Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold442
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: 407032
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.32
Warning! 25515 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:297811 original size:43 final size:42
Alignment explanation
Indices: 297740--297977 Score: 228
Period size: 42 Copynumber: 5.6 Consensus size: 42
297730 GGCGCTTTTC
* * ** * *
297740 AAAAACGCCGCTAAAGGACATGACCTTTAGCCAAGTTTTAGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTT-GGG
* * *
297783 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGATGTTTTTGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTTGGG
* *
297825 AAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTT-TGGG
* * *
297868 -AAAGCGCCGCTAAAAGTCATGTTCTTTAACGGCG-TTTGTGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTTG-GG
* * * * *
297909 TAAAGCGCCGCTGAAGGTCATGTTCTTTAGTGGCATTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTT-TGGG
* * *
297952 GAAAGCACCGTTAAAGGTCATGTTCT
1 AAAAGCGCCGCTAAAGGTCATGTTCT
297978 ATAACGTCAT
Statistics
Matches: 167, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
40 2 0.01
41 4 0.02
42 98 0.59
43 61 0.37
44 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTTGGG
Found at i:297845 original size:42 final size:42
Alignment explanation
Indices: 297781--297977 Score: 241
Period size: 42 Copynumber: 4.7 Consensus size: 42
297771 CAAGTTTTAG
* * ** *
297781 GGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGATGTTTTT
1 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
297823 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
1 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
* *
297865 GGGAAAGCGCCGCTAAAAGTCATGTTCTTTAACGGCGTTTGT
1 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
* * * * *
297907 GGTAAAGCGCCGCTGAAGGTCATGTTCTTTAGTGGCATTTGT
1 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
* * * *
297949 GGGGAAAGCACCGTTAAAGGTCATGTTCT
1 -GGAAAAGCGCCGCTAAAAGTCATGTTCT
297978 ATAACGTCAT
Statistics
Matches: 137, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 113 0.82
43 24 0.18
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (42 bp):
GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
Found at i:297887 original size:84 final size:85
Alignment explanation
Indices: 297784--297993 Score: 269
Period size: 84 Copynumber: 2.5 Consensus size: 85
297774 GTTTTAGGGA
** * *
297784 AAAGCGCCGCTAAAGGTCATGTTCTTTAGTGATGTTTTTGGAAAAGCGCCGCTAAAAGTCATGTT
1 AAAGCGCCGCTAAAGGTCATGTTCTTTAACGACGTTTGTGGAAAAGCGCCGCTAAAAGTCATGTT
*
297849 CTTTAGCGGCGTTTGT-GGG
66 CTTTAGCGGCATTTGTGGGG
* * * * *
297868 AAAGCGCCGCTAAAAGTCATGTTCTTTAACGGCGTTTGTGGTAAAGCGCCGCTGAAGGTCATGTT
1 AAAGCGCCGCTAAAGGTCATGTTCTTTAACGACGTTTGTGGAAAAGCGCCGCTAAAAGTCATGTT
*
297933 CTTTAGTGGCATTTGTGGGG
66 CTTTAGCGGCATTTGTGGGG
* * * * *
297953 AAAGCACCGTTAAAGGTCATGTTCTATAACGTCATTTGTGG
1 AAAGCGCCGCTAAAGGTCATGTTCTTTAACGACGTTTGTGG
297994 GGTAGTGCCG
Statistics
Matches: 108, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 70 0.65
85 38 0.35
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (85 bp):
AAAGCGCCGCTAAAGGTCATGTTCTTTAACGACGTTTGTGGAAAAGCGCCGCTAAAAGTCATGTT
CTTTAGCGGCATTTGTGGGG
Found at i:298005 original size:85 final size:84
Alignment explanation
Indices: 297826--297994 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 84
297816 TGTTTTTGGA
* *
297826 AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAAGTCATGTT
1 AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCATTTGTGGGAAAGCACCGCTAAAAGTCATGTT
* * *
297891 CTTTAACGGCGTTTGTGGT
66 CTATAACGGCATTTGTGGG
* * * * *
297910 AAAGCGCCGCTGAAGGTCATGTTCTTTAGTGGCATTTGTGGGGAAAGCACCGTTAAAGGTCATGT
1 AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCATTTGT-GGGAAAGCACCGCTAAAAGTCATGT
*
297975 TCTATAACGTCATTTGTGGG
65 TCTATAACGGCATTTGTGGG
297995 GTAGTGCCGC
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 35 0.48
85 38 0.52
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (84 bp):
AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCATTTGTGGGAAAGCACCGCTAAAAGTCATGTT
CTATAACGGCATTTGTGGG
Found at i:300246 original size:21 final size:21
Alignment explanation
Indices: 300196--300247 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
300186 CAATTCTGAA
*
300196 AATTTTAAAATATCTTAAAAT
1 AATTTTAAAATAACTTAAAAT
* * *
300217 AAATATAAAATAAGTTAAAAT
1 AATTTTAAAATAACTTAAAAT
*
300238 ATTTTTAAAA
1 AATTTTAAAA
300248 ATAATTTGAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTTTAAAATAACTTAAAAT
Found at i:300566 original size:10 final size:11
Alignment explanation
Indices: 300539--300577 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
300529 TAAGGTCAAC
*
300539 ATATTTTAAAA
