Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 119 of 198
Found at i:38255092 original size:3 final size:3
Alignment explanation
Indices: 38255079--38255126 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
38255069 ATAATTGTAA
38255079 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38255125 AA
1 AA
38255127 AAAATCAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38256099 original size:145 final size:146
Alignment explanation
Indices: 38255668--38256299 Score: 1117
Period size: 145 Copynumber: 4.3 Consensus size: 146
38255658 NNNNNNNNNN
38255668 AGCGGCGTTTTCTATAAAAACGCCGC-AAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
1 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
38255732 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCACTTTATAAGAAGCGCC
66 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCACTTTATAAGAAGCGCC
*
38255797 GCTAAAGGTAAGCAAT
131 GCTAAAGGTAACCAAT
* *
38255813 AGCGGCGTTTTCTATAAAAATGCCACAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
1 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
* * *
38255878 GAATAGCAAAACGGTGTCATTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCC
66 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCACTTTATAAGAAGCGCC
38255943 GCTAAAGGTAACCAAT
131 GCTAAAGGTAACCAAT
*
38255959 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAT-AAAAAATTTTA
1 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
* * *
38256023 GAATAGCAAAACGGCGTCGTTTGGTTCAAAATGAAAAAATTTTGCGGCGCTTTACAAGAAGCGCC
66 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCACTTTATAAGAAGCGCC
38256088 GCTAAAGGTAACCAAT
131 GCTAAAGGTAACCAAT
* *
38256104 AACGGCGTTTTCTATAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAAT-AAAAAAATTTA
1 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
* *
38256168 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCACTTTATAACAAGCGCC
66 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCACTTTATAAGAAGCGCC
38256233 GCTAAAGGTAACCAAT
131 GCTAAAGGTAACCAAT
38256249 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
1 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
38256300 TTTCCCAAAA
Statistics
Matches: 463, Mismatches: 23, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
145 297 0.64
146 166 0.36
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (146 bp):
AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCACTTTATAAGAAGCGCC
GCTAAAGGTAACCAAT
Found at i:38256165 original size:20 final size:20
Alignment explanation
Indices: 38256130--38256167 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38256120 AAAACGCCAC
**
38256130 AAAAAATAAATCAATTTATA
1 AAAAAATAAAAAAATTTATA
38256150 AAAAAATAAAAAAATTTA
1 AAAAAATAAAAAAATTTA
38256168 GAATAGCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATAAAAAAATTTATA
Found at i:38256208 original size:291 final size:291
Alignment explanation
Indices: 38255668--38256299 Score: 1126
Period size: 291 Copynumber: 2.2 Consensus size: 291
38255658 NNNNNNNNNN
38255668 AGCGGCGTTTTCTATAAAAACGCCGC-AAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
1 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
* *
38255732 GAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCACTTTATAAGAAGCGCC
66 GAATAGCAAAACGGCGTCGTTTGGTTCAAAATGAAAAAATTTTGCGGCACTTTACAAGAAGCGCC
* * *
38255797 GCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAATGCCACAAAAAATAAATCAATTTATAAAA
131 GCTAAAGGTAACCAATAACGGCGTTTTCTATAAAAACGCCACAAAAAATAAATCAATTTATAAAA
* *
38255862 AAATAAAAAAAATTTAGAATAGCAAAACGGTGTCATTTTGTTCAAAATGAAAAAATTTTGCGGCG
196 AAATAAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAA-TTTGCGGCA
*
38255927 CTTTATAAGAAGCGCCGCTAAAGGTAACCAAT
260 CTTTATAACAAGCGCCGCTAAAGGTAACCAAT
*
38255959 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAT-AAAAAATTTTA
1 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
*
38256023 GAATAGCAAAACGGCGTCGTTTGGTTCAAAATGAAAAAATTTTGCGGCGCTTTACAAGAAGCGCC
66 GAATAGCAAAACGGCGTCGTTTGGTTCAAAATGAAAAAATTTTGCGGCACTTTACAAGAAGCGCC
38256088 GCTAAAGGTAACCAATAACGGCGTTTTCTATAAAAACGCCACAAAAAATAAATCAATTTATAAAA
131 GCTAAAGGTAACCAATAACGGCGTTTTCTATAAAAACGCCACAAAAAATAAATCAATTTATAAAA
*
38256153 AAAT-AAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCA
196 AAATAAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATG-AAAAAATTTGCGGCA
38256217 CTTTATAACAAGCGCCGCTAAAGGTAACCAAT
260 CTTTATAACAAGCGCCGCTAAAGGTAACCAAT
38256249 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
1 AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
38256300 TTTCCCAAAA
Statistics
Matches: 328, Mismatches: 11, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
290 132 0.40
291 170 0.52
292 26 0.08
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (291 bp):
AGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTA
GAATAGCAAAACGGCGTCGTTTGGTTCAAAATGAAAAAATTTTGCGGCACTTTACAAGAAGCGCC
GCTAAAGGTAACCAATAACGGCGTTTTCTATAAAAACGCCACAAAAAATAAATCAATTTATAAAA
AAATAAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAATTTGCGGCAC
TTTATAACAAGCGCCGCTAAAGGTAACCAAT
Found at i:38256593 original size:15 final size:15
Alignment explanation
Indices: 38256573--38256602 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38256563 AAATCTCCCT
38256573 AAATCGATTCCCCAG
1 AAATCGATTCCCCAG
38256588 AAATCGATTCCCCAG
1 AAATCGATTCCCCAG
38256603 TAATGCTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
AAATCGATTCCCCAG
Found at i:38260783 original size:13 final size:13
Alignment explanation
Indices: 38260765--38260807 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
38260755 TTTTATTTTG
*
38260765 ATTTAAAATTAGA
1 ATTTAAAATTAAA
*
38260778 ATTTAAAAATAAA
1 ATTTAAAATTAAA
* *
38260791 ATTCAAAATTACA
1 ATTTAAAATTAAA
38260804 ATTT
1 ATTT
38260808 TGCATTGAGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (13 bp):
ATTTAAAATTAAA
Found at i:38262348 original size:43 final size:43
Alignment explanation
Indices: 38262270--38262435 Score: 201
Period size: 43 Copynumber: 3.9 Consensus size: 43
38262260 TTTTTGGCAG
* *
38262270 AAGCGCCGCAAAAGGTCATGATCTTTTAGCGGCGTTTGTAATAA
1 AAGCGCCGCTAAAGGTCATGA-CCTTTAGCGGCGTTTGTAATAA
* * *
38262314 AAGCGTCGCTAAAGGTCCTGACCTTTAGCGGCGTTTGTAAGAA
1 AAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGTTTGTAATAA
* * * * *
38262357 AAGCGCCACTAAAGGTCCTGGCCTTTTGCGGCGTTT-T-TTAA
1 AAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGTTTGTAATAA
* *
38262398 AAGCGCCGCTAAAAGTCATGACCTTTAGCGACGTTTGT
1 AAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGTTTGT
38262436 TTCTAAAAAC
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
41 32 0.31
42 2 0.02
43 52 0.50
44 18 0.17
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGTTTGTAATAA
Found at i:38267938 original size:7 final size:7
Alignment explanation
Indices: 38267926--38267955 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
38267916 TGAACACCAA
38267926 TCTCTTC
1 TCTCTTC
38267933 TCTCTTC
1 TCTCTTC
38267940 TCTCTTC
1 TCTCTTC
38267947 TCTCTTC
1 TCTCTTC
38267954 TC
1 TC
38267956 ATTAGACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
TCTCTTC
Found at i:38269564 original size:128 final size:128
Alignment explanation
Indices: 38269336--38269587 Score: 495
Period size: 128 Copynumber: 2.0 Consensus size: 128
38269326 AACTTACTGG
38269336 CAATTGTTGAGAAAATGTTATATGGCATATTTTACTAAATACCATCTGACTCTTAGCACAATACA
1 CAATTGTTGAGAAAATGTTATATGGCATATTTTACTAAATACCATCTGACTCTTAGCACAATACA
38269401 GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGCACTT
66 GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGCACTT
*
38269464 CAATTGTTGAGAAAATGTTATATGGCTTATTTTACTAAATACCATCTGACTCTTAGCACAATACA
1 CAATTGTTGAGAAAATGTTATATGGCATATTTTACTAAATACCATCTGACTCTTAGCACAATACA
38269529 GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGC
66 GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGC
38269588 TTTGAAGTGC
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 123 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (128 bp):
CAATTGTTGAGAAAATGTTATATGGCATATTTTACTAAATACCATCTGACTCTTAGCACAATACA
GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGCACTT
Found at i:38281851 original size:3 final size:3
Alignment explanation
Indices: 38281845--38281870 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38281835 ATTTTTTTCT
38281845 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
38281871 TAACTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:38296448 original size:16 final size:16
Alignment explanation
Indices: 38296427--38296459 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38296417 TCTGCTTTTA
38296427 AAAAAAAAGAGAAAAT
1 AAAAAAAAGAGAAAAT
*
38296443 AAAAAAAAGGGAAAAT
1 AAAAAAAAGAGAAAAT
38296459 A
1 A
38296460 GAGAAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAAAAAAGAGAAAAT
Found at i:38299562 original size:17 final size:17
Alignment explanation
Indices: 38299542--38299580 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
38299532 TTGTTAGTTT
38299542 TTGATTAAAGGATT-GAA
1 TTGATTAAAGG-TTAGAA
*
38299559 TTGATTAAATGTTAGAA
1 TTGATTAAAGGTTAGAA
38299576 TTGAT
1 TTGAT
38299581 AGGGAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (17 bp):
TTGATTAAAGGTTAGAA
Found at i:38300262 original size:20 final size:20
Alignment explanation
Indices: 38300239--38300302 Score: 87
Period size: 19 Copynumber: 3.3 Consensus size: 20
38300229 GCATTTCGGC
38300239 GCCTCTGTTTGCACTTTGGT
1 GCCTCTGTTTGCACTTTGGT
* *
38300259 GCCTCTG-TTACACTTCGGT
