Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 1 of 82
Found at i:116 original size:21 final size:21
Alignment explanation
Indices: 69--136 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
59 TTTTTAAGTA
69 TTTTTAAGGTCCTTTT-AAAGA-
1 TTTTTAAGGT--TTTTAAAAGAT
*
90 TATTTAAGGTTTTTAAAAGAT
1 TTTTTAAGGTTTTTAAAAGAT
* **
111 TTTTTAATGAATTTAAAAGAT
1 TTTTTAAGGTTTTTAAAAGAT
132 TTTTT
1 TTTTT
137 TTTGTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 4 0.10
20 5 0.12
21 31 0.77
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.51
Consensus pattern (21 bp):
TTTTTAAGGTTTTTAAAAGAT
Found at i:205 original size:20 final size:22
Alignment explanation
Indices: 170--230 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
160 TTTTTTAATT
*
170 ATTTATTACG-ATTTTT-AAGG
1 ATTTATTAAGAATTTTTCAAGG
190 ATTTATTAAGAATTTTTCAAGG
1 ATTTATTAAGAATTTTTCAAGG
* *
212 ATTT-TTAGGCATTTTTCAA
1 ATTTATTAAGAATTTTTCAA
231 AGATGTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.25
21 19 0.53
22 8 0.22
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (22 bp):
ATTTATTAAGAATTTTTCAAGG
Found at i:215 original size:11 final size:10
Alignment explanation
Indices: 179--333 Score: 64
Period size: 10 Copynumber: 14.8 Consensus size: 10
169 TATTTATTAC
179 GATTTTTAAG
1 GATTTTTAAG
189 GATTTATTAAG
1 GATTT-TTAAG
*
200 AATTTTTCAAG
1 GATTTTT-AAG
211 GATTTTT-AG
1 GATTTTTAAG
*
220 GCATTTTTCAAA
1 G-ATTTTT-AAG
*
232 GATGTTTAAG
1 GATTTTTAAG
*
242 G-TCATTCTAAG
1 GAT--TTTTAAG
* *
253 CATTTTAAAG
1 GATTTTTAAG
* **
263 GTTTTTTTCATT
1 G-ATTTTT-AAG
* *
275 GATTTTAAAA
1 GATTTTTAAG
285 GATTTTTAAG
1 GATTTTTAAG
*
295 G-TGTTTTCAAA
1 GAT-TTTT-AAG
* *
306 GAATTTTATG
1 GATTTTTAAG
316 GATTTTTAAG
1 GATTTTTAAG
*
326 GTTTTTTA
1 GATTTTTA
334 GGTAATTTTT
Statistics
Matches: 104, Mismatches: 28, Indels: 26
0.66 0.18 0.16
Matches are distributed among these distances:
9 5 0.05
10 51 0.49
11 43 0.41
12 5 0.05
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (10 bp):
GATTTTTAAG
Found at i:225 original size:21 final size:21
Alignment explanation
Indices: 180--241 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
170 ATTTATTACG
180 ATTTTT-AAGGATTTATTAAGA
1 ATTTTTCAAGGATTT-TTAAGA
* *
201 ATTTTTCAAGGATTTTTAGGC
1 ATTTTTCAAGGATTTTTAAGA
* *
222 ATTTTTCAAAGATGTTTAAG
1 ATTTTTCAAGGATTTTTAAG
242 GTCATTCTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 27 0.77
22 8 0.23
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (21 bp):
ATTTTTCAAGGATTTTTAAGA
Found at i:227 original size:22 final size:21
Alignment explanation
Indices: 161--215 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
151 ATTTTTAATT
** *
161 TTTTTAATTATTTATTACG-A
1 TTTTTAAGGATTTATTAAGAA
181 TTTTTAAGGATTTATTAAGAA
1 TTTTTAAGGATTTATTAAGAA
202 TTTTTCAAGGATTT
1 TTTTT-AAGGATTT
216 TTAGGCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 16 0.53
21 6 0.20
22 8 0.27
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.55
Consensus pattern (21 bp):
TTTTTAAGGATTTATTAAGAA
Found at i:643 original size:10 final size:10
Alignment explanation
Indices: 604--684 Score: 65
Period size: 11 Copynumber: 7.7 Consensus size: 10
594 TTTCCATGGA
604 TTTCAAAGGATT
1 TTTC-AAGGA-T
*
616 TTTAAAGGAAT
1 TTTCAAGG-AT
627 TTTCAAGGAT
1 TTTCAAGGAT
637 TTTCAAGGAAT
1 TTTCAAGG-AT
*
648 TTT-ATGGAT
1 TTTCAAGGAT
* *
657 TTTTAAGGTT
1 TTTCAAGGAT
*
667 CTTTCGAGGAT
1 -TTTCAAGGAT
678 TTTCAAG
1 TTTCAAG
685 AAAATTTATG
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
9 5 0.09
10 23 0.41
11 24 0.43
12 4 0.07
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (10 bp):
TTTCAAGGAT
Found at i:644 original size:21 final size:21
Alignment explanation
Indices: 604--684 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
594 TTTCCATGGA
*
604 TTTCAAAGGATTTTTAAAGGAAT
1 TTTC-AAGGA-TTTTCAAGGAAT
627 TTTCAAGGATTTTCAAGGAAT
1 TTTCAAGGATTTTCAAGGAAT
* * *
648 TTT-ATGGATTTTTAAGG-TT
1 TTTCAAGGATTTTCAAGGAAT
*
667 CTTTCGAGGATTTTCAAG
1 -TTTCAAGGATTTTCAAG
685 AAAATTTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 1 0.02
20 15 0.31
21 24 0.49
22 5 0.10
23 4 0.08
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (21 bp):
TTTCAAGGATTTTCAAGGAAT
Found at i:798 original size:21 final size:21
Alignment explanation
Indices: 772--811 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
762 ATTCACATAT
*
772 TTTTAAGCATTTTTAAGGTCC
1 TTTTAAGCATATTTAAGGTCC
*
793 TTTTAAGGATATTTAAGGT
1 TTTTAAGCATATTTAAGGT
812 TTTTTAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.47
Consensus pattern (21 bp):
TTTTAAGCATATTTAAGGTCC
Found at i:817 original size:10 final size:10
Alignment explanation
Indices: 609--826 Score: 63
Period size: 10 Copynumber: 21.0 Consensus size: 10
599 ATGGATTTCA
609 AAGGATTTTT
1 AAGGATTTTT
*
619 AAAGGAATTTTC
1 -AAGG-ATTTTT
*
631 AAGGATTTTC
1 AAGGATTTTT
*
641 AAGGAATTTT
1 AAGGATTTTT
*
651 ATGGATTTTT
1 AAGGATTTTT
661 AAGG-TTCTTT
1 AAGGATT-TTT
* *
671 CGAGGATTTTC
1 -AAGGATTTTT
* **
682 AAGAAAATTT
1 AAGGATTTTT
*
692 ATGGA-TTTT
1 AAGGATTTTT
*
701 AAAG-TTTTGT
1 AAGGATTTT-T
*
711 AAGTTATTTTT
1 AAG-GATTTTT
* *
722 AAAAGCTTTTT
1 -AAGGATTTTT
*
733 AA-AATCTTTT
1 AAGGAT-TTTT
*
743 GAAGCATTTTT
1 -AAGGATTTTT
*
754 AAGGTTTTATT
1 AAGGATTT-TT
*
765 CACA-TATTTTT
1 -A-AGGATTTTT
*
776 AAGCATTTTT
1 AAGGATTTTT
786 AAGG-TCCTTTT
1 AAGGAT--TTTT
*
797 AAGGATATTT
1 AAGGATTTTT
807 AAGG-TTTTT
1 AAGGATTTTT
*
816 TAGAGATTTTT
1 AAG-GATTTTT
827 CAAAGAATTT
Statistics
Matches: 151, Mismatches: 35, Indels: 42
0.66 0.15 0.18
Matches are distributed among these distances:
9 19 0.13
10 69 0.46
11 42 0.28
12 20 0.13
13 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (10 bp):
AAGGATTTTT
Found at i:961 original size:21 final size:21
Alignment explanation
Indices: 908--966 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
898 TGTATTACGA
* *
908 TTTTTAAAGATTTCTTGAGGTTC
1 TTTTTAAGGATTT-TT-AGGGTC
*
931 -TTTAAAGGATTTTTAGGGTC
1 TTTTTAAGGATTTTTAGGGTC
*
951 TTTTTAAGGATGTTTA
1 TTTTTAAGGATTTTTA
967 AGATCATTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.17
21 15 0.50
22 10 0.33
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (21 bp):
TTTTTAAGGATTTTTAGGGTC
Found at i:1012 original size:73 final size:73
Alignment explanation
Indices: 935--1090 Score: 206
Period size: 73 Copynumber: 2.1 Consensus size: 73
925 AGGTTCTTTA
* * * *
935 AAGGATTTTTAGGGTCTTTTTAAGGATGTTTAAGATCATTCTAAACAT-TTTGAAGTTTTTTTTG
1 AAGGATTTTTAAGGCCTTTTTAAGGATATTTAAGATCATTCTAAACATGTTT-AAGGTTTTTTTG
*
999 TTAATTTTT
65 TTAATTTCT
* * *
1008 AAGGATTTTTAAGGCCTTTTTAAGGATATTTAAGGTCTTTCTAAGCATGTTTAAGGTTTTTTTGT
1 AAGGATTTTTAAGGCCTTTTTAAGGATATTTAAGATCATTCTAAACATGTTTAAGGTTTTTTTGT
*
1073 TGATTTCT
66 TAATTTCT
*
1081 AAAGATTTTT
1 AAGGATTTTT
1091 TAGGTATTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 69 0.96
74 3 0.04
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (73 bp):
AAGGATTTTTAAGGCCTTTTTAAGGATATTTAAGATCATTCTAAACATGTTTAAGGTTTTTTTGT
TAATTTCT
Found at i:1017 original size:11 final size:10
Alignment explanation
Indices: 1002--1446 Score: 109
Period size: 10 Copynumber: 43.0 Consensus size: 10
992 TTTTTTGTTA
1002 ATTTTTAAGG
1 ATTTTTAAGG
1012 ATTTTTAAGG
1 ATTTTTAAGG
*
1022 CCTTTTTAAGG
1 -ATTTTTAAGG
*
1033 ATATTTAAGG
1 ATTTTTAAGG
*
1043 -TCTTTCTAAGC
1 AT-TTT-TAAGG
*
1054 ATGTTTAAGG
1 ATTTTTAAGG
**
1064 -TTTTTTTGTTG
1 ATTTTTAAG--G
* *
1075 ATTTCTAAAG
1 ATTTTTAAGG
*
1085 ATTTTTTAGG
1 ATTTTTAAGG
* *
1095 TATTTTCAAAG
1 -ATTTTTAAGG
* *
1106 ATTTTCAAGA
1 ATTTTTAAGG
**
1116 AAATTTAAGG
1 ATTTTTAAGG
1126 ATTTTTAAGG
1 ATTTTTAAGG