1 ATATATTAAAA
300550 ATATATTAAAA
1 ATATATTAAAA
300561 AT-TATTAAAA
1 ATATATTAAAA
300571 ATATATT
1 ATATATT
300578 GAAGGTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATATTAAAA
Found at i:303477 original size:18 final size:18
Alignment explanation
Indices: 303454--303488 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
303444 ACACGGGCGT
*
303454 GTGGCTTGGCCTTGTGGC
1 GTGGCTTGGCCGTGTGGC
303472 GTGGCTTGGCCGTGTGG
1 GTGGCTTGGCCGTGTGG
303489 TACAAGTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.49, T:0.31
Consensus pattern (18 bp):
GTGGCTTGGCCGTGTGGC
Found at i:304906 original size:21 final size:21
Alignment explanation
Indices: 304867--304908 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
304857 TTTGCCTAAG
* *
304867 ATATGAATTGGATTGAATTGA
1 ATATGAATTAGATTAAATTGA
*
304888 ATATGAATTATATTAAATTGA
1 ATATGAATTAGATTAAATTGA
304909 GTTAAATTTA
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:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
ATATGAATTAGATTAAATTGA
Found at i:305400 original size:26 final size:26
Alignment explanation
Indices: 305371--305428 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
305361 CTCGATGTAT
305371 GGCT-TTTCGTGAGCTTCCTGATTAAA
1 GGCTCTTT-GTGAGCTTCCTGATTAAA
* *
305397 GGCTCTTTGTGAGCTTCTTGATTAAT
1 GGCTCTTTGTGAGCTTCCTGATTAAA
305423 GGCTCT
1 GGCTCT
305429 CCAGAGCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCTGATTAAA
Found at i:307277 original size:13 final size:13
Alignment explanation
Indices: 307256--307286 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
307246 AAAATACATA
*
307256 TAAATGAAAAAGT
1 TAAAAGAAAAAGT
307269 TAAAAGAAAAAGT
1 TAAAAGAAAAAGT
307282 TAAAA
1 TAAAA
307287 TTTTAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (13 bp):
TAAAAGAAAAAGT
Found at i:316272 original size:14 final size:12
Alignment explanation
Indices: 316245--316279 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
316235 TAATTTAAAC
316245 AAATAAAAACAA
1 AAATAAAAACAA
316257 AAATAAATAGACAA
1 AAATAAA-A-ACAA
316271 AAATAAAAA
1 AAATAAAAA
316280 AATAACAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.38
13 2 0.10
14 11 0.52
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (12 bp):
AAATAAAAACAA
Found at i:322206 original size:3 final size:3
Alignment explanation
Indices: 322198--322228 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
322188 CAAAACTTGC
322198 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
322229 GTCATCACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:323249 original size:15 final size:15
Alignment explanation
Indices: 323229--323259 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
323219 ATTAAAACGC
323229 ATTATCTTTTTATTT
1 ATTATCTTTTTATTT
323244 ATTATCTTTTTATTT
1 ATTATCTTTTTATTT
323259 A
1 A
323260 AAAATTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTATCTTTTTATTT
Found at i:325368 original size:21 final size:22
Alignment explanation
Indices: 325342--325387 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
325332 TTGTATTCAC
*
325342 AAAAAATAATATTATTTATATTTA
1 AAAAAAT-A-ATTATATATATTTA
325366 AAAAAATAAATTATATATATTT
1 AAAAAAT-AATTATATATATTT
325388 TACTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAAATAATTATATATATTTA
Found at i:325378 original size:23 final size:25
Alignment explanation
Indices: 325325--325387 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
325315 TCTTAAATTT
* *
325325 ATATTATTTGTATTCACAAAAAATA
1 ATATTATTTATATTTACAAAAAATA
325350 ATATTATTTATATTTA-AAAAAATA
1 ATATTATTTATATTTACAAAAAATA
*
325374 A-ATTATATATATTT
1 ATATTATTTATATTT
325388 TACTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 12 0.34
24 9 0.26
25 14 0.40
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATTATTTATATTTACAAAAAATA
Found at i:328503 original size:28 final size:27
Alignment explanation
Indices: 328463--328520 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
328453 TTCAATTTAT
* *
328463 TGTCATTTCAAATAAAAATAAAAATTGA
1 TGTCAATTAAAATAAAAAT-AAAATTGA
* * *
328491 TGTCAATTAAAATTAAGATAAATTTGA
1 TGTCAATTAAAATAAAAATAAAATTGA
328518 TGT
1 TGT
328521 ATTTTAGGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (27 bp):
TGTCAATTAAAATAAAAATAAAATTGA
Found at i:329610 original size:3 final size:3
Alignment explanation
Indices: 329602--329636 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
329592 TTTTATTGAG
329602 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
329637 TGTCTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:342479 original size:30 final size:30
Alignment explanation
Indices: 342407--342480 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
342397 CTTGGGCTGT
*
342407 CACATGCTCGTGTGACACACATGACCTAGCTA
1 CACA-GCT-GTGTGACACACACGACCTAGCTA