1 GCCTCTGTTTGCACTTTGGT
*
38300278 TCC-CTGTTTGCACTTTGGT
1 GCCTCTGTTTGCACTTTGGT
38300297 GCCTCT
1 GCCTCT
38300303 ATTACGCATC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 3 0.08
19 24 0.67
20 9 0.25
ACGTcount: A:0.06, C:0.30, G:0.22, T:0.42
Consensus pattern (20 bp):
GCCTCTGTTTGCACTTTGGT
Found at i:38300291 original size:19 final size:20
Alignment explanation
Indices: 38300227--38300302 Score: 84
Period size: 19 Copynumber: 3.9 Consensus size: 20
38300217 TTATATGGGA
* *
38300227 TTGCATTTCGGCGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
*
38300247 TTGCACTTTGGTGCCTCTG-
1 TTGCACTTCGGTGCCTCTGT
* *
38300266 TTACACTTCGGTTCC-CTGT
1 TTGCACTTCGGTGCCTCTGT
*
38300285 TTGCACTTTGGTGCCTCT
1 TTGCACTTCGGTGCCTCT
38300303 ATTACGCATC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
18 3 0.07
19 24 0.53
20 18 0.40
ACGTcount: A:0.07, C:0.29, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGT
Found at i:38306847 original size:28 final size:28
Alignment explanation
Indices: 38306816--38306869 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
38306806 GTAAAAGGTA
*
38306816 CTTTTA-AAAAGCAGTGTATACCAAACCG
1 CTTTTAGAAAA-CACTGTATACCAAACCG
*
38306844 CTTTTAGAAAACACTTTATACCAAAC
1 CTTTTAGAAAACACTGTATACCAAAC
38306870 ACACTTCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (28 bp):
CTTTTAGAAAACACTGTATACCAAACCG
Found at i:38308167 original size:12 final size:12
Alignment explanation
Indices: 38308137--38308169 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
38308127 ATAACTAATA
*
38308137 CTAACTACTCTG
1 CTAACTGCTCTG
38308149 CTAACTGCTCTG
1 CTAACTGCTCTG
38308161 CTAACTGCT
1 CTAACTGCT
38308170 AACTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (12 bp):
CTAACTGCTCTG
Found at i:38312834 original size:12 final size:12
Alignment explanation
Indices: 38312804--38312836 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
38312794 ATGACTAATA
*
38312804 CTAACTACTCTG
1 CTAACTGCTCTG
38312816 CTAACTGCTCTG
1 CTAACTGCTCTG
38312828 CTAACTGCT
1 CTAACTGCT
38312837 AACTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (12 bp):
CTAACTGCTCTG
Found at i:38317926 original size:20 final size:18
Alignment explanation
Indices: 38317885--38317927 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
38317875 TACTAGTTTT
* *
38317885 AATTGACTTGATTAATTT
1 AATTTACTTGATTAATTA
38317903 AATTTACTTGATCATAATTA
1 AATTTACTTGAT--TAATTA
38317923 AATTT
1 AATTT
38317928 TCTAAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (18 bp):
AATTTACTTGATTAATTA
Found at i:38320099 original size:51 final size:51
Alignment explanation
Indices: 38320037--38320253 Score: 371
Period size: 51 Copynumber: 4.3 Consensus size: 51
38320027 GATCACATTT
*
38320037 ATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
38320088 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
* ** *
38320139 ATCACTTGTCACTTGTCACTGATCAGATAAGCGTAGCTAAAGCTGTCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
38320190 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
38320241 ATCTCTTGTCACT
1 ATCACTTGTCACT
38320254 GATCAGAAGT
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 157 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
Found at i:38323360 original size:30 final size:30
Alignment explanation
Indices: 38323325--38323385 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
38323315 TCTAATTTGA
38323325 ACACAATAATCACTTGTTCATCCTAAAAAC
1 ACACAATAATCACTTGTTCATCCTAAAAAC
*
38323355 ACACAATAATCATTTGTTCATCCTAAAAAC
1 ACACAATAATCACTTGTTCATCCTAAAAAC
38323385 A
1 A
38323386 GACCTCTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.03, T:0.28
Consensus pattern (30 bp):
ACACAATAATCACTTGTTCATCCTAAAAAC
Found at i:38325316 original size:26 final size:25
Alignment explanation
Indices: 38325287--38325342 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
38325277 AATAAAATAA
*
38325287 AAAAATTTAAAACAT-GTTTGTTAATT
1 AAAAATTTAAAA-ATAG-TTATTAATT
*
38325313 AAAAATTTGAAAATAGTTATTAATT
1 AAAAATTTAAAAATAGTTATTAATT
38325338 AAAAA
1 AAAAA
38325343 CATTAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (25 bp):
AAAAATTTAAAAATAGTTATTAATT
Found at i:38328240 original size:2 final size:2
Alignment explanation
Indices: 38328233--38328261 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38328223 TTTGCCCCTT
38328233 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38328262 TTACTTCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38332445 original size:28 final size:28
Alignment explanation
Indices: 38332413--38332510 Score: 142
Period size: 28 Copynumber: 3.5 Consensus size: 28
38332403 TGACTTTCGA
*
38332413 CACTAAGTGTGAGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATGGTAAAG
38332441 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATGGTAAAG
* ** **
38332469 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATGGTAAAG
38332497 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
38332511 ACTTATTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATGGTAAAG
Found at i:38333342 original size:93 final size:93
Alignment explanation
Indices: 38333245--38333956 Score: 1298
Period size: 93 Copynumber: 7.7 Consensus size: 93
38333235 AAATGCTGCT
* *
38333245 CAAATTGGTATATATATGCTACCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATATATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
*
38333310 CGGTCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
*
38333338 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
*
38333403 CTGTCAAATTTTGTGTATAAGTGTTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
*
38333431 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCTAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
*
38333496 TTGTCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
* *
38333524 CAAATTGGTATATATATGCCGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATAGATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
38333589 CTGTCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
*
38333617 CAAATTGGTATATATATGCAGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
38333682 CTGTCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
38333710 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
*
38333775 CTATCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
* *
38333803 CAAATTGGTATATATATGTTGCTCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
*
38333868 CTGTCAAATTTTGTGTATAATTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
38333896 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATA
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATA
38333957 TATATATATG
Statistics
Matches: 596, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 596 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (93 bp):
CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
CTGTCAAATTTTGTGTATAAGTGCTGTC
Found at i:38333987 original size:29 final size:28
Alignment explanation
Indices: 38333904--38333987 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 28
38333894 TCCAAATTGG
* *
38333904 TATATATATGCTGCCCAATTTTGGTG-A
1 TATATATATGCTGCTCAATTTTGATGTA
*
38333931 -ATA-A-ATGCTG-TCCAATTTTGTATATA
1 TATATATATGCTGCT-CAATTTTG-ATGTA
38333957 TATATATATGCTGCTCAATTTCTGATGTA
1 TATATATATGCTGCTCAATTT-TGATGTA
38333986 TA
1 TA
38333988 AGAGCTGTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
24 14 0.31
25 2 0.04
26 4 0.09
27 3 0.07
28 1 0.02
29 18 0.40
30 3 0.07
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (28 bp):
TATATATATGCTGCTCAATTTTGATGTA
Found at i:38340817 original size:25 final size:25
Alignment explanation
Indices: 38340789--38340855 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
38340779 TACAGTCTAT
* *
38340789 CTATAGTAGTCTCAGTATATACTAC
1 CTATAATAGTCTCAGGATATACTAC
* *
38340814 CTATAATAGTTTCAGGATATACTAT
1 CTATAATAGTCTCAGGATATACTAC
* * *
38340839 CAAAAATAGTTTCAGGA
1 CTATAATAGTCTCAGGA
38340856 AACTTACTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (25 bp):
CTATAATAGTCTCAGGATATACTAC
Found at i:38347448 original size:32 final size:30
Alignment explanation
Indices: 38347412--38347480 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
38347402 ATTGTAAAAC
*
38347412 AAAATAATACAAATGTGTTAAAATCATTAATT
1 AAAATAACACAAATGTGTTAAAATC--TAATT
* *
38347444 AAAATAACACAACTGTGTTAATATCTAATT
1 AAAATAACACAAATGTGTTAAAATCTAATT
38347474 ACAAATA
1 A-AAATA
38347481 TTTAATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 6 0.18
31 5 0.15
32 22 0.67
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (30 bp):
AAAATAACACAAATGTGTTAAAATCTAATT
Found at i:38351291 original size:3 final size:3
Alignment explanation
Indices: 38351283--38351334 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
38351273 GTATGTATAT
38351283 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38351331 ATA A
1 ATA A
38351335 ATAGGGATTA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:38352692 original size:43 final size:44
Alignment explanation
Indices: 38352628--38352739 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 44
38352618 CTTGGGTCCA
* * * * *
38352628 CTCCACTGTAACTTCAAGGAGATAAAATTATCGG-TTTTATCTG
1 CTCCACTGCAACTTCAGGGAGATAAAATTATCGGCCTTAATATG
* * *
38352671 CTCCACTGCAACTTCAGGGAGATAAGATTATTGGCCTTAATATT
1 CTCCACTGCAACTTCAGGGAGATAAAATTATCGGCCTTAATATG
* *
38352715 CTCCACTGCAACTTTAGGGAAATAA
1 CTCCACTGCAACTTCAGGGAGATAA
38352740 GATTCGCCCA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