**
1136 -TTTTGTAAATT
1 ATTTT-T-AAGG
* *
1147 ATTTTAACAAG
1 ATTTTTA-AGG
*
1158 ATTTTTAATGC
1 ATTTTTAA-GG
* * *
1169 CTTTTGAAGC
1 ATTTTTAAGG
*
1179 ATTTTTTAA-T
1 A-TTTTTAAGG
* *
1189 ATCTTTTTTATGC
1 A---TTTTTAAGG
1202 ATTTTTAAGG
1 ATTTTTAAGG
1212 ATTTTTAAGG
1 ATTTTTAAGG
**
1222 -TCCTTTTAAAT
1 AT--TTTTAAGG
* * *
1233 ATATTAAAGT
1 ATTTTTAAGG
* *
1243 TTTTTTAAAG
1 ATTTTTAAGG
1253 ATTTTTTAAGG
1 A-TTTTTAAGG
* *
1264 AATTTCAAGG
1 ATTTTTAAGG
* *
1274 ATTTTTTATG
1 ATTTTTAAGG
1284 -TTTTTAAGG
1 ATTTTTAAGG
*
1293 AATTTTTAA-T
1 -ATTTTTAAGG
* **
1303 TTTTTTAATT
1 ATTTTTAAGG
*
1313 ATTTATT-ACG
1 ATTT-TTAAGG
*
1323 ATATTTAAGG
1 ATTTTTAAGG
*
1333 ATTTTCAAGG
1 ATTTTTAAGG
*
1343 -TTTTTAATG
1 ATTTTTAAGG
1352 ACTTTTTAAAGG
1 A-TTTTT-AAGG
*
1364 ATTTTTAGGG
1 ATTTTTAAGG
*
1374 TTTTTTAAAGG
1 ATTTTT-AAGG
*
1385 ATGTTTAAGG
1 ATTTTTAAGG
*
1395 -TCATTTTAAGC
1 AT--TTTTAAGG
*
1406 ATTTTTAAGT
1 ATTTTTAAGG
* *
1416 TTTTTTCATGG
1 ATTTTT-AAGG
*
1427 ATTTTAAAGG
1 ATTTTTAAGG
*
1437 ATATTTAAGG
1 ATTTTTAAGG
1447 TGTTTTCAAA
Statistics
Matches: 308, Mismatches: 93, Indels: 68
0.66 0.20 0.14
Matches are distributed among these distances:
9 35 0.11
10 153 0.50
11 97 0.31
12 22 0.07
13 1 0.00
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (10 bp):
ATTTTTAAGG
Found at i:1027 original size:21 final size:21
Alignment explanation
Indices: 1003--1063 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
993 TTTTTGTTAA
*
1003 TTTTTAAGGATTTTTAAGGCC
1 TTTTTAAGGATATTTAAGGCC
*
1024 TTTTTAAGGATATTTAAGGTC
1 TTTTTAAGGATATTTAAGGCC
* * *
1045 TTTCTAAGCATGTTTAAGG
1 TTTTTAAGGATATTTAAGG
1064 TTTTTTTGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (21 bp):
TTTTTAAGGATATTTAAGGCC
Found at i:1378 original size:21 final size:21
Alignment explanation
Indices: 1354--1436 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1344 TTTTAATGAC
*
1354 TTTTTAAAGGATTTTTAGGGT
1 TTTTTAAAGGATTTTTAAGGT
*
1375 TTTTTAAAGGATGTTTAAGGT
1 TTTTTAAAGGATTTTTAAGGT
* * *
1396 CATTTT-AAGCATTTTTAAGTT
1 -TTTTTAAAGGATTTTTAAGGT
* * *
1417 TTTTTCATGGATTTTAAAGG
1 TTTTTAAAGGATTTTTAAGG
1437 ATATTTAAGG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 4 0.08
21 41 0.84
22 4 0.08
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.51
Consensus pattern (21 bp):
TTTTTAAAGGATTTTTAAGGT
Found at i:1843 original size:11 final size:10
Alignment explanation
Indices: 1804--1842 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1794 TTTAAAATAT
1804 TTTTTAAGTC
1 TTTTTAAGTC
* *
1814 TTTTGAAGTA
1 TTTTTAAGTC
1824 TTTTTAAGGTC
1 TTTTTAA-GTC
1835 TTTTTAAG
1 TTTTTAAG
1843 GATATTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.56
Consensus pattern (10 bp):
TTTTTAAGTC
Found at i:1850 original size:21 final size:20
Alignment explanation
Indices: 1806--1850 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1796 TAAAATATTT
* *
1806 TTTAAGTCTTTTGAAGTATT
1 TTTAAGTCTTTTGAAGGATA
*
1826 TTTAAGGTCTTTTTAAGGATA
1 TTTAA-GTCTTTTGAAGGATA
1847 TTTA
1 TTTA
1851 TGGATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (20 bp):
TTTAAGTCTTTTGAAGGATA
Found at i:2197 original size:21 final size:20
Alignment explanation
Indices: 2173--2225 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
2163 TCATGGTTGC
2173 TTCAGCATTTTTAAGGTTCTT
1 TTCAG-ATTTTTAAGGTTCTT
*
2194 TTCAAGATATTTAAGGTT-TT
1 TTC-AGATTTTTAAGGTTCTT
2214 TT-AGATTTTTAA
1 TTCAGATTTTTAA
2226 AGTCTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 9 0.31
20 4 0.14
21 14 0.48
22 2 0.07
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (20 bp):
TTCAGATTTTTAAGGTTCTT
Found at i:2242 original size:21 final size:20
Alignment explanation
Indices: 2179--2266 Score: 83
Period size: 21 Copynumber: 4.3 Consensus size: 20
2169 TTGCTTCAGC
*
2179 ATTTTTAAGGTTCTTTTCAAG
1 ATTTTTAAGG-TCTTTTTAAG
*
2200 ATATTTAAGGT-TTTTT-AG
1 ATTTTTAAGGTCTTTTTAAG
*
2218 ATTTTTAAAGTCTTTTTAAG
1 ATTTTTAAGGTCTTTTTAAG
*
2238 CA-TTTTAAGGTCCTTTTAAAAG
1 -ATTTTTAAGGT-CTTTT-TAAG
2260 ATTTTTA
1 ATTTTTA
2267 TGTGTTTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
18 11 0.20
19 9 0.16
20 11 0.20
21 16 0.29
22 8 0.15
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTTTAAGGTCTTTTTAAG
Found at i:2255 original size:39 final size:39
Alignment explanation
Indices: 2179--2255 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
2169 TTGCTTCAGC
* *
2179 ATTTTTAAGGTTCTTTTCAAGATATTTAAGGTTTTTTAG
1 ATTTTTAAAGTTCTTTTCAAGATATTTAAGGTCTTTTAG
*
2218 ATTTTTAAAG-TCTTTTTAAGCAT-TTTAAGGTCCTTTTA
1 ATTTTTAAAGTTCTTTTCAAG-ATATTTAAGGT-CTTTTA
2256 AAAGATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (39 bp):
ATTTTTAAAGTTCTTTTCAAGATATTTAAGGTCTTTTAG
Found at i:2374 original size:21 final size:21
Alignment explanation
Indices: 2350--2396 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2340 TTTTCATAGA
**
2350 TTTTTAAGCATTTTTAAGGTC
1 TTTTTAAGCATAATTAAGGTC
* *
2371 TTTTTAAGGATAATTAAGGTT
1 TTTTTAAGCATAATTAAGGTC
2392 TTTTT
1 TTTTT
2397 TATAGATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.55
Consensus pattern (21 bp):
TTTTTAAGCATAATTAAGGTC
Found at i:2433 original size:53 final size:53
Alignment explanation
Indices: 2331--2434 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 53
2321 TAAAGCAATT
* * **
2331 TTAAAGTTTTTTTCATAGATTTTTAAGCATTTTTAAGGTCTTTTTAAGGATAA
1 TTAAAGTTTTTTTCATAGATTTTTAAGCATTTTTAAGGCCATTGGAAGGATAA
* * * *
2384 TTAAGGTTTTTTTTATAGATTTTTGAGTATTTTTAAGGCCATTGGAAGGAT
1 TTAAAGTTTTTTTCATAGATTTTTAAGCATTTTTAAGGCCATTGGAAGGAT
2435 TTGAAAGGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.50
Consensus pattern (53 bp):
TTAAAGTTTTTTTCATAGATTTTTAAGCATTTTTAAGGCCATTGGAAGGATAA
Found at i:2503 original size:31 final size:29
Alignment explanation
Indices: 2463--2547 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
2453 AATTTTTTAC
2463 ATTTTTTAAGTTTTATATGTTATTTTTAAA-
1 ATTTTTTAAGTTTTATATG--ATTTTTAAAG
* *
2493 ATATTTTTAAGGTTTATTACGATTTTTAAAG
1 AT-TTTTTAAGTTTTA-TATGATTTTTAAAG
*
2524 ATTTTTT-AGTTTTGTATGATTTTT
1 ATTTTTTAAGTTTTATATGATTTTT
2548 TGGGTCTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
28 9 0.19
29 5 0.11
30 16 0.34
31 14 0.30
32 3 0.06
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.61
Consensus pattern (29 bp):
ATTTTTTAAGTTTTATATGATTTTTAAAG
Found at i:2617 original size:22 final size:22
Alignment explanation
Indices: 2585--2642 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2575 ATTCAAAGCA
2585 TTTTAAA-ATTTTT-TGGT-TGT
1 TTTTAAAGATTTTTATGGTCT-T
2605 TTTCTAAAGATTTTTATGGTCTT
1 TTT-TAAAGATTTTTATGGTCTT
*
2628 TTTAAAAGATTTTTA
1 TTTTAAAGATTTTTA
2643 AGGGTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 4 0.12
22 17 0.52
23 8 0.24
24 1 0.03
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.59
Consensus pattern (22 bp):
TTTTAAAGATTTTTATGGTCTT
Found at i:2880 original size:9 final size:10
Alignment explanation
Indices: 2740--2880 Score: 57
Period size: 10 Copynumber: 14.5 Consensus size: 10
2730 TTTTTCATGA
**
2740 ATTTTTAACT
1 ATTTTTAAGG
2750 ATTTTTAAGG
1 ATTTTTAAGG
*
2760 TCTTTTTAAGG
1 -ATTTTTAAGG
** *
2771 AAATTTAATG
1 ATTTTTAAGG
*
2781 -TTTTTTAGAG
1 ATTTTTAAG-G
*
2791 ATTTTCAAGG
1 ATTTTTAAGG
* *
2801 AATTTGAAGG
1 ATTTTTAAGG
*
2811 ATTTTT---T
1 ATTTTTAAGG
2818 ATTTTTAAGGG
1 ATTTTTAA-GG
*
2829 ATTTTTAA-T
1 ATTTTTAAGG
2838 ATTTTTAA-G
1 ATTTTTAAGG
*
2847 TTTTATTACA--
1 ATTT-TTA-AGG
2857 ATTTTTAAGG
1 ATTTTTAAGG
2867 ATTTTTAAGG
1 ATTTTTAAGG
2877 -TTTT
1 ATTTT
2881 GTATGAATTT
Statistics
Matches: 97, Mismatches: 23, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
7 6 0.06
