Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 33 of 141
Found at i:11040620 original size:45 final size:46
Alignment explanation
Indices: 11040548--11040642 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 46
11040538 CATTGAAAAA
11040548 TTTTGAAATTTCGCCATTGTTGCTGTAGAGGAAATTAAATTAGGGC
1 TTTTGAAATTTCGCCATTGTTGCTGTAGAGGAAATTAAATTAGGGC
11040594 TTTTGAAATTTCG-CATTGTTGCTGTAGAGGAAATTAAATTAGGGC
1 TTTTGAAATTTCGCCATTGTTGCTGTAGAGGAAATTAAATTAGGGC
11040639 TTTT
1 TTTT
11040643 TTTTTCTCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 36 0.73
46 13 0.27
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.40
Consensus pattern (46 bp):
TTTTGAAATTTCGCCATTGTTGCTGTAGAGGAAATTAAATTAGGGC
Found at i:11044519 original size:5 final size:5
Alignment explanation
Indices: 11044504--11044535 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
11044494 NNNNNTTGGT
11044504 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
11044536 CCAAGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:11045798 original size:43 final size:43
Alignment explanation
Indices: 11045694--11045980 Score: 314
Period size: 43 Copynumber: 6.7 Consensus size: 43
11045684 TTTTTGCGAG
** *
11045694 AAGCGTCC-CTAAAGGT-TTGTTCTATAGCGGCGTTTGTGG-TA
1 AAGCG-CCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAA
* * *
11045735 AAGCTCCGCTAAAGGTCTTGAGATATAGCGGCATTTGTGGAAA
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAA
* *
11045778 AAGAGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAA
* * * *
11045821 AAGCACCGTTAAAGGTCTTGATCTATAGCGGCGTTTGT-GCAA
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAA
* ** * * *
11045863 AAGTGCCGCTAAAGGTCCCGATCTAGAGCGGCGTTTATGGAAA
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAA
* * * *
11045906 AAGCGCCGCTAAAGGTCCTGATCTGTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAA
*
11045949 AAGCGCCGCTAAAGGTCATG-GTCTATAGCGGC
1 AAGCGCCGCTAAAGGTCTTGAG-CTATAGCGGC
11045981 ATTTATTTCT
Statistics
Matches: 208, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
40 2 0.01
41 12 0.06
42 53 0.25
43 141 0.68
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGAAA
Found at i:11045874 original size:85 final size:86
Alignment explanation
Indices: 11045702--11045980 Score: 323
Period size: 85 Copynumber: 3.3 Consensus size: 86
11045692 AGAAGCGTCC
** * * **
11045702 CTAAAGGT-TTGTTCTATAGCGGCGTTTGT-GGTAAAGCTCCGCTAAAGGTCTTGAGATATAGCG
1 CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGATCTATAGCG
*
11045765 GCATTTGTGGAAAAAGAGCCG
66 GCGTTTGTGGAAAAAGAGCCG
*
11045786 CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCGTTAAAGGTCTTGATCTATAGCG
1 CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGATCTATAGCG
* *
11045851 GCGTTTGT-GCAAAAGTGCCG
66 GCGTTTGTGGAAAAAGAGCCG
** * * * * * * *
11045871 CTAAAGGTCCCGATCTAGAGCGGCGTTTATGGAAAAAGCGCCGCTAAAGGTCCTGATCTGTAGCG
1 CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGATCTATAGCG
* *
11045936 GCGTTTGTGGGAAAAGCGCCG
66 GCGTTTGTGGAAAAAGAGCCG
*
11045957 CTAAAGGTCATG-GTCTATAGCGGC
1 CTAAAGGTCTTGAG-CTATAGCGGC
11045981 ATTTATTTCT
Statistics
Matches: 165, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
84 8 0.05
85 92 0.56
86 65 0.39
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (86 bp):
CTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGATCTATAGCG
GCGTTTGTGGAAAAAGAGCCG
Found at i:11045893 original size:128 final size:128
Alignment explanation
Indices: 11045702--11045980 Score: 373
Period size: 128 Copynumber: 2.2 Consensus size: 128
11045692 AGAAGCGTCC
* ** ** *
11045702 CTAAAGGT-TTGTTCTATAGCGGCGTTTGTGGTAAAGCTCCGCTAAAGGTCTTGAGATATAGCGG
1 CTAAAGGTCTTGATCTATAGCGGCGTTTGTGCAAAAGCTCCGCTAAAGGTCCCGAGATAGAGCGG
* *
11045766 CATTTGTGGAAAAAGAGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCG
66 CATTTATGGAAAAAGAGCCGCTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCG
* **
11045829 TTAAAGGTCTTGATCTATAGCGGCGTTTGTGCAAAAG-TGCCGCTAAAGGTCCCGATCTAGAGCG
1 CTAAAGGTCTTGATCTATAGCGGCGTTTGTGCAAAAGCT-CCGCTAAAGGTCCCGAGATAGAGCG
* * * * *
11045893 GCGTTTATGGAAAAAGCGCCGCTAAAGGTCCTGATCTGTAGCGGCGTTTGTGGGAAAAGCGCCG
65 GCATTTATGGAAAAAGAGCCGCTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCG
* *
11045957 CTAAAGGTCATGGTCTATAGCGGC
1 CTAAAGGTCTTGATCTATAGCGGC
11045981 ATTTATTTCT
Statistics
Matches: 131, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
127 8 0.06
128 123 0.94
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (128 bp):
CTAAAGGTCTTGATCTATAGCGGCGTTTGTGCAAAAGCTCCGCTAAAGGTCCCGAGATAGAGCGG
CATTTATGGAAAAAGAGCCGCTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGGAAAAGCACCG
Found at i:11048456 original size:21 final size:21
Alignment explanation
Indices: 11048430--11048496 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
11048420 AAAATTGACT
*
11048430 GAGAAATTAAGAGGGAATTGA
1 GAGAAATTAAGAGAGAATTGA
*
11048451 GAGAAATTTAAGAGAGATTTGA
1 GAGAAA-TTAAGAGAGAATTGA
* *
11048473 GA-AAATGAGAGAGATAAGTTGA
1 GAGAAATTA-AGAGAGAA-TTGA
11048495 GA
1 GA
11048497 TTGAATTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.05
21 15 0.39
22 21 0.55
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (21 bp):
GAGAAATTAAGAGAGAATTGA
Found at i:11048464 original size:22 final size:22
Alignment explanation
Indices: 11048430--11048478 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
11048420 AAAATTGACT
*
11048430 GAGAAA-TTAAGAGGGAATTGA
1 GAGAAATTTAAGAGAGAATTGA
*
11048451 GAGAAATTTAAGAGAGATTTGA
1 GAGAAATTTAAGAGAGAATTGA
11048473 GA-AAAT
1 GAGAAAT
11048479 GAGAGAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (22 bp):
GAGAAATTTAAGAGAGAATTGA
Found at i:11053030 original size:36 final size:35
Alignment explanation
Indices: 11052948--11053036 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 35
11052938 CAGTATTTAA
*
11052948 TTAATATTAAAAAATATTTTTTTGTACTTTTTAATGATTT
1 TTAA-ATTAAAAAATA---TTTTATACTTTTT-ATGATTT
*
11052988 TTAAATTTAAAAATATTTTATACTTTTT-TGAATTT
1 TTAAATTAAAAAATATTTTATACTTTTTATG-ATTT
11053023 TTAAAATTAAAAAA
1 TT-AAATTAAAAAA
11053037 ATTAATTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
34 2 0.05
35 6 0.14
36 22 0.50
39 10 0.23
40 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (35 bp):
TTAAATTAAAAAATATTTTATACTTTTTATGATTT
Found at i:11053033 original size:35 final size:35
Alignment explanation
Indices: 11052967--11053035 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
11052957 AAAAATATTT
* *
11052967 TTTTGTACTTTTTAATGATTTTTAAATTTAAAAATA
1 TTTTATACTTTTT-ATGATTTTTAAAATTAAAAATA
11053003 TTTTATACTTTTT-TGAATTTTTAAAATTAAAAA
1 TTTTATACTTTTTATG-ATTTTTAAAATTAAAAA
11053036 AATTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 2 0.07
35 16 0.53
36 12 0.40
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (35 bp):
TTTTATACTTTTTATGATTTTTAAAATTAAAAATA
Found at i:11059812 original size:18 final size:17
Alignment explanation
Indices: 11059766--11059816 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
11059756 ACAGCTCATA
*
11059766 CTTTGATGTGCTCGCAG
1 CTTTGATGAGCTCGCAG
*
11059783 CTTTGATGAGCTCGCAT
1 CTTTGATGAGCTCGCAG
*
11059800 CTTTAGGTGAGCTCGCA
1 CTTT-GATGAGCTCGCA
11059817 AGGATAGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 19 0.63
18 11 0.37
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (17 bp):
CTTTGATGAGCTCGCAG
Found at i:11064286 original size:35 final size:35
Alignment explanation
Indices: 11064237--11064307 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
11064227 CAGCTCACAC
* *
11064237 TTTGATGTGCTCGCAACTTGAGTTGAGCTTGCAAG
1 TTTGATGAGCTCGCAACTTGAGGTGAGCTTGCAAG
* * *
11064272 TTTGATGAGTTCGCATCTTTAGGTGAGCTTGCAAG
1 TTTGATGAGCTCGCAACTTGAGGTGAGCTTGCAAG
11064307 T
1 T
11064308 GTAGAGCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.37
Consensus pattern (35 bp):
TTTGATGAGCTCGCAACTTGAGGTGAGCTTGCAAG
Found at i:11064334 original size:18 final size:18
Alignment explanation
Indices: 11064311--11064352 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
11064301 TGCAAGTGTA
*
11064311 GAGCTCACATACTTG-TTT
1 GAGCTCACA-ACTTGAGTT
11064329 GAGCTCACAACTTGAGTT
1 GAGCTCACAACTTGAGTT
11064347 GAGCTC
1 GAGCTC
11064353 GTAGCTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (18 bp):
GAGCTCACAACTTGAGTT
Found at i:11065601 original size:21 final size:21
Alignment explanation
Indices: 11065563--11065602 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11065553 AATCAACATT
* **
11065563 AAAAATGTTGTATTTAGAAGG
1 AAAAATATTGTACGTAGAAGG
11065584 AAAAATATTGTACGTAGAA
1 AAAAATATTGTACGTAGAA
11065603 CACAAACAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (21 bp):
AAAAATATTGTACGTAGAAGG
Found at i:11066144 original size:12 final size:12
Alignment explanation
Indices: 11066096--11066137 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
11066086 GTCCAAATGA
11066096 AAGCGAGGACCC
1 AAGCGAGGACCC
* *
11066108 AAGTGAGGAACC
1 AAGCGAGGACCC
11066120 AAGCGAGGACCC
1 AAGCGAGGACCC
11066132 AAGCGA
1 AAGCGA
11066138 AGGCCCAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.38, C:0.26, G:0.33, T:0.02
Consensus pattern (12 bp):
AAGCGAGGACCC
Found at i:11072414 original size:28 final size:28
Alignment explanation
Indices: 11072372--11072474 Score: 93
Period size: 28 Copynumber: 3.7 Consensus size: 28
11072362 AGATGCAGAA
* *
11072372 TCATATATACAGACTCATAAGTACGGAT
1 TCATATATGCGGACTCATAAGTACGGAT
* * * *
11072400 TCATATATGTGGACTCA-AAGATGCAGAA
1 TCATATATGCGGACTCATAAG-TACGGAT
*
11072428 TCATATATGCGGATTCATAAGTACAGG-T
1 TCATATATGCGGACTCATAAGTAC-GGAT
* *
11072456 TCATAAATGCGGATTCATA
1 TCATATATGCGGACTCATA
11072475 GATATAGATT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
27 3 0.05
28 53 0.88
29 4 0.07
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (28 bp):
TCATATATGCGGACTCATAAGTACGGAT
Found at i:11072426 original size:56 final size:56
