAAGTTTAGTGCAATGCATCTCATTTAAATTACA
Found at i:28257577 original size:44 final size:44
Alignment explanation
Indices: 28257528--28257639 Score: 154
Period size: 44 Copynumber: 2.5 Consensus size: 44
28257518 TATTTTACAG
*
28257528 AGTTTGTTTCAATGTATCTAATTTAAATTACAAAGTTTGTTCCA
1 AGTTTGTTTCAATGCATCTAATTTAAATTACAAAGTTTGTTCCA
* * * *
28257572 AGTTTGGTGCAATGCATCTTATTTAAATTATAAAGTTTGTTCCA
1 AGTTTGTTTCAATGCATCTAATTTAAATTACAAAGTTTGTTCCA
*
28257616 AATTT-TTTCCAATGCATCTAATTT
1 AGTTTGTTT-CAATGCATCTAATTT
28257640 TTGCATGGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 57 0.98
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (44 bp):
AGTTTGTTTCAATGCATCTAATTTAAATTACAAAGTTTGTTCCA
Found at i:28259969 original size:14 final size:14
Alignment explanation
Indices: 28259950--28259993 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
28259940 ATCAAAACAC
28259950 ATAAATATAATACA
1 ATAAATATAATACA
28259964 ATAAATAT--TACA
1 ATAAATATAATACA
*
28259976 ATAAATGTAATACA
1 ATAAATATAATACA
28259990 ATAA
1 ATAA
28259994 TATCATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAAATATAATACA
Found at i:28259979 original size:26 final size:28
Alignment explanation
Indices: 28259950--28260009 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
28259940 ATCAAAACAC
28259950 ATAAATATAATACAATAA-AT-ATTACA
1 ATAAATATAATACAATAATATCATTACA
*
28259976 ATAAATGTAATACAATAATATCATTACA
1 ATAAATATAATACAATAATATCATTACA
28260004 A-AAATA
1 ATAAATA
28260010 CTAAACAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 17 0.57
27 6 0.20
28 7 0.23
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (28 bp):
ATAAATATAATACAATAATATCATTACA
Found at i:28260003 original size:14 final size:12
Alignment explanation
Indices: 28259950--28260009 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 12
28259940 ATCAAAACAC
28259950 ATAAATATAATACA
1 ATAAATAT--TACA
28259964 ATAAATATTACA
1 ATAAATATTACA
*
28259976 ATAAATGTAATACA
1 ATAAA--TATTACA
28259990 ATAATATCATTACA
1 ATAA-AT-ATTACA
28260004 A-AAATA
1 ATAAATA
28260010 CTAAACAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 1 0.03
12 11 0.28
13 3 0.08
14 24 0.60
15 1 0.03
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (12 bp):
ATAAATATTACA
Found at i:28260592 original size:22 final size:20
Alignment explanation
Indices: 28260552--28260611 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
28260542 CTTATTTACT
*
28260552 TATTATA-TAAATAAATATTA
1 TATTATATTAAA-AATTATTA
*
28260572 TTTTATCATTAAAATATTATTA
1 TATTAT-ATTAAAA-ATTATTA
28260594 TATTATATTAAAAATTAT
1 TATTATATTAAAAATTAT
28260612 ATTATATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 15 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTATATTAAAAATTATTA
Found at i:28260614 original size:22 final size:21
Alignment explanation
Indices: 28260566--28260620 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
28260556 ATATAAATAA
*
28260566 ATATTATTTTATCATTAAAAT
1 ATATTATATTATCATTAAAAT
28260587 ATTATTATATTAT-ATTAAAAATT
1 A-TATTATATTATCATT-AAAA-T
28260610 ATATTATATTA
1 ATATTATATTA
28260621 ATATAATGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.13
22 24 0.80
23 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTATATTATCATTAAAAT
Found at i:28261047 original size:21 final size:20
Alignment explanation
Indices: 28261006--28261054 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
28260996 TCATGTTGAA
**
28261006 TAAATTGATAAATTAGGAGT
1 TAAATTGATAAATTACAAGT
*
28261026 TAAATTGATAGAATTTCAAGT
1 TAAATTGATA-AATTACAAGT
28261047 TAGAATTG
1 TA-AATTG
28261055 GTTAAAGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.42
21 9 0.38
22 5 0.21
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (20 bp):
TAAATTGATAAATTACAAGT
Found at i:28262880 original size:17 final size:17
Alignment explanation
Indices: 28262844--28262880 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28262834 CATGTTGAAC
*
28262844 AAATCACAATAAACACT
1 AAATCACAATAAACAAT
*
28262861 AAATCACAATAAATAAT
1 AAATCACAATAAACAAT
28262878 AAA
1 AAA
28262881 CTAAACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATCACAATAAACAAT
Found at i:28263168 original size:3 final size:3
Alignment explanation
Indices: 28263160--28263191 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28263150 CTCTATTGCT
28263160 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
28263192 TTTTTAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:28263499 original size:21 final size:22
Alignment explanation
Indices: 28263456--28263507 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
28263446 CCATTTTCGT
*
28263456 ATTTTGACCCCTATTTTAACCC
1 ATTTTGACCCATATTTTAACCC
* *
28263478 ATTTTGACTCATA-TTTATCCC
1 ATTTTGACCCATATTTTAACCC
28263499 ATTTTGACC
1 ATTTTGACC
28263508 TGTATACGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.23, C:0.27, G:0.06, T:0.44
Consensus pattern (22 bp):
ATTTTGACCCATATTTTAACCC
Found at i:28272584 original size:18 final size:20
Alignment explanation
Indices: 28272547--28272586 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
28272537 CAAGAAGTAA
*
28272547 AAAAAGAGAAATAAAGAAAG
1 AAAAAGAGAAATAAAAAAAG
28272567 AAAAAGA-AAA-AAAAAAAG
1 AAAAAGAGAAATAAAAAAAG
28272585 AA
1 AA
28272587 GCAAAACCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 3 0.16
20 7 0.37
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (20 bp):
AAAAAGAGAAATAAAAAAAG
Found at i:28276437 original size:15 final size:14
Alignment explanation
Indices: 28276382--28276438 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
28276372 AACTCCTACT
28276382 ATATTTATATT-TA
1 ATATTTATATTATA
* *
28276395 ATAATTTAATTTTTTTA
1 AT-ATTT-A-TATTATA
28276412 ATATTTATATTATA
1 ATATTTATATTATA
28276426 ATATTATATATTA
1 ATATT-TATATTA
28276439 CTATAAAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.06
14 14 0.39
15 9 0.25
16 7 0.19
17 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATTTATATTATA
Found at i:28277288 original size:17 final size:18
Alignment explanation
Indices: 28277241--28277367 Score: 73
Period size: 17 Copynumber: 6.8 Consensus size: 18
28277231 ATATTTTCTT
*
28277241 AATATATTTAAAATTTTA
1 AATATATTTAAAAATTTA
*
28277259 AA-AAATTTAAAAAATTTA
1 AATATATTT-AAAAATTTA
*
28277277 AATATATTAAAAAATATTA
1 AATATATTTAAAAAT-TTA
* *
28277296 AGTATAACCAAATTT-AAAATTTT
1 A--AT----ATATTTAAAAATTTA
*
28277319 AATATATTTAATATATTTA
1 AATATATTTAA-AAATTTA
*
28277338 AATATA-TTAAAAATTTG
1 AATATATTTAAAAATTTA
*
28277355 AACATA-TTAAAAA
1 AATATATTTAAAAA
28277368 AAATTTAAGT
Statistics
Matches: 85, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
17 27 0.32
18 23 0.27
19 19 0.22
21 4 0.05
23 3 0.04
24 5 0.06
25 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATATTTAAAAATTTA
Found at i:28277301 original size:19 final size:18
Alignment explanation
Indices: 28277241--28277368 Score: 71
Period size: 18 Copynumber: 6.8 Consensus size: 18
28277231 ATATTTTCTT
* *
28277241 AATATATTTAAAATTTTA
1 AATATATTAAAAAATTTA
*
28277259 AA-AAATTTAAAAAATTTA
1 AATATA-TTAAAAAATTTA
28277277 AATATATTAAAAAATATTA
1 AATATATTAAAAAAT-TTA
* ** *
28277296 AGTATAACCAAATTTAAAATTTT
1 AATAT-A-TTAA---AAAATTTA
* *
28277319 AATATATTTAATATATTTA
1 AATATA-TTAAAAAATTTA
*
28277338 AATATATT-AAAAATTTG
1 AATATATTAAAAAATTTA
*
28277355 AACATATTAAAAAA
1 AATATATTAAAAAA
28277369 AATTTAAGTA
Statistics
Matches: 82, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
17 15 0.18
18 30 0.37
19 20 0.24
20 1 0.01
21 2 0.02
22 3 0.04
23 6 0.07
24 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATATTAAAAAATTTA
Found at i:28277341 original size:10 final size:10
Alignment explanation
Indices: 28277241--28277345 Score: 55
Period size: 9 Copynumber: 10.8 Consensus size: 10
28277231 ATATTTTCTT
28277241 AATATATTTA
1 AATATATTTA
28277251 AA-AT-TTTA
1 AATATATTTA
*
28277259 AA-AAATTTA
1 AATATATTTA
*
28277268 AA-AAATTTA
1 AATATATTTA
*
28277277 AATATATTAA
1 AATATATTTA
*
28277287 AAAATATTAAGTA
1 AATATATT---TA
* *
28277300 TAACCAAATTTA
1 -AA-TATATTTA
28277312 AA-AT-TTT-
1 AATATATTTA
28277319 AATATATTT-
1 AATATATTTA
28277328 AATATATTTA
1 AATATATTTA
28277338 AATATATT
1 AATATATT
28277346 AAAAATTTGA
Statistics
Matches: 77, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
7 2 0.03
8 12 0.16
9 30 0.39
10 22 0.29
11 2 0.03
12 2 0.03
13 1 0.01
14 2 0.03
15 4 0.05
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (10 bp):
AATATATTTA
Found at i:28277391 original size:79 final size:79
Alignment explanation