8 1 0.01
9 22 0.23
10 44 0.45
11 24 0.25
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.54
Consensus pattern (10 bp):
ATTTTTAAGG
Found at i:3272 original size:21 final size:21
Alignment explanation
Indices: 3235--3281 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3225 TAAAAATATT
* * *
3235 TTTAAGGTCTTTTTAAGGATG
1 TTTAAGGTCATTCTAAGCATG
*
3256 TTTAAGGTCATTCTAAGCATT
1 TTTAAGGTCATTCTAAGCATG
3277 TTTAA
1 TTTAA
3282 TTTTTTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.47
Consensus pattern (21 bp):
TTTAAGGTCATTCTAAGCATG
Found at i:3523 original size:19 final size:19
Alignment explanation
Indices: 3499--3535 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3489 GAAATTTGAA
3499 AGATTTTT-ATGTTTTTAAG
1 AGATTTTTAAT-TTTTTAAG
3518 AGATTTTTAATTTTTTAA
1 AGATTTTTAATTTTTTAA
3536 TTATTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (19 bp):
AGATTTTTAATTTTTTAAG
Found at i:3772 original size:20 final size:21
Alignment explanation
Indices: 3749--3792 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3739 TTTAAGAATT
3749 TTTTTATGG-ATTTAT-AAGGA
1 TTTTTATGGAATTT-TGAAGGA
3769 TTTTTATGGAATTTTGAAGGA
1 TTTTTATGGAATTTTGAAGGA
3790 TTT
1 TTT
3793 GGGAATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.52
Consensus pattern (21 bp):
TTTTTATGGAATTTTGAAGGA
Found at i:3991 original size:19 final size:19
Alignment explanation
Indices: 3963--4022 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
3953 AAAGAATTTG
3963 AAAGATTTTTTATATTTTT
1 AAAGATTTTTTATATTTTT
* *
3982 AAAGAATTTTGA-ATTTTT
1 AAAGATTTTTTATATTTTT
* *
4000 TAATATTTTTTTATGATTTTT
1 AAAGA-TTTTTTAT-ATTTTT
4021 AA
1 AA
4023 GGATCTTTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
18 9 0.29
19 15 0.48
21 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
AAAGATTTTTTATATTTTT
Found at i:3993 original size:30 final size:28
Alignment explanation
Indices: 3946--4009 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
3936 CTTTTTGGAG
3946 ATTTTTCAAAGAATTTGAAAGATTTTTT-AT
1 ATTTTTCAAAGAATTTG--A-ATTTTTTAAT
3976 ATTTTT-AAAGAATTTTGAATTTTTTAAT
1 ATTTTTCAAAGAA-TTTGAATTTTTTAAT
4004 ATTTTT
1 ATTTTT
4010 TTATGATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
27 7 0.22
28 9 0.28
29 6 0.19
30 10 0.31
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (28 bp):
ATTTTTCAAAGAATTTGAATTTTTTAAT
Found at i:4000 original size:29 final size:29
Alignment explanation
Indices: 3946--4009 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
3936 CTTTTTGGAG
*
3946 ATTTTTCAAAGAATTTGAAAGATTTTTTAT
1 ATTTTTCAAAGAATTTGAAA-ATTTTTAAT
*
3976 ATTTTT-AAAGAATTTTG-AATTTTTTAAT
1 ATTTTTCAAAGAA-TTTGAAAATTTTTAAT
4004 ATTTTT
1 ATTTTT
4010 TTATGATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 13 0.42
29 8 0.26
30 10 0.32
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (29 bp):
ATTTTTCAAAGAATTTGAAAATTTTTAAT
Found at i:4426 original size:21 final size:21
Alignment explanation
Indices: 4393--4448 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
4383 TTCGTATGGG
* **
4393 TTTTTAAAAGATTTTTAAGGTC
1 TTTTT-AAGGATTTTTAACATC
4415 TTTTTAAGGATTTTTAACATC
1 TTTTTAAGGATTTTTAACATC
*
4436 TTTTGAAGGATTT
1 TTTTTAAGGATTT
4449 GCAAAGGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTTTAAGGATTTTTAACATC
Found at i:4550 original size:20 final size:21
Alignment explanation
Indices: 4527--4573 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
4517 TTTTCATGGA
* *
4527 TTTTTAAGCAT-TTTAAGTTC
1 TTTTTAAGAATATTTAAGGTC
*
4547 -TTTTAATAATATTTAAGGTC
1 TTTTTAAGAATATTTAAGGTC
4567 TTTTTAA
1 TTTTTAA
4574 AGGTTTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 8 0.36
20 8 0.36
21 6 0.27
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTTTAAGAATATTTAAGGTC
Found at i:4895 original size:10 final size:10
Alignment explanation
Indices: 4822--4896 Score: 62
Period size: 11 Copynumber: 7.0 Consensus size: 10
4812 TTTGTAGGTT
4822 ATTTTTAAAAG
1 ATTTTT-AAAG
4833 ATTTTTAAAG
1 ATTTTTAAAG
4843 -TCTTTTAAAG
1 AT-TTTTAAAG
*
4853 CATTTTTAAGG
1 -ATTTTTAAAG
* *
4864 TTTTTTTATATG
1 -ATTTTTA-AAG
4876 ATTTTTTAAAG
1 A-TTTTTAAAG
4887 ATTTTTAAAG
1 ATTTTTAAAG
4897 TCCTTTCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 1 0.02
10 21 0.40
11 22 0.42
12 9 0.17
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (10 bp):
ATTTTTAAAG
Found at i:5433 original size:20 final size:20
Alignment explanation
Indices: 5401--5467 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
5391 AATTTGAAAG
*
5401 ATTTTGAAG-GATTTTTTAT
1 ATTTTTAAGTGATTTTTTAT
5420 ATTTTTAAGTGATTTTTTAT
1 ATTTTTAAGTGATTTTTTAT
* * *
5440 -TATTTAA-TAATTTTTTACG
1 ATTTTTAAGTGATTTTTTA-T
5459 ATTTTTAAG
1 ATTTTTAAG
5468 AACCTTTCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.23
19 14 0.36
20 16 0.41
ACGTcount: A:0.28, C:0.01, G:0.10, T:0.60
Consensus pattern (20 bp):
ATTTTTAAGTGATTTTTTAT
Found at i:5440 original size:18 final size:18
Alignment explanation
Indices: 5411--5456 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
5401 ATTTTGAAGG
* *
5411 ATTTTTTATATTTTTAAGTG
1 ATTTTTTAT-TATTTAA-TA
5431 ATTTTTTATTATTTAATA
1 ATTTTTTATTATTTAATA
5449 ATTTTTTA
1 ATTTTTTA
5457 CGATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 6 0.25
20 9 0.38
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
ATTTTTTATTATTTAATA
Found at i:5555 original size:10 final size:10
Alignment explanation
Indices: 5541--5626 Score: 52
Period size: 10 Copynumber: 8.5 Consensus size: 10
5531 CATTTTAAGC
5541 ATTTTTATGG
1 ATTTTTATGG
*
5551 TTTTTTTATGG
1 -ATTTTTATGG
*
5562 ATTTCTATGG
1 ATTTTTATGG
*
5572 ATTTTTA-AG
1 ATTTTTATGG
* *
5581 TTCTTTTCAAGG
1 AT-TTTT-ATGG
*
5593 ATTTTCAATGG
1 ATTTT-TATGG
5604 -TTTTTATGG
1 ATTTTTATGG
*
5613 AATTTT-TGG
1 ATTTTTATGG
5622 ATTTT
1 ATTTT
5627 GGAGGTTTAG
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
9 13 0.23
10 26 0.46
11 16 0.28
12 2 0.04
ACGTcount: A:0.20, C:0.05, G:0.17, T:0.58
Consensus pattern (10 bp):
ATTTTTATGG
Found at i:5565 original size:21 final size:21
Alignment explanation
Indices: 5500--5577 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 21
5490 TTTTCAAAGT
*
5500 ATTTTTA-GGTTTTTTTATAG
1 ATTTTTATGGTTTTTTTATGG
* * ** * *
5520 ATGTTTAAGGTCATTTTAAGC
1 ATTTTTATGGTTTTTTTATGG
5541 ATTTTTATGGTTTTTTTATGG
1 ATTTTTATGGTTTTTTTATGG
* *
5562 ATTTCTATGGATTTTT
1 ATTTTTATGGTTTTTT
5578 AAGTTCTTTT
Statistics
Matches: 43, Mismatches: 14, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.21, C:0.04, G:0.17, T:0.59
Consensus pattern (21 bp):
ATTTTTATGGTTTTTTTATGG
Found at i:5691 original size:21 final size:20
Alignment explanation
Indices: 5642--5694 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
5632 TTTAGTAAGT
5642 TATTTTTTAAAAGATTTTAAA
1 TATTTTTT-AAAGATTTTAAA
*
5663 -AGTCTTTTAAAGCATTTTAAA
1 TA-TTTTTTAAAG-ATTTTAAA
5684 TATTTTTTAAA
1 TATTTTTTAAA
5695 TTTATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.19
21 21 0.78
22 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (20 bp):
TATTTTTTAAAGATTTTAAA
Found at i:5803 original size:20 final size:18
Alignment explanation
Indices: 5780--5845 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 18
5770 TTTTTTTATA
*
5780 TTTTTAAGATATTTTGAATT
1 TTTTTAAGAT-TTTT-AAAT
*
5800 TTTTTAATGATTTTTTACAAC
1 TTTTTAA-GA-TTTTTA-AAT
*
5821 TTTTTAAGATGTTTTAAGT
1 TTTTTAAGAT-TTTTAAAT
5840 TTTTTA
1 TTTTTA
5846 TGGTTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
19 8 0.21
20 15 0.39
21 14 0.37
22 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (18 bp):
TTTTTAAGATTTTTAAAT