* * *
342439 TACGGTTGTGTGACACACACGACCTAGCTA
1 CACAGCTGTGTGACACACACGACCTAGCTA
342469 CACAGCTGTGTG
1 CACAGCTGTGTG
342481 TCACTTGTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 31 0.89
31 2 0.06
32 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (30 bp):
CACAGCTGTGTGACACACACGACCTAGCTA
Found at i:349526 original size:20 final size:20
Alignment explanation
Indices: 349501--349546 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
349491 TAGTAAATCT
349501 TAACAACCTATTT-AAATAA
1 TAACAACCTATTTGAAATAA
349520 GTAACAACCTATTTGAAATAA
1 -TAACAACCTATTTGAAATAA
349541 TAACAA
1 TAACAA
349547 AATATTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (20 bp):
TAACAACCTATTTGAAATAA
Found at i:349552 original size:20 final size:20
Alignment explanation
Indices: 349509--349552 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
349499 CTTAACAACC
**
349509 TATTTAAATAAGTAACAACC
1 TATTTAAATAAGTAACAAAA
349529 TATTTGAAATAA-TAACAAAA
1 TATTT-AAATAAGTAACAAAA
349549 TATT
1 TATT
349553 AACAGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (20 bp):
TATTTAAATAAGTAACAAAA
Found at i:353812 original size:2 final size:2
Alignment explanation
Indices: 353805--353837 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
353795 AATGGTAGAG
353805 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 T
353838 GTAGATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:355041 original size:15 final size:15
Alignment explanation
Indices: 355021--355050 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
355011 AGCTTACATC
355021 ATGATTTTAAAATAT
1 ATGATTTTAAAATAT
*
355036 ATGATTTTTAAATAT
1 ATGATTTTAAAATAT
355051 TAATAAAATA
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
ATGATTTTAAAATAT
Found at i:356176 original size:55 final size:55
Alignment explanation
Indices: 356117--356281 Score: 150
Period size: 55 Copynumber: 3.1 Consensus size: 55
356107 TTTTGAAAAG
356117 TGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATTTTGAGTGTTTGGTAT
1 TGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATTTTGAGTGTTTGGTAT
** * ** * * ** *
356172 TGCTGTCAAAAAATACTTTTGAGAAAT-TAATTT-GACAACTTTTGA-------AAAG
1 TGCTGTGGAAAGATGTTTTTGAGAAGTGT--TTTCGA-AAATTTTGAGTGTTTGGTAT
356221 TGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATTTTGAGTGTTTGGTAT
1 TGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATTTTGAGTGTTTGGTAT
356276 TGCTGT
1 TGCTGT
356282 CAAAAAAAAT
Statistics
Matches: 78, Mismatches: 20, Indels: 24
0.64 0.16 0.20
Matches are distributed among these distances:
48 11 0.14
49 24 0.31
50 1 0.01
54 1 0.01
55 30 0.38
56 11 0.14
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (55 bp):
TGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATTTTGAGTGTTTGGTAT
Found at i:356213 original size:104 final size:106
Alignment explanation
Indices: 356092--356302 Score: 390
Period size: 104 Copynumber: 2.0 Consensus size: 106
356082 GAGCTTAGGG
356092 TTAATTTGACAATACTTTTGAAAAGTGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATT
1 TTAATTTGACAATACTTTTGAAAAGTGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATT
*
356157 TTGAGTGTTTGGTATTGCTGTCAAAAAATACTTTTGAGAAA
66 TTGAGTGTTTGGTATTGCTGTCAAAAAAAACTTTTGAGAAA
356198 TTAATTTGAC-A-ACTTTTGAAAAGTGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATT
1 TTAATTTGACAATACTTTTGAAAAGTGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATT
*
356261 TTGAGTGTTTGGTATTGCTGTCAAAAAAAATTTTTGAGAAA
66 TTGAGTGTTTGGTATTGCTGTCAAAAAAAACTTTTGAGAAA
356302 T
1 T
356303 AAAATGTTCA
Statistics
Matches: 103, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
104 92 0.89
105 1 0.01
106 10 0.10
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (106 bp):
TTAATTTGACAATACTTTTGAAAAGTGCTGTGGAAAGATGTTTTTGAGAAGTGTTTTCGAAAATT
TTGAGTGTTTGGTATTGCTGTCAAAAAAAACTTTTGAGAAA
Found at i:368088 original size:105 final size:105
Alignment explanation
Indices: 367963--368162 Score: 285
Period size: 105 Copynumber: 1.9 Consensus size: 105
367953 AAAGTACATC
* ** *
367963 TTATTTATATTTTTATTAAGTAGCAAATGTACATACTGGACGTGTTTTTATGTA-CAAAGGAATT
1 TTATTTATATTTTTATTAAGTAACAAACATACATACTGGACGCGTTTTTATGTACCAAA-GAATT
** *
368027 TGATTGGAAAGTGCTCTTCCTCGTGGTAGCAGTACTATTGG
65 TGATCAGAAAGAGCTCTTCCTCGTGGTAGCAGTACTATTGG
* *
368068 TTATTTATATTTTTATTAAGTAACAAACATACGTAGTGGACGCGTTTTTATGTACCAAAGAATTT
1 TTATTTATATTTTTATTAAGTAACAAACATACATACTGGACGCGTTTTTATGTACCAAAGAATTT
* *
368133 GATCAGAAAGAGCTCTTTCTTGTGGTAGCA
66 GATCAGAAAGAGCTCTTCCTCGTGGTAGCA
368163 ATTTTGAAGG
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
105 79 0.95
106 4 0.05
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (105 bp):
TTATTTATATTTTTATTAAGTAACAAACATACATACTGGACGCGTTTTTATGTACCAAAGAATTT
GATCAGAAAGAGCTCTTCCTCGTGGTAGCAGTACTATTGG
