Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 42 of 125
Found at i:12973210 original size:21 final size:21
Alignment explanation
Indices: 12973186--12973231 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12973176 TTTTCTTTCA
*
12973186 CCTCTTCAACA-CAAACTTCCT
1 CCTCTCCAACATC-AACTTCCT
12973207 CCTCTCCAACATCAACTTCCT
1 CCTCTCCAACATCAACTTCCT
12973228 CCTC
1 CCTC
12973232 AACAGTAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (21 bp):
CCTCTCCAACATCAACTTCCT
Found at i:12978087 original size:23 final size:25
Alignment explanation
Indices: 12978035--12978087 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
12978025 AATGGGTGAT
12978035 TTTTTTTAAAAAAAAGAAAGTTTAG
1 TTTTTTTAAAAAAAAGAAAGTTTAG
*
12978060 -ATTTTTAAAAAATAA-AAA-TTT-G
1 TTTTTTTAAAAAA-AAGAAAGTTTAG
12978082 TTTTTT
1 TTTTTT
12978088 AGTCATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
22 1 0.04
23 7 0.29
24 14 0.58
25 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTTTTAAAAAAAAGAAAGTTTAG
Found at i:12978443 original size:148 final size:145
Alignment explanation
Indices: 12978035--12978619 Score: 705
Period size: 148 Copynumber: 4.0 Consensus size: 145
12978025 AATGGGTGAT
12978035 TTTTTTTAAAAAAAAGAAAGTTTAGATTTTTAAAAAATAAAAATTTGTTTTTTAGTCATTTTAAA
1 TTTTTTTAAAAAAAAGAAAGTTTAGATTTTT-AAAAATAAAAA-TTGTTTTTTAGTCATTTT-AA
* *
12978100 AGGAAAAAA-TTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTT
63 AGGAAAAAATTTAAATTTTTAAACAAA-TTTTGA-TTTTTTTAAC-ATTTTGAAATAAAAGTTTT
12978164 GATTTTTAAGAAAAATAG-TA
125 GATTTTTAAGAAAAATAGTTA
* * * * *
12978184 ATTTTTTAAAAAAAATAGAGTTTAGATTTTTAAAAATAAAAATT-TCTTTTTAGTTATTTCAAAG
1 TTTTTTTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATTGT-TTTTTAGTCATTTTAAAG
* * * * *
12978248 GAAAAAGTTTAAATTTTTAAATAAAATTTTAATTTTTTTACCTATTTTGAAATAACAGTTTT-AC
65 GAAAAAATTTAAATTTTTAAA-CAAATTTTGATTTTTTTAAC-ATTTTGAAATAAAAGTTTTGA-
12978312 TTTTTAAGAAAAATAGTTA
127 TTTTTAAGAAAAATAGTTA
*
12978331 TTTTTTTTAAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAA
1 -TTTTTTTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAAT-TGTTTTTTAGTCATTTTAAA
* *
12978396 GGAAAAAAATTTAAATTTTTAAACAAACTTTTTATTTTTTTAA-ATTTTTCGAAATGAAAGTTTT
64 GG-AAAAAATTTAAATTTTTAAACAAA-TTTTGATTTTTTTAACA-TTTT-GAAATAAAAGTTTT
* *
12978460 GATTTTTAAGAAAAGTAGTGA
125 GATTTTTAAGAAAAATAGTTA
** * ** *
12978481 -TTTTAAAAAAAAAACAAAGTTTAGATTTTTAAAAATAAAAATCCATTTTTTAGTCATTTTAAAA
1 TTTTTTTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAAT-TGTTTTTTAGTCATTTTAAAG
* * * * * *
12978545 GAAAAAATTTAAAATTTTAAACAAAGTTTGGTTTTTTTAACCATTTTGAATTAAAAGCTTTAATT
65 GAAAAAATTTAAATTTTTAAACAAATTTTGATTTTTTTAA-CATTTTGAAATAAAAGTTTTGATT
12978610 TTTAAGAAAA
129 TTTAAGAAAA
12978620 GCACTGATTT
Statistics
Matches: 380, Mismatches: 41, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
145 1 0.00
146 90 0.24
147 61 0.16
148 112 0.29
149 53 0.14
150 62 0.16
151 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (145 bp):
TTTTTTTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATTGTTTTTTAGTCATTTTAAAGG
AAAAAATTTAAATTTTTAAACAAATTTTGATTTTTTTAACATTTTGAAATAAAAGTTTTGATTTT
TAAGAAAAATAGTTA
Found at i:12978582 original size:296 final size:297
Alignment explanation
Indices: 12978033--12978619 Score: 835
Period size: 296 Copynumber: 2.0 Consensus size: 297
12978023 AAAATGGGTG
* *
12978033 ATTTTTTTTAAAAAAAAGAAAGTTTAGATTTTTAAAAAATAAAAATTTGTTTTTTAGTCATTTTA
1 ATTTTTTTTAAAAAAAAGAAAATTTAGATTTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTA
* * *
12978098 AAAGGAAAAAATTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTT
66 AAAGGAAAAAATTAAATTTTTAAACAAACTTTTGATTTTTTTTAAATATTTCGAAATAAAAGTTT
** * * *
12978163 TGATTTTTAAGAAAAATAGTAATTTTTTAAAAAAAATAGAGTTTAGATTTTTAAAAATAAAAATT
131 TGATTTTTAAGAAAAATAGTAATTTTAAAAAAAAAACAAAGTTTAGATTTTTAAAAATAAAAATA
* * * * *
12978228 TCTTTTTAGTTATTTCAAAGGAAAAAGTTTAAATTTTTAAATAAAATTTTAATTTTTTT-ACCTA
196 TCTTTTTAGTCATTTCAAAAGAAAAAATTTAAAATTTTAAATAAAAGTTTAATTTTTTTAACC-A
* * *
12978292 TTTTGAAATAACAGTTTTACTTTTTAAGAAAAATAGTT
260 TTTTGAAATAAAAGCTTTAATTTTTAAGAAAAATAGTT
12978330 ATTTTTTTTAAAAAAAAGAAAATTTAGATTTTT-AAAAATAAAAATATGTTTTTTAGTCATTTT-
1 ATTTTTTTTAAAAAAAAGAAAATTTAGATTTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTA
* * *
12978393 AAAGGAAAAAAATTTAAATTTTTAAACAAACTTTTTA-TTTTTTTAAATTTTTCGAAATGAAAGT
66 AAAGG-AAAAAA-TTAAATTTTTAAACAAACTTTTGATTTTTTTTAAATATTTCGAAATAAAAGT
* *
12978457 TTTGATTTTTAAGAAAAGTAGTGATTTTAAAAAAAAAACAAAGTTTAGATTTTTAAAAATAAAAA
129 TTTGATTTTTAAGAAAAATAGTAATTTTAAAAAAAAAACAAAGTTTAGATTTTTAAAAATAAAAA
* * **
12978522 TCCAT-TTTTTAGTCATTTTAAAAGAAAAAATTTAAAATTTTAAA-CAAAGTTTGGTTTTTTTAA
194 T--ATCTTTTTAGTCATTTCAAAAGAAAAAATTTAAAATTTTAAATAAAAGTTTAATTTTTTTAA
*
12978585 CCATTTTGAATTAAAAGCTTTAATTTTTAAGAAAA
257 CCATTTTGAAATAAAAGCTTTAATTTTTAAGAAAA
12978620 GCACTGATTT
Statistics
Matches: 257, Mismatches: 28, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
295 5 0.02
296 161 0.63
297 90 0.35
298 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (297 bp):
ATTTTTTTTAAAAAAAAGAAAATTTAGATTTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTA
AAAGGAAAAAATTAAATTTTTAAACAAACTTTTGATTTTTTTTAAATATTTCGAAATAAAAGTTT
TGATTTTTAAGAAAAATAGTAATTTTAAAAAAAAAACAAAGTTTAGATTTTTAAAAATAAAAATA
TCTTTTTAGTCATTTCAAAAGAAAAAATTTAAAATTTTAAATAAAAGTTTAATTTTTTTAACCAT
TTTGAAATAAAAGCTTTAATTTTTAAGAAAAATAGTT
Found at i:12979230 original size:16 final size:15
Alignment explanation
Indices: 12979199--12979248 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
12979189 TTATTTATTC
*
12979199 TTATTTTATCTTTAT
1 TTATTTTATGTTTAT
12979214 TTATTTTCATGTTTAT
1 TTATTTT-ATGTTTAT
*
12979230 TTATATTTATGTTTTT
1 TTAT-TTTATGTTTAT
12979246 TTA
1 TTA
12979249 CACATTCCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
15 7 0.23
16 21 0.68
17 3 0.10
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (15 bp):
TTATTTTATGTTTAT
Found at i:12984011 original size:110 final size:110
Alignment explanation
Indices: 12983806--12984015 Score: 271
Period size: 110 Copynumber: 1.9 Consensus size: 110
12983796 ATAAGTAAAC
** *
12983806 TTATCGATTTTAAAATAGATGTTCAATTACTTAGGTTTCAAGAAAAAACCATACCCAATACATTA
1 TTATCGATTTTAAAATAGATACTCAATTACTTAGGTTTAAAGAAAAAACCATACCCAATACATTA
* * *
12983871 TGACATAATTTCTCGAGTTCCTTAAAATAAAAGAACATTAAGCGT
66 GGACACAATTTCTCGAATTCCTTAAAATAAAAGAACATTAAGCGT
* * * **
12983916 TTATCGATTTT-AAATAGGATACTCAATTATTTAGGTTTAAAGAAAAAATCGTACCCAATATGTT
1 TTATCGATTTTAAAATA-GATACTCAATTACTTAGGTTTAAAGAAAAAACCATACCCAATACATT
* *
12983980 AGGGCACAATTTCTCGAATT-CTCTAACATAAAAGAA
65 AGGACACAATTTCTCGAATTCCT-TAAAATAAAAGAA
12984016 AATTGCCTTG
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
109 7 0.08
110 78 0.92
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (110 bp):
TTATCGATTTTAAAATAGATACTCAATTACTTAGGTTTAAAGAAAAAACCATACCCAATACATTA
GGACACAATTTCTCGAATTCCTTAAAATAAAAGAACATTAAGCGT
Found at i:12984328 original size:31 final size:30
Alignment explanation
Indices: 12984290--12984415 Score: 89
Period size: 31 Copynumber: 4.2 Consensus size: 30
12984280 AATAAAAGGT
*
12984290 AATTTTAA-AAGAAATAAAAATAAAAGGGTTA
1 AATTTTAACAA-AAA-AAAAATAAAAGGATTA
* *
12984321 AATTTTAACAAAAACACAAATAAAAGGATTT
1 AATTTTAACAAAAA-AAAAATAAAAGGATTA
* * *
12984352 AA-TTTAA-AAAAACAAAATAAATGG-GTA
1 AATTTTAACAAAAAAAAAATAAAAGGATTA
* * * *
12984379 AAATTTAATAGAGAAAAACAATAAAAAGATTA
1 AATTTTAACA-A-AAAAAAAATAAAAGGATTA
12984411 AATTT
1 AATTT
12984416 AAATTGAAAC
Statistics
Matches: 74, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
27 3 0.04
28 14 0.19
29 6 0.08
30 6 0.08
31 37 0.50
32 8 0.11
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.25
Consensus pattern (30 bp):
AATTTTAACAAAAAAAAAATAAAAGGATTA
Found at i:12984369 original size:59 final size:59
Alignment explanation
Indices: 12984306--12984418 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
12984296 AAAAGAAATA
* * * *
12984306 AAAATAAAAGGGTTAAATTTTAACA-A-AAACACAAATAAAAGGATTTAATTTAAAAAAAC
1 AAAATAAAAGGG-TAAAATTTAACAGAGAAAAAC-AATAAAAAGATTAAATTTAAAAAAAC
* *
12984365 AAAATAAATGGGTAAAATTTAATAGAGAAAAACAATAAAAAGATTAAATTTAAA
1 AAAATAAAAGGGTAAAATTTAACAGAGAAAAACAATAAAAAGATTAAATTTAAA
12984419 TTGAAACAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 10 0.22
59 31 0.67
60 5 0.11
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.24
Consensus pattern (59 bp):
AAAATAAAAGGGTAAAATTTAACAGAGAAAAACAATAAAAAGATTAAATTTAAAAAAAC
Found at i:12986128 original size:42 final size:42
Alignment explanation
Indices: 12986076--12986487 Score: 446
Period size: 42 Copynumber: 10.0 Consensus size: 42
12986066 TAAGATATTA
* *
12986076 GATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * * *
12986118 GATGTCTTCAATCTGCCTCATGATTGAGGTAAAAGATT--A-
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * * * * *
12986157 GATGGCTTTAATCTACTCCATGGTTGGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
*
12986199 GATGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * * *
12986241 G--G-CTTCAATTTGCCCCATGGTCGAGGTAAGAGATTGAAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* *
12986280 GATGTCTTCAATCTGCCTCATGGTCGGGGTAAGAGATT--A-
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * *
12986319 GATGACTTCAATATGCCCCATGGTCGGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
** * * * *
12986361 GATGTCTTCAATCTGCCTTATGATTGAGGTAGGTGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* *
12986403 GATGTCTTCAATCTGCCTCATGATCGGGGTAAAAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * * * *
12986445 GATATCTTCAATTTTCCCCATGATCGAGGTAAAAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
12986487 G
1 G
12986488 GTAGCTTTGC
Statistics
Matches: 309, Mismatches: 52, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
39 98 0.32
40 3 0.01
41 3 0.01
42 205 0.66
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (42 bp):
GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
Found at i:12986170 original size:81 final size:81
Alignment explanation
Indices: 12986066--12986488 Score: 524
Period size: 81 Copynumber: 5.2 Consensus size: 81
12986056 ATGATTTGGA