Found at i:5870 original size:20 final size:21
Alignment explanation
Indices: 5840--5886 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
5830 TGTTTTAAGT
5840 TTTTTATGGTTTTTTAAAATA
1 TTTTTATGGTTTTTTAAAATA
*
5861 TTTTTA-GGTTTTTTTAAATA
1 TTTTTATGGTTTTTTAAAATA
*
5881 TGTTTA
1 TTTTTA
5887 AAGTAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.64
Consensus pattern (21 bp):
TTTTTATGGTTTTTTAAAATA
Found at i:5916 original size:10 final size:10
Alignment explanation
Indices: 5901--5936 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
5891 AATTCTAATA
5901 ATTTTTAAGG
1 ATTTTTAAGG
*
5911 ATTTTTAATGA
1 ATTTTTAA-GG
5922 ATTTTTAAGG
1 ATTTTTAAGG
5932 ATTTT
1 ATTTT
5937 CAAGATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (10 bp):
ATTTTTAAGG
Found at i:5936 original size:360 final size:356
Alignment explanation
Indices: 5397--7758 Score: 1102
Period size: 360 Copynumber: 6.7 Consensus size: 356
5387 AAAGAATTTG
* * * *
5397 AAAGATTTTGAAGGATTTTTTATATTTTTAAG-TGATTTTTTA-TTATTTAATAATTTTTTACGA
1 AAAGAATTTGAAGGATTTTTTATATTTTTAAGAT-ATTTTTAATTTTTTTAATAATTTTTTACAA
* * * * * *
5460 -TTTTTAAGAACCTTTCAGGTTTTGTT-TTGTTTTTCAAAGTATTTTTAGGTTTTTTTATAGATG
65 CTTTTTAAG-ATCTTTTAGGTTTT-TTATAGTTTTTTAAAATATTTTTAGGTTTTTTTAAAGATG
* * * * * *
5523 TTTAAGGTCATTTTAAGCATTTTTATGGTTTTTTTATGGATTTCTATGGATTTTTAAGTTCTTTT
128 TTTAAGGTCATTCTAAGCATTTTTAAGGATTTTTAAT-GATTTTTAAGGATTTTTAAG-TCTTTT
* ** * *
5588 CAAGGATTTTCAATGGTTTTTATGGAATTTT-TGGATTTTGGAGGTTTAGTAAGTTATTTTTTAA
191 CAAGGATTTTCAATAGTTTTTATGGAATTTTATAAATTTTGGAGGTTTAGTAAGTTA-TATTGAA
* **
5652 AAGATTTTAAAAGTCTTTTAAAGCATTTTAAATATTTT-TTAAATTTATTTTTAAACATTTT-AT
255 AAGATTTTAAAAGTCTTTTAAAGCATTTTAAAGATTTTATT-AATAGATTTTTAAACATTTTGA-
* *
5715 GAT-TCTTTTAAGGATA-TATAAGGT-TGTTTAGCGATTTTTA
318 GATCT-TTTTAAGGATACT-TAAGGTAT-TTTAGAG-GTTTTA
* *
5755 AAAGAATTTGAAGGATTTTTTTATATTTTTAAGATATTTTGAATTTTTTTAATGATTTTTTACAA
1 AAAGAATTTGAAGGA-TTTTTTATATTTTTAAGATATTTTTAATTTTTTTAATAATTTTTTACAA
* * * *
5820 CTTTTTAAGATGTTTTAAGTTTTTTATGGTTTTTTAAAATATTTTTAGGTTTTTTTAAATATGTT
65 CTTTTTAAGATCTTTTAGGTTTTTTATAGTTTTTTAAAATATTTTTAGGTTTTTTTAAAGATGTT
* * ** *
5885 TAAAGTAATTCTAATAATTTTTAAGGATTTTTAATGAATTTTTAAGGATTTTCAAGATCTTTTCA
130 TAAGGTCATTCTAAGCATTTTTAAGGATTTTTAATG-ATTTTTAAGGATTTTTAAG-TCTTTTCA
* * * ** ** * *
5950 TGGATTTCCAATAATTTTTATAAAATTTTATAAATTTTTTAGGTTTTGTACGTTATATTGAAAAG
193 AGGATTTTCAATAGTTTTTATGGAATTTTATAAATTTTGGAGGTTTAGTAAGTTATATTGAAAAG
* * * * * *
6015 ATTTTTATAGTCTTTTAAAGCATTTTTAAGGTTTTATTCATAGATTTTTAAGCATTTTGAGATCT
258 ATTTTAAAAGTCTTTTAAAGCATTTTAAAGATTTTATTAATAGATTTTTAAACATTTTGAGATCT
*
6080 TTTTAAGGATACTTAAGGTATTTTAGAGGTTTTC
323 TTTTAAGGATACTTAAGGTATTTTAGAGGTTTTA
* * * * * *
6114 AAGGAATTTGAAGGATTTTCTATGTTTTTAAGAGATTTTTAATTTTGTTAATAATTTTTTTTACC
1 AAAGAATTTGAAGGATTTTTTATATTTTTAAGATATTTTTAATTTTTTTAATAA--TTTTTTACA
* * * * * *
6179 ACTTTTAAAGATTTTTTAGGTTTTGTACAGTTTTTTCAAAGATTTTATA--TTCTTTTTAAAGAT
64 ACTTTTTAAGATCTTTTAGGTTTTTTATAGTTTTTTAAAATATTTT-TAGGTT-TTTTTAAAGAT
6242 GTTTAAGGTCATTCTAAGCATTTTTAA-GATTTCTTTTACA-GATTTTTAAGGATTTTTAAAGTC
127 GTTTAAGGTCATTCTAAGCATTTTTAAGGA--T-TTTTA-ATGATTTTTAAGGATTTTT-AAGTC
* * ** * * *
6305 TTTTCAAAGATTTTCAATAGTTTTCATGGAATTTTAT--ATTTTTTAAGTTTTGAAAGTTACT-T
187 TTTTCAAGGATTTTCAATAGTTTTTATGGAATTTTATAAATTTTGGAGGTTTAGTAAGTTA-TAT
* * * * * ** ** * * * * *
6367 TTAAATGATTTTTATAA-TGTTTTAATGTGTGCATAAGGTTTTTGTTCATAGATTTTTAAAAATT
251 TGAAAAGA-TTTTAAAAGTCTTTTAAAGCAT-TTTAAAGATTTTATTAATAGATTTTTAAACA-T
* * * * * * * * *
6431 TTTAAGGTCCTTTTAAAGATATTTAAGATTTTTTAGAGATTTTCC
313 TTTGAGATCTTTTTAAGGATACTTAAGGTATTTTAGAGGTTTT-A
* * * * * *
6476 AAGGAATTTGAAGGATTTCTAATATATTTAAGGTATTTTTAATTTTTTTAGTAA-TTTTTA-AGA
1 AAAGAATTTGAAGGATTTTTTATATTTTTAAGATATTTTTAATTTTTTTAATAATTTTTTACA-A
* *** * * * *
6539 C-TTTTAAGGGT-TTTTTTTTTTTTGTATGGTTTTTTAAAAAAATTTTATGGTATTTTT-AAG--
65 CTTTTTAA-GATCTTTTAGGTTTTT-TATAGTTTTTTAAAATATTTTTA-GGTTTTTTTAAAGAT
* *
6599 G--T----T-ATTCTAAGCATTTTTAA--TTTTTTCTAT-ATTTTTAAGG----TT-A---TTTT
127 GTTTAAGGTCATTCTAAGCATTTTTAAGGATTTTT-AATGATTTTTAAGGATTTTTAAGTCTTTT
* ** * * * *
6646 -ATGGATTTT-AA-AGGAATTT-T---A-TTTAT---TTTT-TAGGTTTTGTAAGTTATTTTTAA
191 CAAGGATTTTCAATA-GTTTTTATGGAATTTTATAAATTTTGGAGGTTTAGTAAGTTATATTGAA
* * * ** * * *
6699 AAGATATTT-AAAGTCTTTTAAAGCATTTTTAAAGGTTTT-TTCATGGATTTAAAAAAAATTTAA
255 AAGAT-TTTAAAAGTCTTTTAAAGCA-TTTTAAAGATTTTATTAATAGATTTTTAAACATTTTGA
* * * * * *
6762 G-GCTTTTTTAACGATATTTAA-GT-TTTTGTGAGATTATTC
318 GATC-TTTTTAAGGATACTTAAGGTATTTT-AGAGGTT-TTA
* ** * * *
6801 AAAGAATTTGAAGGATTTTTTATGTTTTTAAGGGACTTTT-ACTTTTTTAATAA-TTTTTATGAA
1 AAAGAATTTGAAGGATTTTTTATATTTTTAAGATATTTTTAATTTTTTTAATAATTTTTTA-CAA
* ** * * * * * * *
6864 --TTTTAAGGATCTTTTAGGCTTAGTATTGTTTTTCAAAGTACTTTAAGGGTCTTTTTAAGGATG
65 CTTTTTAA-GATCTTTTAGGTTTTTTATAGTTTTTTAAAATATTTTTA-GGTTTTTTTAAAGATG
* * * * * * *
6927 TTTCAA-GTCATTATAAGCATTTTT-ATGATTTTTTTTATGGGTTTCTGAGGGTTTTTAAGTTCT
128 TTT-AAGGTCATTCTAAGCATTTTTAAGGA--TTTTTAAT-GATTTTTAAGGATTTTTAAG-TCT
* ** * * * *
6990 TTTCAAGGATTTTCAATAGTTTTTATGGAATTTT-TAGATTTTTTAGATTTCGTAAGTT-TTTTT
188 TTTCAAGGATTTTCAATAGTTTTTATGGAATTTTATAAATTTTGGAGGTTTAGTAAGTTATATTG
* * * * * * *
7053 TAAAGATTTTTATAA-TCTTTTAAAGTATTTTTAAG-TTTTTTTGATAGATTTTTAATCATTTTT
253 AAAAGA-TTTTAAAAGTCTTTTAAAGCATTTTAAAGATTTTATTAATAGATTTTTAAACA-TTTT
* * * * * * *
7116 AAGGTCCTTTTT-AGGATATTTAAGGTTTTTTTACA-TTTTTC
316 GAGAT-CTTTTTAAGGATACTTAAGG-TATTTTAGAGGTTTTA
* * * ** *
7157 AAGGAATTTGAATGA-TTTTTAAAGTTTTTAAGGGATTTTTAATTATTTTAAT-A-TTTTTA-AG
1 AAAGAATTTGAAGGATTTTTTATA-TTTTTAAGATATTTTTAATTTTTTTAATAATTTTTTACA-
* * * * *
7218 A-TTTTTAATGAT-TTTTCTGGGTTTGTATAGTTTTTTAAAAGATTTTTAGGGTCTTTTT-AAGA
64 ACTTTTTAA-GATCTTTT-AGGTTTTTTATAGTTTTTTAAAATATTTTTA-GGTTTTTTTAAAG-
* * * * * *** * * * *
7280 ATTTTTAAAGTTAGTCTAGGCATTTTTAATTTTTTTTTATAGATTTTTACGAATTTTT-AGACTT
125 ATGTTTAAGGTCATTCTAAGCATTTTTAAGGATTTTTAAT-GATTTTTAAGGATTTTTAAGTC-T
** ** * * *
7344 ATTTCAAGGATTTT-AAT-G-----A---AATTTTATTGATTTTTTAGATTTTGTAAGTTATTTT
188 -TTTCAAGGATTTTCAATAGTTTTTATGGAATTTTATAAATTTTGGAGGTTTAGTAAGTTATATT
* * * * * * * * ** *
7399 AAAAAGATTTTTAATGTCTTTTAAAGTATTTTTAAGGTTTTTTTTCAT-GGCTTTTAAATAATTT
252 GAAAAGATTTTAAAAGTCTTTTAAAGCA-TTTTAAAGATTTTATTAATAGATTTTTAAA-CA-TT
* * * * *
7463 TTAAGGT-TCTTTTAAGGATATTTAAGG-ATTTTTAGAGAATTTTC
314 TTGAGATCT-TTTTAAGGATACTTAAGGTA-TTTTAGAG-GTTTTA
* * * * * * *
7507 AAAGAATTTGAAAGATTTTTAATGTTTTTAAGAGATTTTTAAATTTTTTAATGATTTTTTACTA-
1 AAAGAATTTGAAGGATTTTTTATATTTTTAAGATATTTTTAATTTTTTTAATAATTTTTTACAAC
* * * * * * * *
7571 TTTTTAAGGATCTTTTCGATTTTCTATTGATTTTTCAAAGTAGTTTTAGAG-TCTTTTAAAGGAT
66 TTTTTAA-GATCTTTTAGGTTTTTTATAG-TTTTTTAAAATATTTTTAG-GTTTTTTTAAA-GAT
* * * * ** * * *
7635 GTTTAAAGCCATGCTAAGCATATTTATAGTTTTTTTTTATGGATTTCTAATGATTTTT-AGTTCT
127 GTTTAAGGTCATTCTAAGCATTTTTA-AG-GATTTTTAAT-GATTTTTAAGGATTTTTAAG-TCT
* *** * *
7699 TTTCAAGAATTTTCAATAGTTTTTATGGAATTTT-TGGTTTTTTGAGGTTTTGTAAGTTAT
188 TTTCAAGGATTTTCAATAGTTTTTATGGAATTTTATAAATTTTGGAGGTTTAGTAAGTTAT
7759 TTTTAATGGA
Statistics
Matches: 1569, Mismatches: 301, Indels: 263
0.74 0.14 0.12
Matches are distributed among these distances:
324 55 0.04
325 51 0.03
326 24 0.02
327 20 0.01
328 41 0.03
329 6 0.00
330 5 0.00
331 1 0.00
333 2 0.00
334 16 0.01
335 5 0.00
336 10 0.01
337 9 0.01
338 7 0.00
340 1 0.00
342 4 0.00
343 1 0.00
345 6 0.00
346 42 0.03
347 27 0.02
348 32 0.02
349 39 0.02
350 62 0.04
351 7 0.00
352 30 0.02
353 46 0.03
354 28 0.02
355 96 0.06
356 144 0.09
357 36 0.02
358 65 0.04
359 116 0.07
360 330 0.21
361 121 0.08
362 55 0.04
363 23 0.01
364 6 0.00
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (356 bp):