Indices: 28277239--28277412 Score: 246
Period size: 79 Copynumber: 2.2 Consensus size: 79
28277229 AAATATTTTC
* * *
28277239 TTAATATATTTAAAAT-TTTAAAAAATTTAAAAAATTTAAATATATTAAAAAATATTAAGTATAA
1 TTAATATATTTAATATATTTAAAAAATTTAAAAAATTTAAACATATTAAAAAAAATTAAGTATAA
28277303 CCAAATTTAAAATT
66 CCAAATTTAAAATT
* *
28277317 TTAATATATTTAATATATTT-AAATATATT-AAAAATTTGAACATATTAAAAAAAATTTAAGTAT
1 TTAATATATTTAATATATTTAAAAAAT-TTAAAAAATTTAAACATATTAAAAAAAA-TTAAGTAT
* *
28277380 AACTAATTTTAAAATT
64 AACCAAATTTAAAATT
28277396 TTAATATATTTAATATA
1 TTAATATATTTAATATA
28277413 ATTTTTAAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 42 0.49
79 44 0.51
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (79 bp):
TTAATATATTTAATATATTTAAAAAATTTAAAAAATTTAAACATATTAAAAAAAATTAAGTATAA
CCAAATTTAAAATT
Found at i:28281986 original size:35 final size:35
Alignment explanation
Indices: 28281930--28282121 Score: 240
Period size: 35 Copynumber: 5.5 Consensus size: 35
28281920 TACACGGTTA
* *
28281930 ACCATCCAACACAGCATATGCTCATAAGAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* * *
28281965 ACCATCCAGCACACTAGATGCTCCTAAGAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* *
28282000 ACCATCCAACACACCATATACTCATAAGAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* ** * * *
28282035 ACCATTCAGTACACTAGATGCTCCTAAAAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
*
28282070 ACCATCCAACACACCAGATGCTCATAAGAGTCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* *
28282105 ACCATCTAGCACACCAG
1 ACCATCCAACACACCAG
28282122 GTAACACTGT
Statistics
Matches: 130, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 130 1.00
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.18
Consensus pattern (35 bp):
ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
Found at i:28282049 original size:70 final size:70
Alignment explanation
Indices: 28281930--28282118 Score: 306
Period size: 70 Copynumber: 2.7 Consensus size: 70
28281920 TACACGGTTA
* *
28281930 ACCATCCAACACAGCATATGCTCATAAGAGCCAGTACCATCCAGCACACTAGATGCTCCTAAGAG
1 ACCATCCAACACACCATATGCTCATAAGAGCCAGTACCATCCAGCACACTAGATGCTCCTAAAAG
28281995 CCAGT
66 CCAGT
* * *
28282000 ACCATCCAACACACCATATACTCATAAGAGCCAGTACCATTCAGTACACTAGATGCTCCTAAAAG
1 ACCATCCAACACACCATATGCTCATAAGAGCCAGTACCATCCAGCACACTAGATGCTCCTAAAAG
28282065 CCAGT
66 CCAGT
* * *
28282070 ACCATCCAACACACCAGATGCTCATAAGAGTCAGTACCATCTAGCACAC
1 ACCATCCAACACACCATATGCTCATAAGAGCCAGTACCATCCAGCACAC
28282119 CAGGTAACAC
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 108 1.00
ACGTcount: A:0.36, C:0.33, G:0.13, T:0.18
Consensus pattern (70 bp):
ACCATCCAACACACCATATGCTCATAAGAGCCAGTACCATCCAGCACACTAGATGCTCCTAAAAG
CCAGT
Found at i:28289305 original size:50 final size:51
Alignment explanation
Indices: 28289228--28289356 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
28289218 GACCATGGAA
*
28289228 ACAAGTGATAAGTGATAGCTTTGGCTACACTTACCTGATCAA-GGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTACCTGATCAATGG-CAAATG
*
28289279 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGGCAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTACCTGATCAATGGCAAATG
* * *
28289329 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
28289357 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 45 0.63
51 26 0.37
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTACCTGATCAATGGCAAATG
Found at i:28289646 original size:49 final size:49
Alignment explanation
Indices: 28289574--28289670 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
28289564 AATGAAAGTG
28289574 ATAAGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCA
1 ATAAGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCA
28289623 ATAAGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
1 ATAAGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
28289671 GATGTATGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (49 bp):
ATAAGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCA
Found at i:28289703 original size:42 final size:41
Alignment explanation
Indices: 28289642--28289753 Score: 145
Period size: 42 Copynumber: 2.7 Consensus size: 41
28289632 ATGTGATTAC
* *
28289642 GTGTAAGACCATAGCTGGGCTATGGCATCGATGTA-TGAATAT
1 GTGTAAGACCATAGTTGGGCTATGGCATC-AT-TAGTGAAGAT
*
28289684 GTGTAAGACCATAGTTGGGCTACGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCATTA-GTGAAGAT
**
28289726 GTGTAAGACCATAGTTGAACTATGGCAT
1 GTGTAAGACCATAGTTGGGCTATGGCAT
28289754 TGAGAAAACG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.03
41 2 0.03
42 58 0.94
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (41 bp):
GTGTAAGACCATAGTTGGGCTATGGCATCATTAGTGAAGAT
Found at i:28291217 original size:22 final size:22
Alignment explanation
Indices: 28291191--28291232 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28291181 GTAAAATCCC
28291191 TAAAACC-CTAAACATTAAAACT
1 TAAAACCAC-AAACATTAAAACT
*
28291213 TAAAACCACAAACTTTAAAA
1 TAAAACCACAAACATTAAAA
28291233 AACCCTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAAACCACAAACATTAAAACT
Found at i:28292383 original size:20 final size:18
Alignment explanation
Indices: 28292336--28292384 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
28292326 CAAGATAAAC
28292336 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
28292353 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
28292373 ATTAAATTAATA
1 ATTAAATTAATA
28292385 AAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:28295138 original size:15 final size:15
Alignment explanation
Indices: 28295118--28295147 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28295108 CTATGCATGC
28295118 AAAATATAAAAGACA
1 AAAATATAAAAGACA
28295133 AAAATATAAAAGACA
1 AAAATATAAAAGACA
28295148 TAACAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAATATAAAAGACA
Found at i:28295847 original size:20 final size:18
Alignment explanation
Indices: 28295800--28295906 Score: 53
Period size: 20 Copynumber: 5.8 Consensus size: 18
28295790 CAAGATAAAC
28295800 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
*
28295817 ACTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
**
28295837 ATTAAATTAATAAAATAAT
1 ATTAAATTAAT-ATTTAAT
28295856 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
* *
28295873 ATTAAATTTCATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
28295893 ATTAAAATAATATT
1 ATTAAATTAATATT
28295907 ATTTTTGAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
16 1 0.01
17 14 0.21
18 9 0.13
19 21 0.31
20 23 0.34
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:28301272 original size:44 final size:43
Alignment explanation
Indices: 28301134--28301429 Score: 192
Period size: 44 Copynumber: 6.7 Consensus size: 43
28301124 ATAGCTTTGA
* **
28301134 TCTGCTCTACTGCAATTTCAAAGAGATAAGATTTGCTATCTTCAG
1 TCTGCTCCACTGCAATTTCAGGGAGATAAGA-TTG-TATCTTCAG
* * * * * *
28301179 TCTACTCTACTGCAACTTCAGGGAGATAAAACTCGTAGT-TTCAA
1 TCTGCTCCACTGCAATTTCAGGGAGATAAGA-TTGTA-TCTTCAG
* *
28301223 CCTGCTCCACTGCAATTTCAGGGAGATAAGATTGGTATCTTTAG
1 TCTGCTCCACTGCAATTTCAGGGAGATAAGATT-GTATCTTCAG
* * * *
28301267 TCTGCTCCACTACAACTTCAGAGAGATAAGACTTGTAACTTCA-
1 TCTGCTCCACTGCAATTTCAGGGAGATAAGA-TTGTATCTTCAG
* * * * * *
28301310 ACTTG-TCCCACTGCAACTTCAGGGGGACAAGGTT-TATGGCTT-TG
1 TC-TGCT-CCACTGCAATTTCAGGGAGATAAGATTGTAT--CTTCAG
*
28301354 ATCTACTCCACTGCAACTTT-AGGGAGATAAGATCTGTCATCTTCAG
1 -TCTGCTCCACTGCAA-TTTCAGGGAGATAAGAT-TGT-ATCTTCAG
* *
28301400 TCTGTTCCACTGTAACTTT-AGGGAGATAAG
1 TCTGCTCCACTGCAA-TTTCAGGGAGATAAG
28301430 GCCTTCAATC
Statistics
Matches: 195, Mismatches: 40, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
42 2 0.01
43 6 0.03
44 117 0.60
45 66 0.34
46 2 0.01
47 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
TCTGCTCCACTGCAATTTCAGGGAGATAAGATTGTATCTTCAG
Found at i:28301310 original size:88 final size:89
Alignment explanation
Indices: 28301135--28301333 Score: 240
Period size: 88 Copynumber: 2.2 Consensus size: 89
28301125 TAGCTTTGAT
* ** * *
28301135 CTGCTCTACTGCAATTTCAAAGAGATAAGATTTGCTATCTTCAGTCTACTCTACTGCAACTTCAG
1 CTGCTCCACTGCAATTTCAGGGAGATAAGATTTGCTATCTTCAGTCTACTCCACTACAACTTCAG
* **
28301200 GGAGATAAAACTCGTAGTTTCAAC
66 AGAGATAAAACTCGTAACTTCAAC
* * *
28301224 CTGCTCCACTGCAATTTCAGGGAGATAAGA-TTGGTATCTTTAGTCTGCTCCACTACAACTTCAG
1 CTGCTCCACTGCAATTTCAGGGAGATAAGATTTGCTATCTTCAGTCTACTCCACTACAACTTCAG
* *
28301288 AGAGATAAGACTTGTAACTTCAAC
66 AGAGATAAAACTCGTAACTTCAAC
* *
28301312 TTG-TCCCACTGCAACTTCAGGG
1 CTGCT-CCACTGCAATTTCAGGG
28301334 GGACAAGGTT