Found at i:378041 original size:2 final size:2
Alignment explanation
Indices: 377986--378025 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
377976 CTTTAATTGC
* *
377986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
378026 GTGTGTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:380228 original size:5 final size:6
Alignment explanation
Indices: 380211--380238 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
380201 TGGGATTGAT
380211 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
380239 TATTAGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:386181 original size:123 final size:124
Alignment explanation
Indices: 385926--386228 Score: 378
Period size: 123 Copynumber: 2.4 Consensus size: 124
385916 AAACGACGCC
* * * * *
385926 GTTTCACTACAGG-AAGTAAGTTTTTTTAGTAGCGTTTTGATTGAAAATGCCGCAAAGGTGATAC
1 GTTTCACTACAGGAAATTAA--ATTTTTAGTGGCGTTTTGACTGAAAACGCCGCAAAGGTGATAC
* * * * * * *
385990 ATTAGTGGCGTTTTTTATAAACGCTGCAAAATTGCAATACCAATTCGAGTTAAACGTCGTT
64 ATTAGTGGCGATTTTCATAAACGCCGCAAAATTACAATACAAATTCGACTTAAACGGCGTT
* * *
386051 GTTTCACTACA-GAACATTAAATTTTTAGTGGCATTTTGACTGAAAACGCTGCAAAGGTTATACA
1 GTTTCACTACAGGAA-ATTAAATTTTTAGTGGCGTTTTGACTGAAAACGCCGCAAAGGTGATACA
*
386115 TTAGTGGC-ATTTTCATAAACGCCGCAAAATTACAATACAAATTTGACTTAAACGGCGTT
65 TTAGTGGCGATTTTCATAAACGCCGCAAAATTACAATACAAATTCGACTTAAACGGCGTT
* ** *
386174 GTTTCACTACAGGGAATTAAGGTTTTAGTGGCGTTTTGACCGAAAACGCCGCAAA
1 GTTTCACTACAGGAAATTAAATTTTTAGTGGCGTTTTGACTGAAAACGCCGCAAA
386229 ATTACAATAC
Statistics
Matches: 153, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
123 89 0.58
124 48 0.31
125 12 0.08
126 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (124 bp):
GTTTCACTACAGGAAATTAAATTTTTAGTGGCGTTTTGACTGAAAACGCCGCAAAGGTGATACAT
TAGTGGCGATTTTCATAAACGCCGCAAAATTACAATACAAATTCGACTTAAACGGCGTT
Found at i:386344 original size:84 final size:84
Alignment explanation
Indices: 386115--386379 Score: 399
Period size: 84 Copynumber: 3.1 Consensus size: 84
386105 AGGTTATACA
* * *
386115 TTAGTGGCA-TTTTCATAAACGCCGCAAAATTACAATACAAATTTGACTTAAACGGCGTTGTTTC
1 TTAGTGGCATTTTTCATAAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGTTTC
* *
386179 ACTACAGGGAATTAAGGTT
66 ACTATAGGGAATTAAGTTT
* *
386198 TTAGTGGCGTTTTGACCGA-AAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGT
1 TTAGTGGCATTTT--TC-ATAAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGT
386262 TTCACTATAGGGAATTAAGTTT
63 TTCACTATAGGGAATTAAGTTT
* *
386284 TTAGTGGCATTTTTCATAAACGCCGCAAAATTGCAATACCAATTTGACTTAAACGTTGTCGTTTC
1 TTAGTGGCATTTTTCATAAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGTTTC
*
386349 ACTATAAGGAATTAAGTTT
66 ACTATAGGGAATTAAGTTT
386368 TTAGTGGCATTT
1 TTAGTGGCATTT
386380 GGCTTGAAAA
Statistics
Matches: 165, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
83 9 0.05
84 80 0.48
86 75 0.45
87 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (84 bp):
TTAGTGGCATTTTTCATAAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGTTTC
ACTATAGGGAATTAAGTTT
Found at i:388694 original size:43 final size:44
Alignment explanation
Indices: 388588--388839 Score: 234
Period size: 43 Copynumber: 5.9 Consensus size: 44
388578 ATGTTTTTGG
* * *
388588 GAAAAGCGCTGCTAAAGGTCATGTTTTTTAGCGGCGTTTG-TGT
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
*** *
388631 G-AAAGCGCCATTAAATGTCATGTTCTTTAGTGGCATTTGTTG-
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
* * * *
388673 GAAAAGCGTTGCTAAAGGTCATGTTCTTTAGCGGCGTATGTTG-
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
* * * *
388716 GAAGAGTGCTGCAAAAGGTCATGTTCTTTAGCT-ACATTTG-TGT
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAG-TGGCATTTGTTGT
* * * * *
388759 TAAAAGCGCCGCTAAAGGTCATGTTCTATAGTGGCGTTT-TCGT
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
*
388802 GAGAAA-CGCTGCTAAAGGTCATG-TCTATAGTGGCATTT
1 GA-AAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTT
388840 TTCACATAAA
Statistics
Matches: 167, Mismatches: 35, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
42 49 0.29
43 115 0.69
44 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (44 bp):
GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
Found at i:397440 original size:15 final size:16
Alignment explanation
Indices: 397415--397447 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
397405 TATCCCTTTC
*
397415 TTTATATTTTATTATA
1 TTTATATTTTATGATA
397431 TTTA-ATTTTATGATA
1 TTTATATTTTATGATA
397446 TT
1 TT
397448 ATTTTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTATATTTTATGATA
Found at i:398136 original size:20 final size:20
Alignment explanation
Indices: 398113--398152 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
398103 CCCTAGCCCT
398113 GCCACCGCCACGGTCACGTC
1 GCCACCGCCACGGTCACGTC