*
12986066 TAAGATATTAGATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATC
1 TAAGAGATTAGATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATC
12986131 TGCCTCATGATTGAGG
66 TGCCTCATGATTGAGG
* * * * *
12986147 TAAAAGATTAGATGGCTTTAATCTACTCCATGGTTGGGGTAAGAGATTGGATGATGTCTTCAATC
1 TAAGAGATTAGATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATC
* *
12986212 TGCCCCATGA-TCAGGG
66 TGCCTCATGATTGA-GG
* * * *
12986228 TAAGAGATTGGATGGCTTCAATTTGCCCCATGGTCGAGGTAAGAGATTGAATGATGTCTTCAATC
1 TAAGAGATTAGATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATC
* * *
12986293 TGCCTCATGGTCGGGG
66 TGCCTCATGATTGAGG
* *
12986309 TAAGAGATTAGATGACTTCAATATGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATC
1 TAAGAGATTAGATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATC
*
12986374 TGCCTTATGATTGAGG
66 TGCCTCATGATTGAGG
* * * * * * *
12986390 TAGGTGATTGGATGATGTCTTCAATCTGCCTCATGATCGGGGTAAAAGATTGGATGATATCTTCA
1 TAAGAGATT--A-GATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCA
* * * *
12986455 ATTTTCCCCATGATCGAGG
63 ATCTGCCTCATGATTGAGG
* *
12986474 TAAAAGATTGGATGG
1 TAAGAGATTAGATGG
12986489 TAGCTTTGCG
Statistics
Matches: 288, Mismatches: 49, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
80 2 0.01
81 219 0.76
83 1 0.00
84 66 0.23
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (81 bp):
TAAGAGATTAGATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATC
TGCCTCATGATTGAGG
Found at i:12986620 original size:47 final size:47
Alignment explanation
Indices: 12986569--12986910 Score: 126
Period size: 47 Copynumber: 7.1 Consensus size: 47
12986559 AACTTTAGGA
*
12986569 AGATAGGATTTGGTGTAGCTTGATCTTGCTCCACTGCAACTTCAAGG
1 AGATAGGATTTGGTGTAGCTTAATCTTGCTCCACTGCAACTTCAAGG
** * * ** * * * *
12986616 AGATAAATATTTGCTACT-GCTTTAAT-TCACTTCACTACAACTTCACGA
1 AGAT-AGGATTTGGT-GTAGC-TTAATCTTGCTCCACTGCAACTTCAAGG
* * * *
12986664 AGATAGGATTTGGTGTGGTTTCATCTTGCTCCACTGCAACTT-TAGAG
1 AGATAGGATTTGGTGTAGCTTAATCTTGCTCCACTGCAACTTCAAG-G
* * * * * * * *
12986711 ACATAAAGATCTGCCAATGCTAGTTTTAATC-CGATCC-TTGCAACTTCAAGG
1 AGAT-AGGATTTG---GTG-TAG-CTTAATCTTGCTCCACTGCAACTTCAAGG
* * *
12986762 ATATAGGATTTGGTGTTGTAGCTTTATCTTGCTCCATTGCAACTTC-AGAG
1 AGATAGGATTT-G-G-TGTAGCTTAATCTTGCTCCACTGCAACTTCAAG-G
* * * ** * *
12986812 AGATAAAGA-TTGCTACT-GCTTTAATC-TGCTTTACTGCAACTTTAAGA
1 AGAT-AGGATTTGGT-GTAGC-TTAATCTTGCTCCACTGCAACTTCAAGG
* * * * *
12986859 AGATAGGATTTGGTGTGGCTTCATCTTCCTTCACTGCAACTTCAGGG
1 AGATAGGATTTGGTGTAGCTTAATCTTGCTCCACTGCAACTTCAAGG
12986906 AGATA
1 AGATA
12986911 AAGATTTGCC
Statistics
Matches: 208, Mismatches: 62, Indels: 50
0.65 0.19 0.16
Matches are distributed among these distances:
46 15 0.07
47 75 0.36
48 48 0.23
49 15 0.07
50 23 0.11
51 18 0.09
52 8 0.04
53 6 0.03
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (47 bp):
AGATAGGATTTGGTGTAGCTTAATCTTGCTCCACTGCAACTTCAAGG
Found at i:12986641 original size:95 final size:96
Alignment explanation
Indices: 12986541--12986919 Score: 362
Period size: 95 Copynumber: 3.9 Consensus size: 96
12986531 TTGTTATTGT
* *
12986541 TTTAATCCACTTCACTATAACTTTAGGAAGATAGGATTTGGTGTAGCTTGATCTTGCTCCACTGC
1 TTTAATCCACTTCACTACAACTTTAGGAAGATAGGATTTGGTGTAGCTTCATCTTGCTCCACTGC
*
12986606 AACTTCAAG-GAGATAAATATTTGCTACTGC
66 AACTTCAAGAGAGATAAAGATTTGCTACTGC
* * * * *
12986636 TTTAATTCACTTCACTACAACTTCACGAAGATAGGATTTGGTGTGGTTTCATCTTGCTCCACTGC
1 TTTAATCCACTTCACTACAACTTTAGGAAGATAGGATTTGGTGTAGCTTCATCTTGCTCCACTGC
* * * * *
12986701 AACTT-TAGAGACATAAAGATCTGCCAATGCTAGT
66 AACTTCAAGAGAGATAAAGATTTG-C--TACT-GC
* * * *
12986735 TTTAATCCGA--TC-CTTGCAACTTCAAGG-ATATAGGATTTGGTGTTGTAGCTTTATCTTGCTC
1 TTTAATCC-ACTTCAC-TACAACTT-TAGGAAGATAGGATTT-G-G-TGTAGCTTCATCTTGCTC
*
12986796 CATTGCAACTTC-AGAGAGATAAAGA-TTGCTACTGC
60 CACTGCAACTTCAAGAGAGATAAAGATTTGCTACTGC
** * * * * * *
12986831 TTTAATCTGCTTTACTGCAACTTTAAGAAGATAGGATTTGGTGTGGCTTCATCTTCCTTCACTGC
1 TTTAATCCACTTCACTACAACTTTAGGAAGATAGGATTTGGTGTAGCTTCATCTTGCTCCACTGC
*
12986896 AACTTC-AGGGAGATAAAGATTTGC
66 AACTTCAAGAGAGATAAAGATTTGC
12986920 CAATGTTAGT
Statistics
Matches: 229, Mismatches: 38, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
94 39 0.17
95 79 0.34
96 12 0.05
97 23 0.10
98 23 0.10
99 12 0.05
100 4 0.02
101 37 0.16
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (96 bp):
TTTAATCCACTTCACTACAACTTTAGGAAGATAGGATTTGGTGTAGCTTCATCTTGCTCCACTGC
AACTTCAAGAGAGATAAAGATTTGCTACTGC
Found at i:12986915 original size:195 final size:196
Alignment explanation
Indices: 12986571--12986973 Score: 575
Period size: 195 Copynumber: 2.1 Consensus size: 196
12986561 CTTTAGGAAG
*
12986571 ATAGGATTT-G-G-TGTAGCTTGATCTTGCTCCACTGCAACTTCAAGGAGATAAATATTTGCTAC
1 ATAGGATTTGGTGTTGTAGCTTGATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGCTAC
* * *
12986633 TGCTTTAATTCACTTCACTACAACTTCACGAAGATAGGATTTGGTGTGGTTTCATCTTGCTCCAC
66 TGCTTTAATTCACTTCACTACAACTTCAAGAAGATAGGATTTGGTGTGGCTTCATCTTCCTCCAC
*
12986698 TGCAACTTTAGAGACATAAAGATCTGCCAATGCTAGTTTTAATCCGATCCTTGCAACTTCAAGGA
131 TGCAACTTCAGAGACATAAAGATCTGCCAATGCTAGTTTTAATCCGATCCTTGCAACTTCAAGGA
12986763 T
196 T
* *
12986764 ATAGGATTTGGTGTTGTAGCTTTATCTTGCTCCATTGCAACTTC-AGAGAGATAAAGA-TTGCTA
1 ATAGGATTTGGTGTTGTAGCTTGATCTTGCTCCACTGCAACTTCAAG-GAGATAAAGATTTGCTA
* * * * *
12986827 CTGCTTTAA-TCTGCTTTACTGCAACTTTAAGAAGATAGGATTTGGTGTGGCTTCATCTTCCTTC
65 CTGCTTTAATTC-ACTTCACTACAACTTCAAGAAGATAGGATTTGGTGTGGCTTCATCTTCCTCC
* * * * **
12986891 ACTGCAACTTCAGGGAGATAAAGATTTGCCAATGTTAGTTTTAATTTGATCCTTGCAACTTCAAG
129 ACTGCAACTTCAGAGACATAAAGATCTGCCAATGCTAGTTTTAATCCGATCCTTGCAACTTCAAG
12986956 GAT
194 GAT
*
12986959 ATAGGATTTGTTGTT
1 ATAGGATTTGGTGTT
12986974 TCGTTGATTC
Statistics
Matches: 186, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
193 9 0.05
194 3 0.02
195 137 0.74
196 37 0.20
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (196 bp):
ATAGGATTTGGTGTTGTAGCTTGATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGCTAC
TGCTTTAATTCACTTCACTACAACTTCAAGAAGATAGGATTTGGTGTGGCTTCATCTTCCTCCAC
TGCAACTTCAGAGACATAAAGATCTGCCAATGCTAGTTTTAATCCGATCCTTGCAACTTCAAGGA
T
Found at i:12987566 original size:20 final size:20
Alignment explanation
Indices: 12987543--12987580 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12987533 ATTATAAAAA
*
12987543 TTGGTAAAAAATGGAAAATG
1 TTGGTAAAAAATAGAAAATG
12987563 TTGGTAAAAAATAGAAAA
1 TTGGTAAAAAATAGAAAA
12987581 CATTGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (20 bp):
TTGGTAAAAAATAGAAAATG
Found at i:12988829 original size:20 final size:18
Alignment explanation
Indices: 12988800--12988860 Score: 74
Period size: 17 Copynumber: 3.4 Consensus size: 18
12988790 CATCTTAATT
12988800 TTTTCTTCTTTCCTTTTTC
1 TTTTCTTCTTT-CTTTTTC
12988819 TTTTC-TCTCTT-TTTTTC
1 TTTTCTTCT-TTCTTTTTC
*
12988836 TTTTCTTCTTTCATTTT-
1 TTTTCTTCTTTCTTTTTC
12988853 TTTTCTTC
1 TTTTCTTC
12988861 ATCTTGACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 21 0.55
18 10 0.26
19 7 0.18
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCTTCTTTCTTTTTC
Found at i:12988876 original size:36 final size:35
Alignment explanation
Indices: 12988798--12988876 Score: 81
Period size: 36 Copynumber: 2.2 Consensus size: 35
12988788 TTCATCTTAA
* **
12988798 TTTTTTCTTCTTTCCTTTTTCTTTTCTCTCTTTTT
1 TTTTTTCTTCTTTCATTTTTCTTTTCTCTCTTACT
12988833 TTCTTTTCTTCTTTCA-TTTT-TTTTCTTCATCTTGACT
1 TT-TTTTCTTCTTTCATTTTTCTTTTC-TC-TCTT-ACT
12988870 TTTTTTC
1 TTTTTTC
12988877 ATCTCCTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 5 0.14
35 8 0.22
36 21 0.57
37 3 0.08
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.73
Consensus pattern (35 bp):
TTTTTTCTTCTTTCATTTTTCTTTTCTCTCTTACT
Found at i:13020719 original size:22 final size:22
Alignment explanation
Indices: 13020694--13020744 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
13020684 ATAGTATTAG
* *
13020694 TTAATTAAATATTTAATTGTAT
1 TTAATTAAATAATTAATTATAT
13020716 TTAATTAAATAATTAATTATAT
1 TTAATTAAATAATTAATTATAT
13020738 TTAATTA
1 TTAATTA
13020745 TAAAAACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTAAATAATTAATTATAT
Found at i:13020743 original size:10 final size:10
Alignment explanation
Indices: 13020702--13020746 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
13020692 AGTTAATTAA
13020702 ATATTTAATT
1 ATATTTAATT
*
13020712 GTATTTAATT
1 ATATTTAATT
*
13020722 AAATAATTAATT
1 --ATATTTAATT
13020734 ATATTTAATT
1 ATATTTAATT
13020744 ATA
1 ATA
13020747 AAAACAACCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 21 0.72
12 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
ATATTTAATT
Found at i:13020770 original size:32 final size:34
Alignment explanation
Indices: 13020734--13020799 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
13020724 ATAATTAATT
13020734 ATATTTAATT-ATAAAAACAACCC-AATATTTAA
1 ATATTTAATTAATAAAAACAACCCAAATATTTAA
13020766 ATATTTAATTAATAAAAACAACCCAAATATTTAA
1 ATATTTAATTAATAAAAACAACCCAAATATTTAA
13020800 GTAAAATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 10 0.31
33 13 0.41
34 9 0.28
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (34 bp):
ATATTTAATTAATAAAAACAACCCAAATATTTAA
Found at i:13020833 original size:32 final size:32
Alignment explanation
Indices: 13020795--13020860 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
13020785 AACCCAAATA
*
13020795 TTTAAGTAAAATGTTGTCACTTATATATATTT
1 TTTAAGTAAAATGTTGTCACTAATATATATTT
13020827 TTTAAGTAAAATGTTGTCACTAATATATATTT
1 TTTAAGTAAAATGTTGTCACTAATATATATTT
13020859 TT
1 TT
13020861 AAATTTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (32 bp):
TTTAAGTAAAATGTTGTCACTAATATATATTT
Found at i:13026272 original size:15 final size:15
Alignment explanation
Indices: 13026252--13026284 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
13026242 ATTTGAAGTT
13026252 ATTGGTTGAATTTGA
1 ATTGGTTGAATTTGA
*
13026267 ATTGGTTGGATTTGA
1 ATTGGTTGAATTTGA
13026282 ATT
1 ATT
13026285 TATAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
ATTGGTTGAATTTGA
Found at i:13026470 original size:43 final size:42
Alignment explanation
Indices: 13026380--13026750 Score: 481