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 1 0.01
88 66 0.70
89 27 0.29
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (89 bp):
CTGCTCCACTGCAATTTCAGGGAGATAAGATTTGCTATCTTCAGTCTACTCCACTACAACTTCAG
AGAGATAAAACTCGTAACTTCAAC
Found at i:28301363 original size:88 final size:87
Alignment explanation
Indices: 28301135--28301425 Score: 239
Period size: 88 Copynumber: 3.3 Consensus size: 87
28301125 TAGCTTTGAT
* * ** * * *
28301135 CTGCTCTACTGCAATTTCAAAGAGATAAGATTTGCTATCTTCAGTCTACTCTACTGCAACTTCAG
1 CTGCTCCACTGCAACTTCAGGGAGACAAGA-TTG-TATCTTTAGTCTACTCCACTGCAACTTCAG
* **
28301200 GGAGATAAAACTCGTAGTTTCAAC
64 GGAGATAAGACTCGTAACTTCAAC
* * * * *
28301224 CTGCTCCACTGCAATTTCAGGGAGATAAGATTGGTATCTTTAGTCTGCTCCACTACAACTTCAGA
1 CTGCTCCACTGCAACTTCAGGGAGACAAGATT-GTATCTTTAGTCTACTCCACTGCAACTTCAGG
*
28301289 GAGATAAGACTTGTAACTTCAAC
65 GAGATAAGACTCGTAACTTCAAC
* * * *
28301312 TTG-TCCCACTGCAACTTCAGGGGGACAAGGTT-TATGGCTTT-GATCTACTCCACTGCAACTTT
1 CTGCT-CCACTGCAACTTCAGGGAGACAAGATTGTAT--CTTTAG-TCTACTCCACTGCAACTTC
* **
28301374 AGGGAGATAAGA-TCTGTCATCTTCAGT
62 AGGGAGATAAGACTC-GT-AACTTCAAC
* * *
28301401 CTGTTCCACTGTAACTTTAGGGAGA
1 CTGCTCCACTGCAACTTCAGGGAGA
28301426 TAAGGCCTTC
Statistics
Matches: 165, Mismatches: 29, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
86 3 0.02
87 3 0.02
88 105 0.64
89 53 0.32
90 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (87 bp):
CTGCTCCACTGCAACTTCAGGGAGACAAGATTGTATCTTTAGTCTACTCCACTGCAACTTCAGGG
AGATAAGACTCGTAACTTCAAC
Found at i:28301424 original size:45 final size:46
Alignment explanation
Indices: 28301360--28301453 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 46
28301350 TTTGATCTAC
*
28301360 TCCACTGCAACTTTAGGGAGATAAGATCTGTC-ATCTTCAGTCTG-T
1 TCCACTGCAACTTTAGGGAGATAAGACCT-TCAATCTTCAGTCTGCT
* *
28301405 TCCACTGTAACTTTAGGGAGATAAGGCCTTCAATCTTCAGTCTGCT
1 TCCACTGCAACTTTAGGGAGATAAGACCTTCAATCTTCAGTCTGCT
28301451 TCC
1 TCC
28301454 TTGCTGCCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 2 0.05
45 38 0.86
46 4 0.09
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (46 bp):
TCCACTGCAACTTTAGGGAGATAAGACCTTCAATCTTCAGTCTGCT
Found at i:28301661 original size:44 final size:45
Alignment explanation
Indices: 28301558--28301857 Score: 131
Period size: 44 Copynumber: 6.7 Consensus size: 45
28301548 TGTAGCTTGA
* * * * *
28301558 TCTGCTTCATTGCAACTTCAAGGAGATAAGATCTGCTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACTTCAC
28301603 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTG-TAACTTCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATC-TGCTAACTTC-AC
* * * * *
28301648 T-TGC-CCTACTGCAACTTCAGGGGGATAAGGTTTG-TTA--TGAC
1 TCTGCTCC-ACTGCAACTTCAGGGAGATAAGATCTGCTAACTTCAC
* * * * * ** *
28301689 -CTACTCTACTGCAACTTCAGAGAGATAATATATTTTTATTTATAGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGAT-A-AGA--TCT-GCTA-A-CTTCAC
*** * * * *
28301740 TCCATTCCACTGCATCTTCAGGGAAATAAGATC-GCTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACTTCAC
* * *
28301784 TCTGTTCCACTGCAACATT-ATGGAGATAAGA-CTCACT-ACTTCAAC
1 TCTGCTCCACTGCAAC-TTCAGGGAGATAAGATCT-GCTAACTTC-AC
*
28301829 -CTGCTCCACTGCAACTTCAGGGAAATAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG
28301858 GTCTTCAATC
Statistics
Matches: 190, Mismatches: 43, Indels: 45
0.68 0.15 0.16
Matches are distributed among these distances:
41 21 0.11
42 3 0.02
43 6 0.03
44 90 0.47
45 40 0.21
46 2 0.01
47 1 0.01
48 2 0.01
50 2 0.01
51 3 0.02
52 20 0.11
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACTTCAC
Found at i:28313719 original size:42 final size:43
Alignment explanation
Indices: 28313609--28313729 Score: 178
Period size: 41 Copynumber: 2.9 Consensus size: 43
28313599 CTTGTATAAA
* * *
28313609 ACACCGGCA-CAGAGCCTGCTAGGTAATAAACCTGAT-TCAAT
1 ACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGATATCAAT
28313650 ACACCGGCAT-AAAGCCTGCTAGGCAATAAGCCTGATATC-AT
1 ACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGATATCAAT
*
28313691 ACACCGGCATCAAAGCCTGCTAGGCAATATGCCTGATAT
1 ACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGATAT
28313730 ATCACTGTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
41 44 0.60
42 29 0.40
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (43 bp):
ACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGATATCAAT
Found at i:28313913 original size:20 final size:20
Alignment explanation
Indices: 28313888--28313927 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28313878 TTCAACAACG
28313888 TTTATTGCTTATAAACTAAC
1 TTTATTGCTTATAAACTAAC
28313908 TTTATTGCTTATAAACTAAC
1 TTTATTGCTTATAAACTAAC
28313928 CTCGGATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTATTGCTTATAAACTAAC
Found at i:28331419 original size:5 final size:5
Alignment explanation
Indices: 28331405--28331466 Score: 58
Period size: 5 Copynumber: 12.4 Consensus size: 5
28331395 GCAACCCAAT
* *
28331405 TTTTA TTTTTA TTTTCA TTTCA TTTTA TTTT- TATTTA TTTTA TCTTA
1 TTTTA -TTTTA TTTT-A TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA
28331452 --TTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
28331467 CAGATATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
3 3 0.06
4 1 0.02
5 34 0.71
6 10 0.21
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:28332729 original size:26 final size:25
Alignment explanation
Indices: 28332692--28332778 Score: 120
Period size: 26 Copynumber: 3.4 Consensus size: 25
28332682 NNNNNNNNNN
*
28332692 CCATTATCATGGAATATTTACCTAA
1 CCATTATCATGGAACATTTACCTAA
*
28332717 TTCATTATCATGGAACATTTACCTAA
1 -CCATTATCATGGAACATTTACCTAA
*
28332743 CCTATTATCATTGAACATTTACCTAA
1 CC-ATTATCATGGAACATTTACCTAA
28332769 CCTATTATCA
1 CC-ATTATCA
28332779 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
25 1 0.02
26 55 0.98
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (25 bp):
CCATTATCATGGAACATTTACCTAA
Found at i:28333912 original size:96 final size:95
Alignment explanation
Indices: 28333742--28333995 Score: 402
Period size: 96 Copynumber: 2.6 Consensus size: 95
28333732 GACGTGACTA
*
28333742 GCTGAGTAACCGGGGTAAGGTGCTTGGGTTGTCATC-CTATTTCGCGTCAAAAGGTTCGATATGT
1 GCTGAGTAACCGGGGT-AGGTGCTT-GGTTGTCATCTCT-CTTCGCGTCAAAAGGTTCGATATGT
* *
28333806 TCTTAGGAAAAATAAAAATTAGGAATGTTTTGG
63 TCTTACGAAAAATAAAAATTAGGAATGTGTTGG
*
28333839 GCTGAGTAACCGGGGTGAGGTGCTTGGTTGTCATCTCTCTTCGCGTCAAAAGATTCGATATGTTC
1 GCTGAGTAACCGGGGT-AGGTGCTTGGTTGTCATCTCTCTTCGCGTCAAAAGGTTCGATATGTTC
28333904 TTACGAAAAATAAAAATTAGGAATGTGTTGG
65 TTACGAAAAATAAAAATTAGGAATGTGTTGG
* *
28333935 GCTGAGTAACCGGGGTAGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAATAT
1 GCTGAGTAACCGGGGTA-GGTGCTTGGTTGTCATCTCTCTTCGCGTCAAAAGGTTCGATAT
28333996 TTTTCCTAAG
Statistics
Matches: 147, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
95 1 0.01
96 120 0.82
97 26 0.18
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (95 bp):
GCTGAGTAACCGGGGTAGGTGCTTGGTTGTCATCTCTCTTCGCGTCAAAAGGTTCGATATGTTCT
TACGAAAAATAAAAATTAGGAATGTGTTGG
Found at i:28334670 original size:27 final size:27
Alignment explanation
Indices: 28334631--28334693 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
28334621 ACTCCATTTT
28334631 ATTTATATTAGGA-TAATTAATATTAAG
1 ATTT-TATTAGGATTAATTAATATTAAG
* * *
28334658 ATTATTATTAGGATTATTTAATTTTAGG
1 ATT-TTATTAGGATTAATTAATATTAAG
28334686 ATTTTATT
1 ATTTTATT
28334694 TTAATTATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (27 bp):
ATTTTATTAGGATTAATTAATATTAAG
Found at i:28340460 original size:26 final size:26
Alignment explanation
Indices: 28340424--28340476 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28340414 CTTGGTCTAA
28340424 ATAATCAATTTCAATCCATTTAGTAT
1 ATAATCAATTTCAATCCATTTAGTAT
28340450 ATAATCAATTTCAATCCATTTAGTAT
1 ATAATCAATTTCAATCCATTTAGTAT
28340476 A
1 A
28340477 CATTCTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (26 bp):
ATAATCAATTTCAATCCATTTAGTAT
Found at i:28342933 original size:24 final size:25
Alignment explanation
Indices: 28342878--28342934 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
28342868 ATTAAAATAT
28342878 TATAAATATATATTATACATTAACA
1 TATAAATATATATTATACATTAACA
28342903 TAT-AATATATATTCATA-ATTAA-A
1 TATAAATATATATT-ATACATTAACA
*
28342926 TTTAAATAT
1 TATAAATAT
28342935 TAAAATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.10
24 20 0.69
25 6 0.21
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
TATAAATATATATTATACATTAACA
Found at i:28346085 original size:15 final size:14
Alignment explanation
Indices: 28346064--28346098 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28346054 CCCGTATGAC