Alignment explanation
Indices: 11072348--11072469 Score: 158
Period size: 56 Copynumber: 2.2 Consensus size: 56
11072338 ATACAAAATC
*
11072348 ATATGTGGATCCAGAGATGCAGAATCATATATACAGACTCATAAGTAC-GGATTCAT
1 ATATGTGGATCCAAAGATGCAGAATCATATATACAGACTCATAAGTACAGG-TTCAT
* * *
11072404 ATATGTGGA-CTCAAAGATGCAGAATCATATATGCGGATTCATAAGTACAGGTTCAT
1 ATATGTGGATC-CAAAGATGCAGAATCATATATACAGACTCATAAGTACAGGTTCAT
* *
11072460 AAATGCGGAT
1 ATATGTGGAT
11072470 TCATAGATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
55 1 0.02
56 54 0.95
57 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (56 bp):
ATATGTGGATCCAAAGATGCAGAATCATATATACAGACTCATAAGTACAGGTTCAT
Found at i:11072445 original size:14 final size:14
Alignment explanation
Indices: 11072395--11072474 Score: 56
Period size: 14 Copynumber: 5.7 Consensus size: 14
11072385 CTCATAAGTA
11072395 CGGATTCATATATG
1 CGGATTCATATATG
* * * *
11072409 TGGACTCAAAGATG
1 CGGATTCATATATG
* *
11072423 CAGAATCATATATG
1 CGGATTCATATATG
*
11072437 CGGATTCATA-AGTA
1 CGGATTCATATA-TG
*
11072451 CAGG-TTCATAAATG
1 C-GGATTCATATATG
11072465 CGGATTCATA
1 CGGATTCATA
11072475 GATATAGATT
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
13 3 0.06
14 43 0.88
15 3 0.06
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (14 bp):
CGGATTCATATATG
Found at i:11072486 original size:28 final size:28
Alignment explanation
Indices: 11072386--11072487 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 28
11072376 ATATACAGAC
* * * *
11072386 TCATAAGTACGGATTCATATATGTGGAC
1 TCATAAGTACAGATTCATAAATGCGGAT
* * *
11072414 TCA-AAGATGCAGAATCATATATGCGGAT
1 TCATAAG-TACAGATTCATAAATGCGGAT
*
11072442 TCATAAGTACAGGTTCATAAATGCGGAT
1 TCATAAGTACAGATTCATAAATGCGGAT
*
11072470 TCAT-AGATATAGATTCAT
1 TCATAAG-TACAGATTCAT
11072488 GCGTATGGAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
27 5 0.08
28 52 0.87
29 3 0.05
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (28 bp):
TCATAAGTACAGATTCATAAATGCGGAT
Found at i:11072855 original size:55 final size:55
Alignment explanation
Indices: 11072782--11072955 Score: 348
Period size: 55 Copynumber: 3.2 Consensus size: 55
11072772 GCAAAAAAGG
11072782 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATAT
1 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATAT
11072837 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATAT
1 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATAT
11072892 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATAT
1 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATAT
11072947 GGTCACACG
1 GGTCACACG
11072956 ATCGTGTCAC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 119 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (55 bp):
GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATAT
Found at i:11073000 original size:110 final size:110
Alignment explanation
Indices: 11072782--11073000 Score: 251
Period size: 110 Copynumber: 2.0 Consensus size: 110
11072772 GCAAAAAAGG
*
11072782 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATATGGTCACACGG
1 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATATGGTCACACGA
** * ** * *** *** *
11072847 GCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATAT
66 GCATGTCACAAACCGTGTGAAACATCACCTGAAAATTTAAAATAT
11072892 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATATGGTCACACGA
1 GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATATGGTCACACGA
* * ** *
11072957 TCGTGTCACGGACCGTGTGAAACCTACACCT-AAAATTTAAAATA
66 GCATGTCACAAACCGTGTGAAACAT-CACCTGAAAATTTAAAATA
11073001 CACTACCGTG
Statistics
Matches: 89, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
110 87 0.98
111 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (110 bp):
GGTCACACGGGCATGTCGTAAACCTTGTGTCAGATCGTGTGTGTATTTGAAATATGGTCACACGA
GCATGTCACAAACCGTGTGAAACATCACCTGAAAATTTAAAATAT
Found at i:11074479 original size:36 final size:36
Alignment explanation
Indices: 11074439--11074532 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
11074429 GTGCCCAACT
11074439 TAGTTGGATAAACCAACAATGTTTTACGCCAAGCAG-
1 TAGTTGGATAAACCAACAATGTTTTACGCCAAGC-GC
* * *
11074475 TAGTTGGATAAATCGACAATGTTTTACGCCTAGCGC
1 TAGTTGGATAAACCAACAATGTTTTACGCCAAGCGC
11074511 TAGTTGGATAAACCAACAATGT
1 TAGTTGGATAAACCAACAATGT
11074533 CAAATGTGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
35 1 0.02
36 51 0.98
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (36 bp):
TAGTTGGATAAACCAACAATGTTTTACGCCAAGCGC
Found at i:11076117 original size:37 final size:37
Alignment explanation
Indices: 11076076--11076161 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
11076066 TCTAACGATT
* * * * * *
11076076 TGTCTTTGTTTGAAACACGAGGACAAGTCCAGCGGAC
1 TGTCTTAGCTTGAAACACAAGAAAAAGTCCAGCGAAC
*
11076113 TGTCTTAGCTTGAAACATAAGAAAAAGTCCAGCGAAC
1 TGTCTTAGCTTGAAACACAAGAAAAAGTCCAGCGAAC
*
11076150 TGTCTTACCTTG
1 TGTCTTAGCTTG
11076162 CGTATGTCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (37 bp):
TGTCTTAGCTTGAAACACAAGAAAAAGTCCAGCGAAC
Found at i:11081724 original size:49 final size:49
Alignment explanation
Indices: 11081664--11081762 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
11081654 ACCATTCTTC
11081664 TATTCTCTCATTTCCTCTCTTCATTCTCATACATAGCATCCCATAGTCT
1 TATTCTCTCATTTCCTCTCTTCATTCTCATACATAGCATCCCATAGTCT
* * *
11081713 TATTCTTTCATTTCCTCTCTTCATTCTCATGCATAGCATCTCATAGTCT
1 TATTCTCTCATTTCCTCTCTTCATTCTCATACATAGCATCCCATAGTCT
11081762 T
1 T
11081763 TCTTTTCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.19, C:0.30, G:0.05, T:0.45
Consensus pattern (49 bp):
TATTCTCTCATTTCCTCTCTTCATTCTCATACATAGCATCCCATAGTCT
Found at i:11087517 original size:22 final size:22
Alignment explanation
Indices: 11087491--11087536 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11087481 AGCTTAGCTT
*
11087491 TAGGTTTAGGTTTAG-TTTTCTC
1 TAGGTTT-GCTTTAGATTTTCTC
*
11087513 TAGGTTTTCTTTAGATTTTCTC
1 TAGGTTTGCTTTAGATTTTCTC
11087535 TA
1 TA
11087537 CACTTTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.15, C:0.11, G:0.17, T:0.57
Consensus pattern (22 bp):
TAGGTTTGCTTTAGATTTTCTC
Found at i:11091754 original size:11 final size:11
Alignment explanation
Indices: 11091735--11091819 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
11091725 AATTTTTAAA
11091735 ATTTCTTTATAT
1 ATTT-TTTATAT
*
11091747 ATTTTTTAGA-
1 ATTTTTTATAT
*
11091757 ATTTTTGTAGA-
1 ATTTTT-TATAT
11091768 ATTTTTTATA-
1 ATTTTTTATAT
11091778 ATTTTTTTAAAATAT
1 A-TTTTTT---ATAT
*
11091793 AATTTTTATAT
1 ATTTTTTATAT
* *
11091804 ATTTTATAAAT
1 ATTTTTTATAT
11091815 ATTTT
1 ATTTT
11091820 GAATTTTAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
10 10 0.16
11 38 0.62
12 4 0.07
14 8 0.13
15 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:11091762 original size:10 final size:10
Alignment explanation
Indices: 11091727--11091784 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 10
11091717 AAATTTTTAA
*
11091727 TTTTTAAAAT
1 TTTTTAGAAT
*
11091737 TTCTTTATATAT
1 TT-TTTAGA-AT
11091749 TTTTTAGAAT
1 TTTTTAGAAT
11091759 TTTTGTAGAAT
1 TTTT-TAGAAT
*
11091770 TTTTTATAAT
1 TTTTTAGAAT
11091780 TTTTT
1 TTTTT
11091785 TAAAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 18 0.43
11 20 0.48
12 4 0.10
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (10 bp):
TTTTTAGAAT
Found at i:11091825 original size:18 final size:19
Alignment explanation
Indices: 11091804--11091839 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11091794 ATTTTTATAT
*
11091804 ATTTTATAAA-TATTTTGA
1 ATTTTAAAAATTATTTTGA
11091822 ATTTTAAAAATTATTTTG
1 ATTTTAAAAATTATTTTG
11091840 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTTAAAAATTATTTTGA
Found at i:11091872 original size:50 final size:51
Alignment explanation
Indices: 11091801--11091902 Score: 188
Period size: 50 Copynumber: 2.0 Consensus size: 51
11091791 ATAATTTTTA
11091801 TATATTTTATAAATATTTTGAATTTTAAAAATTATTTTGTTTTTTTTTTTGT
1 TATATTTTAT-AATATTTTGAATTTTAAAAATTATTTTGTTTTTTTTTTTGT
11091853 TATATTTTAT-ATATTTTGAATTTTAAAAATTATTTTGTTTTTTTTTTTGT
1 TATATTTTATAATATTTTGAATTTTAAAAATTATTTTGTTTTTTTTTTTGT
11091903 AATTTTTGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 40 0.80
52 10 0.20
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (51 bp):
TATATTTTATAATATTTTGAATTTTAAAAATTATTTTGTTTTTTTTTTTGT
Found at i:11092384 original size:41 final size:40
Alignment explanation
Indices: 11092265--11092391 Score: 125
Period size: 40 Copynumber: 3.2 Consensus size: 40
11092255 TGGCACCCAG
* * * *
11092265 TGCCTCATCAGATAATTCGAAGTAATAATTTTACACCCAA
1 TGCCTCATCAGATAATCCGAAGTAATAATTTGACACCTAT
* * * * *
11092305 TGTCTCATCGGCTAAACCGAAGT-A-AA-TTGGCACCTAT
1 TGCCTCATCAGATAATCCGAAGTAATAATTTGACACCTAT
*
11092342 TGCCTCATCAAATATATCCGAAGTAATAATTTGACACCTAT
1 TGCCTCATCAGATA-ATCCGAAGTAATAATTTGACACCTAT
*
11092383 TGTCTCATC
1 TGCCTCATC
11092392 GACTCGAAGT
Statistics
Matches: 67, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
37 17 0.25
38 10 0.15
39 2 0.03
40 20 0.30
41 18 0.27
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.31
Consensus pattern (40 bp):
TGCCTCATCAGATAATCCGAAGTAATAATTTGACACCTAT
Found at i:11094344 original size:12 final size:12
Alignment explanation
Indices: 11094327--11094357 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
11094317 TAATGTATAT
11094327 GGTAAGTGTTAA
1 GGTAAGTGTTAA
*
11094339 GGTAAGTGTTGA
1 GGTAAGTGTTAA
11094351 GGTAAGT
1 GGTAAGT
11094358 AATTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.39, T:0.32
Consensus pattern (12 bp):
GGTAAGTGTTAA
Found at i:11099365 original size:11 final size:11
Alignment explanation
Indices: 11099349--11099373 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11099339 CATAGATGCA
11099349 GAATCACATAT
1 GAATCACATAT
11099360 GAATCACATAT
1 GAATCACATAT
11099371 GAA
1 GAA
11099374 GATTCATAAG
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:0.16, G:0.12, T:0.24