Period size: 43 Copynumber: 8.6 Consensus size: 42
13026370 AAAACTCCGT
* * * ** * *
13026380 TAAAGAACATTTTCTATAGCGGCATTTGTGGGTAAAAGCACCAC
1 TAAAGACCATGTTCTTTAGCGGTGTTTGT-GGT-AAAGCGCCGC
* *
13026424 TAAACACCATGTTCTTTAGCGGTGTTTGTGGCTAAAGCGCCAC
1 TAAAGACCATGTTCTTTAGCGGTGTTTGTGG-TAAAGCGCCGC
* *
13026467 TAAAGACCATGTTCTTTAGCGGTGTTTGTAGGGAAAGCGCCAC
1 TAAAGACCATGTTCTTTAGCGGTGTTTGT-GGTAAAGCGCCGC
* *
13026510 TACAGACCATGTTCTTTAGCGGTGTTTGTGCGGAAAGCGCCGC
1 TAAAGACCATGTTCTTTAGCGGTGTTTGTG-GTAAAGCGCCGC
* *
13026553 TAAAGACCATGTTCTATAGCGGCGTTTGTGGTAGAAGCGCCGC
1 TAAAGACCATGTTCTTTAGCGGTGTTTGTGGTA-AAGCGCCGC
*
13026596 TAAAGACCATGTTCTTTAGCGGTGTTTGTGGGGAAAGCGCCGC
1 TAAAGACCATGTTCTTTAGCGGTGTTTGT-GGTAAAGCGCCGC
* *
13026639 TAAAGACCATGTTCTATAGCGGCGTTTGTGGTAGAAGCGCCGC
1 TAAAGACCATGTTCTTTAGCGGTGTTTGTGGTA-AAGCGCCGC
* *
13026682 TAAAGACCATGTTCTTTAGCGGTGTTTGTAGTAAAGTGCCGC
1 TAAAGACCATGTTCTTTAGCGGTGTTTGTGGTAAAGCGCCGC
*
13026724 TAAAGACCATGTTCTTTAGCGGCGTTT
1 TAAAGACCATGTTCTTTAGCGGTGTTT
13026751 TTCCTCATAA
Statistics
Matches: 295, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
42 40 0.14
43 226 0.77
44 29 0.10
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (42 bp):
TAAAGACCATGTTCTTTAGCGGTGTTTGTGGTAAAGCGCCGC
Found at i:13026769 original size:86 final size:86
Alignment explanation
Indices: 13026361--13026750 Score: 532
Period size: 86 Copynumber: 4.5 Consensus size: 86
13026351 TTTAGTGGCA
* * * * * * * * * *
13026361 TTTGTGGGAAAAACTCCGTTAAAGAACATTTTCTATAGCGGCATTTGTGGGTAAAAGCACCACTA
1 TTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTTGT-GGTAGAAGCGCCGCTA
*
13026426 AACACCATGTTCTTTAGCGGTG
65 AAGACCATGTTCTTTAGCGGTG
** * * * * *
13026448 TTTGTGGCTAAAGCGCCACTAAAGACCATGTTCTTTAGCGGTGTTTGTAGGGA-AAGCGCCACTA
1 TTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTTGT-GGTAGAAGCGCCGCTA
*
13026512 CAGACCATGTTCTTTAGCGGTG
65 AAGACCATGTTCTTTAGCGGTG
*
13026534 TTTGTGCGGAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGTAGAAGCGCCGCTAA
1 TTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGTAGAAGCGCCGCTAA
13026599 AGACCATGTTCTTTAGCGGTG
66 AGACCATGTTCTTTAGCGGTG
13026620 TTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGTAGAAGCGCCGCTAA
1 TTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGTAGAAGCGCCGCTAA
13026685 AGACCATGTTCTTTAGCGGTG
66 AGACCATGTTCTTTAGCGGTG
* * * *
13026706 TTTGT-AGTAAAGTGCCGCTAAAGACCATGTTCTTTAGCGGCGTTT
1 TTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTT
13026751 TTCCTCATAA
Statistics
Matches: 272, Mismatches: 30, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
85 39 0.14
86 193 0.71
87 40 0.15
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (86 bp):
TTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGTAGAAGCGCCGCTAA
AGACCATGTTCTTTAGCGGTG
Found at i:13039354 original size:17 final size:17
Alignment explanation
Indices: 13039332--13039367 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
13039322 GTTAGTGCAC
13039332 ATTGTCATTGCATTTTA
1 ATTGTCATTGCATTTTA
13039349 ATTGTCATTGCATTTTA
1 ATTGTCATTGCATTTTA
13039366 AT
1 AT
13039368 ATTAGTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (17 bp):
ATTGTCATTGCATTTTA
Found at i:13044105 original size:27 final size:25
Alignment explanation
Indices: 13044047--13044105 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
13044037 GGCTTCGAGT
*
13044047 AATAAACCAAAATTAAAAAAAAGTA
1 AATAAAACAAAATTAAAAAAAAGTA
*
13044072 AAGAAAACAAAATATGAAAAATAAA-TA
1 AATAAAACAAAAT-T-AAAAA-AAAGTA
13044099 AATAAAA
1 AATAAAA
13044106 TAAATTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 11 0.39
26 1 0.04
27 13 0.46
28 3 0.11
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (25 bp):
AATAAAACAAAATTAAAAAAAAGTA
Found at i:13044429 original size:18 final size:18
Alignment explanation
Indices: 13044406--13044440 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13044396 TAAAGAGCAT
13044406 AAAATA-AAAGAGAAAAGA
1 AAAATAGAAA-AGAAAAGA
13044424 AAAATAGAAAAGAAAAG
1 AAAATAGAAAAGAAAAG
13044441 CAAGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (18 bp):
AAAATAGAAAAGAAAAGA
Found at i:13047982 original size:13 final size:13
Alignment explanation
Indices: 13047964--13047990 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13047954 CTTCCTTTAC
13047964 TTCTATTTTATTT
1 TTCTATTTTATTT
13047977 TTCTATTTTATTT
1 TTCTATTTTATTT
13047990 T
1 T
13047991 ATGCTCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTATTTTATTT
Found at i:13056438 original size:41 final size:41
Alignment explanation
Indices: 13056382--13056462 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
13056372 TCGGTACCAT
* *
13056382 ATATTTCTTGGGAGAAGGAGTGAAAGCTTTCTTGAATTAGC
1 ATATTTCTTGGGAGAAGGAGTGAAACCCTTCTTGAATTAGC
13056423 ATATTTCTTGGGAGAAGGAGTGAAACCCTTCTTGAATTAG
1 ATATTTCTTGGGAGAAGGAGTGAAACCCTTCTTGAATTAG
13056463 TAGAAGTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (41 bp):
ATATTTCTTGGGAGAAGGAGTGAAACCCTTCTTGAATTAGC
Found at i:13063571 original size:20 final size:21
Alignment explanation
Indices: 13063532--13063571 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
13063522 CGATTAATCA
13063532 AATTCGATTAGTTAACCGAATT
1 AATTCGATTA-TTAACCGAATT
*
13063554 AATTCGATT-TTAATCGAA
1 AATTCGATTATTAACCGAA
13063572 ATTTATACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
AATTCGATTATTAACCGAATT
Found at i:13064383 original size:9 final size:9
Alignment explanation
Indices: 13064371--13064458 Score: 51
Period size: 9 Copynumber: 9.9 Consensus size: 9
13064361 TAATTTTTTT
13064371 AAATTTAAA
1 AAATTTAAA
13064380 AAATTT---
1 AAATTTAAA
13064386 AAATTTATAA
1 AAATTTA-AA
* *
13064396 AAATATATA
1 AAATTTAAA
13064405 AAATTT-AA
1 AAATTTAAA
13064413 AAA-TTAAA
1 AAATTTAAA
*
13064421 ATTATTTGAAA
1 A-AATTT-AAA
*
13064432 ATATTTAAA
1 AAATTTAAA
* *
13064441 AACTATAAA
1 AAATTTAAA
13064450 AATATTTAA
1 AA-ATTTAA
13064459 TAATTTTTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
6 6 0.10
7 2 0.03
8 7 0.12
9 24 0.40
10 17 0.28
11 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (9 bp):
AAATTTAAA
Found at i:13064414 original size:34 final size:34
Alignment explanation
Indices: 13064371--13064441 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
13064361 TAATTTTTTT
*
13064371 AAATTTAAAAAATTTAAATT-TATAAAAATATATA
1 AAATTT-AAAAATTAAAATTATATAAAAATATATA
* * *
13064405 AAATTTAAAAATTAAAATTATTTGAAAATATTTA
1 AAATTTAAAAATTAAAATTATATAAAAATATATA
13064439 AAA
1 AAA
13064442 ACTATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 12 0.38
34 20 0.62
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (34 bp):
AAATTTAAAAATTAAAATTATATAAAAATATATA
Found at i:13065864 original size:87 final size:86
Alignment explanation
Indices: 13065743--13065979 Score: 225
Period size: 87 Copynumber: 2.7 Consensus size: 86
13065733 TATTTTTTTT
* * *
13065743 AAATTTTACAGTTTTACCACTGGATTTT-TAGATTTTACAATTTTGCCATTATTTTCCAAAATTT
1 AAATTTTATAGTTTTGCAACT-GATTTTCTAGATTTTACAATTTTGCCATTATTTTCC-AAATTT
*
13065807 TATAATTCTGCCACTA-TTTTCCA
64 TACAATTCTGCCACTAGTTTT-CA
* * *
13065830 AAATTTTATAGTTTTGCAACTGATTTTCTAGATTTTACAATTCTACCAATGT-TTTTCCAGATTT
1 AAATTTTATAGTTTTGCAACTGATTTTCTAGATTTTACAATTTTGCC-AT-TATTTTCCAAATTT
* * *
13065894 TACAGTTTTGTCACTAGTTTTCA
64 TACAATTCTGCCACTAGTTTTCA
* * * * * *
13065917 AAATTTT-TCAGTTCTGCCAA-T-TTTTTCTAGATTTTATAGTTTTGCCACTATTTTTCAAATTT
1 AAATTTTAT-AGTTTTG-CAACTGATTTTCTAGATTTTACAATTTTGCCATTATTTTCCAAATTT
13065979 T
64 T
13065980 GTAGTTTTGC
Statistics
Matches: 124, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
84 1 0.01
85 12 0.10
86 27 0.22
87 68 0.55
88 15 0.12
89 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (86 bp):
AAATTTTATAGTTTTGCAACTGATTTTCTAGATTTTACAATTTTGCCATTATTTTCCAAATTTTA
CAATTCTGCCACTAGTTTTCA
Found at i:13065986 original size:28 final size:29
Alignment explanation
Indices: 13065717--13066006 Score: 169
Period size: 29 Copynumber: 10.0 Consensus size: 29
13065707 TTTTACAGAC
* * **
13065717 TTTATAGTTATGTCACTATTTTTTTTAAAT
1 TTTATAGTTTTGCCACTA-TTTTTCAAAAT
* * *
13065747 TTTACAGTTTTACCACTGGATTTTT--AGAT
1 TTTATAGTTTTGCCACT--ATTTTTCAAAAT
* * * *
13065776 TTTACAATTTTGCCATTATTTTCCAAAAT
1 TTTATAGTTTTGCCACTATTTTTCAAAAT
* * *
13065805 TTTATAATTCTGCCACTATTTTCCAAAAT
1 TTTATAGTTTTGCCACTATTTTTCAAAAT
* * *
13065834 TTTATAGTTTTGCAACTGA-TTTTCTAGAT
1 TTTATAGTTTTGCCACT-ATTTTTCAAAAT
* * * * * * * *
13065863 TTTACAATTCTACCAATGTTTTTCCAGAT
1 TTTATAGTTTTGCCACTATTTTTCAAAAT
* * *
13065892 TTTACAGTTTTGTCACTAGTTTTCAAAAT
1 TTTATAGTTTTGCCACTATTTTTCAAAAT
* * * *
13065921 TTT-TCAGTTCTGCCAAT-TTTTTCTAGAT
1 TTTAT-AGTTTTGCCACTATTTTTCAAAAT
13065949 TTTATAGTTTTGCCACTATTTTTC-AAAT
1 TTTATAGTTTTGCCACTATTTTTCAAAAT
* * *
13065977 TTTGTAGTTTTGCTACTATTCTTTAAAAAT
1 TTTATAGTTTTGCCACTATT-TTTCAAAAT
13066007 AATTACAATT
Statistics
Matches: 200, Mismatches: 49, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
27 5 0.03
28 42 0.21
29 129 0.64
30 18 0.09
31 5 0.03
32 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (29 bp):
TTTATAGTTTTGCCACTATTTTTCAAAAT
Found at i:13067213 original size:3 final size:3
Alignment explanation
Indices: 13067198--13067252 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
13067188 AAATAGATTG
13067198 TTA TTA GTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
13067244 TTA CTA TTA
1 TTA TTA TTA
13067253 CTACTACCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13074313 original size:34 final size:35
Alignment explanation
Indices: 13074275--13074343 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
13074265 AGTAGTTTTA
* *
13074275 CTTGATTGTTTATGAT-TAAGAATGAATTGAAATT
1 CTTGATAGTTTATAATATAAGAATGAATTGAAATT
**
13074309 CTTGATAGTTTATAATATGTGAATGAATTGAAATT
1 CTTGATAGTTTATAATATAAGAATGAATTGAAATT
13074344 TCTAAACCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 14 0.47
35 16 0.53
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.43
Consensus pattern (35 bp):
CTTGATAGTTTATAATATAAGAATGAATTGAAATT
Found at i:13075368 original size:29 final size:29
Alignment explanation
Indices: 13075336--13075622 Score: 156
Period size: 29 Copynumber: 9.9 Consensus size: 29