*
28346064 TTTTTTTATATTAT
1 TTTTTTTATATAAT
28346078 TATTTTTTATATAAT
1 T-TTTTTTATATAAT
28346093 TTTTTT
1 TTTTTT
28346099 AAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTATATAAT
Found at i:28351070 original size:35 final size:36
Alignment explanation
Indices: 28351022--28351097 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 36
28351012 AAAAGCTTTC
*
28351022 GTAATCTTCATTAAGGCTCGAATTTGGTTGTATGGT
1 GTAATCTTCATTAAGGCTCGAATTCGGTTGTATGGT
* *
28351058 GTAA-CTTGATTAAGGCTTGAATTCGGTTGTATGGT
1 GTAATCTTCATTAAGGCTCGAATTCGGTTGTATGGT
28351093 GTAAT
1 GTAAT
28351098 ATAAATGTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 32 0.89
36 4 0.11
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (36 bp):
GTAATCTTCATTAAGGCTCGAATTCGGTTGTATGGT
Found at i:28358220 original size:31 final size:31
Alignment explanation
Indices: 28358185--28358243 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
28358175 GATACAATTA
*
28358185 TATACGTGAAACTCTAATTGTGGTTTAAATG
1 TATACGTGAAACTCTAATTGTGATTTAAATG
* * *
28358216 TATACTTGAAACTTTAATTTTGATTTAA
1 TATACGTGAAACTCTAATTGTGATTTAA
28358244 TCATACACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (31 bp):
TATACGTGAAACTCTAATTGTGATTTAAATG
Found at i:28358658 original size:29 final size:28
Alignment explanation
Indices: 28358625--28358685 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
28358615 TATACCAAAC
* *
28358625 AATTT-TATAATATAAATTTAATATTTATA
1 AATTTCTATAATA-AAAGTTAATAATT-TA
*
28358654 AATTTCTATACTAAAAGTTAATAATTTA
1 AATTTCTATAATAAAAGTTAATAATTTA
28358682 AATT
1 AATT
28358686 CATCATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 16 0.57
30 6 0.21
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (28 bp):
AATTTCTATAATAAAAGTTAATAATTTA
Found at i:28359946 original size:20 final size:21
Alignment explanation
Indices: 28359909--28359947 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28359899 CATTAAATTT
*
28359909 TTTTTATATATAAGATTTTAC
1 TTTTTATATATAAAATTTTAC
*
28359930 TTTTTA-ATTTAAAATTTT
1 TTTTTATATATAAAATTTT
28359948 TTCATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTTATATATAAAATTTTAC
Found at i:28374480 original size:29 final size:30
Alignment explanation
Indices: 28374436--28374493 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
28374426 TTATATTAAA
* * *
28374436 TTAGTCCATTTGTTATT-AAATGGATCAAT
1 TTAGTCCATGTATTATTAAAAAGGATCAAT
28374465 TTAGTCCATGTATTATTAAAAAGGATCAA
1 TTAGTCCATGTATTATTAAAAAGGATCAA
28374494 ATAAGGCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (30 bp):
TTAGTCCATGTATTATTAAAAAGGATCAAT
Found at i:28377697 original size:158 final size:158
Alignment explanation
Indices: 28377406--28377719 Score: 398
Period size: 158 Copynumber: 2.0 Consensus size: 158
28377396 TATACCATCC
* ** * **
28377406 TTTTTTGGCTTCTAGTTCTTGTACTCGTTCTAGACTAAGACAAAAAAATCACAACCCCCTATTAG
1 TTTTTTGGCTTCTAGTTCTTGTAATCGCACTAGACTAAGA-AAAAAAATCAAAACCCCAAATTAG
* * *
28377471 ATTTAAATATTTTAAAACTTGACAGTAAAAAAGTGTTTACGATATACCTATGATCCAGTTGTGGT
65 ACTTAAATATTTTAAAACTTGACAGTAAAAAAGTGTTAACGATATACCTATGATCCAGTTCTGGT
* *
28377536 AGGTTGATTGCATGATCTTCTGTTGTTCT
130 AGGTTGAATGCATGATCTTCTATTGTTCT
* * *
28377565 TTTTTTGGCTTTTAGTTCTTGTAATGGCACTAGACTAAG-AAAAAAATGTAAAACCCCAAATTAG
1 TTTTTTGGCTTCTAGTTCTTGTAATCGCACTAGACTAAGAAAAAAAAT-CAAAACCCCAAATTAG
* * * * * * *
28377629 ACTTAAATA-TTTAAGAACTTGATAGTGAAAAAGTGTTAATGATATATCTATGATCTATTTCTGT
65 ACTTAAATATTTTAA-AACTTGACAGTAAAAAAGTGTTAACGATATACCTATGATCCAGTTCTGG
28377693 TAGGTTGAATGCATGATCTTCTATTGT
129 TAGGTTGAATGCATGATCTTCTATTGT
28377720 GACTCTCACC
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
157 13 0.10
158 85 0.64
159 34 0.26
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (158 bp):
TTTTTTGGCTTCTAGTTCTTGTAATCGCACTAGACTAAGAAAAAAAATCAAAACCCCAAATTAGA
CTTAAATATTTTAAAACTTGACAGTAAAAAAGTGTTAACGATATACCTATGATCCAGTTCTGGTA
GGTTGAATGCATGATCTTCTATTGTTCT
Found at i:28379431 original size:31 final size:31
Alignment explanation
Indices: 28379372--28379431 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
28379362 TATACATGAA
*
28379372 ATATATGGAAATGATGGTACATGATATATTG
1 ATATATGGAAATGATGATACATGATATATTG
* *
28379403 ATATATTGAAATGGATGATATATG-TATAT
1 ATATATGGAAAT-GATGATACATGATATAT
28379432 GAAAAAACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (31 bp):
ATATATGGAAATGATGATACATGATATATTG
Found at i:28384342 original size:24 final size:24
Alignment explanation
Indices: 28384310--28384358 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28384300 TTTACATGCA
28384310 TTTCTGAAGCTAGCTTTCTTTGTG
1 TTTCTGAAGCTAGCTTTCTTTGTG
28384334 TTTCTGAAGCTAGCTTTCTTTGTG
1 TTTCTGAAGCTAGCTTTCTTTGTG
28384358 T
1 T
28384359 CTCCCTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.51
Consensus pattern (24 bp):
TTTCTGAAGCTAGCTTTCTTTGTG
Found at i:28390760 original size:29 final size:29
Alignment explanation
Indices: 28390717--28390775 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
28390707 AACCACTTAG
28390717 ACTAAGGTTCATTTCATATTAGTTTTATT
1 ACTAAGGTTCATTTCATATTAGTTTTATT
*
28390746 ACTAAGGTTCCTTTCATATTAGTTTTATT
1 ACTAAGGTTCATTTCATATTAGTTTTATT
28390775 A
1 A
28390776 ATACTAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (29 bp):
ACTAAGGTTCATTTCATATTAGTTTTATT
Found at i:28395878 original size:40 final size:40
Alignment explanation
Indices: 28395804--28396114 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
28395794 AACCCAAGTA
* *
28395804 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
28395843 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28395883 CCTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
28395926 CCTTCGGGACTTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGA---CTTAGCCCGGATATAGTCACTAGCACAAATG
* *
28395969 CCTTCGGGACTTAGCCCGGGTATAGCAACCACTCA-CACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG---TCACT-AGCACAAATG
*
28396012 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
** *
28396052 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
28396092 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28396115 CATCCGAATA
Statistics
Matches: 242, Mismatches: 15, Indels: 29
0.85 0.05 0.10
Matches are distributed among these distances:
39 14 0.06
40 135 0.56
41 1 0.00
43 71 0.29
44 1 0.00
46 19 0.08
47 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:28395962 original size:86 final size:82
Alignment explanation
Indices: 28395804--28396114 Score: 472
Period size: 86 Copynumber: 3.8 Consensus size: 82
28395794 AACCCAAGTA
*
28395804 CCTTCGGGATTTAG-CCGGATATAGC-AACTCGCACAAATGCCTTCGGG-TCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGCAAACTCGCACAAATGCCTTCGGGATCTTAGCCCGGATAT
28395866 AGTCACTAGCACAAATG
66 AGTCACTAGCACAAATG
*
28395883 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGATATAGCAA--ACTCGCACAAATGCCTTCGGGA--TCTTAGCCCGG
28395948 ATATAGTCACTAGCACAAATG
62 ATATAGTCACTAGCACAAATG
* * *
28395969 CCTTCGGGACTTAGCCCGGGTATAGCAACCACTCACACAAATGCCTTCGGGA-CTTCGCCCGGAT
1 CCTTCGGGACTTAGCCCGGATATAGCAA--ACTCGCACAAATGCCTTCGGGATCTTAGCCCGGAT
28396033 ATAGTCACTAGCACAAATG
64 ATAGTCACTAGCACAAATG
*
28396052 CCTTCGGGACTTAGCCCGGATATAG-GAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGCAAACTCGCACAAATGCCTTCGGGATCTTAGCCCGGATAT
28396115 CATCCGAATA
Statistics
Matches: 216, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
79 13 0.06
80 44 0.20
81 1 0.00
82 1 0.00
83 75 0.35
86 82 0.38
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (82 bp):
CCTTCGGGACTTAGCCCGGATATAGCAAACTCGCACAAATGCCTTCGGGATCTTAGCCCGGATAT
AGTCACTAGCACAAATG
Found at i:28401999 original size:13 final size:14
Alignment explanation
Indices: 28401971--28402003 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
28401961 TTTTTGAAAC
28401971 ACAGAAATTAAAAA
1 ACAGAAATTAAAAA
28401985 ACAGAAATT-AAAA
1 ACAGAAATTAAAAA
28401998 ACAGAA
1 ACAGAA
28402004 TTTGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (14 bp):
ACAGAAATTAAAAA
Found at i:28402011 original size:14 final size:14
Alignment explanation
Indices: 28401964--28402011 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
28401954 TTTGTTTTTT
*
28401964 TTGAAACACAGAAA
1 TTGAAAAACAGAAA
*
28401978 TTAAAAAACAGAAA
1 TTGAAAAACAGAAA
*
28401992 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
28402005 TTGAAAA
1 TTGAAAA
28402012 GACCTCAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.19
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:28402259 original size:145 final size:144