AAAGAATTTGAAGGATTTTTTATATTTTTAAGATATTTTTAATTTTTTTAATAATTTTTTACAAC
TTTTTAAGATCTTTTAGGTTTTTTATAGTTTTTTAAAATATTTTTAGGTTTTTTTAAAGATGTTT
AAGGTCATTCTAAGCATTTTTAAGGATTTTTAATGATTTTTAAGGATTTTTAAGTCTTTTCAAGG
ATTTTCAATAGTTTTTATGGAATTTTATAAATTTTGGAGGTTTAGTAAGTTATATTGAAAAGATT
TTAAAAGTCTTTTAAAGCATTTTAAAGATTTTATTAATAGATTTTTAAACATTTTGAGATCTTTT
TAAGGATACTTAAGGTATTTTAGAGGTTTTA
Found at i:5947 original size:21 final size:21
Alignment explanation
Indices: 5900--5969 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
5890 TAATTCTAAT
*
5900 AATTTTTAAGGATTTTTAATG
1 AATTTTTAAGGATTTTCAATG
5921 AATTTTTAAGGATTTTCAA-G
1 AATTTTTAAGGATTTTCAATG
* *
5941 -ATCTTTTCATGGATTTCCAAT-
1 AAT-TTTT-AAGGATTTTCAATG
5962 AATTTTTA
1 AATTTTTA
5970 TAAAATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.05
20 6 0.14
21 32 0.76
22 2 0.05
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (21 bp):
AATTTTTAAGGATTTTCAATG
Found at i:6504 original size:20 final size:20
Alignment explanation
Indices: 6481--6518 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6471 TTTCCAAGGA
6481 ATTTGAAGG-ATTTCTAATAT
1 ATTT-AAGGTATTTCTAATAT
*
6501 ATTTAAGGTATTTTTAAT
1 ATTTAAGGTATTTCTAAT
6519 TTTTTTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (20 bp):
ATTTAAGGTATTTCTAATAT
Found at i:6738 original size:21 final size:20
Alignment explanation
Indices: 6692--6738 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
6682 TTGTAAGTTA
6692 TTTTTAAAAGATATTTAAAG
1 TTTTTAAAAGATATTTAAAG
*
6712 TCTTTT-AAAGCATTTTTAAAGG
1 T-TTTTAAAAG-ATATTTAAA-G
6734 TTTTT
1 TTTTT
6739 TCATGGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 5 0.22
21 16 0.70
22 2 0.09
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTTTAAAAGATATTTAAAG
Found at i:7094 original size:21 final size:20
Alignment explanation
Indices: 7042--7107 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
7032 TTAGATTTCG
7042 TAAGTTTTTTTTAAAGATTTT
1 TAAG-TTTTTTTAAAGATTTT
* *
7063 TATA-ATCTTTTAAAGTATTTT
1 TA-AGTTTTTTTAAAG-ATTTT
*
7084 TAAGTTTTTTTGATAGATTTT
1 TAAGTTTTTTT-AAAGATTTT
7105 TAA
1 TAA
7108 TCATTTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 10 0.28
21 22 0.61
22 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (20 bp):
TAAGTTTTTTTAAAGATTTT
Found at i:7175 original size:29 final size:28
Alignment explanation
Indices: 7143--7233 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
7133 ATTTAAGGTT
* * *
7143 TTTTTACATTTTTCAAGGAATTTGAATGA
1 TTTTTAAATTTTT-AAGGATTTTTAATGA
*
7172 TTTTTAAAGTTTTTAAGGGATTTTTAATTA
1 TTTTTAAA-TTTTTAA-GGATTTTTAATGA
7202 -TTTTAATATTTTTAA-GATTTTTAATGA
1 TTTTTAA-ATTTTTAAGGATTTTTAATGA
7229 TTTTT
1 TTTTT
7234 CTGGGTTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
27 11 0.21
28 4 0.08
29 22 0.42
30 16 0.30
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (28 bp):
TTTTTAAATTTTTAAGGATTTTTAATGA
Found at i:7441 original size:21 final size:20
Alignment explanation
Indices: 7401--7440 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
7391 GTTATTTTAA
*
7401 AAAGATTTTTAATGTCTTTT
1 AAAGATTTTTAAGGTCTTTT
7421 AAAGTATTTTTAAGGT-TTTT
1 AAAG-ATTTTTAAGGTCTTTT
7441 TTTCATGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (20 bp):
AAAGATTTTTAAGGTCTTTT
Found at i:7443 original size:33 final size:33
Alignment explanation
Indices: 7406--7475 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
7396 TTTAAAAAGA
* *
7406 TTTTTAATGTCTTTTAAAGT-ATTTTTAAGGTTT
1 TTTTTAATGGCTTTTAAA-TAATTTTTAAGGTTC
*
7439 TTTTTCATGGCTTTTAAATAATTTTTAAGGTTC
1 TTTTTAATGGCTTTTAAATAATTTTTAAGGTTC
7472 TTTT
1 TTTT
7476 AAGGATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (33 bp):
TTTTTAATGGCTTTTAAATAATTTTTAAGGTTC
Found at i:7542 original size:20 final size:20
Alignment explanation
Indices: 7519--7557 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
7509 AGAATTTGAA
7519 AGATTTTT-AATGTTTTTAAG
1 AGATTTTTAAAT-TTTTTAAG
7539 AGATTTTTAAATTTTTTAA
1 AGATTTTTAAATTTTTTAA
7558 TGATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
AGATTTTTAAATTTTTTAAG
Found at i:7547 original size:11 final size:11
Alignment explanation
Indices: 7459--7548 Score: 52
Period size: 10 Copynumber: 8.7 Consensus size: 11
7449 CTTTTAAATA
7459 ATTTTTAAG-G
1 ATTTTTAAGAG
*
7469 TTCTTTTAAG-G
1 AT-TTTTAAGAG
*
7480 ATATTTAAG-G
1 ATTTTTAAGAG
7490 ATTTTT-AGAG
1 ATTTTTAAGAG
*
7500 AATTTTCAA-AG
1 -ATTTTTAAGAG
* *
7511 AATTTGAA-AG
1 ATTTTTAAGAG
*
7521 ATTTTTAA-TG
1 ATTTTTAAGAG
7531 -TTTTTAAGAG
1 ATTTTTAAGAG
7541 ATTTTTAA
1 ATTTTTAA
7549 ATTTTTTAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
9 9 0.14
10 30 0.48
11 23 0.37
12 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (11 bp):
ATTTTTAAGAG
Found at i:7566 original size:40 final size:40
Alignment explanation
Indices: 7522--7605 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
7512 ATTTGAAAGA
* *
7522 TTTTTAATGTTTTTAAGAGAT-TTTTAAATTTTTTAATGAT
1 TTTTTAATATTTTTAAG-GATCTTTTAAATTTTCTAATGAT
* ** *
7562 TTTTTACTATTTTTAAGGATCTTTTCGATTTTCTATTGAT
1 TTTTTAATATTTTTAAGGATCTTTTAAATTTTCTAATGAT
7602 TTTT
1 TTTT
7606 CAAAGTAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 3 0.08
40 34 0.92
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.62
Consensus pattern (40 bp):
TTTTTAATATTTTTAAGGATCTTTTAAATTTTCTAATGAT
Found at i:7574 original size:20 final size:19
Alignment explanation
Indices: 7551--7605 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
7541 ATTTTTAAAT
*
7551 TTTTTAATGATTTTTTACTA
1 TTTTTAATGATTTTTT-CGA
* *
7571 TTTTTAAGGATCTTTTCGA
1 TTTTTAATGATTTTTTCGA
*
7590 TTTTCTATTGATTTTT
1 TTTT-TAATGATTTTT
7606 CAAAGTAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTTTAATGATTTTTTCGA
Found at i:7794 original size:21 final size:19
Alignment explanation
Indices: 7757--7826 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 19
7747 TTTGTAAGTT
*
7757 ATTTTTAATGGATTTTTAAG
1 ATTTTTAAT-GTTTTTTAAG
*
7777 CATTTTTAATGTTCTTTTAATT
1 -ATTTTTAATGTT-TTTTAA-G
* *
7799 ATATTTAAGGTTTTTTAGAG
1 ATTTTTAATGTTTTTTA-AG
7819 ATTTTTAA
1 ATTTTTAA
7827 AGAATGTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (19 bp):
ATTTTTAATGTTTTTTAAG
Found at i:8105 original size:32 final size:31
Alignment explanation
Indices: 8069--8198 Score: 90
Period size: 32 Copynumber: 4.1 Consensus size: 31
8059 TTTAAAAGAC
* *
8069 TTTTAAAGTCTTTTAAAGCATTTTTAAGGTTT
1 TTTTAAAGTATTTTAAAG-ATTTTTAAGGTCT
* *
8101 TTTTAATA-AAGTTTT-AAGCATTTTTAAGGTCA
1 TTTTAA-AGTA-TTTTAAAG-ATTTTTAAGGTCT
*
8133 TTTT-AAGTATATTTAAAGTTTTTTAAGAG-CT
1 TTTTAAAGTAT-TTTAAAGATTTTTAAG-GTCT
* *
8164 TTTTCAAGTAATTTGAAAGATTTTTAATGGT-T
1 TTTTAAAGT-ATTTTAAAGATTTTTAA-GGTCT
8196 TTT
1 TTT
8199 AAGGGATTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
30 2 0.03
31 18 0.23
32 51 0.65
33 8 0.10
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.52
Consensus pattern (31 bp):
TTTTAAAGTATTTTAAAGATTTTTAAGGTCT
Found at i:8254 original size:29 final size:31
Alignment explanation
Indices: 8190--8259 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
8180 AAGATTTTTA
* *
8190 ATGG-TTTTTAAGGGATTTTTAATTTGTTTT
1 ATGGTTTTTTAAGGGATTTTTAAGTTGTTGT
*
8220 A-CGTTTTTTAA-GGATTTTTAAGTT-TTGT
1 ATGGTTTTTTAAGGGATTTTTAAGTTGTTGT
8248 ATGGTTTTTTAA
1 ATGGTTTTTTAA
8260 AAGACTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 4 0.12
29 22 0.65
30 8 0.24
ACGTcount: A:0.21, C:0.01, G:0.19, T:0.59
Consensus pattern (31 bp):
ATGGTTTTTTAAGGGATTTTTAAGTTGTTGT
Found at i:8412 original size:21 final size:21
Alignment explanation