13075326 CGTTGTCTTT
* *
13075336 TTTTTCAAATTTTATAGTTTTGCTACTGA
1 TTTTTCAAATTTTACAGTTTTGCCACTGA
* **
13075365 -TTTTCTAGATTTTACAGTTTTAACACT-A
1 TTTTTC-AAATTTTACAGTTTTGCCACTGA
* * * * *
13075393 TTTTTCAGAAATTTACAGTTTTTCAATTGGG
1 TTTTTCA-AATTTTACAGTTTTGCCACT-GA
* * * * *
13075424 CTTTTCAGATTTTGCAATTTCGCCACTG-
1 TTTTTCAAATTTTACAGTTTTGCCACTGA
* *
13075452 TTTTCCAAAATTTTACAGTTTTGCCATTGA
1 TTTTTC-AAATTTTACAGTTTTGCCACTGA
* * * * *
13075482 ATTTCCAGATTTTAAAGTTCTGCCACTG-
1 TTTTTCAAATTTTACAGTTTTGCCACTGA
* * * * *
13075510 TTTTCCAGATTTTACAATTTTGCCATTGG
1 TTTTTCAAATTTTACAGTTTTGCCACTGA
* * * **
13075539 TTTTCCAAATTTT-CAATTCTGCCACTTT
1 TTTTTCAAATTTTACAGTTTTGCCACTGA
*
13075567 TTTTTCAAGATTTTATAGTTTTGCCACT-A
1 TTTTTCAA-ATTTTACAGTTTTGCCACTGA
* *
13075596 TTTTAT-AGATTTTATAGTTTTGCCACT
1 TTTT-TCAAATTTTACAGTTTTGCCACT
13075623 ATTCTTAAAA
Statistics
Matches: 198, Mismatches: 49, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
28 71 0.36
29 93 0.47
30 28 0.14
31 6 0.03
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (29 bp):
TTTTTCAAATTTTACAGTTTTGCCACTGA
Found at i:13075523 original size:28 final size:28
Alignment explanation
Indices: 13075445--13075622 Score: 144
Period size: 28 Copynumber: 6.2 Consensus size: 28
13075435 TTGCAATTTC
* *
13075445 GCCACTGTTTTCCAAAATTTTACAGTTTT
1 GCCACTGTTTTCC-AGATTTTAAAGTTTT
* * *
13075474 GCCATTGAATTTCCAGATTTTAAAGTTCT
1 GCCACTG-TTTTCCAGATTTTAAAGTTTT
13075503 GCCACTGTTTTCCAGATTTTACAA-TTTT
1 GCCACTGTTTTCCAGATTTTA-AAGTTTT
* * * *
13075531 GCCATTGGTTTTCCAAATTTTCAA-TTCT
1 GCCACT-GTTTTCCAGATTTTAAAGTTTT
* * *
13075559 GCCACTTTTTTTTCAAGATTTTATAGTTTT
1 GCCAC--TGTTTTCCAGATTTTAAAGTTTT
* ** *
13075589 GCCACTATTTTATAGATTTTATAGTTTT
1 GCCACTGTTTTCCAGATTTTAAAGTTTT
13075617 GCCACT
1 GCCACT
13075623 ATTCTTAAAA
Statistics
Matches: 121, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
28 56 0.46
29 51 0.42
30 14 0.12
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (28 bp):
GCCACTGTTTTCCAGATTTTAAAGTTTT
Found at i:13075528 original size:86 final size:85
Alignment explanation
Indices: 13075425--13075609 Score: 203
Period size: 86 Copynumber: 2.2 Consensus size: 85
13075415 TCAATTGGGC
* * * *
13075425 TTTTCAGATTTTGCAATTTCGCCACT-GTTTTCCAAAATTTTACAGTTTTGCCA-TTGAATTTCC
1 TTTTCAGATTTTACAATTTCGCCACTGGTTTTCC-AAATTTT-CAATTCTGCCACTTGAATTTCA
*
13075488 AGATTTTAAAGTTCTGCCACTG
64 AGATTTTAAAGTTCTGCCACTA
* * ***
13075510 TTTTCCAGATTTTACAATTTTGCCATTGGTTTTCCAAATTTTCAATTCTGCCACTTTTTTTTCAA
1 TTTT-CAGATTTTACAATTTCGCCACTGGTTTTCCAAATTTTCAATTCTGCCACTTGAATTTCAA
* *
13075575 GATTTTATAGTTTTGCCACTA
65 GATTTTAAAGTTCTGCCACTA
*
13075596 TTTTATAGATTTTA
1 TTTT-CAGATTTTA
13075610 TAGTTTTGCC
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
85 13 0.16
86 63 0.76
87 7 0.08
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (85 bp):
TTTTCAGATTTTACAATTTCGCCACTGGTTTTCCAAATTTTCAATTCTGCCACTTGAATTTCAAG
ATTTTAAAGTTCTGCCACTA
Found at i:13075544 original size:57 final size:56
Alignment explanation
Indices: 13075445--13075592 Score: 179
Period size: 58 Copynumber: 2.6 Consensus size: 56
13075435 TTGCAATTTC
* *
13075445 GCCACTGTTTTCCAAAATTTTACAGTTTTGCCATTGAATTTCCAGATTTTAAAGTTCT
1 GCCACTGTTTTCC-AGATTTTACAGTTTTGCCATTGAATTTCCAAATTTTAAA-TTCT
* ** *
13075503 GCCACTGTTTTCCAGATTTTACAATTTTGCCATTGGTTTTCCAAATTTTCAATTCT
1 GCCACTGTTTTCCAGATTTTACAGTTTTGCCATTGAATTTCCAAATTTTAAATTCT
* * *
13075559 GCCACTTTTTTTTCAAGATTTTATAGTTTTGCCA
1 GCCAC--TGTTTTCCAGATTTTACAGTTTTGCCA
13075593 CTATTTTATA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
56 9 0.12
57 33 0.42
58 36 0.46
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (56 bp):
GCCACTGTTTTCCAGATTTTACAGTTTTGCCATTGAATTTCCAAATTTTAAATTCT
Found at i:13076726 original size:22 final size:21
Alignment explanation
Indices: 13076685--13076726 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
13076675 TACCATTTCA
*
13076685 ATTAAAAAGGTGAGATATTTT
1 ATTAAAAAGGTGAGAAATTTT
13076706 ATTAGAAAA-GTGTAGAAATTT
1 ATTA-AAAAGGTG-AGAAATTT
13076727 GGAGAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (21 bp):
ATTAAAAAGGTGAGAAATTTT
Found at i:13079560 original size:3 final size:3
Alignment explanation
Indices: 13079554--13079597 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
13079544 TTATACAAAA
13079554 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
13079598 GAACAGTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:13082199 original size:28 final size:27
Alignment explanation
Indices: 13082159--13082217 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
13082149 ACATGATTCA
*
13082159 AAATATTATAAAATTATATAAAA-TTATT
1 AAATATTATAAAA-TACATAAAACTTA-T
13082187 AAATATT-TAAAAATACATAAAACTTAT
1 AAATATTAT-AAAATACATAAAACTTAT
13082214 AAAT
1 AAAT
13082218 TTTGTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (27 bp):
AAATATTATAAAATACATAAAACTTAT
Found at i:13083239 original size:19 final size:20
Alignment explanation
Indices: 13083215--13083260 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
13083205 AGGGAAAGAA
13083215 AGTAAAACCC-AGTTGAATT
1 AGTAAAACCCTAGTTGAATT
13083234 AGTAAAACCCTAGTTGAATT
1 AGTAAAACCCTAGTTGAATT
13083254 AGTAAAA
1 AGTAAAA
13083261 TGCATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (20 bp):
AGTAAAACCCTAGTTGAATT
Found at i:13085891 original size:3 final size:3
Alignment explanation
Indices: 13085883--13085927 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
13085873 TCCAAAACCA
*
13085883 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AACT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
13085928 GTGTTGAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:13088448 original size:25 final size:25
Alignment explanation
Indices: 13088418--13088468 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
13088408 GCATATATAT
* * *
13088418 ATACAAACAATTTCATATAGCATTC
1 ATACAAACAAGTTCACATAGAATTC
13088443 ATACAAACAAGTTCACATAGAATTC
1 ATACAAACAAGTTCACATAGAATTC
13088468 A
1 A
13088469 ATAGCACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (25 bp):
ATACAAACAAGTTCACATAGAATTC
Found at i:13091198 original size:19 final size:20
Alignment explanation
Indices: 13091176--13091213 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13091166 TATTTTTATG
13091176 TTTATT-CAATTTAGTCCAA
1 TTTATTGCAATTTAGTCCAA
*
13091195 TTTATTGTAATTTAGTCCA
1 TTTATTGCAATTTAGTCCA
13091214 GTAACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (20 bp):
TTTATTGCAATTTAGTCCAA
Found at i:13091527 original size:22 final size:21
Alignment explanation
Indices: 13091502--13091544 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13091492 AATGATTTTT
13091502 AAAAAATTATTTACTTTTCTAG
1 AAAAAATTA-TTACTTTTCTAG
* *
13091524 AAAAAGTTATTATTTTTCTAG
1 AAAAAATTATTACTTTTCTAG
13091545 TGTTTGGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
AAAAAATTATTACTTTTCTAG
Found at i:13092037 original size:19 final size:19
Alignment explanation
Indices: 13092013--13092063 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
13092003 GCATTACTAG
13092013 TATTACACCACATAATTAA
1 TATTACACCACATAATTAA
13092032 TATTACACCACATAATTAA
1 TATTACACCACATAATTAA
* *
13092051 TAATACATCACAT
1 TATTACACCACAT
13092064 TAAAGAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (19 bp):
TATTACACCACATAATTAA
Found at i:13098286 original size:41 final size:41
Alignment explanation
Indices: 13098170--13098332 Score: 170
Period size: 41 Copynumber: 3.9 Consensus size: 41
13098160 GGTGTATAAA
* * * *
13098170 AAGGAAGACTCATGTCTCTG-GTTGAGCATGAGA-AATTGTAT
1 AAGGAAGACTCATGTCTC-GAGATGAGAATGAGATTA-TGAAT
* * *
13098211 AAATGGAATACTCATGTCTCGAGATAAGAGTGAGATTATGAAT
1 -AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
*
13098254 AAGGAAGACTCATGTCTCG-GAATGAGAATGAGATTATGATT
1 AAGGAAGACTCATGTCTCGAG-ATGAGAATGAGATTATGAAT
* *
13098295 AAGGAAAACTCATGTCTCGAGATGAGAATGAGAATATG
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATG
13098333 GTTAAAGGAA
Statistics
Matches: 103, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
40 1 0.01
41 67 0.65
42 6 0.06
43 28 0.27
44 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.26
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
Found at i:13106237 original size:40 final size:40
Alignment explanation
Indices: 13106147--13106225 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
13106137 CCGGTGTAAT
* ** * **
13106147 AAAACTTAAGCTACGGCTTAGCAGGCTATAAGTCGCTGTC
1 AAAACTCAAGCTTTGGCTTAGCAAGCTATAAGTCAATGTC
13106187 AAAACTCAAGCTTTGGCTTAGCAAGCTATAAGTCAATGT
1 AAAACTCAAGCTTTGGCTTAGCAAGCTATAAGTCAATGT
13106226 ATTAATTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (40 bp):
AAAACTCAAGCTTTGGCTTAGCAAGCTATAAGTCAATGTC
Found at i:13106446 original size:11 final size:11
Alignment explanation
Indices: 13106430--13106455 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13106420 ATAATAGATG
13106430 TTTAAAACAAA
1 TTTAAAACAAA
13106441 TTTAAAACAAA
1 TTTAAAACAAA
13106452 TTTA
1 TTTA
13106456 TTATGTGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (11 bp):
TTTAAAACAAA
Found at i:13122092 original size:20 final size:19
Alignment explanation
Indices: 13122059--13122096 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
13122049 AAGGTAACAA
*
13122059 ATAATATGGTAATAATATC
1 ATAATATGGCAATAATATC
13122078 ATAATAATGGCAATAATAT
1 ATAAT-ATGGCAATAATAT
13122097 TAATCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (19 bp):
ATAATATGGCAATAATATC
Found at i:13122644 original size:16 final size:16
Alignment explanation
Indices: 13122623--13122653 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13122613 ATGACATACA
13122623 AATAAATAAAAATATC
1 AATAAATAAAAATATC
*
13122639 AATAAATAAATATAT
1 AATAAATAAAAATAT
13122654 GAAATGCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAATAAAAATATC
Found at i:13122786 original size:20 final size:21
Alignment explanation
Indices: 13122763--13122811 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
13122753 AACAAACAAG
* *
13122763 ATAATAAATTAAATGTCAA-A
1 ATAATAAACTAAATATCAATA
* *
13122783 ATAAAAAACTAAATATGAATA