*
398133 GCCACCGCCATGGTCACGTC
1 GCCACCGCCACGGTCACGTC
398153 ACCGCCTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.47, G:0.25, T:0.12
Consensus pattern (20 bp):
GCCACCGCCACGGTCACGTC
Found at i:398157 original size:17 final size:18
Alignment explanation
Indices: 398114--398158 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
398104 CCTAGCCCTG
398114 CCACCGCCACGGTCACGT
1 CCACCGCCACGGTCACGT
*
398132 CGCCACCGCCATGGTCACGT
1 --CCACCGCCACGGTCACGT
398152 -CACCGCC
1 CCACCGCC
398159 TACCCACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 7 0.29
20 17 0.71
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (18 bp):
CCACCGCCACGGTCACGT
Found at i:399100 original size:594 final size:583
Alignment explanation
Indices: 398152--399653 Score: 2376
Period size: 594 Copynumber: 2.5 Consensus size: 583
398142 ATGGTCACGT
*
398152 CACCGCCTACCCACTTGCACCGCCACTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
1 CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
*
398217 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTCGGTAACAT
66 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTGGTAACAT
*
398282 TTTCACAGAAATAAAAGCAAAAAAACAAAGGTGATTTCTTTTTTTTTTTTCATTTTCGCATCTCT
131 TTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTC-TTTTTTTTTTTCATTTTCGCATCTCT
* * *
398347 GCTCTTTTCATACCTGTTCATTTTATTTTTATACATATATACATATATTTTTTTAAAAAGAGTTT
195 GCTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATATTTTAAAAAAGAGTTT
*
398412 ATATTCGCGCAAAATACAAAAAGTAAAATTTTTACCTTTTTTTAAATTTTTCGACCACCGCGTAA
260 ATATTCGCGCAAAATACAAAAAGTAAATTTTTTACCTTTTTTTAAATTTTTCGACCACCGCGTAA
*
398477 TATTCTCGTTACCCGACAACGAGCAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGCTT
325 TATTCTCGTTACCCGACAACGAACAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGCTT
398542 AAGACCCAATTAAACCCCAAACCCAAACCACCTAAACCCAAAACCCAAATACAACCCAACAAAAT
390 AAGACCCAATT-------------AAACC-CC-AAACCCAAAACCCAAATACAACCCAACAAAAT
*
398607 TAAACCCAATACCCAAACCCAACAACCCCAATACCCCAGGCCCAAAATAACCCTAGCCCAAAAAC
440 TAAACCCAATACCCAAACCCAACAAACCCAATACCCCAGGCCCAAAATAACCCTAGCCCAAAAAC
*
398672 AAATCAG-AAAAAAAAATAATTTTTTCAAGCCCTAGGTGC-G-G-C-CTTCTGACCAGCAGGCGC
505 AAATCAGAAAAAAAAAACAATTTTTTCAAGCCCTAGGTGCGGTGCCGCTTCTGACCAGCAGGCGC
398732 CGCCCTAGCCCTGC
570 CGCCCTAGCCCTGC
398746 CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
1 CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
*
398811 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTGGTAATAT
66 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTGGTAACAT
*
398876 TTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTC-TTTTTTTTTTCATTTTCGCATCTCTA
131 TTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTCTTTTTTTTTTTCATTTTCGCATCTCTG
398940 CTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATATTTTAAAAAAGAGTTTA
196 CTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATATTTTAAAAAAGAGTTTA
*
399005 TATTCGTGCAAAATACAAAAAAGTAAATTTTTTTACCTTTTTTTAAA-TTTTCTGACCACCGCGT
261 TATTCGCGCAAAATAC-AAAAAGTAAA-TTTTTTACCTTTTTTTAAATTTTTC-GACCACCGCGT
399069 AATATTCTCGTTACCCGACAACGAACAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGC
323 AATATTCTCGTTACCCGACAACGAACAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGC
* *
399134 TTAAGACTCAATTAAACCCCAAACCCAAAACCCAAATACAACTCAACAAAATTAAACCCAATACC
388 TTAAGACCCAATTAAACCCCAAACCCAAAACCCAAATACAACCCAACAAAATTAAACCCAATACC
* *
399199 CAAACCCAGCAAACCCAATACCCCAGGCCCAAAATAACCCTAGCCCAGAAACAAATCAGAAAAAA
453 CAAACCCAACAAACCCAATACCCCAGGCCCAAAATAACCCTAGCCCAAAAACAAATCAG---AAA
399264 AAAAAAACAATTTTTTCAAGCCCTAGGTGCGGTGCACCTAGGGTCTTCTGACCAGCAGGCGCCGC
515 AAAAAAACAATTTTTTCAAGCCCTAGGTGCGGTG--CC----G-CTTCTGACCAGCAGGCGCCGC
*
399329 CCTAGCCTTGC
573 CCTAGCCCTGC
* * *
399340 CATCGTCTACTCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
1 CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
399405 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTTTGGTAAC
66 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTC--TTTTTTTTTGGTAAC
* * * *
399470 ATTTTCACAGAAATAAAAGCAAAAAATCAAAGCTGA---CGTTTTTTTTATCATTTTCGCATCTC
129 ATTTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTCTTTTTTTTTTTCATTTTCGCATCTC
*
399532 TGCTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATGCATATATATTTTTAAAAAAAGAG
194 TGCTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATA-TTTT-AAAAAAGAG
* *
399597 TTTTTATTCGCGCAAAATACAAAAAGTAAAATTTTTTACCCTTTTTTAAATTTTTCG
257 TTTATATTCGCGCAAAATACAAAAAGT-AAATTTTTTACCTTTTTTTAAATTTTTCG
399654 CGATGGCCGG
Statistics
Matches: 853, Mismatches: 30, Indels: 49
0.92 0.03 0.05
Matches are distributed among these distances:
579 100 0.12
580 2 0.00
581 5 0.01
583 31 0.04
584 1 0.00
585 1 0.00
588 1 0.00
592 102 0.12
593 16 0.02