Indices: 8388--8457 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
8378 TGTAAGTTAT
8388 TTTTAAAAGATTTTTAAAGAC
1 TTTTAAAAGATTTTTAAAGAC
8409 TTTT-AAAGCA-TTTTAAAG-C
1 TTTTAAAAG-ATTTTTAAAGAC
* **
8428 TTATTTAATAGATTTTTAATCAC
1 -T-TTTAAAAGATTTTTAAAGAC
8451 TTTTAAA
1 TTTTAAA
8458 GTCATTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
19 1 0.03
20 13 0.33
21 14 0.36
22 10 0.26
23 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTTAAAAGATTTTTAAAGAC
Found at i:8447 original size:11 final size:10
Alignment explanation
Indices: 8386--8446 Score: 61
Period size: 10 Copynumber: 5.8 Consensus size: 10
8376 TTTGTAAGTT
8386 ATTTTTAAAAG
1 ATTTTT-AAAG
8397 ATTTTTAAAG
1 ATTTTTAAAG
*
8407 ACTTTTAAAG
1 ATTTTTAAAG
8417 CA-TTTTAAAG
1 -ATTTTTAAAG
*
8427 CTTATTTAATAG
1 ATT-TTTAA-AG
8439 ATTTTTAA
1 ATTTTTAA
8447 TCACTTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
10 22 0.51
11 17 0.40
12 4 0.09
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (10 bp):
ATTTTTAAAG
Found at i:8465 original size:11 final size:10
Alignment explanation
Indices: 8399--8467 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 10
8389 TTTAAAAGAT
8399 TTTTAAAG-A
1 TTTTAAAGCA
8408 CTTTTAAAGCA
1 -TTTTAAAGCA
*
8419 TTTTAAAGCT
1 TTTTAAAGCA
8429 TATTTAATAG-A
1 T-TTTAA-AGCA
* *
8440 TTTTTAATCA
1 TTTTAAAGCA
8450 CTTTTAAAGTCA
1 -TTTTAAAG-CA
8462 TTTTAA
1 TTTTAA
8468 GAATATTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
9 1 0.02
10 23 0.49
11 19 0.40
12 4 0.09
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (10 bp):
TTTTAAAGCA
Found at i:8475 original size:42 final size:42
Alignment explanation
Indices: 8389--8475 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
8379 GTAAGTTATT
* **
8389 TTTAAAAGATTTTTAAAGACTTTTAAAGCATTTTAAAGCTTA
1 TTTAAAAGATTTTTAAACACTTTTAAAGCATTTTAAAGAATA
* *
8431 TTTAATAGATTTTTAATCACTTTTAAAGTCATTTT-AAGAATA
1 TTTAAAAGATTTTTAAACACTTTTAAAG-CATTTTAAAGAATA
8473 TTT
1 TTT
8476 TAGGTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 33 0.85
43 6 0.15
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (42 bp):
TTTAAAAGATTTTTAAACACTTTTAAAGCATTTTAAAGAATA
Found at i:8917 original size:11 final size:10
Alignment explanation
Indices: 8869--9010 Score: 70
Period size: 11 Copynumber: 13.5 Consensus size: 10
8859 GATTTTCAAT
8869 TTTTTAAGAGA
1 TTTTTAAG-GA
*
8880 TTTTTGA-GA
1 TTTTTAAGGA
* *
8889 TTTTGGATGGCA
1 TTTT-TAAGG-A
*
8901 TTTTAAAGGA
1 TTTTTAAGGA
*
8911 TTTTTAAGGT
1 TTTTTAAGGA
8921 TGTTTTAAGGA
1 T-TTTTAAGGA
* *
8932 TGTTTAAGGTC
1 TTTTTAAGG-A
*
8943 TTTTTAAGTA
1 TTTTTAAGGA
**
8953 TTTTTAAGTT
1 TTTTTAAGGA
*
8963 TATTTTATGGA
1 T-TTTTAAGGA
*
8974 TTTTTTATGGA
1 -TTTTTAAGGA
* *
8985 TTTTCAAGAA
1 TTTTTAAGGA
*
8995 TTTTCAAGGA
1 TTTTTAAGGA
9005 CTTTTT
1 -TTTTT
9011 TTATTATTTT
Statistics
Matches: 100, Mismatches: 23, Indels: 16
0.72 0.17 0.12
Matches are distributed among these distances:
9 6 0.06
10 43 0.43
11 45 0.45
12 6 0.06
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.52
Consensus pattern (10 bp):
TTTTTAAGGA
Found at i:8932 original size:21 final size:20
Alignment explanation
Indices: 8901--8978 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
8891 TTGGATGGCA
*
8901 TTTTAAAGGATTTTTAAGGT
1 TTTTTAAGGATTTTTAAGGT
*
8921 TGTTTTAAGGATGTTTAAGGT
1 T-TTTTAAGGATTTTTAAGGT
* *
8942 CTTTTTAAGTATTTTTAAGTT
1 -TTTTTAAGGATTTTTAAGGT
*
8963 TATTTTATGGATTTTT
1 T-TTTTAAGGATTTTT
8979 TATGGATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 2 0.04
21 45 0.94
22 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.18, T:0.56
Consensus pattern (20 bp):
TTTTTAAGGATTTTTAAGGT
Found at i:9096 original size:34 final size:34
Alignment explanation
Indices: 9049--9118 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 34
9039 TTTTAAAAGA
* * *
9049 TTTTTAAACAATTTGTAAGCATTTTTAAGGTTTTT
1 TTTTTAAACAATTTGTAAAC-GTTTTAAGCTTTTT
* *
9084 TTTTTATA-AATTTTTAAACGTTTTAAGCTTTTT
1 TTTTTAAACAATTTGTAAACGTTTTAAGCTTTTT
9117 TT
1 TT
9119 AAGGATATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 14 0.47
34 9 0.30
35 7 0.23
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.59
Consensus pattern (34 bp):
TTTTTAAACAATTTGTAAACGTTTTAAGCTTTTT
Found at i:9564 original size:9 final size:10
Alignment explanation
Indices: 9532--9575 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
9522 TCTTTAAGAG
9532 ATTTTTAAT-
1 ATTTTTAATA
*
9541 -TTTTTAATT
1 ATTTTTAATA
*
9550 ATTTTTTATA
1 ATTTTTAATA
9560 ATTTTTAATA
1 ATTTTTAATA
9570 ATTTTT
1 ATTTTT
9576 TGAGGTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 8 0.27
10 22 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:9934 original size:10 final size:10
Alignment explanation
Indices: 9849--10197 Score: 101
Period size: 10 Copynumber: 33.7 Consensus size: 10
9839 TTTTTTTGGA
9849 GATTTATTAAG
1 GATTT-TTAAG
* *
9860 GAATTTGAAG
1 GATTTTTAAG
* *
9870 GATTTTTTAT
1 GATTTTTAAG
*
9880 G-CTTTTAAGG
1 GATTTTTAA-G
9890 GATTTTTAA-
1 GATTTTTAAG
*
9899 -ATTTTTAAT
1 GATTTTTAAG
*
9908 AATTATTTAA-
1 GATT-TTTAAG
*
9918 TATTTTTAAG
1 GATTTTTAAG
*
9928 GATTTTTTAG
1 GATTTTTAAG
9938 G-TTTTGTATAG
1 GATTTT-TA-AG
*
9949 G-TTTTTAAA
1 GATTTTTAAG
*
9958 GTTATTTTAAG
1 GAT-TTTTAAG
*
9969 GTCTTTTTAAG
1 G-ATTTTTAAG
*
9980 GATGTTTAAG
1 GATTTTTAAG
*
9990 G-TCATTCTAAG
1 GAT--TTTTAAG
*
10001 CATTTTTAAAG
1 GATTTTT-AAG
** *
10012 TTTTTCTTTATG
1 -GATT-TTTAAG
10024 GATTTTTAAG
1 GATTTTTAAG
*
10034 GATTTTTAAA
1 GATTTTTAAG
10044 G-TCTTTTCAAG
1 GAT-TTTT-AAG
* *
10055 GAGTTTTATG
1 GATTTTTAAG
*
10065 GATTTTTGAG
1 GATTTTTAAG
*
10075 GTTTTTTAAG
1 GATTTTTAAG
* *
10085 TTATTTTTAAA
1 -GATTTTTAAG
* *
10096 AAGTTTTTAAA
1 GA-TTTTTAAG
10107 G-TCTTTTAAAG
1 GAT-TTTT-AAG
*
10118 CATTTTT-AG
1 GATTTTTAAG
*
10127 GTTTTTTTCCATA-
1 G-ATTTTT--A-AG
10140 GATTTTTAAG
1 GATTTTTAAG
* *
10150 TATTTTAAAG
1 GATTTTTAAG
10160 GTATTTTTAAG
1 G-ATTTTTAAG
*
10171 GATATTTAAG
1 GATTTTTAAG
*
10181 G-TTTTTTAG
1 GATTTTTAAG
10190 AGATTTTT
1 -GATTTTT
10198 TAAGAAATTT
Statistics
Matches: 249, Mismatches: 55, Indels: 68
0.67 0.15 0.18
Matches are distributed among these distances:
8 8 0.03
9 28 0.11
10 107 0.43
11 89 0.36
12 12 0.05
13 4 0.02
14 1 0.00
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (10 bp):
GATTTTTAAG
Found at i:9936 original size:20 final size:20
Alignment explanation
Indices: 9867--9936 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
9857 AAGGAATTTG
**
9867 AAGGATTTTTT-ATGCTTTT
1 AAGGATTTTTTAATATTTTT
9886 AAGGGA-TTTTTAA-ATTTTT
1 AA-GGATTTTTTAATATTTTT
** *
9905 AATAATTATTTAATATTTTT
1 AAGGATTTTTTAATATTTTT
9925 AAGGATTTTTTA
1 AAGGATTTTTTA
9937 GGTTTTGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.03
19 19 0.49
20 19 0.49
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.56
Consensus pattern (20 bp):
AAGGATTTTTTAATATTTTT
Found at i:9975 original size:21 final size:21
Alignment explanation
Indices: 9947--9992 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
9937 GGTTTTGTAT
*
9947 AGGT-TTTTAAAGTTAT-TTTA
1 AGGTCTTTTAAAG-GATGTTTA
*
9967 AGGTCTTTTTAAGGATGTTTA
1 AGGTCTTTTAAAGGATGTTTA
9988 AGGTC
1 AGGTC
9993 ATTCTAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (21 bp):
AGGTCTTTTAAAGGATGTTTA
Found at i:10000 original size:21 final size:21
Alignment explanation
Indices: 9963--10009 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
9953 TTAAAGTTAT
* * *
9963 TTTAAGGTCTTTTTAAGGATG
1 TTTAAGGTCATTCTAAGCATG
*
9984 TTTAAGGTCATTCTAAGCATT
1 TTTAAGGTCATTCTAAGCATG
10005 TTTAA
1 TTTAA
10010 AGTTTTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.47
Consensus pattern (21 bp):