43 30 0.52
44 28 0.48
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAAATTATCGGCCTTAATATG
Found at i:38353005 original size:132 final size:132
Alignment explanation
Indices: 38352768--38353233 Score: 747
Period size: 132 Copynumber: 3.5 Consensus size: 132
38352758 TGCCTCACTG
* * * * *
38352768 CCAATATAAGAAGACAGGATCTGTTATTTTCGATCCACTTCATGCCAATACATGAAGACAAGATC
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
* *
38352833 TACTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTACATCTTCGATCCACTTCC
66 TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCC
38352898 TA
131 TA
* * *
38352900 CCAATATAGGAAGACAAGATCTG-TAATCTTCGATCTATTTCAAGCCAATACATGAAGACAAGAT
1 CCAATATAGGAAGACAGGATCTGCT-ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
38352964 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC
65 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC
38353029 CTA
130 CTA
*
38353032 CCAATATAGGAAGACAGGATCTGCTA-CATTCGATCTACTTCACGCCAATACATGAAGACGAGAT
1 CCAATATAGGAAGACAGGATCTGCTATC-TTCGATCTACTTCACGCCAATACATGAAGACAAGAT
* * * * *
38353096 CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTAGATTCATTTC
65 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC
38353161 CTA
130 CTA
*
38353164 CAAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
38353229 TGCTT
66 TGCTT
38353234 CTTTTTAGCC
Statistics
Matches: 311, Mismatches: 19, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
131 2 0.01
132 307 0.99
133 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (132 bp):
CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCC
TA
Found at i:38353231 original size:44 final size:44
Alignment explanation
Indices: 38352768--38353236 Score: 438
Period size: 44 Copynumber: 10.7 Consensus size: 44
38352758 TGCCTCACTG
* * * * * **
38352768 CCAATATAAGAAGACAGGATCTGTTATTTTCGATCCACTTCATG
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
* * * * *
38352812 CCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACA
* * *
38352857 CCAATATGGGAAGACAAGATCTAC-ATCTTCGATCCACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-A
*
38352900 CCAATATAGGAAGACAAGATCTG-TAATCTTCGATCTATTTCA-A
1 CCAATATAGGAAGACAAGATCTGCT-ATCTTCGATCTACTTCACA
* * * *
38352943 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
1 -CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACA
* *
38352989 CCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-A
* *
38353032 CCAATATAGGAAGACAGGATCTGCTA-CATTCGATCTACTTCACG
1 CCAATATAGGAAGACAAGATCTGCTATC-TTCGATCTACTTCACA
* * * *
38353076 CCAATACATGAAGACGAGATCTGCTTTCTTCGATCTACTTCACCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CA
* * * *
38353121 CCAGTATGGGAAGACAAGATCTGC-ATCTTAGAT-TCATTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCT-ACTTCAC-A
* * *
38353164 CAAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
* *
38353208 CCAATACATGAAGACAAGATCTGCT-TCTT
1 CCAATATAGGAAGACAAGATCTGCTATCTT
38353237 TTTAGCCTGC
Statistics
Matches: 346, Mismatches: 59, Indels: 41
0.78 0.13 0.09
Matches are distributed among these distances:
42 3 0.01
43 73 0.21
44 202 0.58
45 67 0.19
46 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (44 bp):
CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
Found at i:38359915 original size:13 final size:13
Alignment explanation
Indices: 38359870--38359917 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
38359860 AAATGGCTTT
*
38359870 TAAAAGTATATTA
1 TAAAAATATATTA
* *
38359883 TAAAATAAAAATTA
1 TAAAA-ATATATTA
*
38359897 TTAAAATATATTA
1 TAAAAATATATTA
38359910 TAAAAATA
1 TAAAAATA
38359918 ATTCATCACA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
TAAAAATATATTA
Found at i:38364079 original size:38 final size:38
Alignment explanation
Indices: 38364037--38364112 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
38364027 CAAGTACTTG
38364037 ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
1 ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
38364075 ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
1 ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
38364113 TTCGATTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (38 bp):
ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
Found at i:38367838 original size:31 final size:28
Alignment explanation
Indices: 38367800--38367856 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 28
38367790 TTTTTTTAAA
38367800 TGTATGTATATTATTATAAAAAATAATAATG
1 TGTATGTATA-TA-TAT-AAAAATAATAATG
*
38367831 TGTATGTATATATATAATAATAATAA
1 TGTATGTATATATATAAAAATAATAA
38367857 AAATAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 3 0.12
30 2 0.08
31 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
TGTATGTATATATATAAAAATAATAATG
Found at i:38370995 original size:41 final size:41
Alignment explanation
Indices: 38370950--38371029 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
38370940 TCGAAGCCTA
* *
38370950 ATATAACACACCGGCACAAAGCCTACTAGGCACAAAACCTG
1 ATATAACACACCAGCACAAAGCCTACTAGACACAAAACCTG
* * * * *
38370991 ATATAATACATCAGCACTAAGCCTGCTAGACACATAACC
1 ATATAACACACCAGCACAAAGCCTACTAGACACAAAACC
38371030 CGAATATCAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.41, C:0.30, G:0.12, T:0.16
Consensus pattern (41 bp):
ATATAACACACCAGCACAAAGCCTACTAGACACAAAACCTG
Found at i:38371067 original size:22 final size:22
Alignment explanation
Indices: 38371028--38371073 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
38371018 AGACACATAA
** *
38371028 CCCGAATATCACTGGCACAGAG
1 CCCGAATATCACCAGCACAAAG
38371050 CCCGAATATCACCAGCACAAAG
1 CCCGAATATCACCAGCACAAAG
38371072 CC
1 CC
38371074 TGCTAGGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.17, T:0.11
Consensus pattern (22 bp):
CCCGAATATCACCAGCACAAAG
Found at i:38371092 original size:38 final size:38
Alignment explanation
Indices: 38371041--38371127 Score: 147
Period size: 38 Copynumber: 2.3 Consensus size: 38
38371031 GAATATCACT
38371041 GGCACAGAGCCCGAATATCACCAGCACAAAGCCTGCTA
1 GGCACAGAGCCCGAATATCACCAGCACAAAGCCTGCTA
* *
38371079 GGCACAGAGCCCGAATATGACCGGCACAAAGCCTGCTA
1 GGCACAGAGCCCGAATATCACCAGCACAAAGCCTGCTA
*
38371117 GGCACAAAGCC
1 GGCACAGAGCC
38371128 TAAATAATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.33, C:0.33, G:0.24, T:0.09
Consensus pattern (38 bp):
GGCACAGAGCCCGAATATCACCAGCACAAAGCCTGCTA
Found at i:38373972 original size:2 final size:2
Alignment explanation
Indices: 38373965--38373999 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38373955 ATTCCATGTT
38373965 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 T
38374000 TTCATTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38374519 original size:18 final size:19
Alignment explanation
Indices: 38374493--38374533 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
38374483 TTCATTTCGA
38374493 AAAACAATTAAA-TATTAT
1 AAAACAATTAAATTATTAT
* *
38374511 AAAATAATTAAATTATTTT
1 AAAACAATTAAATTATTAT
38374530 AAAA
1 AAAA
38374534 ATATGAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAACAATTAAATTATTAT
Found at i:38378944 original size:22 final size:22
Alignment explanation
Indices: 38378919--38378975 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 22
38378909 CCCTTTTGAC
38378919 ATTAAAATATTATTTTTAATTT
1 ATTAAAATATTATTTTTAATTT
*
38378941 ATT---AT-TT-TATTT-ATTT
1 ATTAAAATATTATTTTTAATTT
38378957 ATTAAAAATATTATTTTTA
1 ATT-AAAATATTATTTTTA
38378976 TAGTTGGTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 13
0.63 0.05 0.32
Matches are distributed among these distances:
16 7 0.27
17 4 0.15
18 2 0.08
19 2 0.08
20 2 0.08
21 2 0.08
22 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTAAAATATTATTTTTAATTT
Found at i:38380213 original size:18 final size:19
Alignment explanation
Indices: 38380176--38380216 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
38380166 TAAATCTTAC
*
38380176 CAAACTAATTATAATAATT
1 CAAACTAATAATAATAATT
*
38380195 CAAAC-AATAATAATCATT
1 CAAACTAATAATAATAATT
38380213 CAAA
1 CAAA
38380217 AGAAACCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (19 bp):
CAAACTAATAATAATAATT
Found at i:38381952 original size:10 final size:10
Alignment explanation
Indices: 38381939--38382047 Score: 56
Period size: 10 Copynumber: 11.5 Consensus size: 10
38381929 ATAAAAAAAT
38381939 AAAATTTATA
1 AAAATTTATA
*
38381949 AAAA-TTATT
1 AAAATTTATA
*
38381958 AAATTTTAATA
1 AAAATTT-ATA
38381969 AATAA-TT-TA
1 AA-AATTTATA
*
38381978 AAATTTTATTA
1 AAAATTTA-TA
38381989 AAAA-TTAT-
1 AAAATTTATA
38381997 --AATTTA-A
1 AAAATTTATA
*
38382004 AAAAATTATA
1 AAAATTTATA
* *
38382014 AAAAATCATA
1 AAAATTTATA
*
38382024 AAATTTTATA
1 AAAATTTATA
*
38382034 AAAA-TCATA
1 AAAATTTATA
38382043 AAAAT
1 AAAAT
38382048 AATTATAAGT
Statistics
Matches: 74, Mismatches: 13, Indels: 24
0.67 0.12 0.22
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 1 0.01
9 27 0.36
10 29 0.39
11 11 0.15
12 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAATTTATA
Found at i:38381981 original size:20 final size:20
Alignment explanation
Indices: 38381937--38382016 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
38381927 ATATAAAAAA
38381937 ATAAAA-TTT-ATAAAAATT
1 ATAAAATTTTAATAAAAATT
*
38381955 ATTAAATTTTAATAAATAATT
1 ATAAAATTTTAATAAA-AATT
*
38381976 -TAAAATTTTATTAAAAATT
1 ATAAAATTTTAATAAAAATT
38381995 AT--AA-TTTAA-AAAAATT
1 ATAAAATTTTAATAAAAATT
38382011 ATAAAA
1 ATAAAA
38382017 AATCATAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
16 9 0.17
17 4 0.08
18 9 0.17
19 7 0.13
20 19 0.37