Consensus pattern (11 bp):
GAATCACATAT
Found at i:11099392 original size:14 final size:14
Alignment explanation
Indices: 11099373--11099478 Score: 56
Period size: 14 Copynumber: 7.6 Consensus size: 14
11099363 TCACATATGA
11099373 AGATTCATA-AGTAC
1 AGATTCATATA-TAC
*
11099387 AGATTCATATATGC
1 AGATTCATATATAC
* *
11099401 AGATTCATAGATGC
1 AGATTCATATATAC
* * **
11099415 AGAATCACATATGG
1 AGATTCATATATAC
*
11099429 GGATTCATA-AGTAC
1 AGATTCATATA-TAC
*
11099443 -GAATTCATATATCC
1 AG-ATTCATATATAC
* *
11099457 AGATTTATAGATAC
1 AGATTCATATATAC
*
11099471 AAATTCAT
1 AGATTCAT
11099479 GCTTACGGAC
Statistics
Matches: 70, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
13 2 0.03
14 65 0.93
15 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (14 bp):
AGATTCATATATAC
Found at i:11099404 original size:28 final size:28
Alignment explanation
Indices: 11099367--11099478 Score: 95
Period size: 28 Copynumber: 4.0 Consensus size: 28
11099357 TATGAATCAC
*
11099367 ATATGAAGATTCATA-AGTACAGATTCAT
1 ATATGCAGATTCATAGA-TACAGATTCAT
* * *
11099395 ATATGCAGATTCATAGATGCAGAATCAC
1 ATATGCAGATTCATAGATACAGATTCAT
**
11099423 ATATGGGGATTCATA-AGTAC-GAATTCAT
1 ATATGCAGATTCATAGA-TACAG-ATTCAT
* * *
11099451 ATATCCAGATTTATAGATACAAATTCAT
1 ATATGCAGATTCATAGATACAGATTCAT
11099479 GCTTACGGAC
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
27 2 0.03
28 61 0.94
29 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (28 bp):
ATATGCAGATTCATAGATACAGATTCAT
Found at i:11099434 original size:56 final size:56
Alignment explanation
Indices: 11099360--11099468 Score: 166
Period size: 56 Copynumber: 1.9 Consensus size: 56
11099350 AATCACATAT
*
11099360 GAATCACATATGAAGATTCATAAGTAC-AGATTCATATATGCAGATTCATAGATGCA
1 GAATCACATATGAAGATTCATAAGTACGA-ATTCATATATCCAGATTCATAGATGCA
** *
11099416 GAATCACATATGGGGATTCATAAGTACGAATTCATATATCCAGATTTATAGAT
1 GAATCACATATGAAGATTCATAAGTACGAATTCATATATCCAGATTCATAGAT
11099469 ACAAATTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 47 0.98
57 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (56 bp):
GAATCACATATGAAGATTCATAAGTACGAATTCATATATCCAGATTCATAGATGCA
Found at i:11099671 original size:37 final size:37
Alignment explanation
Indices: 11099592--11099676 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
11099582 CCAACGGATG
* *
11099592 ATCTTAGCTTGAAACATAAGGATAAGTCCAGCAGACT
1 ATCTTAGCTTGAAACACAAGGACAAGTCCAGCAGACT
* * * *
11099629 GTCTTAGCTTGAAACACGAGGACAAGTCCAGTAGATT
1 ATCTTAGCTTGAAACACAAGGACAAGTCCAGCAGACT
*
11099666 ATCTTACCTTG
1 ATCTTAGCTTG
11099677 CGTATGCCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (37 bp):
ATCTTAGCTTGAAACACAAGGACAAGTCCAGCAGACT
Found at i:11100658 original size:43 final size:43
Alignment explanation
Indices: 11100609--11100694 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
11100599 CTTACCCAAA
*
11100609 ATCCACTGTCTTCTGTTTCTTGCTTCTACCTTTCTTCTCCACT
1 ATCCACTGTCTTCTATTTCTTGCTTCTACCTTTCTTCTCCACT
11100652 ATCCACTGTCTTCTATTTCTTGCTTCTACCTTTCTTCTCCACT
1 ATCCACTGTCTTCTATTTCTTGCTTCTACCTTTCTTCTCCACT
11100695 CTCCTCGCCG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.10, C:0.35, G:0.06, T:0.49
Consensus pattern (43 bp):
ATCCACTGTCTTCTATTTCTTGCTTCTACCTTTCTTCTCCACT
Found at i:11102637 original size:23 final size:23
Alignment explanation
Indices: 11102578--11102638 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
11102568 TTGTTCAACT
**
11102578 CAGGAACATGGCCACAATAAAAA
1 CAGGAACATGGCCTTAATAAAAA
11102601 CAGGAACATGGCCTTAATAAAAA
1 CAGGAACATGGCCTTAATAAAAA
11102624 CAGGAACATGGCCTT
1 CAGGAACATGGCCTT
11102639 CATTTGTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.20, T:0.15
Consensus pattern (23 bp):
CAGGAACATGGCCTTAATAAAAA
Found at i:11103691 original size:92 final size:91
Alignment explanation
Indices: 11103534--11103742 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
11103524 TTGATTTTAG
* * *
11103534 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
11103599 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
11103626 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
11103690 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
11103718 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
11103743 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:11103705 original size:24 final size:25
Alignment explanation
Indices: 11103670--11103717 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
11103660 TTATGAAATT
11103670 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
11103694 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
11103718 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:11103913 original size:16 final size:16
Alignment explanation
Indices: 11103892--11103933 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
11103882 TTATTAAATT
*
11103892 ATATATTTTAATTATA
1 ATATATTTTAATAATA
11103908 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
11103923 AT-TATGTTTAA
1 ATATAT-TTTAA
11103934 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:11103918 original size:15 final size:15
Alignment explanation
Indices: 11103883--11103924 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11103873 TTAAGAATTT
*
11103883 TATTAAATTAT-ATA
1 TATTTAATTATAATA
11103897 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
11103911 TATTTAATAATAAT
1 TATTTAATTATAAT
11103925 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:11112473 original size:24 final size:21
Alignment explanation
Indices: 11112429--11112474 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
11112419 GATCTTTCTT
*
11112429 CTTCCTCTTTCACTTTGGATC
1 CTTCCTCTTTCACTTTAGATC
11112450 CTTCCTCATTTCCACGTTTAGATC
1 CTTCCTC-TTT-CAC-TTTAGATC
11112474 C
1 C
11112475 ATCTCCTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 3 0.14
24 8 0.38
ACGTcount: A:0.13, C:0.35, G:0.09, T:0.43
Consensus pattern (21 bp):
CTTCCTCTTTCACTTTAGATC
Found at i:11122430 original size:2 final size:2
Alignment explanation
Indices: 11122423--11122449 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11122413 TTTAACTTTA
11122423 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11122450 AACTATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11122480 original size:17 final size:15
Alignment explanation
Indices: 11122460--11122504 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
11122450 AACTATTAAC
*
11122460 ATATTATATAGTATGT
1 ATATAATATAGTAT-T
*
11122476 AATATAATATAGCATT
1 -ATATAATATAGTATT
11122492 ATATAATATAGTA
1 ATATAATATAGTA
11122505 GGAGGGCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
17 12 0.48
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (15 bp):
ATATAATATAGTATT
Found at i:11122983 original size:2 final size:2
Alignment explanation
Indices: 11122976--11123007 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11122966 CTAAAACATA
11122976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11123008 CTTAATAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11124212 original size:20 final size:20
Alignment explanation
Indices: 11124187--11124239 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
11124177 TTTTTTCATA
11124187 TTTTAAATAAAAACATAATT
1 TTTTAAATAAAAACATAATT
** *
11124207 TTTTAAA-AAAATGATGATT
1 TTTTAAATAAAAACATAATT
11124226 TTTTAAAATAAAAA
1 TTTT-AAATAAAAA
11124240 ATTATGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.48
20 10 0.37
21 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
TTTTAAATAAAAACATAATT
Found at i:11124295 original size:19 final size:19
Alignment explanation
Indices: 11124266--11124314 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
11124256 AAAACTATTT
11124266 AAAATTC-AAAAA-ACAAA
1 AAAATTCTAAAAATACAAA
* *
11124283 AAATATTTTAAAAATATAAA
1 AAA-ATTCTAAAAATACAAA
11124303 AAAATTCTAAAA
1 AAAATTCTAAAA
11124315 TTCAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 13 0.50
20 7 0.27
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATTCTAAAAATACAAA
Found at i:11125297 original size:21 final size:20
Alignment explanation
Indices: 11125261--11125306 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
11125251 TTTTAGAAAT
*
11125261 TTTTTATATTTTAAAATT-A
1 TTTTTATATTTAAAAATTAA
11125280 TTTTTATATTTAAAAAAATTAA
1 TTTTTATATTT--AAAAATTAA
11125302 TTTTT
1 TTTTT
11125307 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
21 6 0.26
22 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTATATTTAAAAATTAA
Found at i:11129075 original size:90 final size:90
Alignment explanation
Indices: 11128919--11129097 Score: 315
Period size: 90 Copynumber: 2.0 Consensus size: 90
11128909 ATATGCTTGC
* * *
11128919 CCAATTCGAAAGAAAATTAGTAATAACATATCAATTATTTTCTTTCACATTAAACATATAACAGA
1 CCAATCCGAAAGAAAATTAGTAACAACATATCAATTATTTTCTTTCACATTAAACAAATAACAGA
11128984 TGTTCACGAAACTAACATGCAATTT
66 TGTTCACGAAACTAACATGCAATTT
11129009 CCAATCCGAAAGAAAATTAGTAACAACATATCAATTATTTTCTTTCACATTAAACAAATATA-AG
1 CCAATCCGAAAGAAAATTAGTAACAACATATCAATTATTTTCTTTCACATTAAACAAATA-ACAG
11129073 ATGTTCACGAAACTAACATGCAATT
65 ATGTTCACGAAACTAACATGCAATT
11129098 AGTAATTTTC
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
90 84 0.99
91 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (90 bp):
CCAATCCGAAAGAAAATTAGTAACAACATATCAATTATTTTCTTTCACATTAAACAAATAACAGA
TGTTCACGAAACTAACATGCAATTT
Found at i:11133302 original size:22 final size:22
Alignment explanation
Indices: 11133277--11133322 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11133267 GTTTTGAGAA
*
11133277 TACT-CAAATACAGTAACAATGC
1 TACTACAAATACA-TAACAAAGC
*
11133299 TACTACAAATTCATAACAAAGC
1 TACTACAAATACATAACAAAGC
11133321 TA
1 TA
11133323 GTTTACCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.24
Consensus pattern (22 bp):
TACTACAAATACATAACAAAGC
Found at i:11136546 original size:20 final size:20