Alignment explanation
Indices: 28402029--28402290 Score: 427
Period size: 145 Copynumber: 1.8 Consensus size: 144
28402019 GCGTGTGGCC
* * *
28402029 TGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTGAAAAAGTAGAATTTGAAAATACCTCAA
1 TGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTGAAAAAGCAGAAATTGAAAATACCTCAA
*
28402094 TGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATT
66 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATT
28402159 ACCTCAACGTCTCT
131 ACCTCAACGTCTCT
* ** *
28402173 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AGAAGCAGAAATTGAAAATACCTC
1 TGAGACTCAACTCACCTCTCGCAATATGAGTTG-A-TTTGAAAAAGCAGAAATTGAAAATACCTC
28402237 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAC
64 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAC
28402291 TAGACATTAA
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
144 29 0.27
145 75 0.69
146 4 0.04
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (144 bp):
TGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTGAAAAAGCAGAAATTGAAAATACCTCAA
CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATT
ACCTCAACGTCTCT
Found at i:28402304 original size:73 final size:72
Alignment explanation
Indices: 28401995--28402305 Score: 412
Period size: 72 Copynumber: 4.3 Consensus size: 72
28401985 ACAGAAATTA
* * * * * ** *
28401995 AAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGT
28402060 TG-A-TTTG
64 TGAATTTTG
*
28402067 AAAA-AGTAGAATTTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 AAAACAG-A-AA-TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
28402131 TTGAATTTTG
63 TTGAATTTTG
* *
28402141 AAAACAGAAATTGAAATTACCTCAACGTCTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
28402206 AATTTTG
66 AATTTTG
*
28402213 AGAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 A-AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
28402278 GAATTTTG
65 GAATTTTG
* *
28402286 AAAACTAGACATTAAAAATA
1 AAAAC-AGAAATTGAAAATA
28402306 GAAATTGAAA
Statistics
Matches: 213, Mismatches: 18, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
71 2 0.01
72 98 0.46
73 85 0.40
74 26 0.12
75 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (72 bp):
AAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
AATTTTG
Found at i:28402463 original size:72 final size:72
Alignment explanation
Indices: 28402382--28402731 Score: 531
Period size: 72 Copynumber: 4.8 Consensus size: 72
28402372 TGAAAATCAA
*
28402382 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATT
1 CGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATT
*
28402447 ACCTCAA
66 ACCTCAG
* * *
28402454 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAGCAGAAATTGAAAAT
1 CGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATT
28402519 ACCTCAG
66 ACCTCAG
*
28402526 CGTGTCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATT
1 CGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATT
28402591 ACCTCAG
66 ACCTCAG
* * *
28402598 CGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTAAA
1 CGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAA-AACAGAAATTGAA
28402663 ATTACCTCAG
63 ATTACCTCAG
* ** * *
28402673 TGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAACATAAATT
1 CGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
28402732 AAAAGGCTCA
Statistics
Matches: 256, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
72 190 0.74
73 2 0.01
74 6 0.02
75 58 0.23
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (72 bp):
CGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATT
ACCTCAG
Found at i:28414645 original size:38 final size:38
Alignment explanation
Indices: 28414558--28414630 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
28414548 AAAAAAATCA
*
28414558 CGGAAATTTTTTTTAAAACACAGGAATTTTTGAAACAC
1 CGGAAATTTTTTTAAAAACACAGGAATTTTTGAAACAC
28414596 CGGAAATTTTTTTAAAAACACGAGG-ATTTTTGAAA
1 CGGAAATTTTTTTAAAAACAC-AGGAATTTTTGAAA
28414631 ACACGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
38 30 0.91
39 3 0.09
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (38 bp):
CGGAAATTTTTTTAAAAACACAGGAATTTTTGAAACAC
Found at i:28414646 original size:19 final size:19
Alignment explanation
Indices: 28414565--28414649 Score: 70
Period size: 18 Copynumber: 4.5 Consensus size: 19
28414555 TCACGGAAAT
* *
28414565 TTTTTTTAAAACAC-AGGA
1 TTTTTTGAAAACACGAAGA
*
28414583 ATTTTTG-AAACACCGGAA-A
1 TTTTTTGAAAACA-C-GAAGA
* *
28414602 TTTTTTTAAAAACACGAGGA
1 -TTTTTTGAAAACACGAAGA
28414622 -TTTTTGAAAACACGAAGA
1 TTTTTTGAAAACACGAAGA
28414640 TTTTTTGAAA
1 TTTTTTGAAA
28414650 CGCGAGAGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
17 5 0.10
18 22 0.42
19 12 0.23
20 8 0.15
21 5 0.10
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (19 bp):
TTTTTTGAAAACACGAAGA
Found at i:28414650 original size:18 final size:18
Alignment explanation
Indices: 28414566--28414687 Score: 67
Period size: 17 Copynumber: 6.8 Consensus size: 18
28414556 CACGGAAATT
* *
28414566 TTTTTTAAAACAC-AGGA
1 TTTTTTGAAACACGAAGA
*
28414583 ATTTTTGAAACACCGGAA-A
1 TTTTTTGAAACA-C-GAAGA
* *
28414602 TTTTTTTAAAAACACGAGGA
1 -TTTTTT-GAAACACGAAGA
28414622 -TTTTTGAAAACACGAAGA
1 TTTTTTG-AAACACGAAGA
*
28414640 TTTTTTGAAACGCG-AGA
1 TTTTTTGAAACACGAAGA
* * *
28414657 -GTTTAGAAACATGAA-A
1 TTTTTTGAAACACGAAGA
*
28414673 ATTTTTGAAACACGA
1 TTTTTTGAAACACGA
28414688 CAATAACCCG
Statistics
Matches: 79, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
16 10 0.13
17 25 0.32
18 22 0.28
19 9 0.11
20 8 0.10
21 5 0.06
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (18 bp):
TTTTTTGAAACACGAAGA
Found at i:28414745 original size:16 final size:16
Alignment explanation
Indices: 28414724--28414810 Score: 75
Period size: 16 Copynumber: 5.2 Consensus size: 16
28414714 AAAAATATAA
28414724 AAAAATTTTAAAACAC
1 AAAAATTTTAAAACAC
*
28414740 AAAAATTTGTGAAACAC
1 AAAAATTT-TAAAACAC
* *
28414757 GAGAATTATTGAAAACAC
1 AAAAATT-TT-AAAACAC
* *
28414775 GAAAAATTTGAAAATAC
1 -AAAAATTTTAAAACAC
* *
28414792 GAAAATTTAAAAACAC
1 AAAAATTTTAAAACAC
28414808 AAA
1 AAA
28414811 TTTTTTTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
16 23 0.42
17 19 0.35
18 8 0.15
19 5 0.09
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.22
Consensus pattern (16 bp):
AAAAATTTTAAAACAC
Found at i:28414754 original size:17 final size:16
Alignment explanation
Indices: 28414724--28414810 Score: 59
Period size: 17 Copynumber: 5.2 Consensus size: 16
28414714 AAAAATATAA
*
28414724 AAAAATTTTAAAACAC
1 AAAAATTTTGAAACAC
28414740 AAAAATTTGTGAAACAC
1 AAAAATTT-TGAAACAC
* *
28414757 GAGAATTATTGAAAACAC
1 AAAAATT-TTG-AAACAC
*
28414775 GAAAAA-TTTGAAAATAC
1 -AAAAATTTTG-AAACAC
* **
28414792 GAAAATTTAAAAACAC
1 AAAAATTTTGAAACAC
28414808 AAA
1 AAA
28414811 TTTTTTTTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
16 19 0.35
17 25 0.45
18 8 0.15
19 3 0.05
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.22
Consensus pattern (16 bp):
AAAAATTTTGAAACAC
Found at i:28414825 original size:22 final size:23
Alignment explanation
Indices: 28414800--28414847 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
28414790 ACGAAAATTT
28414800 AAAAACAC-A-AATTTTTTTTTTA
1 AAAAACACGACAA-TTTTTTTTTA
28414822 AAAAACACGACAATTTTTTTTTA
1 AAAAACACGACAATTTTTTTTTA
28414845 AAA
1 AAA
28414848 TATAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 14 0.58
24 2 0.08
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAAACACGACAATTTTTTTTTA
Found at i:28414902 original size:18 final size:17
Alignment explanation
Indices: 28414853--28414964 Score: 113
Period size: 17 Copynumber: 6.4 Consensus size: 17
28414843 TAAAATATAA
28414853 AAAATTTT-AAAACACG
1 AAAATTTTGAAAACACG
*
28414869 AGAATTTGTG-AAACACG
1 AAAATTT-TGAAAACACG
*
28414886 AGAATTGTTGAAAACACG
1 AAAATT-TTGAAAACACG
28414904 AAAATTTTGAAAACACG
1 AAAATTTTGAAAACACG
*
28414921 AAAATTTTTG-AAACATAG
1 AAAA-TTTTGAAAACA-CG
*
28414939 AAATTTTTAGAAAAACACG
1 AAAATTTT-G-AAAACACG
28414958 AAAATTT
1 AAAATTT
28414965 GAANNNNNNN
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.07
17 40 0.49
18 23 0.28
19 7 0.09
20 5 0.06
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (17 bp):
AAAATTTTGAAAACACG
Found at i:28414910 original size:35 final size:35
Alignment explanation
Indices: 28414853--28414963 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 35
28414843 TAAAATATAA
*
28414853 AAAATT-TT-AAAACACGAGAATTTGTG-AAACACG
1 AAAATTGTTGAAAACACGAAAATTT-TGAAAACACG