21 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAATTTTAATAAAAATT
Found at i:38382001 original size:38 final size:36
Alignment explanation
Indices: 38381937--38382016 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 36
38381927 ATATAAAAAA
38381937 ATAAAATTTATAAAAATTATTAAATTTTAATAAATAATT
1 ATAAAATTTATAAAAATTATTAAA-TTTAA-AAA-AATT
38381976 -TAAAATTTTATTAAAAATTA-T-AATTTAAAAAAATT
1 ATAAAA-TTTA-TAAAAATTATTAAATTTAAAAAAATT
38382011 ATAAAA
1 ATAAAA
38382017 AATCATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
35 4 0.11
36 8 0.21
37 5 0.13
38 7 0.18
39 5 0.13
40 9 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
ATAAAATTTATAAAAATTATTAAATTTAAAAAAATT
Found at i:38382017 original size:26 final size:25
Alignment explanation
Indices: 38381970--38382024 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
38381960 ATTTTAATAA
** * *
38381970 ATAATTTAAAATTTTATTAAAAATT
1 ATAATTTAAAAAATTATAAAAAATC
38381995 ATAATTTAAAAAAATTATAAAAAATC
1 ATAATTT-AAAAAATTATAAAAAATC
38382021 ATAA
1 ATAA
38382025 AATTTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAATTTAAAAAATTATAAAAAATC
Found at i:38382036 original size:19 final size:18
Alignment explanation
Indices: 38382005--38382045 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
38381995 ATAATTTAAA
38382005 AAAATTATAAAAAATCAT
1 AAAATTATAAAAAATCAT
*
38382023 AAAATTTTATAAAAATCAT
1 AAAATTATA-AAAAATCAT
38382042 AAAA
1 AAAA
38382046 ATAATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTATAAAAAATCAT
Found at i:38382960 original size:20 final size:20
Alignment explanation
Indices: 38382935--38382989 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
38382925 TACGATAATG
38382935 TTTATAATTTTTTTACGA-AT
1 TTTATAATTTTTTTAC-ATAT
* *
38382955 TTTAT-ATTTCTTTACATTT
1 TTTATAATTTTTTTACATAT
*
38382974 TTTATAATTTTCTTAC
1 TTTATAATTTTTTTAC
38382990 CACTTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTATAATTTTTTTACATAT
Found at i:38383112 original size:10 final size:10
Alignment explanation
Indices: 38383002--38383113 Score: 51
Period size: 10 Copynumber: 11.6 Consensus size: 10
38382992 CTTTATAAAA
*
38383002 TTTTATAATTT
1 TTTTAT-ATAT
*
38383013 TTTTCTATAT
1 TTTTATATAT
*
38383023 TTCTATATA-
1 TTTTATATAT
38383032 TTTTATA-AT
1 TTTTATATAT
38383041 TATTT-TATGAT
1 T-TTTATAT-AT
* *
38383052 TTTTATAAAA
1 TTTTATATAT
* *
38383062 ATTTACAT-T
1 TTTTATATAT
38383071 TTTTATAT-T
1 TTTTATATAT
*
38383080 TTTT-TACGA-
1 TTTTATA-TAT
*
38383089 TTTT-TATAC
1 TTTTATATAT
38383098 TTTTATATAT
1 TTTTATATAT
38383108 TTTTAT
1 TTTTAT
38383114 TAAAATTTAA
Statistics
Matches: 76, Mismatches: 16, Indels: 19
0.68 0.14 0.17
Matches are distributed among these distances:
8 4 0.05
9 30 0.39
10 32 0.42
11 10 0.13
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:38383118 original size:57 final size:58
Alignment explanation
Indices: 38383032--38383152 Score: 135
Period size: 57 Copynumber: 2.1 Consensus size: 58
38383022 TTTCTATATA
* * *
38383032 TTTTATAATTATTTTATGATTTTTATAAAAATTT-A-CATTTTT-TATATTTTTTTACGAT
1 TTTTATAATTATTATATGATTTTTAT-AAAATTTAATCATTTTTATAAATTTTATT--GAT
*
38383090 TTTTATACTT-TTATAT-ATTTTTATTAAAATTTAATCATTTTTATAAATTTTATTGAT
1 TTTTATAATTATTATATGATTTTTA-TAAAATTTAATCATTTTTATAAATTTTATTGAT
38383147 TTTTAT
1 TTTTAT
38383153 TTTTTATTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
56 14 0.25
57 16 0.29
58 16 0.29
59 9 0.16
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (58 bp):
TTTTATAATTATTATATGATTTTTATAAAATTTAATCATTTTTATAAATTTTATTGAT
Found at i:38383139 original size:18 final size:18
Alignment explanation
Indices: 38382993--38383152 Score: 58
Period size: 19 Copynumber: 8.3 Consensus size: 18
38382983 TTCTTACCAC
*
38382993 TTTATAAAATTTTATAATTTT
1 TTTAT-AAA-TTTAT-ATATT
* * *
38383014 TTTCTATATTTCTATATAT
1 TTTATAAATTTATATAT-T
38383033 TTTATAATTATTT-TATGATT
1 TTTATAA--ATTTATAT-ATT
*
38383053 TTTATAAAAATTTACAT-TT
1 TTTAT--AAATTTATATATT
** * *
38383072 TTTATATTTTTTTACGATT
1 TTTATAAATTTATA-TATT
**
38383091 TTTATACTTTTATATATT
1 TTTATAAATTTATATATT
38383109 TTTATTAAAATTTA-ATCATT
1 TTTA-T-AAATTTATAT-ATT
38383129 TTTATAAATTT-TATTGATT
1 TTTATAAATTTATA-T-ATT
38383148 TTTAT
1 TTTAT
38383153 TTTTTATTAT
Statistics
Matches: 107, Mismatches: 18, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
17 5 0.05
18 17 0.16
19 44 0.41
20 27 0.25
21 12 0.11
22 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTATAAATTTATATATT
Found at i:38385885 original size:33 final size:30
Alignment explanation
Indices: 38385812--38385889 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 30
38385802 TTTAAGTAAT
*
38385812 TAATATT-AATTATTTTTAAAATTTAATTA
1 TAATATTAAATTATTTTTAAAATTTAAATA
*
38385841 GAATATATAAATTATATTTTAAATATTTAAATA
1 TAATAT-TAAATTAT-TTTTAAA-ATTTAAATA
38385874 TAATCATTAAA-TATTT
1 TAAT-ATTAAATTATTT
38385890 ATAATTAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 5 0.12
30 1 0.02
31 8 0.20
32 10 0.24
33 15 0.37
34 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TAATATTAAATTATTTTTAAAATTTAAATA
Found at i:38385903 original size:21 final size:19
Alignment explanation
Indices: 38385809--38385904 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 19
38385799 ATTTTTAAGT
*
38385809 AATTAATATTAATTATTTTTAA
1 AATTAATATTAA--ATATTT-A
* *
38385831 AATTTA-ATTAGAATATATA
1 AATTAATATTA-AATATTTA
*
38385850 AATTATATTTTAAATATTTA
1 AATTA-ATATTAAATATTTA
38385870 AATATAATCATTAAATATTTA
1 AAT-TAAT-ATTAAATATTTA
38385891 TAATTAGATATTAA
1 -AATTA-ATATTAA
38385905 TACAGTTGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
19 5 0.08
20 17 0.28
21 27 0.45
22 11 0.18
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTAATATTAAATATTTA
Found at i:38388952 original size:10 final size:11
Alignment explanation
Indices: 38388940--38389055 Score: 52
Period size: 11 Copynumber: 10.8 Consensus size: 11
38388930 TTATTTTAAA
38388940 ATTTTAAAAA-
1 ATTTTAAAAAT
*
38388950 A-TTAAAAAAGT
1 ATTTTAAAAA-T
38388961 ATTTTAAAAAT
1 ATTTTAAAAAT
38388972 ATTTT--AAA-
1 ATTTTAAAAAT
38388980 A--TTAAAAA-
1 ATTTTAAAAAT
**
38388988 A-TAAAAAAAGT
1 ATTTTAAAAA-T
38388999 ATTTTAAAAAT
1 ATTTTAAAAAT
*
38389010 ATTTTAAAATTAAA
1 ATTTT-AAA--AAT
* **
38389024 AATAAAAAAAGT
1 ATTTTAAAAA-T
38389036 ATTTTAAAAAT
1 ATTTTAAAAAT
38389047 ATTTTAAAA
1 ATTTTAAAA
38389056 TTAAAAAAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
6 2 0.03
8 5 0.06
9 15 0.19
10 1 0.01
11 26 0.33
12 23 0.29
13 3 0.04
14 4 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:38388971 original size:30 final size:29
Alignment explanation
Indices: 38388931--38388988 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
38388921 ACCAAAAATT
38388931 TATTTTAAAAT-TTTAAAAAATTAAAAAAG
1 TATTTTAAAATATTT-AAAAATTAAAAAAG
*
38388960 TATTTTAAAAATATTTTAAAATTAAAAAA
1 TATTTT-AAAATATTTAAAAATTAAAAAA
38388989 TAAAAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.23
30 17 0.65
31 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TATTTTAAAATATTTAAAAATTAAAAAAG
Found at i:38388995 original size:38 final size:38
Alignment explanation
Indices: 38388931--38389072 Score: 241
Period size: 38 Copynumber: 3.7 Consensus size: 38
38388921 ACCAAAAATT
*
38388931 TATTTTAAAATTTTAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAA--TTAAAAAATAAAAAAAGTATTTTAAAAA
38388971 TATTTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAA
38389009 TATTTTAAAATT-AAAAATAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAA
38389046 TATTTTAAAATTAAAAAAATAAAAAAA
1 TATTTTAAAATT-AAAAAATAAAAAAA
38389073 ATAAATATAT
Statistics
Matches: 99, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
37 37 0.37
38 39 0.39
39 13 0.13
40 10 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (38 bp):
TATTTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAA
Found at i:38401644 original size:39 final size:39
Alignment explanation
Indices: 38401535--38401651 Score: 189
Period size: 39 Copynumber: 3.0 Consensus size: 39
38401525 TAGCAACTAT
* **
38401535 CAAAATCTCTCAACTATTACTAAATTCCCTATTGGAAAC
1 CAAAATCTCTCAACTATCACTAAATTTTCTATTGGAAAC
*
38401574 CAAAATCTCTCAAATCATCACTAAATTTTCTATTGGAAAC
1 CAAAATCTCTCAACT-ATCACTAAATTTTCTATTGGAAAC
38401614 CAAAATCTCTCAACTATCACTAAATTTTCTATTGGAAA
1 CAAAATCTCTCAACTATCACTAAATTTTCTATTGGAAA
38401652 ATAAATTCCA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
39 37 0.51
40 35 0.49
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.32
Consensus pattern (39 bp):
CAAAATCTCTCAACTATCACTAAATTTTCTATTGGAAAC
Found at i:38401718 original size:39 final size:36
Alignment explanation
Indices: 38401664--38401800 Score: 130
Period size: 39 Copynumber: 3.6 Consensus size: 36
38401654 AAATTCCATA
*
38401664 ACTAAAATTCCTATTGGAAAATCAATTTTGTAACAAAAT
1 ACTAAAATTCCTATT-GAAAAACAATTTT-TAAC-AAAT
* * * *
38401703 ACTAAAATTTCTATTGAAAAACAAAATCTTTCAACTATT
1 ACTAAAATTCCTATTGAAAAAC--AAT-TTTTAACAAAT
*
38401742 ACTAAAATTCCTATTGAAAAAACATTTTTATAACCAAAT
1 ACTAAAATTCCTATTG-AAAAACAATTTT-TAA-CAAAT
*
38401781 ACTATAATTCCTATTGAAAA
1 ACTAAAATTCCTATTGAAAA
38401801 CACATGTGAC
Statistics
Matches: 81, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
37 3 0.04
38 14 0.17
39 49 0.60
40 12 0.15
41 3 0.04
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (36 bp):
ACTAAAATTCCTATTGAAAAACAATTTTTAACAAAT
Found at i:38401899 original size:21 final size:21
Alignment explanation
Indices: 38401873--38401921 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
38401863 ATTCTAGAAA
38401873 TTATAATGTCAAAAATTATTT