594 481 0.56
595 30 0.04
596 83 0.10
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (583 bp):
CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTGGTAACAT
TTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTCTTTTTTTTTTTCATTTTCGCATCTCTG
CTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATATTTTAAAAAAGAGTTTA
TATTCGCGCAAAATACAAAAAGTAAATTTTTTACCTTTTTTTAAATTTTTCGACCACCGCGTAAT
ATTCTCGTTACCCGACAACGAACAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGCTTA
AGACCCAATTAAACCCCAAACCCAAAACCCAAATACAACCCAACAAAATTAAACCCAATACCCAA
ACCCAACAAACCCAATACCCCAGGCCCAAAATAACCCTAGCCCAAAAACAAATCAGAAAAAAAAA
ACAATTTTTTCAAGCCCTAGGTGCGGTGCCGCTTCTGACCAGCAGGCGCCGCCCTAGCCCTGC
Found at i:400214 original size:3 final size:3
Alignment explanation
Indices: 400206--400257 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
400196 TTATTTTAAC
400206 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
400254 ATT A
1 ATT A
400258 ATTTGAGGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:400862 original size:43 final size:42
Alignment explanation
Indices: 400814--400950 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 42
400804 GTTTTTCTCT
* *
400814 CAAACGCCGTACTAGGCCCTGATCTATAGCTGCGCTTCGACCA
1 CAAACGCCGAAATA-GCCCTGATCTATAGCTGCGCTTCGACCA
* * * * *
400857 CAAACGCCACGAAATA-ACCTAATCTTTAG-TGGCGCTTTC-CCCT
1 CAAACG-C-CGAAATAGCCCTGATCTATAGCT-GCGC-TTCGACCA
* *
400900 CAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCA
1 CAAACGCCGAAATAG-CCCTGATCTATAGCTGCGCTTCGACCA
400943 CAAACGCC
1 CAAACGCC
400951 ACTAAAGAAC
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
41 6 0.08
42 5 0.07
43 52 0.72
44 4 0.06
45 5 0.07
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (42 bp):
CAAACGCCGAAATAGCCCTGATCTATAGCTGCGCTTCGACCA
Found at i:400938 original size:86 final size:86
Alignment explanation
Indices: 400793--401019 Score: 312
Period size: 86 Copynumber: 2.6 Consensus size: 86
400783 AAGATCAGGG
* * * * * * *
400793 TCTTTAGCGGCGTTTTTCTCTCAAACGCCGTACTAGGCCCTGATCTATAGCTGCGCTTCGACCAC
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
*
400858 AAACGCCACGAAATAACCTAA
66 AAACGCCACGAAAGAACCTAA
*
400879 TCTTTAGTGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
*
400944 AAACGCCACTAAAGAACCTAA
66 AAACGCCACGAAAGAACCTAA
* * * *
400965 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAA-AGACCATGATCTTTAGTGGCG
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGC-AATAGACCCTGATCTATAGCGGCG
401020 TTTTTTTTAA
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 123 0.98
87 2 0.02
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.24
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
AAACGCCACGAAAGAACCTAA
Found at i:400973 original size:43 final size:43
Alignment explanation
Indices: 400835--401019 Score: 171
Period size: 43 Copynumber: 4.3 Consensus size: 43
400825 CTAGGCCCTG
* * * *
400835 ATCTATAGCTGCGC-TTCGACCACAAACGCCACGAAATAACCTA
1 ATCTTTAGCGGCGCTTTC-ACCACAAACGCCACTAAAGAACCTA
* * * * * *
400878 ATCTTTAGTGGCGCTTTCCCCTCAAACGCCGC-AATAGACCCTG
1 ATCTTTAGCGGCGCTTTCACCACAAACGCCACTAA-AGAACCTA
*
400921 ATCTATAGCGGCGC-TTCGACCACAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTC-ACCACAAACGCCACTAAAGAACCTA
* * *
400964 ATCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAG-ACCATG
1 ATCTTTAGCGGCGCTTTCACCACAAACGCCACTAAAGAACC-TA
*
401007 ATCTTTAGTGGCG
1 ATCTTTAGCGGCG
401020 TTTTTTTTAA
Statistics
Matches: 115, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
42 8 0.07
43 99 0.86
44 8 0.07
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
ATCTTTAGCGGCGCTTTCACCACAAACGCCACTAAAGAACCTA
Found at i:402787 original size:114 final size:114
Alignment explanation
Indices: 402587--403119 Score: 863
Period size: 114 Copynumber: 4.7 Consensus size: 114
402577 NNNNNNNNNN
*
402587 GTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATAAAAACG
1 GTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATAGAAACG
402652 CCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAAT
66 CCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAAT
* * * * * *
402701 GTCACCGAAGTGTCTCCAAATGAAGTCGTTTGGGTTTTAGTTTTTCCGGCATTTTTGTAGAAACG
1 GTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATAGAAACG
*
402766 CCGCTAATACTCATATTATTAGCGGCGCTATT-AGAAAAACGCCACTAAA
66 CCGCTAATACTCATATTATTAGCGGCGCTATTCA-AAAAACGCCACTAAT
* * *
402815 GTCACCGAAGTGTCTCCAAACGACGTCGTTTGGGGTTTAGTTTTTGTGGCATTTTTATAAAAACG
1 GTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATAGAAACG
* *
402880 CCACTAATACTCATATTATTAGCGGCACTATTCAAAAAACGCCACTAAT
66 CCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAAT
* *
402929 GTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTACAGAAACG
1 GTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATAGAAACG
*
402994 CCGCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAAT
66 CCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAAT
* * * *
403043 GTCACCGAAGTTTCTCCAAATGACGTCATCT-GGGTTTAGTTTTTGCGGCGTTTTTATAGAAACG
1 GTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATAGAAACG
403107 CCGCTAATACTCA
66 CCGCTAATACTCA
403120 ATCGGTTGCA
Statistics
Matches: 385, Mismatches: 32, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
113 44 0.11
114 340 0.88
115 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (114 bp):
GTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATAGAAACG
CCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAAT
Found at i:403823 original size:11 final size:11
Alignment explanation
Indices: 403800--403880 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
403790 AAAATAAAAA
403800 TTAAAAAAGTATT
1 TTAAAAAA--ATT
*
403813 TTAAAAATATT
1 TTAAAAAAATT
403824 TT---AAAA-T
1 TTAAAAAAATT
403831 T-AAAAAAA-T
1 TTAAAAAAATT
*
403840 TAAAAAAAGTATT
1 TTAAAAAA--ATT
403853 TTAAAAAAATT
1 TTAAAAAAATT
*
403864 TCAAAAAAATT
1 TTAAAAAAATT
403875 TTAAAA
1 TTAAAA
403881 TTAAAAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.04
8 3 0.05
9 6 0.11
10 6 0.11
11 23 0.41
12 1 0.02
13 15 0.27
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:403841 original size:51 final size:49
Alignment explanation
Indices: 403783--403904 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 49
403773 AATTTATTTT
* *
403783 AAAAATTAAAATAAAA-ATTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAA-AAAATATTAAAAAA--ATTTCAAAAAAATTTTAAAATTAA
*
403834 AAAAATTAAAAAAAGTATTTTAAAAAAATTTCAAAAAAATTTTAAAATTAA
1 AAAAATTAAAAAAA--ATATTAAAAAAATTTCAAAAAAATTTTAAAATTAA
403885 AAAAATTAAAAAAAAGTATT
1 AAAAATTAAAAAAAA-TATT
403905 TTAAAGTTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
49 1 0.02
50 6 0.10
51 47 0.75
52 1 0.02
53 8 0.13
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (49 bp):
AAAAATTAAAAAAAATATTAAAAAAATTTCAAAAAAATTTTAAAATTAA
Found at i:403844 original size:8 final size:9
Alignment explanation
Indices: 403826--403898 Score: 58
Period size: 9 Copynumber: 7.4 Consensus size: 9
403816 AAAATATTTT
403826 AAAATTAAA
1 AAAATTAAA
403835 AAAATTAAAA
1 AAAATT-AAA
403845 AAAGTATTTTAAA
1 AAA--A--TTAAA
403858 AAAATTTCAAA
1 AAAA-TT-AAA
**
403869 AAAATT-TT
1 AAAATTAAA
403877 AAAATTAAA
1 AAAATTAAA
403886 AAAATTAAA
1 AAAATTAAA
403895 AAAA
1 AAAA
403899 AGTATTTTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
8 6 0.11
9 19 0.36
10 11 0.21
11 8 0.15
12 1 0.02
13 6 0.11
14 2 0.04
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (9 bp):
AAAATTAAA
Found at i:403854 original size:40 final size:41
Alignment explanation
Indices: 403777--403869 Score: 127
Period size: 40 Copynumber: 2.2 Consensus size: 41
403767 ACCAAAAATT
403777 TATTTTAAAAATTAAAATAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAATAAAAATTAAAAAAGTATTTTAAAAA
403820 TATTTTAAAATT-AA-AAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAATAAAAATT-AAAAAAGTATTTTAAAAA
* *
403860 AATTTCAAAA
1 TATTTTAAAA
403870 AAATTTTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 7 0.15
40 28 0.60
42 6 0.13
43 6 0.13
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (41 bp):
TATTTTAAAATTAAATAAAAATTAAAAAAGTATTTTAAAAA
Found at i:403859 original size:23 final size:22
Alignment explanation
Indices: 403830--403880 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
403820 TATTTTAAAA
403830 TTAAAAAAA-TTAAAAAAAGTATT
1 TTAAAAAAATTTAAAAAAA--ATT
*
403853 TTAAAAAAATTTCAAAAAAATT
1 TTAAAAAAATTTAAAAAAAATT
403875 TTAAAA
1 TTAAAA
403881 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 9 0.35
24 8 0.31
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAAAAAATTTAAAAAAAATT
Found at i:403889 original size:52 final size:53
Alignment explanation
Indices: 403800--403909 Score: 179
Period size: 51 Copynumber: 2.1 Consensus size: 53
403790 AAAATAAAAA
* *
403800 TTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT-AAAAAAAGTATT
1 TTAAAAAAG-ATTTCAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAAGTATT
403853 TTAAAAAA-ATTTCAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAAGTATT
1 TTAAAAAAGATTTCAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAAGTATT
403905 TTAAA
1 TTAAA
403910 GTTAAAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 29 0.54
52 17 0.31
53 8 0.15
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (53 bp):
TTAAAAAAGATTTCAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAAGTATT
Found at i:403925 original size:7 final size:7
Alignment explanation
Indices: 403913--403937 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
403903 TTTTAAAGTT
403913 AAAAATA
1 AAAAATA