TTTAAGGTCATTCTAAGCATG
Found at i:10071 original size:21 final size:20
Alignment explanation
Indices: 10018--10071 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
10008 AAAGTTTTTC
*
10018 TTTATGGATTTTTAAGGATT
1 TTTATGGATTTTTAAGGAGT
**
10038 TTTAAAG-TCTTTTCAAGGAGT
1 TTTATGGAT-TTTT-AAGGAGT
10059 TTTATGGATTTTT
1 TTTATGGATTTTT
10072 GAGGTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.04
20 9 0.35
21 15 0.58
22 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.19, T:0.54
Consensus pattern (20 bp):
TTTATGGATTTTTAAGGAGT
Found at i:10101 original size:41 final size:41
Alignment explanation
Indices: 10018--10102 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
10008 AAAGTTTTTC
* **
10018 TTTATGGATTTTTAAGGATTTTTAAAGTCTTTTCAAGGAGT
1 TTTATGGATTTTTAAGGATTTTTAAAGTATTTTCAAAAAGT
* * *
10059 TTTATGGATTTTTGAGG-TTTTTTAAGTTATTTTTAAAAAGT
1 TTTATGGATTTTTAAGGATTTTTAAAG-TATTTTCAAAAAGT
10100 TTT
1 TTT
10103 TAAAGTCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 8 0.22
41 29 0.78
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (41 bp):
TTTATGGATTTTTAAGGATTTTTAAAGTATTTTCAAAAAGT
Found at i:10165 original size:21 final size:19
Alignment explanation
Indices: 10141--10196 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 19
10131 TTTTCCATAG
10141 ATTTTTAAGTATTTTAAAGGT
1 ATTTTTAAG-ATTTT-AAGGT
10162 ATTTTTAAGGATATTTAAGGT
1 ATTTTTAA-GAT-TTTAAGGT
10183 -TTTTTAGAGATTTT
1 ATTTTTA-AGATTTT
10197 TTAAGAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 3 0.09
20 9 0.28
21 16 0.50
22 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (19 bp):
ATTTTTAAGATTTTAAGGT
Found at i:13775 original size:27 final size:27
Alignment explanation
Indices: 13714--13776 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
13704 AATTATAGAC
*
13714 CCTAAACCCCGAACCCCAAACTTTAAA
1 CCTAAACCCCGAACCCCAAACCTTAAA
* *
13741 CCTTAACCCCTAACCCCTAAACCTTAAA
1 CCTAAACCCCGAACCCC-AAACCTTAAA
13769 CC-AAACCC
1 CCTAAACCC
13777 TAAACCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.38, C:0.44, G:0.02, T:0.16
Consensus pattern (27 bp):
CCTAAACCCCGAACCCCAAACCTTAAA
Found at i:13782 original size:27 final size:26
Alignment explanation
Indices: 13714--13779 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
13704 AATTATAGAC
* *
13714 CCTAAACCCCGAACCCCAAACTTTAAA
1 CCTAAA-CCCTAACCCCAAACCTTAAA
*
13741 CCTTAACCCCTAACCCCTAAACCTTAAA
1 CC-TAAACCCTAACCCC-AAACCTTAAA
13769 CC-AAACCCTAA
1 CCTAAACCCTAA
13780 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 8 0.24
27 11 0.33
28 14 0.42
ACGTcount: A:0.39, C:0.42, G:0.02, T:0.17
Consensus pattern (26 bp):
CCTAAACCCTAACCCCAAACCTTAAA
Found at i:29622 original size:71 final size:72
Alignment explanation
Indices: 29522--29712 Score: 226
Period size: 71 Copynumber: 2.7 Consensus size: 72
29512 TGGATAGAAC
* * * * *
29522 CATTTTGTGAAAAATCTATAG-ATACATTTTGACAATGTATCGATACATGCA-ACTCAATTTGGA
1 CATTATGTTAAAAATCTATCGAATACATTTTGACAATATATCGATACATGCAGACT-AATTTAGA
*
29585 ATTCTGAA
65 ACTCTGAA
* * * * * *
29593 TATTCTGTTGAAAATTTATC-AATATATTTTGACAATATATCGATGCATGCAGACTAATTTAGAA
1 CATTATGTTAAAAATCTATCGAATACATTTTGACAATATATCGATACATGCAGACTAATTTAGAA
*
29657 CTCTGAG
66 CTCTGAA
*
29664 CATTATGTTAAAAATCTATCGAATACATTTTGACAATATAACGATACAT
1 CATTATGTTAAAAATCTATCGAATACATTTTGACAATATATCGATACAT
29713 TTAGTATAAA
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
71 70 0.71
72 28 0.29
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36
Consensus pattern (72 bp):
CATTATGTTAAAAATCTATCGAATACATTTTGACAATATATCGATACATGCAGACTAATTTAGAA
CTCTGAA
Found at i:36847 original size:2 final size:2
Alignment explanation
Indices: 36840--36868 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36830 TGCCTTCAAT
36840 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
36869 AAACAATGTT
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:42026 original size:21 final size:22
Alignment explanation
Indices: 41997--42039 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
41987 TATTGAGACA
*
41997 TGACTAC-TTCAAAAGAAAGTAT
1 TGACTACTTTC-AAACAAAGTAT
42019 TGAC-ACTTTCAAACAAAGTAT
1 TGACTACTTTCAAACAAAGTAT
42040 CGAGACTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (22 bp):
TGACTACTTTCAAACAAAGTAT
Found at i:43086 original size:82 final size:82
Alignment explanation
Indices: 42949--43118 Score: 340
Period size: 82 Copynumber: 2.1 Consensus size: 82
42939 TCAATAAGAT
42949 ATGTATAAAATGCATGTATGTTAAGTTGAAATTGGATGTATTGATGATTCCACATACCACACGAG
1 ATGTATAAAATGCATGTATGTTAAGTTGAAATTGGATGTATTGATGATTCCACATACCACACGAG
43014 TTAAGAACAAACACATA
66 TTAAGAACAAACACATA
43031 ATGTATAAAATGCATGTATGTTAAGTTGAAATTGGATGTATTGATGATTCCACATACCACACGAG
1 ATGTATAAAATGCATGTATGTTAAGTTGAAATTGGATGTATTGATGATTCCACATACCACACGAG
43096 TTAAGAACAAACACATA
66 TTAAGAACAAACACATA
43113 ATGTAT
1 ATGTAT
43119 GCTAAGTTAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 88 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (82 bp):
ATGTATAAAATGCATGTATGTTAAGTTGAAATTGGATGTATTGATGATTCCACATACCACACGAG
TTAAGAACAAACACATA
Found at i:45079 original size:57 final size:56
Alignment explanation
Indices: 44970--45079 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 56
44960 TACTTAATAG
* *
44970 TCATCCAATTTATTTTTAAAAAAAAAAGATAATTTAGAGATAAATTCTAAATTTGA
1 TCATCCAATTTATCTTTAAAAAAAAAAGATAATTTAGAGATAAACTCTAAATTTGA
**
45026 TCATCCAATTTATCTTTAAATAAATTAAGATAATTTAGAGATAATACTC-AAATT
1 TCATCCAATTTATCTTTAAA-AAAAAAAGATAATTTAGAGATAA-ACTCTAAATT
45080 CGACCAATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
56 19 0.40
57 26 0.54
58 3 0.06
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.38
Consensus pattern (56 bp):
TCATCCAATTTATCTTTAAAAAAAAAAGATAATTTAGAGATAAACTCTAAATTTGA
Found at i:45406 original size:46 final size:49
Alignment explanation
Indices: 45294--45411 Score: 125
Period size: 51 Copynumber: 2.4 Consensus size: 49
45284 AAAGAAGAAA
*
45294 ATTCTGAAGAACCAAAGCCTCCAAAGTTCCACATATCCAAGAAAAAAGGAAG
1 ATTCTAAAG-ACCAAAGCCTCCAAAGTTCCACATATCC-A-AAAAAAGGAAG
* * * * *
45346 ATTCTGAAGACCAAAGCCTTCAGAGTTCCACATAT-C-TAAAAAGGAAT
1 ATTCTAAAGACCAAAGCCTCCAAAGTTCCACATATCCAAAAAAAGGAAG
*
45393 A-TCTAAAGACCAAAACCTC
1 ATTCTAAAGACCAAAGCCTC
45412 TCTAGATTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
46 15 0.25
47 10 0.17
50 1 0.02
51 24 0.41
52 9 0.15
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.19
Consensus pattern (49 bp):
ATTCTAAAGACCAAAGCCTCCAAAGTTCCACATATCCAAAAAAAGGAAG
Found at i:45542 original size:28 final size:28
Alignment explanation
Indices: 45502--45628 Score: 139
Period size: 28 Copynumber: 4.3 Consensus size: 28
45492 TTCAATTTGT
45502 TCATAAGACCCTTGAGGTCGAGATCAAG
1 TCATAAGACCCTTGAGGTCGAGATCAAG
*
45530 TCATAAGACCCTTGAGGTCGAGACCAAG
1 TCATAAGACCCTTGAGGTCGAGATCAAG
* * * *
45558 TTATAAGACCCTTGAAG-CAAAGCCTCTAATTTG
1 TCATAAGACCCTTGAGGTC-GAG-ATC-AA---G
45591 TTCATAAGACCCTTGAGGTCGAGATCAAG
1 -TCATAAGACCCTTGAGGTCGAGATCAAG
45620 TCATAAGAC
1 TCATAAGAC
45629 TCATAAGACC
Statistics
Matches: 81, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
27 1 0.01
28 53 0.65
29 2 0.02
30 2 0.02
32 2 0.02
33 3 0.04
34 17 0.21
35 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (28 bp):
TCATAAGACCCTTGAGGTCGAGATCAAG
Found at i:45688 original size:38 final size:38
Alignment explanation
Indices: 45646--45893 Score: 143
Period size: 38 Copynumber: 6.7 Consensus size: 38
45636 ACCCTTGAAA
*
45646 AAAATATTCATTCAAGATCAAGTCGTAGACCTTTGTAG
1 AAAATATTCATTCAAGATCAAGTCGTAAACCTTTGTAG
*
45684 AAAATATTCATTCAAGATCAAGTTGTAAACCCCTGAGGTTG-AG