*
28414886 AGAATTGTTGAAAACACGAAAATTTTGAAAACACG
1 AAAATTGTTGAAAACACGAAAATTTTGAAAACACG
* * *
28414921 AAAATTTTTG-AAACATAGAAATTTTTAGAAAAACACG
1 AAAATTGTTGAAAACA-CGAAAATTTT-G-AAAACACG
28414958 AAAATT
1 AAAATT
28414964 TGAANNNNNN
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
33 5 0.08
34 9 0.14
35 37 0.56
36 1 0.02
37 14 0.21
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (35 bp):
AAAATTGTTGAAAACACGAAAATTTTGAAAACACG
Found at i:28414946 original size:128 final size:128
Alignment explanation
Indices: 28414705--28414964 Score: 357
Period size: 128 Copynumber: 2.0 Consensus size: 128
28414695 CCGACAATCT
28414705 TTTTTTTTTAAAAATATAAAAAAATTTTAAAACACAAAAATTTGTGAAACACGAGAATTATTGAA
1 TTTTTTTTTAAAAATATAAAAAAATTTTAAAACACAAAAATTTGTGAAACACGAGAATTATTGAA
* * *
28414770 AACACGAAAAATTTGAAAATACGAAAATTTAAAAACACAAATTTTTTTTTTA-AAAAACACGACA
66 AACACGAAAAATTTGAAAACACGAAAATTTAAAAACACAAA---TATTTTTAGAAAAACACGAAA
28414834 A
128 A
* * *
28414835 TTTTTTTTT-AAAATAT-AAAAAATTTTAAAACACGAGAATTTGTGAAACACGAGAATTGTTGAA
1 TTTTTTTTTAAAAATATAAAAAAATTTTAAAACACAAAAATTTGTGAAACACGAGAATTATTGAA
* ** *
28414898 AACACGAAAATTTTGAAAACACGAAAATTTTTGAAACATAGAA-ATTTTTAGAAAAACACGAAAA
66 AACACGAAAAATTTGAAAACACGAAAA-TTTAAAAACACA-AATATTTTTAGAAAAACACGAAAA
28414962 TTT
1 TTT
28414965 GAANNNNNNN
Statistics
Matches: 117, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
126 6 0.05
127 15 0.13
128 69 0.59
129 16 0.14
130 11 0.09
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (128 bp):
TTTTTTTTTAAAAATATAAAAAAATTTTAAAACACAAAAATTTGTGAAACACGAGAATTATTGAA
AACACGAAAAATTTGAAAACACGAAAATTTAAAAACACAAATATTTTTAGAAAAACACGAAAA
Found at i:28420186 original size:17 final size:18
Alignment explanation
Indices: 28420166--28420200 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28420156 CTTGGAATCG
*
28420166 ACTTTTTTATA-AAAAAT
1 ACTTTTTGATAGAAAAAT
28420183 ACTTTTTGATAGAAAAAT
1 ACTTTTTGATAGAAAAAT
28420201 TTTTTTGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
ACTTTTTGATAGAAAAAT
Found at i:28420205 original size:17 final size:17
Alignment explanation
Indices: 28420168--28420208 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
28420158 TGGAATCGAC
28420168 TTTTTT-ATAAAAAATA
1 TTTTTTGATAAAAAATA
*
28420184 CTTTTTGATAGAAAAAT-
1 TTTTTTGATA-AAAAATA
28420201 TTTTTTGA
1 TTTTTTGA
28420209 ACTAATTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 10 0.48
18 6 0.29
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (17 bp):
TTTTTTGATAAAAAATA
Found at i:28421168 original size:16 final size:15
Alignment explanation
Indices: 28421143--28421194 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 15
28421133 TAAATAAATT
*
28421143 AAAAATTAATTATAA
1 AAAAAATAATTATAA
28421158 AAAAGAATAATTTATTAA
1 AAAA-AATAA-TTA-TAA
28421176 AAATAAATAA-TATAA
1 AAA-AAATAATTATAA
28421191 AAAA
1 AAAA
28421195 TATTCAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
14 1 0.03
15 10 0.31
16 6 0.19
17 3 0.09
18 11 0.34
19 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAAAATAATTATAA
Found at i:28421743 original size:29 final size:29
Alignment explanation
Indices: 28421701--28421758 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28421691 ATTTATAATT
28421701 TCATCATAATTTGAAATACATATTTTTGG
1 TCATCATAATTTGAAATACATATTTTTGG
28421730 TCATCATAATTTGAAATACATATTTTTGG
1 TCATCATAATTTGAAATACATATTTTTGG
28421759 CCACACGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (29 bp):
TCATCATAATTTGAAATACATATTTTTGG
Found at i:28423394 original size:20 final size:20
Alignment explanation
Indices: 28423356--28423403 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
28423346 TAAATTCTAA
* **
28423356 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
28423376 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
28423396 AAA-ATAAA
1 AAAGATAAA
28423404 ATTCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:28423447 original size:15 final size:15
Alignment explanation
Indices: 28423427--28423456 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28423417 ATAATCCTAA
*
28423427 TAATTATCTTAATAT
1 TAATTATCCTAATAT
28423442 TAATTATCCTAATAT
1 TAATTATCCTAATAT
28423457 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:28425054 original size:5 final size:5
Alignment explanation
Indices: 28425035--28425107 Score: 60
Period size: 5 Copynumber: 13.8 Consensus size: 5
28425025 AAAATAATTA
* *
28425035 AAAAT AAAAC AAAAT GAAAT AAAAT AAAAT AAGAA- ATAAAT AATAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT AA-AAT
28425082 AATAAT -AAAT AAAATT AAAATT AAAA
1 AA-AAT AAAAT AAAA-T AAAA-T AAAA
28425108 ATTAAAGATT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
4 3 0.05
5 31 0.53
6 24 0.41
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:28425106 original size:16 final size:16
Alignment explanation
Indices: 28425056--28425106 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
28425046 AAATGAAATA
*
28425056 AAATAAAATAAGAAAT
1 AAATAAAATAAGAATT
*
28425072 AAATAATAATAATAA-T
1 AAATAA-AATAAGAATT
28425088 AAATAAAATTAA-AATT
1 AAATAAAA-TAAGAATT
28425104 AAA
1 AAA
28425107 AATTAAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 4 0.13
16 20 0.65
17 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
AAATAAAATAAGAATT
Found at i:28430906 original size:27 final size:26
Alignment explanation
Indices: 28430876--28430938 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
28430866 AGATAATTAA
28430876 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
28430903 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
28430930 AATATAAAT
1 AATA-AAAT
28430939 AAAATAGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:28430925 original size:15 final size:15
Alignment explanation
Indices: 28430905--28430934 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28430895 ATAATCCTAA
*
28430905 TAATTATCTTAATAT
1 TAATTATCCTAATAT
28430920 TAATTATCCTAATAT
1 TAATTATCCTAATAT
28430935 AAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:28434037 original size:42 final size:42
Alignment explanation
Indices: 28433933--28434037 Score: 106
Period size: 44 Copynumber: 2.5 Consensus size: 42
28433923 AATTATCGTG
* *
28433933 TAAGACCGTGTCTGGGACACGGACATCGATTTGAAATTTACGTG
1 TAAGACCATGTCTGGGACACGGACATCGATTTG--ATTTACGTA
* **
28433977 TAAGACCATGTCTAGGACATC-GACATCGTATTTG-TTTTTGTA
1 TAAGACCATGTCTGGGACA-CGGACATCG-ATTTGATTTACGTA
*
28434019 TAAGACCCTGTCTGGGACA
1 TAAGACCATGTCTGGGACA
28434038 GAGGCATCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 22 0.42
44 24 0.46
45 6 0.12
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACACGGACATCGATTTGATTTACGTA
Found at i:28436172 original size:14 final size:14
Alignment explanation
Indices: 28436153--28436181 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28436143 CCTAATAACG
28436153 TGTTTAATTAGGCT
1 TGTTTAATTAGGCT
28436167 TGTTTAATTAGGCT
1 TGTTTAATTAGGCT
28436181 T
1 T
28436182 TAATTAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (14 bp):
TGTTTAATTAGGCT
Found at i:28436372 original size:16 final size:17
Alignment explanation
Indices: 28436347--28436396 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
28436337 TTTTCTTACT
28436347 TTAT-TAAATTATTATA
1 TTATATAAATTATTATA
*
28436363 TTATAT-AATTATTATT
1 TTATATAAATTATTATA
* *
28436379 TTATTTAAATTATAATA
1 TTATATAAATTATTATA
28436396 T
1 T
28436397 GAATTATAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATAAATTATTATA
Found at i:28437321 original size:51 final size:51
Alignment explanation
Indices: 28437245--28437367 Score: 169
Period size: 51 Copynumber: 2.4 Consensus size: 51
28437235 AGAACTAAGT
* * * *
28437245 TATCCGGATGAAATATGAAGCTCTTGTTGAAACTAGAGCAATAAAGTAATA
1 TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATA
*
28437296 TATCCGGATGAAATATGAAGTTCTTGTTGAAGCCAGAACAACAAAGTAATA
1 TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATA
28437347 -ATTCCGGAT-AAAGTATGAAGT
1 TA-TCCGGATGAAA-TATGAAGT
28437368 AAGTTTGGGA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
50 4 0.06
51 61 0.94
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (51 bp):
TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATA
Found at i:28444058 original size:16 final size:17
Alignment explanation
Indices: 28444033--28444082 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
28444023 TTTTCTTACT
28444033 TTAT-TAAATTATTATA
1 TTATATAAATTATTATA
*
28444049 TTATAT-AATTATTATT
1 TTATATAAATTATTATA
* *
28444065 TTATTTAAATTATAATA
1 TTATATAAATTATTATA