1 ATAATAAACTAAATATCAATA
13122804 ATAATAAA
1 ATAATAAA
13122812 AAATACGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAATAAACTAAATATCAATA
Found at i:13123088 original size:21 final size:20
Alignment explanation
Indices: 13123056--13123095 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13123046 AAAAATTCCC
*
13123056 CTCTGAACAAAAAAGTCCTT
1 CTCTGAACAAAAAAATCCTT
*
13123076 CTCTGAAATAAAAAAATCCT
1 CTCTG-AACAAAAAAATCCT
13123096 CTCAATCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (20 bp):
CTCTGAACAAAAAAATCCTT
Found at i:13123098 original size:20 final size:19
Alignment explanation
Indices: 13123043--13123098 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
13123033 TCAATCTCAT
*
13123043 TAAAAAAATTCCCCTCTGAA
1 TAAAAAAA-TCCTCTCTGAA
* *
13123063 CAAAAAAGTCCTTCTCTGAAA
1 TAAAAAAATCC-TCTCTG-AA
13123084 TAAAAAAATCCTCTC
1 TAAAAAAATCCTCTC
13123099 AATCTTATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.10
20 15 0.52
21 11 0.38
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (19 bp):
TAAAAAAATCCTCTCTGAA
Found at i:13125123 original size:18 final size:18
Alignment explanation
Indices: 13125086--13125134 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
13125076 TATTATTTAA
* *
13125086 AAAAAATTTAAATTTTTTT
1 AAAAATTTTAAA-CTTTTT
* *
13125105 ATACATTTTAAACTTTTT
1 AAAAATTTTAAACTTTTT
13125123 AAAAATTTTAAA
1 AAAAATTTTAAA
13125135 ACTAATTTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAAATTTTAAACTTTTT
Found at i:13134926 original size:24 final size:24
Alignment explanation
Indices: 13134878--13134940 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
13134868 TTAGTTTAAC
13134878 CAAAAAGAAAAGAAGAGTGAAAAAT
1 CAAAAAGAAAA-AAGAGTGAAAAAT
*
13134903 CAAAAAGAAAAAATGAGT-AGAAAT
1 CAAAAAGAAAAAA-GAGTGAAAAAT
*
13134927 -AAAAAAAAAAAAGA
1 CAAAAAGAAAAAAGA
13134941 ATCATGAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 2 0.06
23 11 0.31
24 7 0.20
25 15 0.43
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (24 bp):
CAAAAAGAAAAAAGAGTGAAAAAT
Found at i:13138357 original size:21 final size:21
Alignment explanation
Indices: 13138330--13138380 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
13138320 GGATTATGTA
*
13138330 ATTTGGATTTATAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
13138351 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
13138372 ATTTGGATT
1 ATTTGGATT
13138381 ATGCTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:13139233 original size:18 final size:18
Alignment explanation
Indices: 13139210--13139250 Score: 75
Period size: 17 Copynumber: 2.3 Consensus size: 18
13139200 TTAATTAATA
13139210 TTATTTTTTACTAATTTT
1 TTATTTTTTACTAATTTT
13139228 TTA-TTTTTACTAATTTT
1 TTATTTTTTACTAATTTT
13139245 TTATTT
1 TTATTT
13139251 AATATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTTTTTACTAATTTT
Found at i:13141112 original size:22 final size:22
Alignment explanation
Indices: 13141043--13141113 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
13141033 AAACGAGTTT
13141043 ATAAACGAGCTTGTTCGTGAAC
1 ATAAACGAGCTTGTTCGTGAAC
** * *
13141065 ATAAATAAACTTGTTCGTGGAC
1 ATAAACGAGCTTGTTCGTGAAC
* * *
13141087 ATAAACGAGTTTATTCGTGAAT
1 ATAAACGAGCTTGTTCGTGAAC
13141109 ATAAA
1 ATAAA
13141114 TGAACTAAAC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (22 bp):
ATAAACGAGCTTGTTCGTGAAC
Found at i:13143223 original size:29 final size:29
Alignment explanation
Indices: 13143179--13143245 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
13143169 CACATTATAA
*
13143179 ATTTCATTTCTTAATT-TGCATACAATACC
1 ATTTCATTTCTCAATTCTG-ATACAATACC
*
13143208 ATTTCATTTCTCAATTCTGATATAATACC
1 ATTTCATTTCTCAATTCTGATACAATACC
13143237 ATTTCATTT
1 ATTTCATTT
13143246 ATGCAACAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 33 0.94
30 2 0.06
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.48
Consensus pattern (29 bp):
ATTTCATTTCTCAATTCTGATACAATACC
Found at i:13146706 original size:58 final size:58
Alignment explanation
Indices: 13146616--13146734 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 58
13146606 CATTAACCCT
13146616 CATGGTTCTTATTACAAATTTCATATGATCTTTCAAATGTTATCTTTCAATACCTAAA
1 CATGGTTCTTATTACAAATTTCATATGATCTTTCAAATGTTATCTTTCAATACCTAAA
*
13146674 CATGGTT-TGTATTACAAATTTCATATGATCTTTCAAATGTTATCTTTTAATACCTAAA
1 CATGGTTCT-TATTACAAATTTCATATGATCTTTCAAATGTTATCTTTCAATACCTAAA
13146732 CAT
1 CAT
13146735 TTGTATGCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 1 0.02
58 58 0.98
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.44
Consensus pattern (58 bp):
CATGGTTCTTATTACAAATTTCATATGATCTTTCAAATGTTATCTTTCAATACCTAAA
Found at i:13153160 original size:18 final size:18
Alignment explanation
Indices: 13153139--13153173 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13153129 ATTTCTTTCA
* *
13153139 TTTCTTTCTTCTTCTCTC
1 TTTCTCTCTTCCTCTCTC
13153157 TTTCTCTCTTCCTCTCT
1 TTTCTCTCTTCCTCTCT
13153174 AAAACATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTCTCTCTTCCTCTCTC
Found at i:13153383 original size:21 final size:21
Alignment explanation
Indices: 13153357--13153402 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
13153347 AACTAATGAA
13153357 ACCATTTTCTTCAGTTTTCTT
1 ACCATTTTCTTCAGTTTTCTT
*
13153378 ACCATTTTCTTTAGTTTTCTT
1 ACCATTTTCTTCAGTTTTCTT
13153399 ACCA
1 ACCA
13153403 ACCAAACAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.24, G:0.04, T:0.54
Consensus pattern (21 bp):
ACCATTTTCTTCAGTTTTCTT
Found at i:13168060 original size:30 final size:31
Alignment explanation
Indices: 13168024--13168095 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
13168014 AAAAAAGCTT
13168024 AGGTACCAAATCA-GAAAAAATGCCAAGTTC
1 AGGTACCAAATCAGGAAAAAATGCCAAGTTC
* **
13168054 AGGTACCAAATTAGGAAAAAATGTTAAGTTC
1 AGGTACCAAATCAGGAAAAAATGCCAAGTTC
13168085 AGGTACCAAAT
1 AGGTACCAAAT
13168096 GTTATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (31 bp):
AGGTACCAAATCAGGAAAAAATGCCAAGTTC
Found at i:13179076 original size:21 final size:21
Alignment explanation
Indices: 13179052--13179103 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
13179042 TAGAAGTAAG
13179052 ACTTGTATCGGTAGAACAGTC
1 ACTTGTATCGGTAGAACAGTC
* *
13179073 ACTTTTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
*
13179094 GCTTGTATCG
1 ACTTGTATCG
13179104 ATAAAAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:13191225 original size:37 final size:41
Alignment explanation
Indices: 13191147--13191222 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 41
13191137 TATTTATGTG
* * * *
13191147 TGTATACATTAATTTTTATCTATTTATATGTTTTTTAAATT
1 TGTATACATTAATTTATATATATTTAGATGTTTTCTAAATT
13191188 TGTATACA-T-ATTTATATATATTTAGA-GTTTTCTAA
1 TGTATACATTAATTTATATATATTTAGATGTTTTCTAA
13191223 TTTTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
38 8 0.26
39 14 0.45
40 1 0.03
41 8 0.26
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (41 bp):
TGTATACATTAATTTATATATATTTAGATGTTTTCTAAATT
Found at i:13191659 original size:10 final size:10
Alignment explanation
Indices: 13191644--13191676 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
13191634 GAAGATTTAA
13191644 TATTTATTAG
1 TATTTATTAG
13191654 TATTTATTAG
1 TATTTATTAG
*
13191664 TATTTATAAG
1 TATTTATTAG
13191674 TAT
1 TAT
13191677 AATATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (10 bp):
TATTTATTAG
Found at i:13191702 original size:24 final size:24
Alignment explanation
Indices: 13191665--13191712 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13191655 ATTTATTAGT
*
13191665 ATTTATAAGTATAATATATTTAAC
1 ATTTATAAGCATAATATATTTAAC
* *
13191689 ATTTATTAGCATAATTTATTTAAC
1 ATTTATAAGCATAATATATTTAAC
13191713 CTACAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (24 bp):
ATTTATAAGCATAATATATTTAAC
Found at i:13192730 original size:16 final size:16
Alignment explanation
Indices: 13192711--13192743 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13192701 AAAAAATGTA
13192711 TAAAATTATTA-AATAT
1 TAAAA-TATTATAATAT
13192727 TAAAATATTATAATAT
1 TAAAATATTATAATAT
13192743 T
1 T
13192744 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATATTATAATAT
Found at i:13193746 original size:29 final size:28
Alignment explanation
Indices: 13193676--13193815 Score: 101
Period size: 28 Copynumber: 4.9 Consensus size: 28
13193666 AAGTTTTAAT
*
13193676 AAAAAAATATAAAAATATT-TAAAACTT-A
1 AAAAAAATAT-AAAAT-TTATAAAAATTGA
* * *
13193704 ATAAAATTAGATAAATTTATAAAAATTGCA
1 AAAAAAATATA-AAATTTATAAAAATTG-A
13193734 AAAAAAATCATAAAATATTAT-AAAATAT-A
1 AAAAAAAT-ATAAAAT-TTATAAAAAT-TGA
*
13193763 AAAAAAATATAAAATTT-TACAAAATCGTA
1 AAAAAAATATAAAATTTATA-AAAATTG-A
* *
13193792 AAAAAGATATAAAATTCATAAAAA
1 AAAAAAATATAAAATTTATAAAAA
13193816 ATTATAAAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
26 1 0.01
27 5 0.06
28 30 0.33
29 29 0.32
30 18 0.20
31 7 0.08
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (28 bp):
AAAAAAATATAAAATTTATAAAAATTGA
Found at i:13193805 original size:19 final size:18
Alignment explanation
Indices: 13193783--13193825 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
13193773 AAAATTTTAC
*
13193783 AAAATCGTAAAAAAGATAT
1 AAAATCATAAAAAA-ATAT
*
13193802 AAAATTCATAAAAAATTAT
1 AAAA-TCATAAAAAAATAT
13193821 AAAAT
1 AAAAT
13193826 TTTCTGTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 11 0.52
20 9 0.43
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAATCATAAAAAAATAT
Found at i:13193816 original size:11 final size:10
Alignment explanation
Indices: 13193674--13193824 Score: 50
Period size: 10 Copynumber: 15.6 Consensus size: 10
13193664 CTAAGTTTTA
*
13193674 ATAAAAAAAT
1 ATAAAAAATT
13193684 ATAAAAATATT
1 ATAAAAA-ATT
*
13193695 -T-AAAACTT
1 ATAAAAAATT
*
13193703 A-ATAAAATT
1 ATAAAAAATT
* * *
13193712 AGATAAATTT
1 ATAAAAAATT
13193722 AT-AAAAATT
1 ATAAAAAATT
* *
13193731 GCAAAAAAAATC
1 --ATAAAAAATT
*
13193743 ATAAAATATT
1 ATAAAAAATT
13193753 AT--AAAA-T
1 ATAAAAAATT
*
13193760 ATAAAAAA-A
1 ATAAAAAATT
*
13193769 ATATAAAATT
1 ATAAAAAATT
* * *
13193779 TTACAAAATC
1 ATAAAAAATT
* *
13193789 GTAAAAAA-G