1 TTATAATGTCAAAAATTATTT
* **
38401894 TTATAATTTGTAAAATTATTT
1 TTATAATGTCAAAAATTATTT
38401915 TTATAAT
1 TTATAAT
38401922 TTTCATACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
TTATAATGTCAAAAATTATTT
Found at i:38401922 original size:21 final size:21
Alignment explanation
Indices: 38401884--38401923 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
38401874 TATAATGTCA
38401884 AAAATTATTTTTATAATTTGT
1 AAAATTATTTTTATAATTTGT
38401905 AAAATTATTTTTATAATTT
1 AAAATTATTTTTATAATTT
38401924 TCATACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AAAATTATTTTTATAATTTGT
Found at i:38401936 original size:21 final size:21
Alignment explanation
Indices: 38401886--38401954 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
38401876 TAATGTCAAA
38401886 AATTATTTTTATAATTTGTA-A-
1 AATT-TTTTTATAATTT-TATAC
38401907 AATTATTTTTATAATTTTCATAC
1 AATT-TTTTTATAATTTT-ATAC
* *
38401930 AATTTTTTTATGATTTTATAT
1 AATTTTTTTATAATTTTATAC
38401951 AATT
1 AATT
38401955 CAACTCAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.02
21 25 0.58
22 13 0.30
23 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (21 bp):
AATTTTTTTATAATTTTATAC
Found at i:38405561 original size:15 final size:15
Alignment explanation
Indices: 38405543--38405572 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38405533 TCTCTTTTCT
38405543 TTATACAAATAAGCA
1 TTATACAAATAAGCA
38405558 TTATACAAATAAGCA
1 TTATACAAATAAGCA
38405573 AGTACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (15 bp):
TTATACAAATAAGCA
Found at i:38405772 original size:3 final size:3
Alignment explanation
Indices: 38405764--38405827 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
38405754 CACCTAAAAA
38405764 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
38405812 TAT CAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
38405828 TTTGCTTACC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38414340 original size:15 final size:15
Alignment explanation
Indices: 38414320--38414350 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38414310 AAGATTTTTT
*
38414320 TTTAAAAACAATTTC
1 TTTAAAAAAAATTTC
38414335 TTTAAAAAAAATTTC
1 TTTAAAAAAAATTTC
38414350 T
1 T
38414351 CTACAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAAAAAATTTC
Found at i:38414560 original size:61 final size:56
Alignment explanation
Indices: 38414457--38414645 Score: 182
Period size: 61 Copynumber: 3.2 Consensus size: 56
38414447 ATTACTTTAA
* * *
38414457 TATTAAATTAATATAATACTCATTAAGATAAATATTAGATTAAATTTAAAATTAAATC
1 TATTAAATTAATAAAATA-TTATTAAGATAAATATTAAATTAAATTTAAAATTAAA-C
* ** *
38414515 TATTAAATTAATAGAATATTTATATACAAGATAAATATTAAATTAAAGATAATCAATTTAA-
1 TATTAAATTAATAAAATA-TTAT-T--AAGATAAATATTAAATTAAATTTAA--AATTAAAC
* * * * *
38414576 TATTAAATTAATAAAATACTATTAATATAAATATTTAATTTAATTTAATATTAAACC
1 TATTAAATTAATAAAATATTATTAAGATAAATATTAAATTAAATTTAAAATTAAA-C
38414633 TATTAAATTAATA
1 TATTAAATTAATA
38414646 TTATTTTTGG
Statistics
Matches: 108, Mismatches: 16, Indels: 15
0.78 0.12 0.11
Matches are distributed among these distances:
55 5 0.05
57 33 0.31
58 20 0.19
59 2 0.02
60 3 0.03
61 39 0.36
63 6 0.06
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (56 bp):
TATTAAATTAATAAAATATTATTAAGATAAATATTAAATTAAATTTAAAATTAAAC
Found at i:38418992 original size:44 final size:43
Alignment explanation
Indices: 38418909--38419028 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 43
38418899 ACAACGCTAT
* *
38418909 CGTCCCAGACGTGGTCTTACATGTAATCACATATTGATGCC-A
1 CGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCAA
*
38418951 CTGTCCTAGACAG-GGTCTTACACGTAAGTCACA-AGTCGATGCCAA
1 C-GTCCCAGAC-GTGGTCTTACACGTAA-TCACATA-TCGATGCCAA
38418996 CGTCCCAGACGTGGTCTTACACGATAA-CACATA
1 CGTCCCAGACGTGGTCTTACACG-TAATCACATA
38419029 ACACAATTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
42 1 0.02
43 27 0.41
44 33 0.50
45 5 0.08
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (43 bp):
CGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCAA
Found at i:38420967 original size:20 final size:20
Alignment explanation
Indices: 38420942--38420982 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
38420932 TGTTAAGTGT
38420942 AAGTTAATATTAATTATTGA
1 AAGTTAATATTAATTATTGA
38420962 AAGTTAATATTAATTATTGA
1 AAGTTAATATTAATTATTGA
38420982 A
1 A
38420983 GTAAGATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (20 bp):
AAGTTAATATTAATTATTGA
Found at i:38420991 original size:20 final size:20
Alignment explanation
Indices: 38420942--38420991 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
38420932 TGTTAAGTGT
*
38420942 AAGTTAATATTAATTATTGA
1 AAGTAAATATTAATTATTGA
*
38420962 AAGTTAATATTAATTATTG-
1 AAGTAAATATTAATTATTGA
38420981 AAGTAAGATAT
1 AAGTAA-ATAT
38420992 ATTACAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (20 bp):
AAGTAAATATTAATTATTGA
Found at i:38421662 original size:63 final size:63
Alignment explanation
Indices: 38421528--38421676 Score: 174
Period size: 63 Copynumber: 2.4 Consensus size: 63
38421518 TATCTCTAGA
* * * *** *
38421528 GAAGGTGTTGATATAGGGAATGATTGCACGTGTTGTGGTGCTTGTGTAAAATAAATTGGTGTT
1 GAAGGTGTTGATACAGAGAATGATTGCACGTGATGTGGTGCTTGTGTAAAATAAACCAGAGTT
* * * *
38421591 AAATGTGTTGATGCAGAGAATGATTGTACGTGATGTGGTGCTTGTGTAAAATAAACCAGAGTT
1 GAAGGTGTTGATACAGAGAATGATTGCACGTGATGTGGTGCTTGTGTAAAATAAACCAGAGTT
*
38421654 GAAGGTGTTTATAC-GAGGAATGA
1 GAAGGTGTTGATACAGA-GAATGA
38421677 GTGTGTGTAC
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
62 2 0.03
63 68 0.97
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.33
Consensus pattern (63 bp):
GAAGGTGTTGATACAGAGAATGATTGCACGTGATGTGGTGCTTGTGTAAAATAAACCAGAGTT
Found at i:38425581 original size:13 final size:13
Alignment explanation
Indices: 38425560--38425593 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38425550 TATTTGATTT
38425560 ATTATTTTATTTTA
1 ATTA-TTTATTTTA
*
38425574 GTTATTTATTTTA
1 ATTATTTATTTTA
38425587 ATTATTT
1 ATTATTT
38425594 TATCTGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
ATTATTTATTTTA
Found at i:38429704 original size:55 final size:55
Alignment explanation
Indices: 38429638--38429747 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
38429628 TACCCATGTG
*
38429638 GACGAAACTAGGGCATTTTCTAAGCCACATTTCTCACCCAAGTTGACACCAACCT
1 GACGAAACTAGGCCATTTTCTAAGCCACATTTCTCACCCAAGTTGACACCAACCT
38429693 GACGAAACTAGGCCATTTTCTAAGCCACATTTCTCACCCAAGTTGACACCAACCT
1 GACGAAACTAGGCCATTTTCTAAGCCACATTTCTCACCCAAGTTGACACCAACCT
38429748 AACCTCAACA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.31, C:0.32, G:0.14, T:0.24
Consensus pattern (55 bp):
GACGAAACTAGGCCATTTTCTAAGCCACATTTCTCACCCAAGTTGACACCAACCT
Found at i:38430337 original size:21 final size:20
Alignment explanation
Indices: 38430297--38430345 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
38430287 ATAAATGAAA
*
38430297 TCATTCATGTCAATTCCCTG
1 TCATTCATGACAATTCCCTG
*
38430317 TCATTCACTGACAATTTCCTG
1 TCATTCA-TGACAATTCCCTG
38430338 TCATTCAT
1 TCATTCAT
38430346 AACTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.41
Consensus pattern (20 bp):
TCATTCATGACAATTCCCTG
Found at i:38430541 original size:18 final size:21
Alignment explanation
Indices: 38430518--38430626 Score: 82
Period size: 21 Copynumber: 5.3 Consensus size: 21
38430508 CGAATACGCC
38430518 AACAGAAG-TC-GAA-AGCTG
1 AACAGAAGCTCAGAAGAGCTG
*
38430536 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCAGAAGAGCTG
* *
38430557 AACAGAAGCT-TGTAAGAGCTA
1 AACAGAAGCTCAG-AAGAGCTG
* * * * *
38430578 AATAGAAACTCATAGGAGTTG
1 AACAGAAGCTCAGAAGAGCTG
* * *
38430599 AACACAAGCTCATAAGAGCTA
1 AACAGAAGCTCAGAAGAGCTG
38430620 AACAGAA
1 AACAGAA
38430627 AGTAAAACAT
Statistics
Matches: 68, Mismatches: 18, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
18 8 0.12
19 2 0.03
20 2 0.03
21 56 0.82
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCAGAAGAGCTG
Found at i:38430557 original size:21 final size:21
Alignment explanation
Indices: 38430531--38430626 Score: 111
Period size: 21 Copynumber: 4.6 Consensus size: 21
38430521 AGAAGTCGAA
38430531 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
**
38430552 AGCTGAACAGAAGCTTGTAAG
1 AGCTGAACAGAAGCTCATAAG
* * * *
38430573 AGCTAAATAGAAACTCATAGG
1 AGCTGAACAGAAGCTCATAAG
* *
38430594 AGTTGAACACAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
*
38430615 AGCTAAACAGAA
1 AGCTGAACAGAA
38430627 AGTAAAACAT
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCATAAG
Found at i:38432567 original size:18 final size:18
Alignment explanation
Indices: 38432544--38432583 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
38432534 AAATCATATC
38432544 TTTGATCTTAAAGATAGT
1 TTTGATCTTAAAGATAGT
*
38432562 TTTGATTTTAAAGATAGT
1 TTTGATCTTAAAGATAGT
38432580 TTTG
1 TTTG
38432584 GTGCATAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (18 bp):
TTTGATCTTAAAGATAGT
Found at i:38439830 original size:124 final size:125
Alignment explanation
Indices: 38439633--38439901 Score: 425
Period size: 124 Copynumber: 2.2 Consensus size: 125
38439623 GTGAAACTGC
* *
38439633 ACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATATTTTTTTTTGATGTTTCTGAGCAAATAGTA
1 ACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATATATTTTTTTGACGTTTCTGAGCAAATAGTA
* *
38439698 TAAAATCGCTTCTAGCAAGATGCTATTTTGAGAAGAATTTGT-AAAATCGAGCCTTCGTGG
66 TAAAATCGCTTCGAGCAAGATGCTA-TTTGAGAAGAATTTGTGAAAATCGAGCCCTCGTGG
* *
38439758 ACGCACTTTTGCTACTGTAGGTCATGGAAGAAATA-ATTTTTTTGACGTTTCTGAGCAAATAGTA