Alignment explanation
Indices: 11136523--11136588 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
11136513 GTAACTCTAT
11136523 ACAGAGGCACTGTAGTGCAA
1 ACAGAGGCACTGTAGTGCAA
*
11136543 ACAGAGGCA-TGATTGTGCAA
1 ACAGAGGCACTG-TAGTGCAA
** * *
11136563 TTAGAGGCACAGAAGTGCAA
1 ACAGAGGCACTGTAGTGCAA
11136583 ACAGAG
1 ACAGAG
11136589 ACACCGTAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.06
20 33 0.92
21 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (20 bp):
ACAGAGGCACTGTAGTGCAA
Found at i:11139707 original size:11 final size:11
Alignment explanation
Indices: 11139683--11139759 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
11139673 ATTTTTTAAA
*
11139683 TTTT-AAATAA
1 TTTTAAAATAT
11139693 TTTTAAAATAT
1 TTTTAAAATAT
11139704 TTTTAAAATACT
1 TTTTAAAATA-T
* *
11139716 TTTT-TATTAT
1 TTTTAAAATAT
*
11139726 TTTT----TAA
1 TTTTAAAATAT
11139733 TTTTAAAATAT
1 TTTTAAAATAT
11139744 TTTTAAAATACT
1 TTTTAAAATA-T
11139756 TTTT
1 TTTT
11139760 TTAATTTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
7 6 0.11
10 9 0.16
11 30 0.55
12 10 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:11139734 original size:40 final size:39
Alignment explanation
Indices: 11139690--11139768 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
11139680 AAATTTTAAA
*
11139690 TAATTTTAAAATATTTTTAAAATACTTTTTTATTATTTTT
1 TAATTTTAAAATATTTTTAAAATACTTTTTT-TAATTTTT
11139730 TAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTT
1 TAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTT
11139769 AAAATAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 7 0.18
40 31 0.82
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
TAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTT
Found at i:11139780 original size:21 final size:21
Alignment explanation
Indices: 11139742--11139781 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11139732 ATTTTAAAAT
**
11139742 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
11139763 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
11139782 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:11139788 original size:22 final size:21
Alignment explanation
Indices: 11139741--11139799 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
11139731 AATTTTAAAA
* *
11139741 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
11139761 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
11139784 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
11139800 GGGCTGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:11140127 original size:26 final size:26
Alignment explanation
Indices: 11140072--11140147 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
11140062 TCTCATCCCT
* **
11140072 ATTTTACCC-TCAACAAAATTTTGATG
1 ATTTTACCCAT-AATAAAATTTTGACA
**
11140098 ATTTTACCCATTGTAAAATTTTGACA
1 ATTTTACCCATAATAAAATTTTGACA
* *
11140124 ATTTTGCCCCTAATAAAATTTTGA
1 ATTTTACCCATAATAAAATTTTGA
11140148 GAAAATATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (26 bp):
ATTTTACCCATAATAAAATTTTGACA
Found at i:11140331 original size:18 final size:18
Alignment explanation
Indices: 11140310--11140347 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
11140300 ATTTTCTTTA
11140310 TTATTTCCATTTCCAGTT
1 TTATTTCCATTTCCAGTT
*
11140328 TTATTTCTATTTCCAGTT
1 TTATTTCCATTTCCAGTT
11140346 TT
1 TT
11140348 GGAAACTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.61
Consensus pattern (18 bp):
TTATTTCCATTTCCAGTT
Found at i:11142120 original size:17 final size:17
Alignment explanation
Indices: 11142098--11142135 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
11142088 CTAGGCAATC
*
11142098 CTATTCGTCAGGTAATT
1 CTATTCGTCAAGTAATT
11142115 CTATTCGTCAAGTAATT
1 CTATTCGTCAAGTAATT
11142132 CTAT
1 CTAT
11142136 CCGCCAGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (17 bp):
CTATTCGTCAAGTAATT
Found at i:11142152 original size:17 final size:17
Alignment explanation
Indices: 11142082--11142184 Score: 62
Period size: 17 Copynumber: 6.1 Consensus size: 17
11142072 TTATGAATCG
* *
11142082 TATCCGCTAGGCAATCC
1 TATCCGCCAGGCAATAC
* * * *
11142099 TATTCGTCAGGTAATTC
1 TATCCGCCAGGCAATAC
* * * * *
11142116 TATTCGTCAAGTAATTC
1 TATCCGCCAGGCAATAC
11142133 TATCCGCCAGGCAATAC
1 TATCCGCCAGGCAATAC
***
11142150 TATTTTCCAGGCAATAC
1 TATCCGCCAGGCAATAC
* *
11142167 TATCTGCCAGGCGATAC
1 TATCCGCCAGGCAATAC
11142184 T
1 T
11142185 TATATGCCAC
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 69 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (17 bp):
TATCCGCCAGGCAATAC
Found at i:11150447 original size:40 final size:40
Alignment explanation
Indices: 11150392--11150467 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
11150382 ATACACATGT
*
11150392 ACTAATAATCGTGTAACATTTGGCCATCATTCTAACACGA
1 ACTAATAATCGTGTAACATTTGACCATCATTCTAACACGA
11150432 ACTAATAATCGTGTAACATTTGACCATCATTCTAAC
1 ACTAATAATCGTGTAACATTTGACCATCATTCTAAC
11150468 TTAATTTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (40 bp):
ACTAATAATCGTGTAACATTTGACCATCATTCTAACACGA
Found at i:11152191 original size:15 final size:16
Alignment explanation
Indices: 11152171--11152200 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11152161 TAATTAAATA
11152171 TAATT-AATTATTTTT
1 TAATTAAATTATTTTT
11152186 TAATTAAATTATTTT
1 TAATTAAATTATTTT
11152201 CTCAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTAAATTATTTTT
Found at i:11158658 original size:24 final size:24
Alignment explanation
Indices: 11158626--11158674 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11158616 TTAGTTACGA
11158626 TATATATAACAAAAGTCGTCTCGG
1 TATATATAACAAAAGTCGTCTCGG
11158650 TATATATAACAAAAGTCGTCTCGG
1 TATATATAACAAAAGTCGTCTCGG
11158674 T
1 T
11158675 TCTATGTTAA
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:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (24 bp):
TATATATAACAAAAGTCGTCTCGG
Found at i:11160290 original size:26 final size:25
Alignment explanation
Indices: 11160255--11160303 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
11160245 GCCTAAACCT
11160255 CTACTCTAAATTTTGAGTGTAAGGG
1 CTACTCTAAATTTTGAGTGTAAGGG
*
11160280 CTACTACTAAATTTTGGGTGTAAG
1 CTACT-CTAAATTTTGAGTGTAAG
11160304 CTTTCTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (25 bp):
CTACTCTAAATTTTGAGTGTAAGGG
Found at i:11169007 original size:11 final size:11
Alignment explanation
Indices: 11168991--11169015 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11168981 GCTCATTTCC
11168991 AACCTTAATAT
1 AACCTTAATAT
11169002 AACCTTAATAT
1 AACCTTAATAT
11169013 AAC
1 AAC
11169016 TAGGGGGTTG
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:0.20, G:0.00, T:0.32
Consensus pattern (11 bp):
AACCTTAATAT
Found at i:11170801 original size:233 final size:233
Alignment explanation
Indices: 11170392--11170857 Score: 905
Period size: 233 Copynumber: 2.0 Consensus size: 233
11170382 CAAATCAAAC
11170392 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAACAGTAAACAAATTGA
1 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAACAGTAAACAAATTGA
11170457 ATCTTCAGGGACTAATCGATAATTTTTGTTTTTCCTTGATTATCTCCAATTTGATTCAATTCTTG
66 ATCTTCAGGGACTAATCGATAATTTTTGTTTTTCCTTGATTATCTCCAATTTGATTCAATTCTTG
*
11170522 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAACCTTTTTTATGTTATGCCATGATATTT
131 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAACATTTTTTATGTTATGCCATGATATTT
11170587 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
196 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
11170625 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAACAGTAAACAAATTGA
1 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAACAGTAAACAAATTGA
*
11170690 ATCTTCAGGGACTAATCGATTATTTTTGTTTTTCCTTGATTATCTCCAATTTGATTCAATTCTTG
66 ATCTTCAGGGACTAATCGATAATTTTTGTTTTTCCTTGATTATCTCCAATTTGATTCAATTCTTG
*
11170755 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAATATTTTTTATGTTATGCCATGATATTT
131 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAACATTTTTTATGTTATGCCATGATATTT
11170820 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
196 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
11170858 TTTTGCATTT
Statistics
Matches: 230, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
233 230 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (233 bp):
ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAACAGTAAACAAATTGA
ATCTTCAGGGACTAATCGATAATTTTTGTTTTTCCTTGATTATCTCCAATTTGATTCAATTCTTG
ATCTAATTAATTATTTTAAATAATTTATCAATACCAAACATTTTTTATGTTATGCCATGATATTT
TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
Found at i:11171355 original size:2 final size:2
Alignment explanation
Indices: 11171348--11171387 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
11171338 ACATGCCTTT
11171348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11171388 GGTTACAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11174966 original size:50 final size:50
Alignment explanation
Indices: 11174867--11175056 Score: 173
Period size: 50 Copynumber: 3.7 Consensus size: 50
11174857 AAAGAGATCT
* * ** *
11174867 CATGTAAGACCATGTCTAGGACATGACATTGGTATCATTGAGATTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGG---CACCGAG---ATGAGAGGTCC
* * *
11174923 CATGTAAGAACATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * **
11174973 CCCGTAAGACCATGTGTGGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* *
11175023 CATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
11175057 GTACAAGAAA
Statistics
Matches: 112, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 78 0.70
53 5 0.04
56 29 0.26
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:11182728 original size:50 final size:50
Alignment explanation
Indices: 11182667--11182811 Score: 173
Period size: 50 Copynumber: 2.9 Consensus size: 50
11182657 CATTGAGATT
* * *