1 ATAAAAAATT
*
13193798 ATATAAAATT
1 ATAAAAAATT
13193808 CATAAAAAATT
1 -ATAAAAAATT
13193819 ATAAAA
1 ATAAAA
13193825 TTTTCTGTAA
Statistics
Matches: 102, Mismatches: 27, Indels: 24
0.67 0.18 0.16
Matches are distributed among these distances:
7 3 0.03
8 5 0.05
9 32 0.31
10 44 0.43
11 12 0.12
12 6 0.06
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:13194162 original size:4 final size:4
Alignment explanation
Indices: 13194145--13194179 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
13194135 ATGATTTGAA
* *
13194145 TATG TATC TATG TATG TATG TATC TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
13194180 ATATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:13194164 original size:16 final size:16
Alignment explanation
Indices: 13194145--13194179 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
13194135 ATGATTTGAA
13194145 TATGTATCTATGTATG
1 TATGTATCTATGTATG
13194161 TATGTATCTATGTATG
1 TATGTATCTATGTATG
13194177 TAT
1 TAT
13194180 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (16 bp):
TATGTATCTATGTATG
Found at i:13194896 original size:11 final size:9
Alignment explanation
Indices: 13194864--13194916 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
13194854 ATATTACAAT
13194864 TTTTTATAA
1 TTTTTATAA
13194873 TTTTTATAA
1 TTTTTATAA
13194882 TTTTTATAA
1 TTTTTATAA
*
13194891 TCTTTTAGCAA
1 T-TTTTA-TAA
* *
13194902 TTTTAATGA
1 TTTTTATAA
13194911 TTTTTA
1 TTTTTA
13194917 ATTTTAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 25 0.68
10 9 0.24
11 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:13194903 original size:20 final size:18
Alignment explanation
Indices: 13194857--13194916 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
13194847 TTTAAAAATA
13194857 TTACAATTTTTTATAATTT
1 TTACAA-TTTTTATAATTT
*
13194876 TTATAATTTTTATAATCTT
1 TTACAATTTTTATAAT-TT
* *
13194895 TTAGCAATTTTAATGATTT
1 TTA-CAATTTTTATAATTT
13194914 TTA
1 TTA
13194917 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 10 0.29
19 15 0.43
20 10 0.29
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (18 bp):
TTACAATTTTTATAATTT
Found at i:13196558 original size:23 final size:23
Alignment explanation
Indices: 13196531--13196944 Score: 563
Period size: 23 Copynumber: 18.1 Consensus size: 23
13196521 TACAAACTAC
13196531 TAAGCATAAATCACATTAACATT
1 TAAGCATAAATCACATTAACATT
* *
13196554 TAAGCATAAATCACATAAACTTT
1 TAAGCATAAATCACATTAACATT
*
13196577 TAAGCATAAATCATATTAACATT
1 TAAGCATAAATCACATTAACATT
*
13196600 TAAGGATAAATCACATTAACATT
1 TAAGCATAAATCACATTAACATT
*
13196623 TAAGCATAAATCATATT-ACAATT
1 TAAGCATAAATCACATTAAC-ATT
* *
13196646 TAAGTATATATCACATTAAC-TGT
1 TAAGCATAAATCACATTAACAT-T
13196669 TAAGCATAAATCACATTAACATT
1 TAAGCATAAATCACATTAACATT
**
13196692 TAAGCATAAATCACATTAATTTT
1 TAAGCATAAATCACATTAACATT
*
13196715 TAAGCATAAATCATATTAACATT
1 TAAGCATAAATCACATTAACATT
* *
13196738 TAAGCATAAAGCACATTAA-TTT
1 TAAGCATAAATCACATTAACATT
*
13196760 TGAAGCATAAATCATATTAACATT
1 T-AAGCATAAATCACATTAACATT
*
13196784 TAAGCATAAATCATATTAACATT
1 TAAGCATAAATCACATTAACATT
*
13196807 T-A--ATAAATCACATTAA-TTT
1 TAAGCATAAATCACATTAACATT
*
13196826 TGAAGCATAAATCATATTAACATT
1 T-AAGCATAAATCACATTAACATT
13196850 TAAGCATAAATCACATTAACATT
1 TAAGCATAAATCACATTAACATT
*
13196873 TAAGCATAAATCATATTAACATT
1 TAAGCATAAATCACATTAACATT
* *
13196896 TAAGTATAAATCACATTAACTTT
1 TAAGCATAAATCACATTAACATT
*
13196919 TAAGCATAAATCATATTAACATT
1 TAAGCATAAATCACATTAACATT
13196942 TAA
1 TAA
13196945 ACACATTTAA
Statistics
Matches: 343, Mismatches: 37, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
19 3 0.01
20 13 0.04
21 1 0.00
22 7 0.02
23 310 0.90
24 9 0.03
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (23 bp):
TAAGCATAAATCACATTAACATT
Found at i:13197429 original size:36 final size:36
Alignment explanation
Indices: 13197346--13197429 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
13197336 TCATAATATA
* *
13197346 ATCACTATCACTTGGCATGAATATCATACCCACATC
1 ATCACTATCACATGGCATGAATAACATACCCACATC
* ** *
13197382 TTTTCTGTCACATGGCATGAATAAACATACCCACAT-
1 ATCACTATCACATGGCATGAAT-AACATACCCACATC
*
13197418 ATCACTTTCACA
1 ATCACTATCACA
13197430 ACAGTTATCA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
36 25 0.68
37 12 0.32
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.30
Consensus pattern (36 bp):
ATCACTATCACATGGCATGAATAACATACCCACATC
Found at i:13199085 original size:13 final size:14
Alignment explanation
Indices: 13199062--13199094 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13199052 GGATCTACTT
13199062 TAAACTCTAAAA-GA
1 TAAA-TCTAAAATGA
13199076 TAAATCTAAAATGA
1 TAAATCTAAAATGA
13199090 TAAAT
1 TAAAT
13199095 ACAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (14 bp):
TAAATCTAAAATGA
Found at i:13207617 original size:28 final size:29
Alignment explanation
Indices: 13207585--13207642 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
13207575 AGGTATTTTA
13207585 CTCTATTTTT-TGGGTTATTTTTCATCAT
1 CTCTATTTTTCTGGGTTATTTTTCATCAT
13207613 CTCTATTTTTCTGGGTTATTTTTCATCAT
1 CTCTATTTTTCTGGGTTATTTTTCATCAT
13207642 C
1 C
13207643 GAATTAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.59
Consensus pattern (29 bp):
CTCTATTTTTCTGGGTTATTTTTCATCAT
Found at i:13207824 original size:31 final size:32
Alignment explanation
Indices: 13207783--13207847 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
13207773 TGACTTCCAA
*
13207783 TTTTATTTCGTA-TATAACTAACTTTTATTTT
1 TTTTAATTCGTATTATAACTAACTTTTATTTT
*
13207814 TTTTAATTCGTATTATATCTAACTTTTATTTT
1 TTTTAATTCGTATTATAACTAACTTTTATTTT
13207846 TT
1 TT
13207848 GTTTTTGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.25, C:0.09, G:0.03, T:0.63
Consensus pattern (32 bp):
TTTTAATTCGTATTATAACTAACTTTTATTTT
Found at i:13207986 original size:9 final size:9
Alignment explanation
Indices: 13207970--13208324 Score: 163
Period size: 9 Copynumber: 38.7 Consensus size: 9
13207960 GTTTTTAAAC
13207970 TGTTATGTA
1 TGTTATGTA
* *
13207979 TATTATGTT
1 TGTTATGTA
13207988 TGTTATGTA
1 TGTTATGTA
13207997 CTGTTATGTA
1 -TGTTATGTA
13208007 TG-TATGTTA
1 TGTTATG-TA
*
13208016 TGTT-TAT-
1 TGTTATGTA
*
13208023 TGTTTTGTA
1 TGTTATGTA
13208032 TGTTATGTA
1 TGTTATGTA
13208041 CTGTTATGTTA
1 -TGTTATG-TA
13208052 TG-TATGTA
1 TGTTATGTA
13208060 TGTTATGGTCCATA
1 TGTTAT-G----TA
13208074 CTGTTATGTA
1 -TGTTATGTA
*
13208084 TATTATGTA
1 TGTTATGTA
13208093 TGTTATGTTTA
1 TGTTATG--TA
*
13208104 CTGTTATGTT
1 -TGTTATGTA
13208114 TGTATAT-T-
1 TGT-TATGTA
13208122 TG-TATGTA
1 TGTTATGTA
13208130 TGTTATGTA
1 TGTTATGTA
13208139 CTGTTATGTA
1 -TGTTATGTA
*
13208149 TATTATGTA
1 TGTTATGTA
13208158 TGTATAATTGTA
1 TGT-T-A-TGTA
13208170 TGTT-TGTTA
1 TGTTATG-TA
*
13208179 TGTGT-TGTT
1 TGT-TATGTA
**
13208188 TACTAT-TA
1 TGTTATGTA
13208196 TGTT-TGTA
1 TGTTATGTA
*
13208204 TATT-TGTA
1 TGTTATGTA
*
13208212 TG-TCTGTTA
1 TGTTATG-TA
*
13208221 CG-TACTGTTA
1 TGTTA-TG-TA
13208231 TGTTATGTA
1 TGTTATGTA
*
13208240 AGTTATGTA
1 TGTTATGTA
* *
13208249 TATTATGCA
1 TGTTATGTA
13208258 TGTTATGT-
1 TGTTATGTA
*
13208266 T-TAATGTTA
1 TGTTATG-TA
*
13208275 TATT-TGTA
1 TGTTATGTA
*
13208283 TATT-TGTA
1 TGTTATGTA
13208291 TG-TATGTTA
1 TGTTATG-TA
13208300 TGTTATGTA
1 TGTTATGTA
*
13208309 CTATTATGTA
1 -TGTTATGTA
13208319 TGTTAT
1 TGTTAT
13208325 ATATTATAAT
Statistics
Matches: 272, Mismatches: 34, Indels: 80
0.70 0.09 0.21
Matches are distributed among these distances:
6 3 0.01
7 12 0.04
8 48 0.18
9 118 0.43
10 60 0.22
11 8 0.03
12 14 0.05
14 3 0.01
15 6 0.02
ACGTcount: A:0.22, C:0.04, G:0.19, T:0.56
Consensus pattern (9 bp):
TGTTATGTA
Found at i:13208004 original size:28 final size:27
Alignment explanation
Indices: 13207970--13208350 Score: 114
Period size: 28 Copynumber: 14.3 Consensus size: 27
13207960 GTTTTTAAAC
13207970 TGTTATGTATATTATGTTTGTTATGTA
1 TGTTATGTATATTATGTTTGTTATGTA
* *
13207997 CTGTTATGTAT-GTATGTTATGTT-TAT-
1 -TGTTATGTATATTATGTT-TGTTATGTA
* * *
13208023 TGTTTTGTATGTTATGTACTGTTATGTTA
1 TGTTATGTATATTATGT-TTGTTATG-TA
* *
13208052 TG-TATGTATGTTATG---GTCCA--TA
1 TGTTATGTATATTATGTTTGT-TATGTA
*
13208074 CTGTTATGTATATTATGTATGTTATGTTTA
1 -TGTTATGTATATTATGTTTGTTATG--TA
*
13208104 CTGTTATGT-T-TGTATATTTG-TATGTA
1 -TGTTATGTATAT-TATGTTTGTTATGTA
* * *
13208130 TGTTATGTACTGTTATGTATATTATGTA
1 TGTTATGTA-TATTATGTTTGTTATGTA
*
13208158 TG-TAT-AAT-TGTATGTTTGTTATG--
1 TGTTATGTATAT-TATGTTTGTTATGTA
* *
13208181 TGTTGTTTACTATTATGTTTGTATATTTGTA
1 TGTTATGTA-TATTATGTTTGT-TA--TGTA
* *
13208212 TG-TCTGT-TACGTACTGTTATGTTATGTA
1 TGTTATGTATA-TTA-TGTT-TGTTATGTA
* **
13208240 AGTTATGTATATTATGCATGTTATGT-
1 TGTTATGTATATTATGTTTGTTATGTA
* * *
13208266 T-TAATGTTATATT-TGTATATT-TGTA
1 TGTTATG-TATATTATGTTTGTTATGTA
* * *
13208291 TG-TATGTTATGTTATGTACTATTATGTA
1 TGTTATG-TATATTATGT-TTGTTATGTA
** *
13208319 TGTTA--TATATTATAATTG-TATGTT
1 TGTTATGTATATTATGTTTGTTATGTA
13208343 TGTTATGT
1 TGTTATGT
13208351 GTTGTTTACT
Statistics
Matches: 267, Mismatches: 41, Indels: 92
0.67 0.10 0.23
Matches are distributed among these distances:
22 2 0.01
23 4 0.01
24 30 0.11
25 52 0.19
26 40 0.15
27 35 0.13
28 56 0.21
29 21 0.08
30 22 0.08
31 5 0.02
ACGTcount: A:0.22, C:0.03, G:0.18, T:0.56
Consensus pattern (27 bp):
TGTTATGTATATTATGTTTGTTATGTA
Found at i:13208081 original size:33 final size:30
Alignment explanation
Indices: 13207998--13208160 Score: 64
Period size: 33 Copynumber: 5.5 Consensus size: 30
13207988 TGTTATGTAC
* * *
13207998 TGTTATGTATGTATGTTATGTTTATTGTTT
1 TGTTATGTATGTATGTTATGTATACTGTTA
13208028 TG-TATGTTATGTACTGTTATGT-TA-TGTATGTA
1 TGTTATG-TATGTA-TGTTATGTATACTG--T-TA
*** * *
13208060 TGTTATGGTCCATACTGTTATGTATATTATGTA
1 TGTTAT-GTATGTA-TGTTATGTATACTGT-TA
13208093 TGTTATGT-T-TACTGTTATGT-T--TG-TA
1 TGTTATGTATGTA-TGTTATGTATACTGTTA
*
13208118 TATT-TGTATGTATGTTATG--TACTGTTA
1 TGTTATGTATGTATGTTATGTATACTGTTA
13208145 TGTATAT-TATGTATGT
1 TGT-TATGTATGTATGT
13208161 ATAATTGTAT
Statistics
Matches: 108, Mismatches: 9, Indels: 34
0.72 0.06 0.23
Matches are distributed among these distances:
24 4 0.04
25 13 0.12
26 4 0.04
27 5 0.05
28 10 0.09
29 8 0.07
30 21 0.19