28444082 T
1 T
28444083 GAATTATAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATAAATTATTATA
Found at i:28445006 original size:51 final size:51
Alignment explanation
Indices: 28444930--28445052 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 51
28444920 TGAACTAAGT
* * * *
28444930 TATCCGGATGAAATATGAAGCTCTTGTTGAAACTAGAGCAATAAAGTAATA
1 TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATA
*
28444981 TATCCGGATGAAATATGAAGTTCTTGTTGAAGCCAGAACAACAAAGTAATA
1 TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATA
*
28445032 -ATTCCGGATGAAGTATGAAGT
1 TA-TCCGGATGAAATATGAAGT
28445053 AAGTTTGGGA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 64 0.98
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (51 bp):
TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATA
Found at i:28445835 original size:28 final size:28
Alignment explanation
Indices: 28445795--28445850 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28445785 GTATGAGAAA
28445795 GAATGTATGAGTTAAATTATAAATTGAT
1 GAATGTATGAGTTAAATTATAAATTGAT
*
28445823 GAATGTATGAGTTAAATTATGAATTGAT
1 GAATGTATGAGTTAAATTATAAATTGAT
28445851 TTAGTATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (28 bp):
GAATGTATGAGTTAAATTATAAATTGAT
Found at i:28449871 original size:13 final size:13
Alignment explanation
Indices: 28449855--28449894 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
28449845 CAATCTCATA
28449855 TCTCAATTTCAAT
1 TCTCAATTTCAAT
28449868 TCTCAA-TTCAATT
1 TCTCAATTTCAA-T
28449881 TCTC-ATTTC-AT
1 TCTCAATTTCAAT
28449892 TCT
1 TCT
28449895 AATAGCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.16
12 7 0.28
13 14 0.56
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (13 bp):
TCTCAATTTCAAT
Found at i:28449873 original size:26 final size:25
Alignment explanation
Indices: 28449835--28449894 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
28449825 AACCTTTTGG
*
28449835 TTCATATTTTCAATCTC-ATATCTCAAT
1 TTCA-ATTCTCAAT-TCAATATCTC-AT
*
28449862 TTCAATTCTCAATTCAATTTCTCAT
1 TTCAATTCTCAATTCAATATCTCAT
28449887 TTC-ATTCT
1 TTCAATTCT
28449895 AATAGCTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.17
25 7 0.23
26 14 0.47
27 4 0.13
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (25 bp):
TTCAATTCTCAATTCAATATCTCAT
Found at i:28449880 original size:18 final size:19
Alignment explanation
Indices: 28449842--28449882 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
28449832 TGGTTCATAT
28449842 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
28449861 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
28449879 TTTC
1 TTTC
28449883 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:28450308 original size:8 final size:10
Alignment explanation
Indices: 28450279--28450319 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
28450269 ATTCTAATAA
*
28450279 TCACATATTT
1 TCACACATTT
28450289 TCACACATTT
1 TCACACATTT
28450299 TCACA-A-TT
1 TCACACATTT
*
28450307 TCATACATTT
1 TCACACATTT
28450317 TCA
1 TCA
28450320 TTCAATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 6 0.22
9 2 0.07
10 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (10 bp):
TCACACATTT
Found at i:28450522 original size:11 final size:11
Alignment explanation
Indices: 28450506--28450530 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28450496 TACATAAATC
28450506 ATATATATATT
1 ATATATATATT
28450517 ATATATATATT
1 ATATATATATT
28450528 ATA
1 ATA
28450531 ATTTCAATCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATATATT
Found at i:28450545 original size:15 final size:15
Alignment explanation
Indices: 28450527--28450576 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
28450517 ATATATATAT
28450527 TATAATTTCAATCAA
1 TATAATTTCAATCAA
*
28450542 TATAAATTCAATCAA
1 TATAATTTCAATCAA
* *
28450557 AATGATTTCAATCAA
1 TATAATTTCAATCAA
28450572 TATAA
1 TATAA
28450577 ATTTGATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (15 bp):
TATAATTTCAATCAA
Found at i:28451584 original size:21 final size:22
Alignment explanation
Indices: 28451531--28451587 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
28451521 CAATTTAAAT
*
28451531 AATAATAACAATAACAATAATA
1 AATAATAATAATAACAATAATA
* *
28451553 ATTAA-ATATAA-AACTATAATA
1 AATAATA-ATAATAACAATAATA
28451574 AATAATAATAATAA
1 AATAATAATAATAA
28451588 TTTAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAATAATAATAACAATAATA
Found at i:28457444 original size:22 final size:22
Alignment explanation
Indices: 28457393--28457452 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
28457383 ATCATTGTTA
28457393 TTTA-TTGTA-TATTAT-TTTT
1 TTTACTTGTATTATTATATTTT
* *
28457412 TTTGCAT-TATTATTATATTTT
1 TTTACTTGTATTATTATATTTT
28457433 TTTACTTGTATTA-TATATTT
1 TTTACTTGTATTATTATATTT
28457453 GTTAATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 16 0.48
22 5 0.15
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTACTTGTATTATTATATTTT
Found at i:28457445 original size:25 final size:26
Alignment explanation
Indices: 28457400--28457451 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
28457390 TTATTTATTG
*
28457400 TATATTATTTTTTTTGCATTAT-TAT
1 TATATTATTTTTCTTGCATTATATAT
*
28457425 TATATT-TTTTTACTTGTATTATATAT
1 TATATTATTTTT-CTTGCATTATATAT
28457451 T
1 T
28457452 TGTTAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.22
25 14 0.61
26 4 0.17
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (26 bp):
TATATTATTTTTCTTGCATTATATAT
Found at i:28457566 original size:18 final size:18
Alignment explanation
Indices: 28457543--28457590 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
28457533 TTACATAACA
**
28457543 TTTATTATATTTTTTATT
1 TTTATTATATTACTTATT
28457561 TTTATTCTATATTACTTATT
1 TTTA-T-TATATTACTTATT
*
28457581 TTTTTTATAT
1 TTTATTATAT
28457591 GTTATGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 9 0.36
19 2 0.08
20 14 0.56
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATTATATTACTTATT
Found at i:28460698 original size:22 final size:22
Alignment explanation
Indices: 28460673--28460723 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
28460663 AATATTAAAG
28460673 TTAATTGAGTTTTCAAAATATT
1 TTAATTGAGTTTTCAAAATATT
28460695 TTAATTGAGTTTTCAAAATATT
1 TTAATTGAGTTTTCAAAATATT
28460717 TTAATTG
1 TTAATTG
28460724 TAACTATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (22 bp):
TTAATTGAGTTTTCAAAATATT
Found at i:28463593 original size:88 final size:83
Alignment explanation
Indices: 28463489--28463910 Score: 258
Period size: 88 Copynumber: 4.9 Consensus size: 83
28463479 ACAGACATTA
**
28463489 AAAACAGAAATTGAAAATAACTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGATTTTGAAAATAACTC-GCACGTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAGT
* *
28463554 TGATTTTTTGAAACTTAACTT
64 TGATTTTTTGAAA-ATAAATT
* * * * *
28463575 GAAAAGCAGATTTTGAAAATACCTCGATATGTGACTGAAGGTTCAACTCACCTCTCGCAATATGA
1 -AAAA-CAGATTTTGAAAATAACTCG-CACGTGAC-CAAGGCTCAACTCACCTCTCGCAATATGA
*
28463640 GTTGA-TTTTTGAAAAACAAAAATT
62 GTTGATTTTTTG--AAA-ATAAATT
* * * ** * * *
28463664 -AAA-AGA--CT-CAACTCAACTCTCGCAAAAATTA-AAAAGCTCAACTCACCTCTCGCAATATG
1 AAAACAGATTTTGAAAAT-AA--CTCGC--ACGTGACCAAGGCTCAACTCACCTCTCGCAATATG
28463723 AGTTGAATTTTTTTG--AA-AAA--
61 AGTTG-A-TTTTTTGAAAATAAATT
* ** * *
28463743 AAAATAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGT
1 AAAACAGATTTTGAAAATAACTC-GCACGTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAGT
28463808 TGA-TTTTTGAAAATAGAATCT
64 TGATTTTTTGAAAATA-AAT-T
* * * * * *
28463829 GAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATATCGCAATGTGA
1 --AAAACAGATTTTGAAAATAACTCG-CACGTGA-CCAAGGCTCAACTCACCTCTCGCAATATGA
28463894 GTTGATTTTTTTGAAAA
62 GTTGA-TTTTTTGAAAA
28463911 ATATAAATTG
Statistics
Matches: 261, Mismatches: 41, Indels: 63
0.72 0.11 0.17
Matches are distributed among these distances:
79 6 0.02
80 6 0.02
81 12 0.05
82 37 0.14
83 7 0.03
84 33 0.13
85 8 0.03
86 3 0.01
87 22 0.08
88 109 0.42
89 8 0.03
90 10 0.04
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (83 bp):
AAAACAGATTTTGAAAATAACTCGCACGTGACCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTGAAAATAAATT
Found at i:28463692 original size:30 final size:30
Alignment explanation
Indices: 28463656--28463718 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
28463646 TTTTGAAAAA
28463656 CAAAAATT-AAAAGACTCAACTCAACTCTCG
1 CAAAAATTAAAAAG-CTCAACTCAACTCTCG
*
28463686 CAAAAATTAAAAAGCTCAACTCACCTCTCG
1 CAAAAATTAAAAAGCTCAACTCAACTCTCG
28463716 CAA
1 CAA