11182667 ATGAGAGGTCCCATGTAAGAACATGTCTAGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * * *
11182717 ATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATGGGCACTGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * *
11182767 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
11182812 GTACAAGAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:11191650 original size:12 final size:12
Alignment explanation
Indices: 11191633--11191658 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11191623 AATGAGACCA
11191633 TTGAGTTGGAAT
1 TTGAGTTGGAAT
11191645 TTGAGTTGGAAT
1 TTGAGTTGGAAT
11191657 TT
1 TT
11191659 ATAAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (12 bp):
TTGAGTTGGAAT
Found at i:11191965 original size:26 final size:26
Alignment explanation
Indices: 11191936--11191988 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
11191926 TAAAAAAAGT
11191936 TCCACGTCATTTACGAAAATAAATTA
1 TCCACGTCATTTACGAAAATAAATTA
* *
11191962 TCCATGTCATTTACGAAACTAAATTA
1 TCCACGTCATTTACGAAAATAAATTA
11191988 T
1 T
11191989 GTTATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (26 bp):
TCCACGTCATTTACGAAAATAAATTA
Found at i:11192801 original size:14 final size:14
Alignment explanation
Indices: 11192782--11192815 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
11192772 TTGACTTTTT
11192782 TTCTAATGATACTA
1 TTCTAATGATACTA
11192796 TTCTAATGATACTA
1 TTCTAATGATACTA
11192810 TTCTAA
1 TTCTAA
11192816 CATGTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (14 bp):
TTCTAATGATACTA
Found at i:11193473 original size:24 final size:24
Alignment explanation
Indices: 11193432--11193478 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11193422 TTAGGGCATA
*
11193432 CGAGCCCGACCCTAAACCCGAGCT
1 CGAGCCCAACCCTAAACCCGAGCT
* *
11193456 CGAGCCCAACCTTGAACCCGAGC
1 CGAGCCCAACCCTAAACCCGAGC
11193479 CAAAGCTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.45, G:0.21, T:0.09
Consensus pattern (24 bp):
CGAGCCCAACCCTAAACCCGAGCT
Found at i:11193663 original size:33 final size:33
Alignment explanation
Indices: 11193626--11193700 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
11193616 CATAGTACAT
* * *
11193626 CACTCCTTCAAGCCCGTATCTACCGCATTACTC
1 CACTCCTCCAAGCCCGTATCCACCGCAATACTC
** *
11193659 CACTCCTCCTCGCTCGTATCCACCGCAATACTC
1 CACTCCTCCAAGCCCGTATCCACCGCAATACTC
11193692 CACTCCTCC
1 CACTCCTCC
11193701 CGGCTCAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.19, C:0.48, G:0.08, T:0.25
Consensus pattern (33 bp):
CACTCCTCCAAGCCCGTATCCACCGCAATACTC
Found at i:11194016 original size:49 final size:49
Alignment explanation
Indices: 11193963--11194316 Score: 534
Period size: 49 Copynumber: 7.3 Consensus size: 49
11193953 GTATTTATTT
* * *
11193963 AATTAGATTA-ATTGCAATATTAAAACTTGGAACAAACTTTGTGGTCATA
1 AATTAGA-TACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
* * *
11194012 AATTAGATACATTACAACATTAAAACTTAGAAAAAACTTTGTGACCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
11194061 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
*
11194110 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGCTCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
* * *
11194159 AATTAGATATATTACAACATTAAAACTTGAAACAAACTTTGTAAT-ATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
11194207 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
* ** * *
11194256 AATTAGATACATTGCAACATTAAAACGAGGAACAAACTTTGTAAT-TTA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
*
11194304 AATTAGGTACATT
1 AATTAGATACATT
11194317 GGATTACATA
Statistics
Matches: 280, Mismatches: 23, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
48 61 0.22
49 219 0.78
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (49 bp):
AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
Found at i:11194274 original size:146 final size:147
Alignment explanation
Indices: 11193963--11194297 Score: 559
Period size: 146 Copynumber: 2.3 Consensus size: 147
11193953 GTATTTATTT
* *
11193963 AATTAGATTA-ATTGCAATATTAAAACTTGGAACAAACTTTGTGGTCATAAATTAGATACATTAC
1 AATTAGA-TACATTGCAACATTAAAACTTGGAACAAACTTTGTGCTCATAAATTAGATACATTAC
*
11194027 AACATTAAAACTTAGAAAAAACTTTGTGACCATAAATTAGATACATTACAACATTAAAACTTGGA
65 AACATTAAAACTTAGAAAAAACTTTGTGAACATAAATTAGATACATTACAACATTAAAACTTGGA
11194092 ACAAACTTTGTGATCATA
130 ACAAACTTTGTGATCATA
* *
11194110 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGCTCATAAATTAGATATATTACA
1 AATTAGATACATTGCAACATTAAAACTTGGAACAAACTTTGTGCTCATAAATTAGATACATTACA
*
11194175 ACATTAAAACTT-GAAACAAACTTTGT-AATATAAATTAGATACATTACAACATTAAAACTTGGA
66 ACATTAAAACTTAGAAA-AAACTTTGTGAACATAAATTAGATACATTACAACATTAAAACTTGGA
11194238 ACAAACTTTGTGATCATA
130 ACAAACTTTGTGATCATA
**
11194256 AATTAGATACATTGCAACATTAAAACGAGGAACAAACTTTGT
1 AATTAGATACATTGCAACATTAAAACTTGGAACAAACTTTGT
11194298 AATTTAAATT
Statistics
Matches: 177, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
146 98 0.55
147 79 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (147 bp):
AATTAGATACATTGCAACATTAAAACTTGGAACAAACTTTGTGCTCATAAATTAGATACATTACA
ACATTAAAACTTAGAAAAAACTTTGTGAACATAAATTAGATACATTACAACATTAAAACTTGGAA
CAAACTTTGTGATCATA
Found at i:11210841 original size:30 final size:31
Alignment explanation
Indices: 11210798--11210863 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
11210788 TCTAAACTTT
* * *
11210798 AATTTGATTAATTT-TAGTTTTGTATTTTTTA
1 AATTTGATCAATTTAT-GTTTTATAGTTTTTA
*
11210829 AATTTG-TCAATTTATGTTTTATAGTTTTTG
1 AATTTGATCAATTTATGTTTTATAGTTTTTA
11210859 AATTT
1 AATTT
11210864 TAAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.62
Consensus pattern (31 bp):
AATTTGATCAATTTATGTTTTATAGTTTTTA
Found at i:11228480 original size:23 final size:24
Alignment explanation
Indices: 11228420--11228482 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
11228410 TCTACTCACT
11228420 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAGAACAATTTCCAGC
*
11228444 AGAC-TATCAA-AACAATTTCCAG-
1 A-ACAAATCAAGAACAATTTCCAGC
11228466 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
11228483 ATCAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 18 0.53
24 6 0.18
25 2 0.06
ACGTcount: A:0.52, C:0.22, G:0.08, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCCAGC
Found at i:11228491 original size:22 final size:22
Alignment explanation
Indices: 11228449--11228494 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11228439 CCAGCAGACT
* *
11228449 ATCAAAACAATTTCCAGAACAA
1 ATCAAAACAATATCCAAAACAA
11228471 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
11228493 AT
1 AT
11228495 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:11236095 original size:43 final size:42
Alignment explanation
Indices: 11236029--11236161 Score: 117
Period size: 43 Copynumber: 3.1 Consensus size: 42
11236019 TATCGTAACC
* * * *
11236029 ATGCC-ATATCCCAGCTATAGTCTTACATGTAATCTCGTATCG
1 ATGCCAATAGCCCAGCCATGGTCTTACATG-AATCTCATATCG
* * *
11236071 ATGCCAATAGCCCAGCCATGGTCTTACACGAAATCACATACCG
1 ATGCCAATAGCCCAGCCATGGTCTTACATG-AATCTCATATCG
* * *
11236114 ATGCTAAT-GTACCAGACATGGTCTTACATGAATTCTCATATCG
1 ATGCCAATAG-CCCAGCCATGGTCTTACATGAA-TCTCATATCG
*
11236157 TTGCC
1 ATGCC
11236162 CTATCCTAGA
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
42 8 0.11
43 64 0.89
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGCCAATAGCCCAGCCATGGTCTTACATGAATCTCATATCG
Found at i:11240819 original size:44 final size:45
Alignment explanation
Indices: 11240756--11240889 Score: 107
Period size: 44 Copynumber: 3.0 Consensus size: 45
11240746 GATCTACTAT
*
11240756 ATTGTAA-CTTCAGAGAGATAAGATCCT-TTATTTTAATCTGCTCC
1 ATTGTAATCTCCAG-GAGATAAGATCCTATTATTTTAATCTGCTCC
* * * *
11240800 ATTGTAATCTCCAGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ATTGTAATCTCCAGGAGATAAGATCCTATTA-TTTTAATCTGCTCC
** * * * *
11240844 GCTGTAATCTCAAGGAGATAAGA-CCTGTTATCTTTAACCAGCTCC
1 ATTGTAATCTCCAGGAGATAAGATCCTATTAT-TTTAATCTGCTCC
11240889 A
1 A
11240890 CTGCAACCGA
Statistics
Matches: 68, Mismatches: 16, Indels: 11
0.72 0.17 0.12
Matches are distributed among these distances:
42 1 0.01
43 2 0.03
44 47 0.69
45 18 0.26
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
ATTGTAATCTCCAGGAGATAAGATCCTATTATTTTAATCTGCTCC
Found at i:11241259 original size:44 final size:44
Alignment explanation
Indices: 11241209--11241346 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 44
11241199 TAATGCGGGA
11241209 AGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
* * * * * **** *
11241253 AGGCAAGGCTTTG-T-T-TTTGATCTGCTTTGTTGTCAATGCG--GG
1 AGGCAA-GATCTGCTATCTTTAACCAGCTCCACTG-CAA-CCGATGG
11241295 AAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
1 -AGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
11241340 AGGCAAG
1 AGGCAAG
11241347 GCTTTGTTTT
Statistics
Matches: 65, Mismatches: 20, Indels: 18
0.63 0.19 0.17
Matches are distributed among these distances:
42 16 0.25
43 13 0.20
44 20 0.31
45 16 0.25
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
Found at i:11241299 original size:176 final size:173
Alignment explanation
Indices: 11240863--11241362 Score: 811
Period size: 176 Copynumber: 2.9 Consensus size: 173
11240853 TCAAGGAGAT
* *
11240863 AAGACCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
11240928 TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
66 TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
* * *
11240993 TAAGGCTTTATTTTCGATCTACTTCGCTGTTAATGCAGGAAGGC
131 -CAGGCTTTGTTTTCAATCTACTTCGCTGTTAATGCAGGAAGGC
11241037 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
11241102 TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGATGG
66 TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACC---GATGG
* * * * *
11241167 AGGCAGGCTTTGTTTTTAATCTGCTTTGTTGTTAATGCGGGAAGGC
128 AGGCAGGCTTTGTTTTCAATCTACTTCGCTGTTAATGCAGGAAGGC
** *
11241213 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