31 9 0.08
32 5 0.05
33 25 0.23
34 3 0.03
35 1 0.01
ACGTcount: A:0.21, C:0.04, G:0.20, T:0.56
Consensus pattern (30 bp):
TGTTATGTATGTATGTTATGTATACTGTTA
Found at i:13208147 original size:98 final size:89
Alignment explanation
Indices: 13208028--13208373 Score: 287
Period size: 86 Copynumber: 3.9 Consensus size: 89
13208018 TTTATTGTTT
*
13208028 TGTATGTTATGTACTGTTATGTTATGTATGTATGTTATGGTCCAT-ACTGTTATGTATATTATGT
1 TGTATGTTATGTACTGTTATGTTATGTAT-TATG-TAT-GT--ATAATTG-TATGTATATTATG-
*
13208092 ATGTTATGTTTACTGTTATGTTTGTATATTTGTA
59 -TG-T-TGTTTACTATTATGTTTGTATATTTGTA
* *
13208126 TGTATGTTATGTACTGTTATG-TA--TATTATGTATGTATAATTGTATGTTTGTTATGTGTTGTT
1 TGTATGTTATGTACTGTTATGTTATGTATTATGTATGTATAATTGTATGTATATTATGTGTTGTT
13208188 TACTATTATGTTTGTATATTTGTA
66 TACTATTATGTTTGTATATTTGTA
* * * *
13208212 TGTCTGTTACGTACTGTTATGTTATGTA--A-GTTATGTAT-A-T-TATGCATGTTA-----TGT
1 TGTATGTTATGTACTGTTATGTTATGTATTATG-TATGTATAATTGTATGTATATTATGTGTTGT
* * *
13208266 TTAATGTTATATTTGTATATTTGTA
65 TTACTATTATGTTTGTATATTTGTA
* * * *
13208291 TGTATGTTATGTTA-TG-TACTATTATGTATGTTATATAT-TATAATTGTATGTTTGTTATGTGT
1 TGTATGTTATG-TACTGTTA-TGTTATGTA--TTATGTATGTATAATTGTATGTATATTATGTGT
*
13208353 TGTTTACTGTTATGTTTGTAT
62 TGTTTACTATTATGTTTGTAT
13208374 GACAGTTTAT
Statistics
Matches: 209, Mismatches: 19, Indels: 48
0.76 0.07 0.17
Matches are distributed among these distances:
78 2 0.01
79 44 0.21
80 2 0.01
82 3 0.01
83 5 0.02
84 10 0.05
85 10 0.05
86 48 0.23
87 11 0.05
88 2 0.01
89 2 0.01
90 32 0.15
91 3 0.01
92 2 0.01
93 3 0.01
94 4 0.02
95 3 0.01
97 2 0.01
98 21 0.10
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.55
Consensus pattern (89 bp):
TGTATGTTATGTACTGTTATGTTATGTATTATGTATGTATAATTGTATGTATATTATGTGTTGTT
TACTATTATGTTTGTATATTTGTA
Found at i:13208170 original size:86 final size:85
Alignment explanation
Indices: 13208080--13208373 Score: 313
Period size: 86 Copynumber: 3.5 Consensus size: 85
13208070 CATACTGTTA
13208080 TGTATATTATG-TATGT-TATGTTTACTGTTATGTTTGTATATTTGTATGTATGTTATGTACTGT
1 TGTATATT-TGTTATGTGT-TGTTTACTGTTATGTTTGTATATTTGTATGTATGTTATGTACTGT
13208143 TATGTATATTATGTATGTATAAT
64 TATGTAT-TTATGTATGTATAAT
* * * *
13208166 TGTATGTTTGTTATGTGTTGTTTACTATTATGTTTGTATATTTGTATGTCTGTTACGTACTGTTA
1 TGTATATTTGTTATGTGTTGTTTACTGTTATGTTTGTATATTTGTATGTATGTTATGTACTGTTA
*
13208231 TG---TTATGTAAGT-T-A-
66 TGTATTTATGTATGTATAAT
* * *
13208245 TGTATATTATG-CATGT-TATGTTTAATGTTATATTTGTATATTTGTATGTATGTTATGTTATGT
1 TGTATATT-TGTTATGTGT-TGTTTACTGTTATGTTTGTATA--T-T-TGTATG-TATGTTATGT
* *
13208308 ACTATTATGTATGTTATATAT-TATAAT
59 ACTGTTATGTAT-TTATGTATGTATAAT
*
13208335 TGTATGTTTGTTATGTGTTGTTTACTGTTATGTTTGTAT
1 TGTATATTTGTTATGTGTTGTTTACTGTTATGTTTGTAT
13208374 GACAGTTTAT
Statistics
Matches: 171, Mismatches: 19, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
78 1 0.01
79 30 0.18
80 3 0.02
81 2 0.01
82 10 0.06
83 6 0.04
84 16 0.09
85 2 0.01
86 58 0.34
87 2 0.01
88 7 0.04
89 3 0.02
90 30 0.18
91 1 0.01
ACGTcount: A:0.22, C:0.03, G:0.18, T:0.56
Consensus pattern (85 bp):
TGTATATTTGTTATGTGTTGTTTACTGTTATGTTTGTATATTTGTATGTATGTTATGTACTGTTA
TGTATTTATGTATGTATAAT
Found at i:13208316 original size:79 final size:77
Alignment explanation
Indices: 13208184--13208331 Score: 183
Period size: 79 Copynumber: 1.9 Consensus size: 77
13208174 TGTTATGTGT
* * * *
13208184 TGTTTACTATTATGTTTGTATATTTGTATGTCTGTTACGTACTGTTATGTTATGTAAGTTATGTA
1 TGTTTAATATTATATTTGTATATTTGTATGTATGTTACGTACTGTTATATTATGTAAGTTA--TA
13208249 TATTATGCATGTTA
64 TATTATGCATGTTA
* * *
13208263 TGTTTAATGTTATATTTGTATATTTGTATGTATGTTATGTTA-TG-TACTATTATGTATGTTATA
1 TGTTTAATATTATATTTGTATATTTGTATGTATGTTACG-TACTGTTA-TATTATGTAAGTTATA
13208326 TATTAT
64 TATTAT
13208332 AATTGTATGT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
77 8 0.13
78 2 0.03
79 48 0.80
80 2 0.03
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.55
Consensus pattern (77 bp):
TGTTTAATATTATATTTGTATATTTGTATGTATGTTACGTACTGTTATATTATGTAAGTTATATA
TTATGCATGTTA
Found at i:13208340 original size:24 final size:25
Alignment explanation
Indices: 13208269--13208348 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 25
13208259 GTTATGTTTA
* *
13208269 ATGTTATATTTGTATATTTGTATGT
1 ATGTTATATATGTATAATTGTATGT
*
13208294 ATGTTATGTTATGTACT-A-T-TATGT
1 ATGTTAT-ATATGTA-TAATTGTATGT
13208318 ATGTTATATAT-TATAATTGTATGT
1 ATGTTATATATGTATAATTGTATGT
*
13208342 TTGTTAT
1 ATGTTAT
13208349 GTGTTGTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.02
22 3 0.07
23 4 0.09
24 23 0.51
25 8 0.18
26 5 0.11
27 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.15, T:0.57
Consensus pattern (25 bp):
ATGTTATATATGTATAATTGTATGT
Found at i:13211694 original size:11 final size:11
Alignment explanation
Indices: 13211674--13211748 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
13211664 AAGCCTCTTA
*
13211674 TCTTTCCTTTC
1 TCTTTTCTTTC
*
13211685 TCTTTTCTTTT
1 TCTTTTCTTTC
*
13211696 TCTCATTCATTTC
1 TCT-TTTC-TTTC
*
13211709 TTTTTTCTTTC
1 TCTTTTCTTTC
13211720 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
13211732 TATTTTCTTCC
1 TCTTTTCTTTC
13211743 TCTTTT
1 TCTTTT
13211749 AATCACACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
11 30 0.59
12 16 0.31
13 5 0.10
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:13211731 original size:12 final size:12
Alignment explanation
Indices: 13211676--13211740 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
13211666 GCCTCTTATC
*
13211676 TTTCCTTTCTCT
1 TTTCTTTTCTCT
13211688 TTTCTTTT-TCT
1 TTTCTTTTCTCT
* * *
13211699 CATTCATTTCTTT
1 -TTTCTTTTCTCT
13211712 TTTC-TTTCTCT
1 TTTCTTTTCTCT
*
13211723 TTTCTTTTCTAT
1 TTTCTTTTCTCT
13211735 TTTCTT
1 TTTCTT
13211741 CCTCTTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
11 13 0.30
12 28 0.65
13 2 0.05
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTTTTCTCT
Found at i:13212172 original size:15 final size:15
Alignment explanation
Indices: 13212148--13212177 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13212138 AACCCACATT
13212148 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
13212163 CATTTGAACCAAACC
1 CATTTAAACCAAACC
13212178 AAATGAACCA
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:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:13212258 original size:11 final size:10
Alignment explanation
Indices: 13212214--13212282 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
13212204 AGTCAAACCA
*
13212214 TTGACCGATG
1 TTGACCGACG
* *
13212224 TTGACTGGCG
1 TTGACCGACG
*
13212234 TTGATCGACG
1 TTGACCGACG
13212244 TTGACCGACCG
1 TTGACCGA-CG
*
13212255 TTGACCGATG
1 TTGACCGACG
**
13212265 TTGATTGATCG
1 TTGACCGA-CG
13212276 TTGACCG
1 TTGACCG
13212283 TTGATCGTTG
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
10 28 0.64
11 16 0.36
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.30
Consensus pattern (10 bp):
TTGACCGACG
Found at i:13212277 original size:21 final size:21
Alignment explanation
Indices: 13212214--13212309 Score: 77
Period size: 21 Copynumber: 4.3 Consensus size: 21
13212204 AGTCAAACCA
*
13212214 TTGACCGATGTTGACTG-GCG
1 TTGACCGATGTTGACTGATCG
* * * *
13212234 TTGATCGACGTTGACCGACCG
1 TTGACCGATGTTGACTGATCG
*
13212255 TTGACCGATGTTGATTGATCG
1 TTGACCGATGTTGACTGATCG
13212276 TTGACCGTTGATCGTTGACTTTGATCG
1 TTGACC---GAT-GTTGAC--TGATCG
13212303 TTGACCG
1 TTGACCG
13212310 TTGACTTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
20 14 0.24
21 24 0.41
24 4 0.07
25 5 0.08
27 12 0.20
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGACCGATGTTGACTGATCG
Found at i:13212279 original size:7 final size:7
Alignment explanation
Indices: 13212269--13212313 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
13212259 CCGATGTTGA
13212269 TTGATCG
1 TTGATCG
*
13212276 TTGACCG
1 TTGATCG
13212283 TTGATCG
1 TTGATCG
*
13212290 TTGA-CT
1 TTGATCG
13212296 TTGATCG
1 TTGATCG
*
13212303 TTGACCG
1 TTGATCG
13212310 TTGA
1 TTGA
13212314 CTTTTTCGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (7 bp):
TTGATCG
Found at i:13212286 original size:14 final size:14
Alignment explanation
Indices: 13212269--13212313 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
13212259 CCGATGTTGA
13212269 TTGATCGTTGACCG
1 TTGATCGTTGACCG
*
13212283 TTGATCGTTGA-CT
1 TTGATCGTTGACCG
13212296 TTGATCGTTGACCG
1 TTGATCGTTGACCG
13212310 TTGA
1 TTGA
13212314 CTTTTTCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (14 bp):
TTGATCGTTGACCG
Found at i:13212304 original size:20 final size:20
Alignment explanation
Indices: 13212276--13212317 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
13212266 TGATTGATCG
*
13212276 TTGACCGTTGATCGTTGACT
1 TTGACCGTTGACCGTTGACT
*
13212296 TTGATCGTTGACCGTTGACT
1 TTGACCGTTGACCGTTGACT
13212316 TT
1 TT
13212318 TTCGAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:13213375 original size:3 final size:3
Alignment explanation
Indices: 13213363--13213395 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
13213353 TATTCTATTC
13213363 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13213396 TTGGGATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:13230516 original size:24 final size:24
Alignment explanation
Indices: 13230458--13230546 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
13230448 TTCCAGGAAT
* * * *
13230458 TTAGCTCATACGAGCTCAGACAGAA
1 TTAGCTCTTACGAGCCCAGATAG-G
13230483 TTAGCTCTTACGAGCCCAGATAGG
1 TTAGCTCTTACGAGCCCAGATAGG
* * *
13230507 TTAGCCCTTACAAACCCAGATAGG
1 TTAGCTCTTACGAGCCCAGATAGG
13230531 TTAGCTCTTACGAGCC
1 TTAGCTCTTACGAGCC
13230547 TAGACAGAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 34 0.63
25 20 0.37
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGATAGG
Found at i:13234361 original size:20 final size:19
Alignment explanation
Indices: 13234333--13234420 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 19
13234323 ATATTATTCC
*
13234333 TTACAAAAATATCTAAGAAT
1 TTACCAAAATATCTAAG-AT
* * *
13234353 TTACCAAAATTTTTAAGGT
1 TTACCAAAATATCTAAGAT
* *
13234372 TATACCAAAAACATCCAACGAT
1 T-TACC-AAAATATCTAA-GAT
* *
13234394 TTACCAATATTTCTAAGAAT
1 TTACCAAAATATCTAAG-AT