1 ACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATATATTTTTTTGACGTTTCTGAGCAAATAGTA
** * *
38439822 TAAAATCGCTTCGATTAGGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGG
66 TAAAATCGCTTCGAGCAAGATGCTATTTGAGAAGAATTTGTGAAAATCGAGCCCTCGTGG
38439882 ACGCGCTTTTGCTACAGTAG
1 ACGCGCTTTTGCTACAGTAG
38439902 CATGTTTGGG
Statistics
Matches: 131, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
123 16 0.12
124 82 0.63
125 33 0.25
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (125 bp):
ACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATATATTTTTTTGACGTTTCTGAGCAAATAGTA
TAAAATCGCTTCGAGCAAGATGCTATTTGAGAAGAATTTGTGAAAATCGAGCCCTCGTGG
Found at i:38443062 original size:23 final size:23
Alignment explanation
Indices: 38443031--38443705 Score: 797
Period size: 23 Copynumber: 30.2 Consensus size: 23
38443021 AGTAAAATTA
*
38443031 TTAATTTAGTTTAGGGTTTTTAAT
1 TTAA-TTAGGTTAGGGTTTTTAAT
* * *
38443055 TAAATTAGTTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
* *
38443078 TAAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443101 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
38443122 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443145 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443168 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443189 TTAATTAGGTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443212 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443235 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443256 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
* *
38443279 TTAA--GGGTTTAGGGTTTTTAAG
1 TTAATTAGG-TTAGGGTTTTTAAT
*
38443301 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
* *
38443322 TAAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
* *
38443345 TTAA--GGGTTTAGGGTTTTTTAT
1 TTAATTAGG-TTAGGGTTTTTAAT
*
38443367 TTAATTAGGTTGGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443390 TTAATTGGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443413 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443436 TTAA--GGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
* *
38443458 TAAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443481 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
38443502 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443525 TTAATTAGGTCAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443548 TTAATTAGGTTAGGG-TTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443570 TTAA--GGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
*
38443592 TAAATT--GTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443613 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
* *
38443636 TTAA--GGGTTTAGGGTTTTTAAG
1 TTAATTAGG-TTAGGGTTTTTAAT
*
38443658 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
38443679 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
38443702 TTAA
1 TTAA
38443706 GGGTATTAAT
Statistics
Matches: 568, Mismatches: 57, Indels: 53
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.00
21 142 0.25
22 94 0.17
23 323 0.57
24 7 0.01
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (23 bp):
TTAATTAGGTTAGGGTTTTTAAT
Found at i:38443128 original size:44 final size:43
Alignment explanation
Indices: 38443041--38443709 Score: 740
Period size: 44 Copynumber: 15.0 Consensus size: 43
38443031 TTAATTTAGT
* * * *
38443041 TTAGGGTTTTTAATTAAATTAGTTTAGAGTTTTTAA-TTAAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTT-AA--GGG
* * * *
38443087 TTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATAGGTTAGGGTTTTTAAGTTAA--GGG
38443131 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAAGGG
* * *
38443175 TTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAA--GGG
* * * *
38443221 TTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATAGGTTAGGGTTTTTAAGTTAA--GGG
* *
38443265 TTAGGGTTTTTAAGTTAA-GGGTTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATAGG-TTAGGGTTTTTAAGTTAAGGG
*
38443308 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAAGGG
* * *
38443352 TTTAGGGTTTTTTATTTAATTAGGTTGGGGTTTTTAATTTAATTGGG
1 -TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAA--GGG
38443399 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAAGGG
*
38443443 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 -TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAAGGG
* *
38443488 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAA--GGG
*
38443534 TCAGGGTTTTTAATTTAATTAGGTTAGGG-TTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAAGGG
* * * *
38443577 TTTAGGGTTTTTAATTAAAT-TGTTAGGGTTTTTAATTTAATTAGG
1 -TTAGGGTTTTTAATTTAATAGGTTAGGGTTTTTAAGTTAA--GGG
* *
38443622 TTAGGGTTTTTAAGTTAA-GGGTTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATAGG-TTAGGGTTTTTAAGTTAAGGG
38443665 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAA-TAGGTTAGGGTTTTTAAGTTAAGGG
38443709 T
1 T
38443710 ATTAATGGTT
Statistics
Matches: 555, Mismatches: 46, Indels: 46
0.86 0.07 0.07
Matches are distributed among these distances:
42 7 0.01
43 50 0.09
44 241 0.43
45 132 0.24
46 122 0.22
47 3 0.01
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (43 bp):
TTAGGGTTTTTAATTTAATAGGTTAGGGTTTTTAAGTTAAGGG
Found at i:38443151 original size:67 final size:67
Alignment explanation
Indices: 38443041--38443709 Score: 964
Period size: 67 Copynumber: 10.0 Consensus size: 67
38443031 TTAATTTAGT
* * * *
38443041 TTAGGGTTTTTAATTAAATTAGTTTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
38443106 GG
66 GG
38443108 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
38443173 GG
66 GG
*
38443175 TTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
38443240 GG
66 GG
* *
38443242 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGTTAA
38443305 GGG
65 GGG
* * * * *
38443308 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTTAGGGTTTTTTATTTAA
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGTTAA
*
38443371 TTAGG
65 --GGG
* *
38443376 TTGGGGTTTTTAATTTAATTGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
38443441 GG
66 GG
* * * *
38443443 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAA
1 -TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
*
38443506 TTAGG
65 --GGG
*
38443511 TTAGGGTTTTTAATTTAATTAGGTCAGGGTTTTTAATTTAATTAGGTTAGGG-TTTTAAGTTAAG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
38443575 GG
66 GG
*
38443577 TTTAGGGTTTTTAATTAAATT--GTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
1 -TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
38443640 GGG
65 GGG
* *
38443643 TTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
1 -TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
38443706 GGG
65 GGG
38443709 T
1 T
38443710 ATTAATGGTT
Statistics
Matches: 551, Mismatches: 37, Indels: 30
0.89 0.06 0.05
Matches are distributed among these distances:
65 32 0.06
66 178 0.32
67 227 0.41
68 88 0.16
69 24 0.04
70 2 0.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (67 bp):
TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
GG
Found at i:38443754 original size:9 final size:9
Alignment explanation
Indices: 38443736--38443777 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
38443726 ATTCTCAAAT
38443736 AATA-TCAA
1 AATATTCAA
38443744 AATATTCAA
1 AATATTCAA
38443753 AATATTCAA
1 AATATTCAA
38443762 AATATTCAA
1 AATATTCAA
*
38443771 AAAATTC
1 AATATTC
38443778 TATTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 4 0.12
9 28 0.88
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (9 bp):
AATATTCAA
Found at i:38443804 original size:25 final size:24
Alignment explanation
Indices: 38443767--38443891 Score: 136
Period size: 25 Copynumber: 5.3 Consensus size: 24
38443757 TTCAAAATAT
38443767 TCAAA-AAATTCTATTTTATTACA
1 TCAAATAAATTCTATTTTATTACA
38443790 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAA-TTCTATTTTATTACA
** *
38443815 TCAAAT-AATATC-A--AAATAAC-
1 TCAAATAAAT-TCTATTTTATTACA
* *
38443835 TAAAAAAAATTCTATTTTATTACA
1 TCAAATAAATTCTATTTTATTACA
38443859 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAA-TTCTATTTTATTACA
38443884 TCAAATAA
1 TCAAATAA
38443892 TATCAAAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.07
21 8 0.10
23 11 0.13
24 14 0.17
25 44 0.53
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (24 bp):
TCAAATAAATTCTATTTTATTACA
Found at i:38443851 original size:69 final size:69
Alignment explanation
Indices: 38443769--38443901 Score: 266
Period size: 69 Copynumber: 1.9 Consensus size: 69
38443759 CAAAATATTC
38443769 AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
38443834 CTAA
66 CTAA
38443838 AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
1 AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
38443902 TTCAAAATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (69 bp):
AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
CTAA
Found at i:38444343 original size:18 final size:18
Alignment explanation
Indices: 38444320--38444359 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38444310 GACTCTGAAA
*
38444320 AGGATACAAATAAGGGTT
1 AGGATACAAATAAGGGCT
*
38444338 AGGATACATATAAGGGCT
1 AGGATACAAATAAGGGCT
38444356 AGGA
1 AGGA
38444360 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.20
Consensus pattern (18 bp):
AGGATACAAATAAGGGCT
Found at i:38445020 original size:7 final size:7
Alignment explanation
Indices: 38445010--38445034 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38445000 TTATATACAT
38445010 AATACTA
1 AATACTA
38445017 AATACTA