* *
11241278 TTTGTTGTCAATGCGGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
66 TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
*
11241343 CAAGGCTTTGTTTTCGATCT
131 C-AGGCTTTGTTTTCAATCT
11241363 TCACTGATCT
Statistics
Matches: 305, Mismatches: 17, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
173 9 0.03
174 136 0.45
176 152 0.50
177 8 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (173 bp):
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
CAGGCTTTGTTTTCAATCTACTTCGCTGTTAATGCAGGAAGGC
Found at i:11241337 original size:263 final size:261
Alignment explanation
Indices: 11240863--11241356 Score: 837
Period size: 263 Copynumber: 1.9 Consensus size: 261
11240853 TCAAGGAGAT
* *
11240863 AAGACCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
1 AAGACCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGC
11240928 TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
66 TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
* *
11240993 TAAGGCTTTATTTTCGATCTACTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCA
131 CAAGGCTTTATTTTCGATCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCA
11241058 GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGTTTTGTTGTTAATGCAGGAAGG
196 GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGTTTTGTTGTTAATGCAGGAAGG
11241123 C
261 C
* *
11241124 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGATGGAGGC-AGGCTTTGTTTTTAATC
1 AAGACCTGCTATCTTTAACCAGCTCCACTGCAACC---GATGGAGGCAAGGCTTTGTTTTAAATC
*
11241188 TGCTTTGTTGTTAATGCGGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
63 TGCTTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
* * * * * *
11241253 AGGCAAGGCTTTGTTTTTGATCTGCTTTGTTGTCAATGCGGGAAGGCAAGATCTGCTATCTTTAA
128 AGGCAAGGCTTTATTTTCGATCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAA
11241318 CCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
193 CCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
11241357 CGATCTTCAC
Statistics
Matches: 217, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
261 33 0.15
263 175 0.81
264 9 0.04
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (261 bp):
AAGACCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGC
TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
CAAGGCTTTATTTTCGATCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCA
GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGTTTTGTTGTTAATGCAGGAAGG
C
Found at i:11241362 original size:87 final size:87
Alignment explanation
Indices: 11240863--11241356 Score: 801
Period size: 87 Copynumber: 5.7 Consensus size: 87
11240853 TCAAGGAGAT
* * *
11240863 AAGACCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGC
11240928 TTTGTTGTTAATGCAGGAAGGC
66 TTTGTTGTTAATGCAGGAAGGC
* * ** *
11240950 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGTAAGGCTTTATTTTCGATCTAC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGC
* *
11241015 TTCGCTGTTAATGCAGGAAGGC
66 TTTGTTGTTAATGCAGGAAGGC
*
11241037 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGC
11241102 TTTGTTGTTAATGCAGGAAGGC
66 TTTGTTGTTAATGCAGGAAGGC
*
11241124 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGATGGAGGC-AGGCTTTGTTTTTAATC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACC---GATGGAGGCAAGGCTTTGTTTTAAATC
*
11241188 TGCTTTGTTGTTAATGCGGGAAGGC
63 TGCTTTGTTGTTAATGCAGGAAGGC
**
11241213 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGC
* *
11241278 TTTGTTGTCAATGCGGGAAGGC
66 TTTGTTGTTAATGCAGGAAGGC
11241300 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
11241357 CGATCTTCAC
Statistics
Matches: 380, Mismatches: 23, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
86 9 0.02
87 288 0.76
89 74 0.19
90 9 0.02
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (87 bp):
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTAAATCTGC
TTTGTTGTTAATGCAGGAAGGC
Found at i:11242563 original size:7 final size:7
Alignment explanation
Indices: 11242551--11242602 Score: 72
Period size: 7 Copynumber: 7.7 Consensus size: 7
11242541 AGCCTCTCCT
11242551 TTTTTCA
1 TTTTTCA
11242558 TTTTTCA
1 TTTTTCA
11242565 -TTTTCA
1 TTTTTCA
*
11242571 ATTTTCA
1 TTTTTCA
11242578 TTTTTCA
1 TTTTTCA
*
11242585 -TTCTCA
1 TTTTTCA
11242591 TTTTTCA
1 TTTTTCA
11242598 TTTTT
1 TTTTT
11242603 TTGACTCAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
6 11 0.28
7 29 0.73
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTTCA
Found at i:11242570 original size:13 final size:13
Alignment explanation
Indices: 11242551--11242601 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
11242541 AGCCTCTCCT
11242551 TTTTTCATTTTTCA
1 TTTTTCA-TTTTCA
11242565 -TTTTCAATTTTCA
1 TTTTTC-ATTTTCA
*
11242578 TTTTTCATTCTCA
1 TTTTTCATTTTCA
11242591 TTTTTCATTTT
1 TTTTTCATTTT
11242602 TTTGACTCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 27 0.82
14 6 0.18
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:11242577 original size:20 final size:20
Alignment explanation
Indices: 11242552--11242602 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
11242542 GCCTCTCCTT
*
11242552 TTTTCATTTTTCATTTTCAA
1 TTTTCATTTTTCATTCTCAA
*
11242572 TTTTCATTTTTCATTCTCAT
1 TTTTCATTTTTCATTCTCAA
11242592 TTTTCATTTTT
1 TTTTCATTTTT
11242603 TTGACTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTCATTTTTCATTCTCAA
Found at i:11243460 original size:15 final size:16
Alignment explanation
Indices: 11243440--11243474 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
11243430 TCTCCTTTTC
*
11243440 TTTTTTCTTTTC-CTT
1 TTTTTTCTTCTCTCTT
11243455 TTTTTTCTTCTCTCTT
1 TTTTTTCTTCTCTCTT
11243471 TTTT
1 TTTT
11243475 CATTTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTCTCTCTT
Found at i:11244243 original size:39 final size:39
Alignment explanation
Indices: 11244199--11244278 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
11244189 TGTATAAATC
* * *
11244199 ATGAATAATTATTTGTATCATATGATTATGAATGAATGA
1 ATGAATAATAATTTGTACCATATGATTATGAACGAATGA
11244238 ATGAATAATAATTTGTACCATATGATTATGAACGAATGA
1 ATGAATAATAATTTGTACCATATGATTATGAACGAATGA
11244277 AT
1 AT
11244279 AATGAATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (39 bp):
ATGAATAATAATTTGTACCATATGATTATGAACGAATGA
Found at i:11249589 original size:10 final size:10
Alignment explanation
Indices: 11249576--11249600 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11249566 TTTTTCTTTT
11249576 TTTTTTGCTA
1 TTTTTTGCTA
11249586 TTTTTTGCTA
1 TTTTTTGCTA
11249596 TTTTT
1 TTTTT
11249601 CTTCTCGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTTGCTA
Found at i:11258196 original size:26 final size:26
Alignment explanation
Indices: 11258167--11258221 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
11258157 ATATGTATAT
11258167 TATAGATAAATA-TT-ATATTAATTTAA
1 TATA-ATAAATATTTAAT-TTAATTTAA
*
11258193 TATAATTAATATTTAATTTAATTTAA
1 TATAATAAATATTTAATTTAATTTAA
11258219 TAT
1 TAT
11258222 TTAACTTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 6 0.23
26 18 0.69
27 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TATAATAAATATTTAATTTAATTTAA
Found at i:11258249 original size:16 final size:17
Alignment explanation
Indices: 11258175--11258251 Score: 70
Period size: 17 Copynumber: 4.4 Consensus size: 17
11258165 ATTATAGATA
11258175 AATATTATA-TTAATTT
1 AATATTATATTTAATTT
11258191 AATATAATTAATATTTAATTT
1 -A-AT-ATT-ATATTTAATTT
*
11258212 AAT-TTAATATTTAACTT
1 AATATT-ATATTTAATTT
*
11258229 GATATTAT-TTTAATTT
1 AATATTATATTTAATTT
11258245 AATATTA
1 AATATTA
11258252 AAGTGATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
16 13 0.25
17 18 0.35
18 4 0.08
19 5 0.10
20 4 0.08
21 7 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
AATATTATATTTAATTT
Found at i:11260614 original size:17 final size:16
Alignment explanation
Indices: 11260592--11260637 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
11260582 TTACAACCTG
11260592 CTAATTTAATATCACGA
1 CTAATTTAATATCAC-A
*
11260609 CTAATTTACATAGCACA
1 CTAATTTA-ATATCACA
*
11260626 CCAATTTAATAT
1 CTAATTTAATAT
11260638 TGCGCCCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.64
18 6 0.24
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (16 bp):
CTAATTTAATATCACA
Found at i:11260619 original size:68 final size:68
Alignment explanation
Indices: 11260525--11261184 Score: 306
Period size: 68 Copynumber: 9.6 Consensus size: 68
11260515 TATAGTTTGT
* * * * *
11260525 TGATTTAATATCACGAATTACCTACATAGCATGCCGATTTAAGATCACGCTCCTATCTTACAACC
1 TGATTTAAGATCACGACTAATCTACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACC
11260590 TGC
66 TGC
* * * * * * ** * * * **
11260593 TAATTTAATATCACGACTAATTTACATAGCACACCAATTTAATATTGCGCCCCTATTTTA-TAGT
1 TGATTTAAGATCACGACTAATCTACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACC
*
11260657 TCGT
66 T-GC
* * * * * *
11260661 TGATTTAAGATCACAACTAACCTACATAGCACACTGATTTAAGATCGCGCTCCTATCTTACTATC
1 TGATTTAAGATCACGACTAATCTACATAGCACGCCGATTTAAGATCACGCTCCTATCTTAC-AAC
*
11260726 C-AC
65 CTGC
* ** * *
11260729 TGATTTAAGAT-ATCGCTCCTATAT-TATTTCTATAGCACATCAATTTAAGATCGCAC-CT-TTA
1 TGATTTAAGATCA-CG--ACTA-ATCTA---C-ATAGCACGCCGATTTAAGAT--CACGCTCCTA
* * **
11260790 TTTTATAGTCTGC
56 TCTTACAACCTGC
* * * *
11260803 TGATTGAAGATCAC-AGCTAATTTACATAGCACGCTGATTTAAGAT-ATCGCTCCTATATTAC-A
1 TGATTTAAGATCACGA-CTAATCTACATAGCACGCCGATTTAAGATCA-CGCTCCTATCTTACAA
** *
11260865 GTTCAC
64 CCT-GC
* * * * * * * * * *
11260871 TGATTTAATATCAC-AGTTAACCTATATAGCACGCCAATTTAAGATCGCACTCTTATCTTATAGC
1 TGATTTAAGATCACGA-CTAATCTACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAAC
**
11260935 CCAC
65 CTGC
** ** * * * *
11260939 CAATTTAAGATCATAACTAATTTACATAGCACGTCGATTTAAGATTGCAC-C-CCTATTTTATAG
1 TGATTTAAGATCACGACTAATCTACATAGCACGCCGATTTAAGA-T-CACGCTCCTATCTTACA-
*
11261002 ATC-GC
63 ACCTGC
* * * *
11261007 TGATTTAAGATCACGGCTAATCTACATAGCACGCCAATTTAAGATCACACTCATATCTTACAATC
1 TGATTTAAGATCACGACTAATCTACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAA-C
11261072 CAT--
65 C-TGC
** * * * * *
11261075 TGATTTAAGATCACGGTTAACCTACATAGGATGCTGATTTAAGATCACGCTCCTATCTTACAACA
1 TGATTTAAGATCACGACTAATCTACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACC
*
11261140 TGT
66 TGC
* * * **
11261143 TGTTTTAAGATCACAACTAATTTACATAGCACGGTGATTTAA
1 TGATTTAAGATCACGACTAATCTACATAGCACGCCGATTTAA
11261185 TAGCTCAATT
Statistics
Matches: 435, Mismatches: 123, Indels: 68
0.69 0.20 0.11
Matches are distributed among these distances:
65 1 0.00
66 5 0.01
67 10 0.02
68 356 0.82
69 5 0.01
70 7 0.02
71 3 0.01
72 5 0.01
73 3 0.01
74 35 0.08
75 3 0.01
76 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (68 bp):
TGATTTAAGATCACGACTAATCTACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACC
TGC
Found at i:11260829 original size:142 final size:142
Alignment explanation
Indices: 11260618--11260878 Score: 346
Period size: 142 Copynumber: 1.8 Consensus size: 142
11260608 ACTAATTTAC
* * * * *
11260618 ATAGCACACCAATTTAATATTGCGCCCCTATTTTATAGTTCGTTGATTTAAGATCACAACTAACC
1 ATAGCACACCAATTTAAGATCGCACCCCTATTTTATAGTTCGCTGATTGAAGATCACAACTAACC
* *
11260683 TACATAGCACACTGATTTAAGATCGCGCTCCTATCTTACTA-TCCACTGATTTAAGATATCGCTC
66 TACATAGCACACTGATTTAAGATAGCGCTCCTATATTAC-AGTCCACTGATTTAAGATATCGCTC
11260747 CTATATTATTTCT
130 CTATATTATTTCT
* ** * *
11260760 ATAGCACATCAATTTAAGATCGCACCTTTATTTTATAG-TCTGCTGATTGAAGATCACAGCTAAT
1 ATAGCACACCAATTTAAGATCGCACCCCTATTTTATAGTTC-GCTGATTGAAGATCACAACTAAC
* * * *
11260824 TTACATAGCACGCTGATTTAAGATATCGCTCCTATATTACAGTTCACTGATTTAA
65 CTACATAGCACACTGATTTAAGATAGCGCTCCTATATTACAGTCCACTGATTTAA
11260879 TATCACAGTT
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
141 3 0.03
142 98 0.97
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (142 bp):
ATAGCACACCAATTTAAGATCGCACCCCTATTTTATAGTTCGCTGATTGAAGATCACAACTAACC
TACATAGCACACTGATTTAAGATAGCGCTCCTATATTACAGTCCACTGATTTAAGATATCGCTCC
TATATTATTTCT
Found at i:11261130 original size:136 final size:135
Alignment explanation
Indices: 11260524--11261175 Score: 487
Period size: 136 Copynumber: 4.7 Consensus size: 135
11260514 TTATAGTTTG
* * * *
11260524 TTGATTTAATATCACGAA-TTACCTACATAGCATGCCGATTTAAGATCACGCTCCTATCTTACAA
1 TTGATTTAAGATCAC-AACTAACCTACATAGCACGCTGATTTAAGATCACGCTCCTATCTTACAA
* * * * * * * * * * *
11260588 CCTGCTAATTTAATATCACGACTAATTTACATAGCACACCAATTTAATATTGCGCCCCTATTTTA
65 TC-GCTGATTTAAGATCACGACTAATCTACATAGCACGCCAATTTAAGATCGCACTCTTATCTTA
* *
11260653 TAGTTCG
129 TAGTCCA
* * *
11260660 TTGATTTAAGATCACAACTAACCTACATAGCACACTGATTTAAGATCGCGCTCCTATCTTACTAT
1 TTGATTTAAGATCACAACTAACCTACATAGCACGCTGATTTAAGATCACGCTCCTATCTTACAAT
* * **
11260725 CCACTGATTTAAGAT-ATCGCTCCTATAT-TATTTCTATAGCACATCAATTTAAGATCGCAC-CT
66 -CGCTGATTTAAGATCA-CG--ACTA-ATCTA---C-ATAGCACGCCAATTTAAGATCGCACTC-
* **
11260787 TTATTTTATAGTCTG
121 TTATCTTATAGTCCA
* * * ** *
11260802 CTGATTGAAGATCACAGCTAATTTACATAGCACGCTGATTTAAGAT-ATCGCTCCTATATTACAG
1 TTGATTTAAGATCACAACTAACCTACATAGCACGCTGATTTAAGATCA-CGCTCCTATCTTACA-
* * * * * *
11260866 TTCACTGATTTAATATCAC-AGTTAACCTATATAGCACGCCAATTTAAGATCGCACTCTTATCTT
64 ATCGCTGATTTAAGATCACGA-CTAATCTACATAGCACGCCAATTTAAGATCGCACTCTTATCTT
*
11260930 ATAGCCCA
128 ATAGTCCA
*** * ** * *
11260938 CCAATTTAAGATCATAACTAATTTACATAGCACG-TCGATTTAAGATTGCAC-C-CCTATTTTAT
1 TTGATTTAAGATCACAACTAACCTACATAGCACGCT-GATTTAAGA-T-CACGCTCCTATCTTAC
* * *
11261000 AGATCGCTGATTTAAGATCACGGCTAATCTACATAGCACGCCAATTTAAGATCACACTCATATCT
63 A-ATCGCTGATTTAAGATCACGACTAATCTACATAGCACGCCAATTTAAGATCGCACTCTTATCT
* *
11261065 TACAATCCA
127 TATAGTCCA
*** * *
11261074 TTGATTTAAGATCACGGTTAACCTACATAGGATGCTGATTTAAGATCACGCTCCTATCTTACAA-
1 TTGATTTAAGATCACAACTAACCTACATAGCACGCTGATTTAAGATCACGCTCCTATCTTACAAT
* * * *
11261138 CATGTTGTTTTAAGATCACAACTAATTTACATAGCACG
66 C--GCTGATTTAAGATCACGACTAATCTACATAGCACG
11261176 GTGATTTAAT
Statistics
Matches: 412, Mismatches: 77, Indels: 54
0.76 0.14 0.10
Matches are distributed among these distances:
134 4 0.01
135 7 0.02
136 278 0.67
137 5 0.01
138 6 0.01
139 4 0.01
140 4 0.01
141 2 0.00
142 100 0.24
143 2 0.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.34
Consensus pattern (135 bp):
TTGATTTAAGATCACAACTAACCTACATAGCACGCTGATTTAAGATCACGCTCCTATCTTACAAT
CGCTGATTTAAGATCACGACTAATCTACATAGCACGCCAATTTAAGATCGCACTCTTATCTTATA
GTCCA
Found at i:11261152 original size:204 final size:204
Alignment explanation
Indices: 11260661--11261184 Score: 480
Period size: 204 Copynumber: 2.5 Consensus size: 204
11260651 TATAGTTCGT
** * ** * * *
11260661 TGATTTAAGATCACAACTAACCTACATAGCACACTGATTTAAGATCGCGCTCCTATCTTACTATC
1 TGATTTAAGATCACAGTTAACCTACATAGCACGCCAATTTAAGATCACACTCCTATCTTAC-AAC
** * ** * * * **
11260726 -CACTGATTTAAGATATCGCTCCTATATTATTTCTATAGCACATCAATTTAAGATCGCACCTTTA
65 ACACCAATTTAAG--ATCACAACTA-A-T-TTAC-ATAGCACGTCGATTTAAGATCGCACCCCTA
* ** *
11260790 TTTTATAGTCTGCTGATTGAAGATCACAGCTAATTTACATAGCACGCTGATTTAAGATATCGCTC
124 TTTTATAGTCTGCTGATTGAAGATCACAGCTAATCTACATAGCACGCCAATTTAAGATATCACTC
* * *
11260855 CTATATTACAGTTCAC
189 ATATATTACAATCCAC
* * * * * * *
11260871 TGATTTAATATCACAGTTAACCTATATAGCACGCCAATTTAAGATCGCACTCTTATCTTATAGCC
1 TGATTTAAGATCACAGTTAACCTACATAGCACGCCAATTTAAGATCACACTCCTATCTTACAACA
* *
11260936 CACCAATTTAAGATCATAACTAATTTACATAGCACGTCGATTTAAGATTGCACCCCTATTTTATA
66 CACCAATTTAAGATCACAACTAATTTACATAGCACGTCGATTTAAGATCGCACCCCTATTTTATA
* * *
11261001 GATC-GCTGATTTAAGATCACGGCTAATCTACATAGCACGCCAATTTAAGATCA-CACTCATATC
131 G-TCTGCTGATTGAAGATCACAGCTAATCTACATAGCACGCCAATTTAAGAT-ATCACTCATATA
*
11261064 TTACAATCCAT
194 TTACAATCCAC
* * * ** *
11261075 TGATTTAAGATCACGGTTAACCTACATAGGATGCTGATTTAAGATCACGCTCCTATCTTACAACA
1 TGATTTAAGATCACAGTTAACCTACATAGCACGCCAATTTAAGATCACACTCCTATCTTACAACA
******
11261140 TGTTGTTTTAAGATCACAACTAATTTACATAGCACGGT-GATTTAA
66 CACCAATTTAAGATCACAACTAATTTACATAGCAC-GTCGATTTAA
11261185 TAGCTCAATT
Statistics
Matches: 256, Mismatches: 54, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
204 177 0.69
205 8 0.03
206 1 0.00
207 1 0.00
208 6 0.02
209 2 0.01
210 61 0.24
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.33
Consensus pattern (204 bp):
TGATTTAAGATCACAGTTAACCTACATAGCACGCCAATTTAAGATCACACTCCTATCTTACAACA
CACCAATTTAAGATCACAACTAATTTACATAGCACGTCGATTTAAGATCGCACCCCTATTTTATA
GTCTGCTGATTGAAGATCACAGCTAATCTACATAGCACGCCAATTTAAGATATCACTCATATATT
ACAATCCAC
Found at i:11261184 original size:34 final size:33
Alignment explanation
Indices: 11260941--11261184 Score: 99
Period size: 34 Copynumber: 7.2 Consensus size: 33
11260931 TAGCCCACCA
*
11260941 ATTTAAGATCATAACTAATTTACATAGCACG-TCG
1 ATTTAAGATCA-CACTAATTTACATAGCACGCT-G
* *
11260975 ATTTAAGATTGCACCCCT-ATTT-TATAG-ATCGCTG
1 ATTTAAGA-T-CA-CACTAATTTACATAGCA-CGCTG
* * **
11261009 ATTTAAGATCACGGCTAATCTACATAGCACGCCA
1 ATTTAAGATCAC-ACTAATTTACATAGCACGCTG
* **
11261043 ATTTAAGATCACACTCATATCTTACA-ATC-CATTG
1 ATTTAAGATCACACT-A-AT-TTACATAGCACGCTG
** ** * *
11261077 ATTTAAGATCACGGTTAACCTACATAGGATGCTG
1 ATTTAAGATCAC-ACTAATTTACATAGCACGCTG
* * * *
11261111 ATTTAAGATCACGCTCCTATCTTACA-A-CATGTTG
1 ATTTAAGATCACACT--AAT-TTACATAGCACGCTG
* *
11261145 TTTTAAGATCACAACTAATTTACATAGCACGGTG
1 ATTTAAGATCAC-ACTAATTTACATAGCACGCTG
11261179 ATTTAA
1 ATTTAA
11261185 TAGCTCAATT
Statistics
Matches: 153, Mismatches: 37, Indels: 40
0.67 0.16 0.17
Matches are distributed among these distances:
31 1 0.01
32 13 0.08
33 14 0.09
34 97 0.63
35 16 0.10
36 12 0.08
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (33 bp):
ATTTAAGATCACACTAATTTACATAGCACGCTG
Found at i:11265141 original size:4 final size:4
Alignment explanation
Indices: 11265132--11265195 Score: 69
Period size: 4 Copynumber: 15.5 Consensus size: 4
11265122 AAAAATACAT
*
11265132 TTTC TTTC TTTC -TT- TTTC TTCTC TTTTC TTTC TTTA TTTC TTCTC ATTTC
1 TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC TTTC TTTC TT-TC -TTTC
11265182 TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TT
11265196 CTCCCTCTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
3 4 0.08
4 36 0.69
5 8 0.15
6 4 0.08
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:11265150 original size:14 final size:14
Alignment explanation
Indices: 11265131--11265188 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
11265121 TAAAAATACA
11265131 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
11265145 TTTTCTTCTCTTT-T
1 TTTTCTT-TCTTTCT
* *
11265159 CTTTCTTTATTTC-
1 TTTTCTTTCTTTCT
*
11265172 TTCTCATTTCTTTCT
1 TTTTC-TTTCTTTCT
11265187 TT
1 TT
11265189 CTTTCTTCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 7 0.20
14 21 0.60
15 7 0.20
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:11265174 original size:22 final size:21
Alignment explanation
Indices: 11265136--11265198 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
11265126 ATACATTTTC
*
11265136 TTTCTTTC-TTTTTCTTCTCT
1 TTTCTTTCTTTTTTCTTCTCA
11265156 TTTCTTTCTTTATTTCTTCTCA
1 TTTCTTTCTTT-TTTCTTCTCA
11265178 TTTCTTTCTTTCTTTCTTCTC
1 TTTCTTTCTTT-TTTCTTCTC
11265199 CCTCTATTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.21
21 2 0.05
22 29 0.74
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTCTTTCTTTTTTCTTCTCA
Found at i:11265208 original size:22 final size:22
Alignment explanation
Indices: 11265158--11265209 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
11265148 TCTTCTCTTT
**
11265158 TCTTTCTTTATTTCTTCTCATT
1 TCTTTCTTTATTTCTTCTCACC
*
11265180 TCTTTCTTTCTTTCTTCTC-CC
1 TCTTTCTTTATTTCTTCTCACC
11265201 TCTATTCTT
1 TCT-TTCTT
11265210 CCTTGTGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (22 bp):
TCTTTCTTTATTTCTTCTCACC
Found at i:11265320 original size:27 final size:27
Alignment explanation
Indices: 11265282--11265353 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
11265272 GGCATGCACT
*
11265282 AGTGTCGCCTATCAGATAGAGGTCACC