403920 AAAAATA
1 AAAAATA
403927 AAAAATA
1 AAAAATA
403934 AAAA
1 AAAA
403938 TATTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:403932 original size:51 final size:50
Alignment explanation
Indices: 403826--403937 Score: 124
Period size: 52 Copynumber: 2.2 Consensus size: 50
403816 AAAATATTTT
* **
403826 AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAATTTCAAAAAAATTTT
1 AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAATAT-AAAAAAATTAA
403877 AAAATTAAAAAAATTAAAAAAAAGTATTTTAAAGTTAAAA-AT-AAAAAA-TAA
1 AAAATTAAAAAAATT-AAAAAAAGTATTTTAAA---AAAATATAAAAAAATTAA
403928 AAAA-TAAAAA
1 AAAATTAAAAA
403938 TATTTATTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
50 6 0.11
51 20 0.37
52 23 0.43
54 1 0.02
55 4 0.07
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.27
Consensus pattern (50 bp):
AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAATATAAAAAAATTAA
Found at i:405672 original size:128 final size:129
Alignment explanation
Indices: 405411--405735 Score: 447
Period size: 128 Copynumber: 2.5 Consensus size: 129
405401 CGCACTTTTA
* * ***
405411 ATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGCAACAGTGGAGC
* ** * * *
405476 AGATGAAAGCTACTAATCCTATCTCCCTGAAGTTGTAGTAGAGCGGATTAAAACCACAGATCTT
66 AGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCGAATTAAAACCACAGATCTT
* * *
405540 ATCTCTCTGAAGTTGCAGTAGAGTAAATCGCATCAAGTCTTATCTCCCT-AAGCAATAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGCAACAGTGGAGC
* *
405604 AGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAATTAAAACCA-ATATCTT
66 AGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGC-GAATTAAAACCACAGATCTT
* * **
405668 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCCATGAAGTTACAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGCAACAGTGGAGC
405733 AGA
66 AGA
405736 TCAAAACCAC
Statistics
Matches: 171, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
128 100 0.58
129 71 0.42
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (129 bp):
ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGCAACAGTGGAGC
AGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCGAATTAAAACCACAGATCTT
Found at i:405721 original size:85 final size:85
Alignment explanation
Indices: 405623--405819 Score: 288
Period size: 85 Copynumber: 2.3 Consensus size: 85
405613 AAACCAATCC
* * * *
405623 TATCTCCCTGAAGTTGCAGTGGAGCAGAATTAAAACCA-ATATCTTATCTCTCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTACAGTGGAGCAG-ATCAAAACCACAGATCTTATCTCTCTGAACTTGCAGT
* * * *
405687 AGAGCAGATCGCATCTAGTCT
65 AAAGCAGATCGCATCAAGCCA
*
405708 TATCTCCATGAAGTTACAGTGGAGCAGATCAAAACCACAGATCTTATCTCTCTGAACTTGCAGTA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATCAAAACCACAGATCTTATCTCTCTGAACTTGCAGTA
405773 AAGCAGATCGCATCAAGCCA
66 AAGCAGATCGCATCAAGCCA
*
405793 TATCTCCCTGAAGTTATAGTGGAGCAG
1 TATCTCCCTGAAGTTACAGTGGAGCAG
405820 GTTGAAGATA
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 9 0.09
85 91 0.91
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (85 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATCAAAACCACAGATCTTATCTCTCTGAACTTGCAGTA
AAGCAGATCGCATCAAGCCA
Found at i:405781 original size:44 final size:44
Alignment explanation
Indices: 405411--405781 Score: 250
Period size: 44 Copynumber: 8.7 Consensus size: 44
405401 CGCACTTTTA
* * *
405411 ATCTCTCTGAAGTTGCAGTAGAGCAGATC-ACATC-CAG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* * * * *
405452 ATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCTACTA-ATCCT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCAC-AGATCTT
* * *
405496 ATCTCCCTGAAGTTGTAGTAGAGCGGATTAAAACCACAGATCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* * * ** *
405540 ATCTCTCTGAAGTTGCAGTAGAGTAAATC-GCATCA-AG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
**** * * *
405581 ATCTCCCT-AAGCAATAGTGGAGCAGA-CGAAAGA-AACCA-ATCCT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATC-AAA-ACCA-CAGATCTT
* * *
405624 ATCTCCCTGAAGTTGCAGTGGAGCAGAATTAAAACCA-ATATCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAG-ATCAAAACCACAGATCTT
* ** * *
405668 ATCTCTCTGAAGTTGCAGTAGAGCAGATC-GCATC-TAG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* * *
405709 ATCTCCATGAAGTTACAGTGGAGCAGATCAAAACCACAGATCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* * *
405753 ATCTCTCTGAACTTGCAGTAAAGCAGATC
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATC
405782 GCATCAAGCC
Statistics
Matches: 246, Mismatches: 64, Indels: 37
0.71 0.18 0.11
Matches are distributed among these distances:
39 1 0.00
40 11 0.04
41 67 0.27
42 9 0.04
43 22 0.09
44 131 0.53
45 5 0.02
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (44 bp):
ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
Done.