1 AATACTA
38445024 AATACTA
1 AATACTA
38445031 AATA
1 AATA
38445035 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:38445242 original size:20 final size:20
Alignment explanation
Indices: 38445205--38445242 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38445195 TTTATTTTTA
*
38445205 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
38445225 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
38445243 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:38446160 original size:12 final size:12
Alignment explanation
Indices: 38446136--38446178 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
38446126 ATTTTTACGG
38446136 TTTAAAAAA-AT
1 TTTAAAAAATAT
38446147 TTTAAAAAATAT
1 TTTAAAAAATAT
* *
38446159 TTTTAAAATTA-
1 TTTAAAAAATAT
38446170 TTTAAAAAA
1 TTTAAAAAA
38446179 AGGGAGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAAAAATAT
Found at i:38446268 original size:11 final size:11
Alignment explanation
Indices: 38446248--38446287 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
38446238 AAGAGAATTT
38446248 TTGA-AGGAAA
1 TTGAGAGGAAA
38446258 TTGAGAGGAAA
1 TTGAGAGGAAA
38446269 TTGAGAGGAAA
1 TTGAGAGGAAA
38446280 TTTGAGAG
1 -TTGAGAG
38446288 ATGATTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 17 0.61
12 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:38447085 original size:20 final size:20
Alignment explanation
Indices: 38447060--38447099 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38447050 TGAAAAATGA
*
38447060 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
38447080 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
38447100 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:38447115 original size:14 final size:15
Alignment explanation
Indices: 38447039--38447115 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38447029 GATTGGCAGT
* *
38447039 AAAAT-ATTTTTTGA
1 AAAATGATTTTCTGG
38447053 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
38447067 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
38447087 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
38447102 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
38447116 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:38447454 original size:37 final size:37
Alignment explanation
Indices: 38447404--38447475 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
38447394 CTTATTTTTT
38447404 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
1 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
38447441 CCATTAGATTAGAATTCACTAACTATTTAATTAAT
1 CCATTAGATTAGAATTCACTAACTATTTAATTAAT
38447476 TATGACCAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (37 bp):
CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
Found at i:38448823 original size:44 final size:44
Alignment explanation
Indices: 38448760--38448865 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 44
38448750 TGTAGGCTTT
* * *
38448760 CAAAAAATGCTCAAATCACCTAAACTCAAAATACTGAGTCATCC
1 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
38448804 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
1 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
38448848 CAAAACATGCTCAATATC
1 CAAAACATGCTC-ATATC
38448866 TCTACTTCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
44 53 0.91
45 5 0.09
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (44 bp):
CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
Found at i:38449156 original size:14 final size:14
Alignment explanation
Indices: 38449137--38449180 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
38449127 GTTGCAGGAC
*
38449137 TGGAGGTGGACCGG
1 TGGAGGTGGATCGG
*
38449151 TGGAGGTGGATCAG
1 TGGAGGTGGATCGG
38449165 TGGAGGTGGATCGG
1 TGGAGGTGGATCGG
38449179 TG
1 TG
38449181 CTCGGTGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.16, C:0.09, G:0.55, T:0.20
Consensus pattern (14 bp):
TGGAGGTGGATCGG
Found at i:38449463 original size:14 final size:14
Alignment explanation
Indices: 38449446--38449478 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
38449436 GTGGAGGGCC
38449446 GGAGGTGGACCGGT
1 GGAGGTGGACCGGT
*
38449460 GGAGGTGGATCGGT
1 GGAGGTGGACCGGT
38449474 GGAGG
1 GGAGG
38449479 ACGGAGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.09, G:0.61, T:0.15
Consensus pattern (14 bp):
GGAGGTGGACCGGT
Found at i:38468223 original size:29 final size:29
Alignment explanation
Indices: 38468188--38468260 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
38468178 ACTGTTAACT
*
38468188 GAACCGAAATTTTTTTAAAAAAATTTACC
1 GAACCGAAATTTTTTAAAAAAAATTTACC
38468217 GAACCGAAATTTTTTAAAAAAAATTTACC
1 GAACCGAAATTTTTTAAAAAAAATTTACC
38468246 GAACCGAAATTTTTT
1 GAACCGAAATTTTTT
38468261 CGGTTAATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (29 bp):
GAACCGAAATTTTTTAAAAAAAATTTACC
Found at i:38468289 original size:9 final size:9
Alignment explanation
Indices: 38468277--38468316 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
38468267 ATTCGGTCGG
38468277 TTAACCGAA
1 TTAACCGAA
*
38468286 TTAACCTAA
1 TTAACCGAA
*
38468295 TTACCCGAA
1 TTAACCGAA
*
38468304 TTACCCGAA
1 TTAACCGAA
38468313 TTAA
1 TTAA
38468317 TCAATTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (9 bp):
TTAACCGAA
Found at i:38468468 original size:18 final size:18
Alignment explanation
Indices: 38468445--38468498 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
38468435 AATTTTTATG
38468445 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
38468463 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
38468481 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
38468499 TTAGGTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:38470940 original size:178 final size:178
Alignment explanation
Indices: 38470641--38470992 Score: 650
Period size: 178 Copynumber: 2.0 Consensus size: 178
38470631 CAATGGTAAC
* *
38470641 AATGAGATAAAATAGGATTGTATTGAGTGAACGGATTTAACTCAAAGGAATCAAGGATATCATAT
1 AATGAGATAAAATAGGATTGTATTGAGTGAACAGATTTAACTCAAAAGAATCAAGGATATCATAT
*
38470706 GAGGGTAACACACACATGACGAGATTAGTGGACAAAGCAGTTGGATGAATTGCTTTCATAAAGAG
66 GAGGGTAACACACACATGACGAGATCAGTGGACAAAGCAGTTGGATGAATTGCTTTCATAAAGAG
*
38470771 TATACAATAAGGAGTTTTCAATCATGGTACTTCTTGTGGACTGATGAT
131 TATACAATAAGGAGTATTCAATCATGGTACTTCTTGTGGACTGATGAT
38470819 AATGAGATAAAATAGGATTGTATTGAGTGAACAGATTTAACTCAAAAGAATCAAGGATATCATAT
1 AATGAGATAAAATAGGATTGTATTGAGTGAACAGATTTAACTCAAAAGAATCAAGGATATCATAT
* *
38470884 GAGGGTAACACACACATGACGAGATCATTGGACAAAGCAGTTGGATGAATTGCTTTCGTAAAGAG
66 GAGGGTAACACACACATGACGAGATCAGTGGACAAAGCAGTTGGATGAATTGCTTTCATAAAGAG
38470949 TATACAATAAGGAGTATTCAATCATGGTACTTCTTGTGGACTGA
131 TATACAATAAGGAGTATTCAATCATGGTACTTCTTGTGGACTGA
38470993 CTCCATGATT
Statistics
Matches: 168, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
178 168 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (178 bp):
AATGAGATAAAATAGGATTGTATTGAGTGAACAGATTTAACTCAAAAGAATCAAGGATATCATAT
GAGGGTAACACACACATGACGAGATCAGTGGACAAAGCAGTTGGATGAATTGCTTTCATAAAGAG
TATACAATAAGGAGTATTCAATCATGGTACTTCTTGTGGACTGATGAT
Found at i:38473822 original size:60 final size:61
Alignment explanation
Indices: 38473706--38473823 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 61
38473696 AATGATTATA
* * ** * * *
38473706 TTAATATTTAATTTAATTTAATGTTTCTCTTGCAAATAAACATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATACTTATCTT-CAAATAAACATTATATTAATTTAATAAGAT
*
38473768 TTAATATTAAATTTAATCTAATACTTATCTT-AAATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATACTTATCTTCAAATAAACATTATATTAATTTAATA
38473824 TTAAAGTGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 22 0.46
62 26 0.54
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.49
Consensus pattern (61 bp):
TTAATATTAAATTTAATCTAATACTTATCTTCAAATAAACATTATATTAATTTAATAAGAT
Found at i:38473982 original size:25 final size:26
Alignment explanation
Indices: 38473932--38473984 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
38473922 AGTTGTAGAG
38473932 AGAAAATTCTCTAAAGAGATTATTCT
1 AGAAAATTCTCTAAAGAGATTATTCT
* * *
38473958 AGAAAATT-TCTAGAGATATTTTTCT
1 AGAAAATTCTCTAAAGAGATTATTCT
38473983 AG
1 AG
38473985 TTTACAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTCT
Found at i:38477772 original size:26 final size:26
Alignment explanation
Indices: 38477743--38477823 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 26
38477733 TATCCGAAGC
38477743 TCCTGATTAAAGGCTCTTTGTGAGCT
1 TCCTGATTAAAGGCTCTTTGTGAGCT
* * * *
38477769 TCCTAATTAAAAGTTCTTTGTGAACT
1 TCCTGATTAAAGGCTCTTTGTGAGCT
* *
38477795 TCCTGATT-ATGGCTC-TTATGAGCT
1 TCCTGATTAAAGGCTCTTTGTGAGCT
38477819 TCCTG
1 TCCTG
38477824 TTATATAGCC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
24 12 0.27
25 4 0.09
26 29 0.64
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (26 bp):
TCCTGATTAAAGGCTCTTTGTGAGCT
Found at i:38477847 original size:25 final size:25
Alignment explanation
Indices: 38477817--38477873 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
38477807 CTCTTATGAG
*
38477817 CTTCCTGTTATATAGCCCGGATAAA
1 CTTCCTGTTATATAGCCCAGATAAA
* *
38477842 CTTCCTGTTATATAGCTCAGATAAG
1 CTTCCTGTTATATAGCCCAGATAAA
38477867 CTTCCTG
1 CTTCCTG
38477874 ATAGGCTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (25 bp):
CTTCCTGTTATATAGCCCAGATAAA
Found at i:38477932 original size:26 final size:26
Alignment explanation
Indices: 38477754--38477932 Score: 74
Period size: 25 Copynumber: 7.2 Consensus size: 26
38477744 CCTGATTAAA
* *
38477754 GGCTCTTTGTGAGCTTCCTAATTA-AA