1 AGTGCCGCCTATCAGATAGAGGTCACC
* *
11265309 AGTGCCGCCTATCAGATAGGGGTCACT
1 AGTGCCGCCTATCAGATAGAGGTCACC
*
11265336 GGTGCCGCCTATCAGATA
1 AGTGCCGCCTATCAGATA
11265354 AGCACCACGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (27 bp):
AGTGCCGCCTATCAGATAGAGGTCACC
Found at i:11268273 original size:1 final size:1
Alignment explanation
Indices: 11268267--11268295 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
11268257 TTTCGATCAT
11268267 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11268296 TTTTCTCGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11270664 original size:34 final size:34
Alignment explanation
Indices: 11270605--11270671 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
11270595 TTGAGATTTG
* *
11270605 AAAATTTTGAAGGTGAAGACATTTTTTTAACCTC
1 AAAATTTTGAAGATGAAGACATTTTTTGAACCTC
** *
11270639 AAAATTTTGAAGATGGGGACCTTTTTTGAACCT
1 AAAATTTTGAAGATGAAGACATTTTTTGAACCT
11270672 TAACTAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (34 bp):
AAAATTTTGAAGATGAAGACATTTTTTGAACCTC
Found at i:11272174 original size:54 final size:53
Alignment explanation
Indices: 11272111--11272234 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 53
11272101 ATGAATTACT
* * **
11272111 TAATGCATGACTTCATTAAAAAAAATGCAAACTTTAACTAACATGGGAGTTGCA
1 TAATGCATGACTTAATTAAAAAAAATGCAAAC-TTAACTAACATGAGAGTAACA
* * ** *
11272165 TAATGCATGACATAATT---TATGATGCAATCTTAACTAACATGAGAGTAACA
1 TAATGCATGACTTAATTAAAAAAAATGCAAACTTAACTAACATGAGAGTAACA
*
11272215 TAATGCATGACTTTATTAAA
1 TAATGCATGACTTAATTAAA
11272235 TGCAGAACAC
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
50 33 0.59
51 8 0.14
54 15 0.27
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (53 bp):
TAATGCATGACTTAATTAAAAAAAATGCAAACTTAACTAACATGAGAGTAACA
Found at i:11272882 original size:21 final size:21
Alignment explanation
Indices: 11272856--11272897 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11272846 CAATGTGGCA
* * *
11272856 AGTTAATTGGCCACGTCAGCT
1 AGTTAACTAGCCACATCAGCT
11272877 AGTTAACTAGCCACATCAGCT
1 AGTTAACTAGCCACATCAGCT
11272898 GTCCCGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTTAACTAGCCACATCAGCT
Found at i:11276725 original size:35 final size:35
Alignment explanation
Indices: 11276686--11276797 Score: 111
Period size: 35 Copynumber: 3.1 Consensus size: 35
11276676 AAGATAATCC
11276686 AAAATCTTAAAATATAGATTGTAAAACGGACATAA
1 AAAATCTTAAAATATAGATTGTAAAACGGACATAA
* * ** * **
11276721 AAAATGTTACAGATGAT--ATTGTTAAAAAAGATAATCC
1 AAAATCTTA-AAAT-ATAGATTG-TAAAACGGA-CATAA
11276758 AAAATCTTAAAATATAGATTGTAAAACGGACATAA
1 AAAATCTTAAAATATAGATTGTAAAACGGACATAA
11276793 AAAAT
1 AAAAT
11276798 GTTGAAAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
35 21 0.37
36 20 0.35
37 16 0.28
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.27
Consensus pattern (35 bp):
AAAATCTTAAAATATAGATTGTAAAACGGACATAA
Found at i:11276749 original size:72 final size:72
Alignment explanation
Indices: 11276650--11276800 Score: 284
Period size: 72 Copynumber: 2.1 Consensus size: 72
11276640 ATGCATAGTT
* *
11276650 AAATTTTACAGATGATATTGTTGAAAAAGATAATCCAAAATCTTAAAATATAGATTGTAAAACGG
1 AAATGTTACAGATGATATTGTTAAAAAAGATAATCCAAAATCTTAAAATATAGATTGTAAAACGG
11276715 ACATAAA
66 ACATAAA
11276722 AAATGTTACAGATGATATTGTTAAAAAAGATAATCCAAAATCTTAAAATATAGATTGTAAAACGG
1 AAATGTTACAGATGATATTGTTAAAAAAGATAATCCAAAATCTTAAAATATAGATTGTAAAACGG
11276787 ACATAAA
66 ACATAAA
11276794 AAATGTT
1 AAATGTT
11276801 GAAAAAAATG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (72 bp):
AAATGTTACAGATGATATTGTTAAAAAAGATAATCCAAAATCTTAAAATATAGATTGTAAAACGG
ACATAAA
Found at i:11276762 original size:37 final size:37
Alignment explanation
Indices: 11276650--11276766 Score: 107
Period size: 37 Copynumber: 3.2 Consensus size: 37
11276640 ATGCATAGTT
* *
11276650 AAATTTTACAGATGATATTGTTGAAAAAGATAATCCA
1 AAATCTTACAGATGATATTGTTAAAAAAGATAATCCA
* ** * **
11276687 AAATCTTA-AAAT-ATAGATTG-TAAAACGGA-CATAAA
1 AAATCTTACAGATGAT--ATTGTTAAAAAAGATAATCCA
*
11276722 AAATGTTACAGATGATATTGTTAAAAAAGATAATCCA
1 AAATCTTACAGATGATATTGTTAAAAAAGATAATCCA
11276759 AAATCTTA
1 AAATCTTA
11276767 AAATATAGAT
Statistics
Matches: 58, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
35 16 0.28
36 19 0.33
37 23 0.40
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.30
Consensus pattern (37 bp):
AAATCTTACAGATGATATTGTTAAAAAAGATAATCCA
Found at i:11276779 original size:37 final size:36
Alignment explanation
Indices: 11276673--11276783 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 36
11276663 GATATTGTTG
11276673 AAAAAGATAATCCAAAATCTTAAAATATAGATTGTA
1 AAAAAGATAATCCAAAATCTTAAAATATAGATTGTA
** * ** * *
11276709 AAACGGA-CATAAAAAATGTTACAGATGAT--ATTGTTA
1 AAAAAGATAATCCAAAATCTTA-AAAT-ATAGATTG-TA
11276745 AAAAAGATAATCCAAAATCTTAAAATATAGATTGTA
1 AAAAAGATAATCCAAAATCTTAAAATATAGATTGTA
11276781 AAA
1 AAA
11276784 CGGACATAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
35 16 0.29
36 23 0.42
37 16 0.29
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (36 bp):
AAAAAGATAATCCAAAATCTTAAAATATAGATTGTA
Found at i:11277580 original size:2 final size:2
Alignment explanation
Indices: 11277573--11277609 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11277563 AAGGTTTAAT
11277573 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11277610 TTCTCCCCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11280588 original size:2 final size:2
Alignment explanation
Indices: 11280581--11280611 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11280571 AACAAATGTT
11280581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11280612 TGTTAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11280877 original size:2 final size:2
Alignment explanation
Indices: 11280870--11280901 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11280860 CCATCACACG
11280870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11280902 ACAGTCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11285398 original size:31 final size:31
Alignment explanation
Indices: 11285338--11285399 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
11285328 TTTAAATTAG
11285338 AGTTTAGGGTTTTTTTAGATTGTAAGTGTTTA
1 AGTTTAGGGTTTTTTTA-ATTGTAAGTGTTTA
*
11285370 AGTTTAGGGTTTTATTT-ATTTTAAGTGTTT
1 AGTTTAGGGTTTT-TTTAATTGTAAGTGTTT
11285400 TTTAATTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 12 0.43
32 13 0.46
33 3 0.11
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.56
Consensus pattern (31 bp):
AGTTTAGGGTTTTTTTAATTGTAAGTGTTTA
Found at i:11290103 original size:26 final size:26
Alignment explanation
Indices: 11290063--11290132 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
11290053 TTTTACATCG
* *
11290063 TTGCTCACACAAGCTGTGAAATGAGT
1 TTGCTCACACGAGCTGTGAAATGAGC
*
11290089 TTGCTCACACGAGCTGTGAAATGGGC
1 TTGCTCACACGAGCTGTGAAATGAGC
* *
11290115 CTGCTCACTCGAGCTGTG
1 TTGCTCACACGAGCTGTG
11290133 GGTCAGAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (26 bp):
TTGCTCACACGAGCTGTGAAATGAGC
Found at i:11293095 original size:28 final size:26
Alignment explanation
Indices: 11293063--11293114 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
11293053 AATACTATAA
11293063 TGGGCTAAGGCCCACACTGTTACTGTAT
1 TGGGCTAAGG-CCACACTG-TACTGTAT
11293091 TGGGCTAAGGCCACACTGTACTGT
1 TGGGCTAAGGCCACACTGTACTGT
11293115 TGCTGAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 6 0.25
27 8 0.33
28 10 0.42
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (26 bp):
TGGGCTAAGGCCACACTGTACTGTAT
Found at i:11293128 original size:32 final size:28
Alignment explanation
Indices: 11293064--11293147 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
11293054 ATACTATAAT
* *
11293064 GGGCTAAGGCCCACACTGTTACTGTATT
1 GGGCTAAGGCCCACACTGTTACTGAATA
*
11293092 GGGCTAAGGCCACACTGTACTGTTGCTGAATA
1 GGGCTAAGGCC-CAC---ACTGTTACTGAATA
* *
11293124 GGGCTCCA-GCCCAGACTGTTACTG
1 GGGCT-AAGGCCCACACTGTTACTG
11293148 CATGTTGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
28 20 0.44
29 3 0.07
31 2 0.04
32 19 0.42
33 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.25
Consensus pattern (28 bp):
GGGCTAAGGCCCACACTGTTACTGAATA
Found at i:11298027 original size:134 final size:134
Alignment explanation
Indices: 11297784--11298053 Score: 459
Period size: 134 Copynumber: 2.0 Consensus size: 134
11297774 TTCCATCCTC
* *
11297784 AGACAGATGGTTAGTCAGAGAGGGTGATTCAGATACTGGAAGAAATGTTGAGAAGTTGTGTAATG
1 AGACAGATGGTTAGTCAGAGAGGGTGATTCAGATACTGGAAGAAATGTTAAGAAGTTGTGTAATA
*
11297849 GATTTCCAAGGCAGTTGGGAAGACTATTTACCGCTAGCAAAGTTCGCGTATAATAATAGCTACCA
66 GATTTCCAAGGCAGCTGGGAAGACTATTTACCGCTAGCAAAGTTCGCGTATAATAATAGCTACCA
11297914 GTCT
131 GTCT
* *
11297918 AGACAGATGGTTAGTCAGAGAGGGTGATTCAGATATTGGAAGACATGTTAAGAAGTTGTGTAATA
1 AGACAGATGGTTAGTCAGAGAGGGTGATTCAGATACTGGAAGAAATGTTAAGAAGTTGTGTAATA
* * * *
11297983 GATTTCTAAGGTAGCTGGGAAGACTATTTGCCGCTAGCAGAGTTCGCGTATAATAATAGCTACCA
66 GATTTCCAAGGCAGCTGGGAAGACTATTTACCGCTAGCAAAGTTCGCGTATAATAATAGCTACCA
11298048 GTCT
131 GTCT
11298052 AG
1 AG
11298054 TATTCAAATG
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 127 1.00
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (134 bp):
AGACAGATGGTTAGTCAGAGAGGGTGATTCAGATACTGGAAGAAATGTTAAGAAGTTGTGTAATA
GATTTCCAAGGCAGCTGGGAAGACTATTTACCGCTAGCAAAGTTCGCGTATAATAATAGCTACCA
GTCT
Found at i:11314815 original size:43 final size:43
Alignment explanation
Indices: 11314760--11314846 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
11314750 AAATTCATAG
*
11314760 ATAATTTAAAAAATTAAGGCATGATCACTCTCTCCCGATTCAC
1 ATAATTTAAAAAATTAAGGCATGACCACTCTCTCCCGATTCAC
*
11314803 ATAATTTAAAAAATTAAGGCATGACCACTCTCTCTCGATTCAC
1 ATAATTTAAAAAATTAAGGCATGACCACTCTCTCCCGATTCAC
11314846 A
1 A
11314847 AACCCGATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (43 bp):
ATAATTTAAAAAATTAAGGCATGACCACTCTCTCCCGATTCAC
Done.