28463719 TATGAGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.19
Consensus pattern (30 bp):
CAAAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:28463957 original size:79 final size:77
Alignment explanation
Indices: 28463828--28464082 Score: 262
Period size: 79 Copynumber: 3.3 Consensus size: 77
28463818 AAATAGAATC
** ** * * * * *
28463828 TGAAAAACAGATTTTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCACATATCGCAATGT
1 TGAAAAACAGAAATTGAAAATACCTCAG-CGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
28463892 GAGTTGATTTTTT
65 GAGTTGATTTTTT
* * * * * *
28463905 TGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAAT
1 TGAAAAACAGAAATTG--AAAATACCTCAGCGCGTGAGC-CAAGGCTCAACTCACCTCTCGCAAT
28463969 ATGAGTTGATTTTTT
63 ATGAGTTGATTTTTT
* *
28463984 TGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATG
1 TGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATG
*
28464049 ACTTGATTTTTTTT
66 AGTTGA--TTTTTT
**
28464063 TGAAAGGCAGAAATTGAAAA
1 TGAAAAACAGAAATTGAAAA
28464083 ACGGAAATTG
Statistics
Matches: 149, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
76 2 0.01
77 58 0.39
79 87 0.58
80 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (77 bp):
TGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTT
Found at i:28464035 original size:77 final size:78
Alignment explanation
Indices: 28463867--28464082 Score: 265
Period size: 79 Copynumber: 2.7 Consensus size: 78
28463857 ATGTGACCCG
* * * * * *
28463867 AGGCTCAACTCACATATCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG--AAAATACCT
* * * *
28463932 CAGTGTGTGATCTGA
64 CAGCGCGTGAGCTCA
*
28463947 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
28464011 GCGCGTGAGC-CA
66 GCGCGTGAGCTCA
* *
28464023 AGGCTCAACTCACCTCTCGCAATATGACTTGATTTTTTTTTGAAAGGCAGAAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACAGAAATTGAAAA
28464083 ACGGAAATTG
Statistics
Matches: 120, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
76 2 0.02
77 46 0.38
79 71 0.59
80 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
GCGCGTGAGCTCA
Found at i:28464125 original size:249 final size:242
Alignment explanation
Indices: 28463488--28464302 Score: 864
Period size: 254 Copynumber: 3.3 Consensus size: 242
28463478 AACAGACATT
*
28463488 AAAAACAGAAATTGAAAATAACTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** * * * *
28463553 TTGATTTTTTGAAACTTAACTTGAAAAGCAGATTTTGAAAATACCTCGATATGTGACTGAAGGTT
66 TTGATTTTTTGAAACAGAAATTGAAAAACAGATTTTGAAAATACCTCGACATGTGACTG-AGGCT
* *
28463618 CAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATT-AAAAGACTCAACTCAA
130 CAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAA-AAT-ACCTC-A
* * * *
28463680 CTCTCGCAAAAAT-TAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTG
192 GTGT-G----TATCT--GAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTG
* *
28463738 AAAAAAAAATAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATA
1 ----AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATA
* *
28463803 TGAGTTGA-TTTTTGAAA-ATAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCC
62 TGAGTTGATTTTTTGAAACAGA-AAT-TGAAAAACAGATTTTGAAAATACCTCGACATGTGA-CT
* * * * *
28463866 GAGGCTCAACTCACATATCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACC
124 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAAAATACC
28463931 TCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
189 TCAGTGTGT-ATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * *
28463986 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAC
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* ** * *
28464051 TTGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACATG
66 TTGA---TTTTTTGAAA--CAGAAATTGAAAAACAGATTTTGAAAATACCTCGACATGTGAC-TG
* * * * * *
28464116 AGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTTG-ACAACAGAAATTG--AAATTACC
125 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAAAAATTGAAAAAATACC
* * *
28464178 TCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
189 TCAGTGTGTATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * * ** ** *
28464231 AAAAACAGAAATTAAAAATACCTCAGCA--TG-TCTTGAGGCTCAACTCATTTCTCACAATATGA
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
28464293 GTTGATTTTT
65 GTTGATTTTT
28464303 AAAAAAAAAA
Statistics
Matches: 487, Mismatches: 56, Indels: 50
0.82 0.09 0.08
Matches are distributed among these distances:
240 5 0.01
242 1 0.00
243 30 0.06
244 64 0.13
245 66 0.14
247 15 0.03
248 19 0.04
249 98 0.20
250 13 0.03
251 3 0.01
252 2 0.00
253 12 0.02
254 130 0.27
255 6 0.01
256 19 0.04
257 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (242 bp):
AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAACAGAAATTGAAAAACAGATTTTGAAAATACCTCGACATGTGACTGAGGCTC
AACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAAAATACCTCAGTGT
GTATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:28464147 original size:170 final size:168
Alignment explanation
Indices: 28463923--28464229 Score: 440
Period size: 170 Copynumber: 1.8 Consensus size: 168
28463913 ATAAATTGAA
* * *
28463923 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGA
1 AAAATACCTCAGCGTGTGATCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTTGA
*
28463987 AAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAC
66 AA-ACAGAAATTGAAAATACCTCA--GCGTG-GCCTAAGGCTCAACTCACCTCTCGCAATATGAC
28464051 TTGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
127 TTGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
* * *
28464093 AAAATACCTCGGCGTGTGA-CATGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTTG
1 AAAATACCTCAGCGTGTGATC-TGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTTG
* * * * *
28464157 ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
65 AAAACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGACTTG
28464222 ATTTTTTT
130 ATTTTTTT
28464230 GAAAAACAGA
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
167 2 0.02
168 43 0.35
169 1 0.01
170 66 0.54
171 10 0.08
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (168 bp):
AAAATACCTCAGCGTGTGATCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTTGA
AAACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGACTTGA
TTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
Found at i:28464148 original size:93 final size:91
Alignment explanation
Indices: 28463983--28464172 Score: 233
Period size: 93 Copynumber: 2.1 Consensus size: 91
28463973 GTTGATTTTT
* * * * *
28463983 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGACAAGGCTCAACTCACCTCTCACAATAC
28464048 GACTTGATTTTTTTTTGA-AAGGCAGAAA
66 GACTTGA-TTTTTTTTGACAA--CAGAAA
* * *
28464076 TTGAAAAACGGAAATTGAAAATACCTC-G-GCGTGTGACATGAGGCTCAACTCGCCTCTCACAAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGACA--AGGCTCAACTCACCTCTCACAAT
*
28464139 ACGAGTTGATTTTTTTTGACAACAGAAA
64 ACGACTTGATTTTTTTTGACAACAGAAA
28464167 TTGAAA
1 TTGAAA
28464173 TTACCTCAGC
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
91 20 0.24
92 11 0.13
93 54 0.64
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (91 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGACAAGGCTCAACTCACCTCTCACAATAC
GACTTGATTTTTTTTGACAACAGAAA
Found at i:28464214 original size:75 final size:74
Alignment explanation
Indices: 28464080--28464426 Score: 351
Period size: 75 Copynumber: 4.6 Consensus size: 74
28464070 CAGAAATTGA
* * * * *
28464080 AAAACGGAAATTGAAAATACCTCGGCGTGTGACATGAGGCTCAACTCGCCTCTCACAATACGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCACAATATGAGT
28464145 TGATTTTTTTTG
64 TGA-TTTTTTTG
* * *
28464157 ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
28464222 ATTTTTTTG
66 ATTTTTTTG
* * * **
28464231 AAAAACAGAAATTAAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTT
1 -AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTT
***
28464296 GATTTTTAAAAAA
65 GATTTTT---TTG
* * ** *
28464309 AAAACAGAAATTGAAAATACCTCAGCATGT-CT-ATTGGCTCAACTAATTTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGA--GGCTCAACTCACCTCTCACAATATGAGT
*
28464372 TGA--ATTTTG
64 TGATTTTTTTG
* * * *
28464381 AAAATAGAAATTGAAATTACCTCAGCGGGTCTTGAGGCTCAACTCA
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA
28464427 TTTTGAACAG
Statistics
Matches: 229, Mismatches: 33, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
72 36 0.16
73 1 0.00
74 9 0.04
75 98 0.43
76 1 0.00
77 84 0.37
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (74 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
ATTTTTTTG
Done.