13234414 TTACCAA
1 TTACCAA
13234421 TGCTTCTAAA
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.06
20 34 0.67
21 11 0.22
22 3 0.06
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (19 bp):
TTACCAAAATATCTAAGAT
Found at i:13234419 original size:41 final size:40
Alignment explanation
Indices: 13234351--13234454 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 40
13234341 ATATCTAAGA
* * * *
13234351 ATTTACCAAAATTTTTAAGGTTATACCAAAAACATCCAACG
1 ATTTACCAATATTTCTAAGATTATACC-AAAACATCCAAAG
** * *
13234392 ATTTACCAATATTTCTAAGAATT-TACCAATGCTTCTAAAG
1 ATTTACCAATATTTCTAAG-ATTATACCAAAACATCCAAAG
13234432 ATTTACCAATATTTCTAAAGATT
1 ATTTACCAATATTTCT-AAGATT
13234455 TCCTTAGTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 27 0.51
41 24 0.45
42 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (40 bp):
ATTTACCAATATTTCTAAGATTATACCAAAACATCCAAAG
Found at i:13234421 original size:20 final size:20
Alignment explanation
Indices: 13234391--13234455 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
13234381 AACATCCAAC
13234391 GATTTACCAATATTTCT-AA
1 GATTTACCAATATTTCTAAA
**
13234410 GAATTTACCAATGCTTCTAAA
1 G-ATTTACCAATATTTCTAAA
13234431 GATTTACCAATATTTCTAAA
1 GATTTACCAATATTTCTAAA
13234451 GATTT
1 GATTT
13234456 CCTTAGTACC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 36 0.90
21 3 0.08
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (20 bp):
GATTTACCAATATTTCTAAA
Found at i:13234520 original size:20 final size:20
Alignment explanation
Indices: 13234495--13234606 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
13234485 TATTTTGACA
13234495 TACCAAAATTTCTAAAGGTT
1 TACCAAAATTTCTAAAGGTT
** *
13234515 TACCAAAAACT-TATAAGGTCA
1 TACCAAAATTTCTA-AAGGT-T
** **
13234536 TACCAAAATAACTAAAAATT
1 TACCAAAATTTCTAAAGGTT
* *
13234556 TACCAAAATTTCTAATGTATT
1 TACCAAAATTTCTAAAG-GTT
*
13234577 TACC-AAATTT-TTAAGGTT
1 TACCAAAATTTCTAAAGGTT
13234595 ATACCAAAATTT
1 -TACCAAAATTT
13234607 TCAAGGATTT
Statistics
Matches: 70, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
18 2 0.03
19 9 0.13
20 39 0.56
21 18 0.26
22 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (20 bp):
TACCAAAATTTCTAAAGGTT
Found at i:13235054 original size:30 final size:30
Alignment explanation
Indices: 13235020--13235084 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
13235010 ACTTATTTTG
13235020 TTGTTAATTTTGTTATTATTTTAGATG-TAT
1 TTGTTAATTTTGTTATTATTTTAGA-GATAT
13235050 TTGTTAATTTTGTTATTATTTTAGAGATAT
1 TTGTTAATTTTGTTATTATTTTAGAGATAT
13235080 TTGTT
1 TTGTT
13235085 TGTTAAGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGATAT
Found at i:13235496 original size:19 final size:20
Alignment explanation
Indices: 13235474--13235518 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
13235464 ACTATTTATG
13235474 AATATTTGT-AGGATTTACC
1 AATATTTGTAAGGATTTACC
*
13235493 AATA-ATGTAAGGATTTACC
1 AATATTTGTAAGGATTTACC
13235512 AATATTT
1 AATATTT
13235519 CTTAAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 3 0.14
19 18 0.82
20 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (20 bp):
AATATTTGTAAGGATTTACC
Found at i:13235578 original size:19 final size:19
Alignment explanation
Indices: 13235532--13235580 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
13235522 AAATGTTTGC
*
13235532 CAAAATTTTTAGGATTTAT
1 CAAAATTTTAAGGATTTAT
**
13235551 CAATTTTTTAAGGATTTA-
1 CAAAATTTTAAGGATTTAT
13235569 CTAAAATTTTAA
1 C-AAAATTTTAA
13235581 TATTTTTAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (19 bp):
CAAAATTTTAAGGATTTAT
Found at i:13235625 original size:20 final size:20
Alignment explanation
Indices: 13235577--13235629 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
13235567 TACTAAAATT
*
13235577 TTAATATTTTTAAGGATTTA
1 TTAATATTTCTAAGGATTTA
* *
13235597 TCAAAATTTCTAAGG-TTATA
1 TTAATATTTCTAAGGATT-TA
13235617 TTAATATTTCTAA
1 TTAATATTTCTAA
13235630 TTGTTTACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (20 bp):
TTAATATTTCTAAGGATTTA
Found at i:13235975 original size:20 final size:19
Alignment explanation
Indices: 13235920--13235976 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
13235910 TGTATGACCT
**
13235920 TAAAAATTTTGGTAAATTT
1 TAAAAATTTTGGTAAATAA
*
13235939 TAAAATATTTTGATAAATCAA
1 TAAAA-ATTTTGGTAAAT-AA
*
13235960 TAAAAATATTGGTAAAT
1 TAAAAATTTTGGTAAAT
13235977 TATTTTGATC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (19 bp):
TAAAAATTTTGGTAAATAA
Found at i:13238898 original size:12 final size:12
Alignment explanation
Indices: 13238867--13238925 Score: 68
Period size: 12 Copynumber: 4.8 Consensus size: 12
13238857 GCCACCGTTA
*
13238867 CCACGTCAGCACCG
1 CCACGTCAGCA--T
13238881 CCACGTCAGCAT
1 CCACGTCAGCAT
13238893 CCACGTCAG--T
1 CCACGTCAGCAT
13238903 GCCACGTCAGCAT
1 -CCACGTCAGCAT
13238916 CCACGTCAGC
1 CCACGTCAGC
13238926 CACGTGACTC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 1 0.02
11 9 0.22
12 19 0.46
13 1 0.02
14 11 0.27
ACGTcount: A:0.22, C:0.44, G:0.20, T:0.14
Consensus pattern (12 bp):
CCACGTCAGCAT
Found at i:13238906 original size:23 final size:23
Alignment explanation
Indices: 13238880--13238924 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
13238870 CGTCAGCACC
13238880 GCCACGTCAGCATCCACGTCAGT
1 GCCACGTCAGCATCCACGTCAGT
13238903 GCCACGTCAGCATCCACGTCAG
1 GCCACGTCAGCATCCACGTCAG
13238925 CCACGTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.40, G:0.22, T:0.16
Consensus pattern (23 bp):
GCCACGTCAGCATCCACGTCAGT
Found at i:13238976 original size:17 final size:17
Alignment explanation
Indices: 13238951--13238989 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
13238941 CTGGACCATT
*
13238951 GACTCCTCAACTCCCGA
1 GACTGCTCAACTCCCGA
*
13238968 GACTGCTCAGCTCCCGA
1 GACTGCTCAACTCCCGA
13238985 GACTG
1 GACTG
13238990 TCTCTCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.41, G:0.21, T:0.18
Consensus pattern (17 bp):
GACTGCTCAACTCCCGA
Found at i:13239134 original size:14 final size:15
Alignment explanation
Indices: 13239106--13239136 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
13239096 TGCAACAAAG
13239106 AAACAGAGAACAGCA
1 AAACAGAGAACAGCA
13239121 AAACAGAG-ACAGCA
1 AAACAGAGAACAGCA
13239135 AA
1 AA
13239137 GAACTATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.61, C:0.19, G:0.19, T:0.00
Consensus pattern (15 bp):
AAACAGAGAACAGCA
Found at i:13242756 original size:58 final size:58
Alignment explanation
Indices: 13242595--13242761 Score: 221
Period size: 58 Copynumber: 2.9 Consensus size: 58
13242585 ATATTATATA
* * *
13242595 TTATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
* * *
13242655 ATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
* *
13242712 TTATTATTTTTATTAAATTATATTTAATAATAATTTTATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAAT
13242762 AATAATAATC
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 21 0.22
58 56 0.60
59 9 0.10
60 8 0.09
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:13242770 original size:25 final size:26
Alignment explanation
Indices: 13242719--13242770 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
13242709 TATTTATTAT
*
13242719 TTTTATTAAATTATATTTAATAATAA
1 TTTTATTAAATTATATATAATAATAA
13242745 TTTTATTAAAATT-TA-ATAATAATAA
1 TTTTATT-AAATTATATATAATAATAA
13242770 T
1 T
13242771 CATCTACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
26 9 0.38
27 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTATTAAATTATATATAATAATAA
Found at i:13247001 original size:6 final size:6
Alignment explanation
Indices: 13246982--13247014 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
13246972 GGGTGGGATT
13246982 GAAGGA GATA-GA GAAGGA GAAGGA GAAGGA GAA
1 GAAGGA GA-AGGA GAAGGA GAAGGA GAAGGA GAA
13247015 CGATGGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.04
6 23 0.92
7 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (6 bp):
GAAGGA
Found at i:13253544 original size:17 final size:18
Alignment explanation
Indices: 13253517--13253550 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13253507 GCTTCGGGGA
13253517 ATATGTCAAAATCTTCAC
1 ATATGTCAAAATCTTCAC
*
13253535 ATAT-TCAAAATTTTCA
1 ATATGTCAAAATCTTCA
13253551 TAATTGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (18 bp):
ATATGTCAAAATCTTCAC
Found at i:13256033 original size:32 final size:35
Alignment explanation
Indices: 13255995--13256073 Score: 103
Period size: 34 Copynumber: 2.3 Consensus size: 35
13255985 ATAGTATATA
13255995 TTTTTATAATTTTTA-AAAGA-TAAAAT-TAAATT
1 TTTTTATAATTTTTAGAAAGATTAAAATATAAATT
**
13256027 TTTTTAT-ATTTTTAGAGTGATTAAAATATAAATT
1 TTTTTATAATTTTTAGAAAGATTAAAATATAAATT
13256061 TTTTTATTAATTT
1 TTTTTA-TAATTT
13256074 AAAATTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
31 7 0.17
32 10 0.25
33 6 0.15
34 12 0.30
35 1 0.03
36 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (35 bp):
TTTTTATAATTTTTAGAAAGATTAAAATATAAATT
Found at i:13259613 original size:11 final size:11
Alignment explanation
Indices: 13259593--13259667 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
13259583 AAGCCTCTTA
*
13259593 TCTTTCCTTTC
1 TCTTTTCTTTC
*
13259604 TCTTTTCTTTT
1 TCTTTTCTTTC
*
13259615 TCTCATTCATTTC
1 TCT-TTTC-TTTC
*
13259628 TTTTTTCTTTC
1 TCTTTTCTTTC
13259639 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
13259651 TATTTTCTTCC
1 TCTTTTCTTTC
13259662 TCTTTT
1 TCTTTT
13259668 AATCACACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
11 30 0.59
12 16 0.31
13 5 0.10
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:13259650 original size:12 final size:12
Alignment explanation
Indices: 13259595--13259659 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
13259585 GCCTCTTATC
*
13259595 TTTCCTTTCTCT
1 TTTCTTTTCTCT
13259607 TTTCTTTT-TCT
1 TTTCTTTTCTCT
* * *
13259618 CATTCATTTCTTT
1 -TTTCTTTTCTCT
13259631 TTTC-TTTCTCT
1 TTTCTTTTCTCT
*
13259642 TTTCTTTTCTAT
1 TTTCTTTTCTCT
13259654 TTTCTT
1 TTTCTT
13259660 CCTCTTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
11 13 0.30
12 28 0.65
13 2 0.05
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTTTTCTCT
Done.