1 GGCTCTTTGTGAGCTTCCT-GTTATAT
* * * *
38477780 AGTTCTTTGTGAACTTCCTGAT-TAT
1 GGCTCTTTGTGAGCTTCCTGTTATAT
*
38477805 GGCTC-TTATGAGCTTCCTGTTATAT
1 GGCTCTTTGTGAGCTTCCTGTTATAT
* ** * *
38477830 AGC-C-CGGATAAACTTCCTGTTATAT
1 GGCTCTTTG-TGAGCTTCCTGTTATAT
* * *
38477855 AGCTC--AGATAAGCTTCCTG--ATA-
1 GGCTCTTTG-TGAGCTTCCTGTTATAT
* ** *
38477877 GGCTCTTTGTGAGCTTTTCAATTA-AA
1 GGCTCTTTGTGAGC-TTCCTGTTATAT
38477903 GGCTCTTTGTGAGCTTCCTGTTATAT
1 GGCTCTTTGTGAGCTTCCTGTTATAT
38477929 GGCT
1 GGCT
38477933 TGAGAGAGGA
Statistics
Matches: 113, Mismatches: 29, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
22 4 0.04
23 7 0.06
24 18 0.16
25 47 0.42
26 37 0.33
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCTGTTATAT
Found at i:38490905 original size:22 final size:22
Alignment explanation
Indices: 38490851--38490911 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
38490841 ATAATTATTT
* *
38490851 TTTATAA-ATATATATTTAATG
1 TTTATAATATAAATATTTAATA
*
38490872 TTT-TAATGATAAATATTTACTA
1 TTTATAAT-ATAAATATTTAATA
38490894 TTTATAATATAAAATATT
1 TTTATAATAT-AAATATT
38490912 AAACAATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.09
21 3 0.09
22 16 0.48
23 11 0.33
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTATAATATAAATATTTAATA
Found at i:38492689 original size:15 final size:14
Alignment explanation
Indices: 38492671--38492705 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
38492661 ATTAATTCTT
38492671 AAAATTTTAAAATTA
1 AAAATTTTAAAA-TA
*
38492686 AAAAATTTAAAATA
1 AAAATTTTAAAATA
38492700 AAAATT
1 AAAATT
38492706 ATTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATTTTAAAATA
Found at i:38492692 original size:16 final size:15
Alignment explanation
Indices: 38492671--38492713 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
38492661 ATTAATTCTT
38492671 AAAATTTTAAAATTAA
1 AAAATTTTAAAA-TAA
38492687 AAAA-TTTAAAATAA
1 AAAATTTTAAAATAA
*
38492701 AAATTATTTAAAA
1 AAAAT-TTTAAAA
38492714 ATTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.25
15 7 0.29
16 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTTTAAAATAA
Found at i:38506854 original size:4 final size:4
Alignment explanation
Indices: 38506845--38506896 Score: 95
Period size: 4 Copynumber: 13.0 Consensus size: 4
38506835 CTAAGAAGTA
*
38506845 TATG TATG TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
38506893 TATG
1 TATG
38506897 ATTGAAGTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:38513050 original size:2 final size:2
Alignment explanation
Indices: 38513043--38513068 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38513033 TTAAAAGTAA
38513043 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
38513069 TGAAAGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38518825 original size:2 final size:2
Alignment explanation
Indices: 38518818--38518844 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38518808 GAATTCCAAT
38518818 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 T
38518845 CTTTCAAACC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38518987 original size:28 final size:27
Alignment explanation
Indices: 38518935--38518987 Score: 63
Period size: 26 Copynumber: 1.9 Consensus size: 27
38518925 AATTAATTCA
* *
38518935 AAATCTATATTTCAGCATCCTAATATC
1 AAATCTATATGTCAGCATCCAAATATC
38518962 AAAT-TATATGTCATGCATGCCAAATA
1 AAATCTATATGTCA-GCAT-CCAAATA
38518988 AACCTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 8 0.36
27 8 0.36
28 6 0.27
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (27 bp):
AAATCTATATGTCAGCATCCAAATATC
Found at i:38520583 original size:17 final size:16
Alignment explanation
Indices: 38520548--38520587 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
38520538 AATATGATGT
* *
38520548 AAAGAAATGGAAAAGA
1 AAAGAAAAGGAAAAAA
38520564 AAAGAAAAGAGAAAAAA
1 AAAGAAAAG-GAAAAAA
38520581 AAAGAAA
1 AAAGAAA
38520588 TACAGGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGGAAAAAA
Found at i:38520956 original size:8 final size:8
Alignment explanation
Indices: 38520943--38520969 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
38520933 ATTGATTAGG
38520943 TTTTATTA
1 TTTTATTA
38520951 TTTTATTA
1 TTTTATTA
38520959 TTTTATTA
1 TTTTATTA
38520967 TTT
1 TTT
38520970 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTATTA
Found at i:38530744 original size:18 final size:18
Alignment explanation
Indices: 38530729--38530763 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38530719 CAGCCCAATA
*
38530729 CCATCATTTGGCCCAAAG
1 CCATCAATTGGCCCAAAG
38530747 CCATCAATTGGCCCAAA
1 CCATCAATTGGCCCAAA
38530764 ATTGCGAGTA
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:0.31, C:0.34, G:0.14, T:0.20
Consensus pattern (18 bp):
CCATCAATTGGCCCAAAG
Found at i:38530796 original size:15 final size:15
Alignment explanation
Indices: 38530776--38530805 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38530766 TGCGAGTAAA
38530776 TCCACCATTAGGCCC
1 TCCACCATTAGGCCC
*
38530791 TCCACCATTCGGCCC
1 TCCACCATTAGGCCC
38530806 ACTTGATTGT
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:0.17, C:0.50, G:0.13, T:0.20
Consensus pattern (15 bp):
TCCACCATTAGGCCC
Found at i:38530922 original size:63 final size:63
Alignment explanation
Indices: 38530786--38530931 Score: 161
Period size: 63 Copynumber: 2.3 Consensus size: 63
38530776 TCCACCATTA
* *
38530786 GGCCCTCCACCATTCGGCCCACTTGATTGTGGCCTATACACATTATTGTCAAAAGTCGGCCTG
1 GGCCCTCCACCATTCGGCCCACTTGATTGTGGCCTATACACATTATTGTCAAAACTCGACCTG
** * * * * *
38530849 ACCCCTCCACCATTTGGCCCACTTGGTTGTGGCCTATACGCA-TGTTGCTCAACAC-CTGACCTG
1 GGCCCTCCACCATTCGGCCCACTTGATTGTGGCCTATACACATTATTG-TCAAAACTC-GACCTG
* *
38530912 GGCCCACCACCAATCGGCCC
1 GGCCCTCCACCATTCGGCCC
38530932 TGCATACTGA
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
62 5 0.07
63 62 0.93
ACGTcount: A:0.19, C:0.37, G:0.20, T:0.24
Consensus pattern (63 bp):
GGCCCTCCACCATTCGGCCCACTTGATTGTGGCCTATACACATTATTGTCAAAACTCGACCTG
Found at i:38544390 original size:30 final size:32
Alignment explanation
Indices: 38544350--38544412 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
38544340 TAAACATTAA
*
38544350 AAAATTATTTTAAAAATAAAAAA-ATAT-TTT
1 AAAAGTATTTTAAAAATAAAAAATATATATTT
*
38544380 AAAAGTATTTTAAAATTAAAAAATATATATTT
1 AAAAGTATTTTAAAAATAAAAAATATATATTT
38544412 A
1 A
38544413 TTATATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 21 0.72
31 4 0.14
32 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (32 bp):
AAAAGTATTTTAAAAATAAAAAATATATATTT
Found at i:38544402 original size:19 final size:19
Alignment explanation
Indices: 38544347--38544383 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
38544337 TAATAAACAT
*
38544347 TAAAAAATTATTTTAAAAA
1 TAAAAAAATATTTTAAAAA
38544366 TAAAAAAATATTTTAAAA
1 TAAAAAAATATTTTAAAA
38544384 GTATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAAATATTTTAAAAA
Found at i:38548386 original size:5 final size:5
Alignment explanation
Indices: 38548376--38548406 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
38548366 TATATTTTTT
*
38548376 TATTA TATTA TATTA TATCA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA T
38548407 TCCTTTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:38553284 original size:56 final size:57
Alignment explanation
Indices: 38553214--38553325 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 57
38553204 ACACTAAAGC
* *
38553214 ATGAAAATGATCAATTTGAAACACTAAAACAGCAG-CTTGATTCAATTTAAGACAGT
1 ATGAAAATGATCAATTTGAAACACTAAAACAACAGTCTTAATTCAATTTAAGACAGT
* * * *
38553270 ATGAAAATGCTCAATTTGAAACACTCAAACAACAGTTTTAATTCAATTTATGACAG
1 ATGAAAATGATCAATTTGAAACACTAAAACAACAGTCTTAATTCAATTTAAGACAG
38553326 CAAGCAAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 32 0.65
57 17 0.35
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (57 bp):
ATGAAAATGATCAATTTGAAACACTAAAACAACAGTCTTAATTCAATTTAAGACAGT
Found at i:38554152 original size:18 final size:18
Alignment explanation
Indices: 38554129--38554182 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
38554119 AATTTTTATG
38554129 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
38554147 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
38554165 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
38554183 TTAGGTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:38554506 original size:24 final size:25
Alignment explanation
Indices: 38554462--38554578 Score: 71
Period size: 24 Copynumber: 4.5 Consensus size: 25
38554452 TTTTGGATTC
38554462 AAATTATAAAAATTAAAAAAAATTA
1 AAATTATAAAAATTAAAAAAAATTA
*
38554487 AAATTA-AAAAA-TATAGAAAAATT-
1 AAATTATAAAAATTA-AAAAAAATTA
* *
38554510 AAATATATATATAATTCAAAAAATATATCA
1 AAAT-TATA-AAAATT-AAAAAA-A-ATTA
* * *
38554540 AAATTTTAAAATTTCAAAATAAAAATA
1 AAATTATAAAAATT-AAAA-AAAATTA
*
38554567 AAAATA-AAAAAT
1 AAATTATAAAAAT
38554579 ATAGAAAACT
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
23 6 0.09
24 15 0.21
25 7 0.10
26 8 0.11
27 11 0.16
28 12 0.17
29 7 0.10
30 4 0.06
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.29
Consensus pattern (25 bp):
AAATTATAAAAATTAAAAAAAATTA
Found at i:38555629 original size:20 final size:20
Alignment explanation
Indices: 38555600--38555637 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38555590 TAAATTCGTA
* *
38555600 TTAAAGCATTTTTGATATTT
1 TTAAAACATTTTTAATATTT
38555620 TTAAAACATTTTTAATAT
1 TTAAAACATTTTTAATAT
38555638 ATTAAATGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
TTAAAACATTTTTAATATTT
Done.