1 AAAATATTCATTCAAGATCAAGTCGTAAA--CCT----TTGTAG
** * * * * *
45727 ATCA-AGTCA-T-AAGACTC-A-T--AAAACCCTAGAAG
1 AAAATATTCATTCAAGA-TCAAGTCGTAAACCTTTGTAG
* *
45759 AAAATATTCATTAAAGATCAAGTCGTAGATCC-TTGTAG
1 AAAATATTCATTCAAGATCAAGTCGTA-AACCTTTGTAG
* * *
45797 AAAATATTCTTTCAAGATCAAGTTGTAAACC-AT-TA-
1 AAAATATTCATTCAAGATCAAGTCGTAAACCTTTGTAG
* *
45832 AAACTA---ATTCAAGATCAAGTCATAAACCTTT-TA-
1 AAAATATTCATTCAAGATCAAGTCGTAAACCTTTGTAG
45865 AACACATATTCATTCAAGATCAAGTCGTA
1 AA-A-ATATTCATTCAAGATCAAGTCGTA
45894 GACCCTTGAA
Statistics
Matches: 161, Mismatches: 27, Indels: 44
0.69 0.12 0.19
Matches are distributed among these distances:
31 2 0.01
32 23 0.14
33 9 0.06
34 4 0.02
35 14 0.09
36 3 0.02
37 7 0.04
38 73 0.45
39 4 0.02
40 8 0.05
41 3 0.02
42 4 0.02
43 4 0.02
44 3 0.02
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (38 bp):
AAAATATTCATTCAAGATCAAGTCGTAAACCTTTGTAG
Found at i:45802 original size:113 final size:113
Alignment explanation
Indices: 45599--45827 Score: 379
Period size: 113 Copynumber: 2.0 Consensus size: 113
45589 TGTTCATAAG
* * * *
45599 ACCCTTGAGGTCGAGATCAAGTCATAAGACTCATAAGACCCTTGAAAAAAATATTCATTCAAGAT
1 ACCCCTGAGGTCGAGATCAAGTCATAAGACTCATAAAACCCTAGAAAAAAATATTCATTAAAGAT
45664 CAAGTCGTAGACCTTTGTAGAAAATATTCATTCAAGATCAAGTTGTAA
66 CAAGTCGTAGACCTTTGTAGAAAATATTCATTCAAGATCAAGTTGTAA
* *
45712 ACCCCTGAGGTTGAGATCAAGTCATAAGACTCATAAAACCCTAGAAGAAAATATTCATTAAAGAT
1 ACCCCTGAGGTCGAGATCAAGTCATAAGACTCATAAAACCCTAGAAAAAAATATTCATTAAAGAT
*
45777 CAAGTCGTAGATCC-TTGTAGAAAATATTCTTTCAAGATCAAGTTGTAA
66 CAAGTCGTAGA-CCTTTGTAGAAAATATTCATTCAAGATCAAGTTGTAA
45825 ACC
1 ACC
45828 ATTAAAACTA
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
113 106 0.98
114 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (113 bp):
ACCCCTGAGGTCGAGATCAAGTCATAAGACTCATAAAACCCTAGAAAAAAATATTCATTAAAGAT
CAAGTCGTAGACCTTTGTAGAAAATATTCATTCAAGATCAAGTTGTAA
Found at i:45851 original size:70 final size:70
Alignment explanation
Indices: 45772--45961 Score: 190
Period size: 70 Copynumber: 2.7 Consensus size: 70
45762 ATATTCATTA
* * * *
45772 AAGATCAAGTCGTAGATCCTTGTAGAA-A-ATATTCTTTCAAGATCAAGTTGTAAACCATTAAAA
1 AAGATCAAGTCATA-AACCTTGTA-AACACATATTCATTCAAGATCAAGTCGTAAACCATTAAAA
*
45835 CTAATTC
64 CAAATTC
* * * * *
45842 AAGATCAAGTCATAAACCTTTTAAACACATATTCATTCAAGATCAAGTCGTAGACCCTTGAAGCA
1 AAGATCAAGTCATAAACCTTGTAAACACATATTCATTCAAGATCAAGTCGTAAACCATTAAAACA
45907 AATTC
66 AATTC
* * *
45912 AAGATCGAGGCATAAAACCCTTAG-AAA-ACATATTCGTTCAAGATCAAGTC
1 AAGATCAAGTCAT-AAA-CCTT-GTAAACACATATTCATTCAAGATCAAGTC
45962 ATCATAACCC
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
68 2 0.02
69 8 0.08
70 59 0.58
71 25 0.25
72 7 0.07
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (70 bp):
AAGATCAAGTCATAAACCTTGTAAACACATATTCATTCAAGATCAAGTCGTAAACCATTAAAACA
AATTC
Found at i:45858 original size:32 final size:32
Alignment explanation
Indices: 45807--45927 Score: 89
Period size: 32 Copynumber: 3.6 Consensus size: 32
45797 AAAATATTCT
**
45807 TTCAAGATCAAGTTGTAAACCATTAAAACTAA
1 TTCAAGATCAAGTCATAAACCATTAAAACTAA
*
45839 TTCAAGATCAAGTCATAAACCTTTTAAACACATATTCA
1 TTCAAGATCAAGTCATAAACC-ATTAAA-AC-TA---A
* * * * * *
45877 TTCAAGATCAAGTCGTAGACCCTTGAAGCAAA
1 TTCAAGATCAAGTCATAAACCATTAAAACTAA
* *
45909 TTCAAGATCGAGGCATAAA
1 TTCAAGATCAAGTCATAAA
45928 ACCCTTAGAA
Statistics
Matches: 70, Mismatches: 13, Indels: 12
0.74 0.14 0.13
Matches are distributed among these distances:
32 35 0.50
33 5 0.07
34 2 0.03
35 3 0.04
36 1 0.01
37 4 0.06
38 20 0.29
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.26
Consensus pattern (32 bp):
TTCAAGATCAAGTCATAAACCATTAAAACTAA
Found at i:45959 original size:71 final size:70
Alignment explanation
Indices: 45800--45961 Score: 191
Period size: 70 Copynumber: 2.3 Consensus size: 70
45790 CTTGTAGAAA
* * * * *
45800 ATATTCTTTCAAGATCAAGTTGTAAACCATTAAAACTAATTCAAGATCAAGTCATAAACCTTTTA
1 ATATTCATTCAAGATCAAGTCGTAAACCATTAAAACAAATTCAAGATCAAGGCATAAACCTCTTA
*
45865 AACAC
66 AAAAC
* * * * *
45870 ATATTCATTCAAGATCAAGTCGTAGACCCTTGAAGCAAATTCAAGATCGAGGCATAAAACC-CTT
1 ATATTCATTCAAGATCAAGTCGTAAACCATTAAAACAAATTCAAGATCAAGGCAT-AAACCTCTT
45934 AGAAAAC
65 A-AAAAC
*
45941 ATATTCGTTCAAGATCAAGTC
1 ATATTCATTCAAGATCAAGTC
45962 ATCATAACCC
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
70 49 0.63
71 29 0.37
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (70 bp):
ATATTCATTCAAGATCAAGTCGTAAACCATTAAAACAAATTCAAGATCAAGGCATAAACCTCTTA
AAAAC
Found at i:47581 original size:34 final size:34
Alignment explanation
Indices: 47543--47630 Score: 133
Period size: 34 Copynumber: 2.6 Consensus size: 34
47533 TTAAGGGCTG
*
47543 GTTTTGGAGGCTGAATAGTGCCATTTTTCTACTA
1 GTTTTGGAGGCTGAAAAGTGCCATTTTTCTACTA
* *
47577 GTTTTGGAGGCTGAAAAGTGCCATTTTTCTGCTG
1 GTTTTGGAGGCTGAAAAGTGCCATTTTTCTACTA
*
47611 GTTTTGGAGG-TCAAAAGTGC
1 GTTTTGGAGGCTGAAAAGTGC
47631 AGAATTTTGC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 9 0.18
34 41 0.82
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (34 bp):
GTTTTGGAGGCTGAAAAGTGCCATTTTTCTACTA
Found at i:47954 original size:5 final size:5
Alignment explanation
Indices: 47936--47976 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
47926 GGTGGGAGAG
*
47936 AAAG- AAAG- AAAGA AAAGA AAAGA AAAGA AAGGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
47977 TAACAAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
4 8 0.24
5 26 0.76
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:48023 original size:27 final size:25
Alignment explanation
Indices: 47975--48065 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 25
47965 AGGAAAAGAA
* * *
47975 AATAACAAGGAAAATGGGCATGGCCC
1 AATAA-AAGAAAAATGGACATGGTCC
*
48001 AATAAGTAAGAAAAATGGACATGGTTC
1 AATAA--AAGAAAAATGGACATGGTCC
* *
48028 AATAAAGGAAAAATGAACATGGTCC
1 AATAAAAGAAAAATGGACATGGTCC
48053 AATTAAAAAGAAA
1 AA-T-AAAAGAAA
48066 TGAGAGAAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
25 19 0.36
26 6 0.11
27 28 0.53
ACGTcount: A:0.52, C:0.11, G:0.21, T:0.16
Consensus pattern (25 bp):
AATAAAAGAAAAATGGACATGGTCC
Found at i:48066 original size:25 final size:24
Alignment explanation
Indices: 48008--48068 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
47998 CCCAATAAGT
* *
48008 AAGAAAAATGGACATGGTTCAATA
1 AAGAAAAATGAACATGGTCCAATA
48032 AAGGAAAAATGAACATGGTCCAATTA
1 AA-GAAAAATGAACATGGTCCAA-TA
48058 AA-AAGAAATGA
1 AAGAA-AAATGA
48069 GAGAAGTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.12
25 24 0.75
26 4 0.12
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (24 bp):
AAGAAAAATGAACATGGTCCAATA
Found at i:59946 original size:45 final size:45
Alignment explanation
Indices: 59791--59964 Score: 167
Period size: 45 Copynumber: 3.9 Consensus size: 45
59781 ATATGTCATG
* * * *
59791 TACAAAAATATGTTACATA-TCA-TGATTAGGTTGTTATC-CGTCATG
1 TACAAAAATATGTGACA-AGTTATTG-TTAGGTTGTTA-CACGCCATA
* * * * * *
59836 TAC-AAAATATGTAACAAGTCATTGTTAGATTATTACACACTATA
1 TACAAAAATATGTGACAAGTTATTGTTAGGTTGTTACACGCCATA
*
59880 TACAAAAATATATGACAAGTTATTGTTAGGTTGTTACACGCCATA
1 TACAAAAATATGTGACAAGTTATTGTTAGGTTGTTACACGCCATA
* * *
59925 TACAAAAACATGTGACGAGTTATGGTTAGGTTGTTACACG
1 TACAAAAATATGTGACAAGTTATTGTTAGGTTGTTACACG
59965 TCATGGTTAG
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
43 2 0.02
44 30 0.28
45 75 0.70
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (45 bp):
TACAAAAATATGTGACAAGTTATTGTTAGGTTGTTACACGCCATA
Found at i:59972 original size:21 final size:21
Alignment explanation
Indices: 59946--59990 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
59936 GTGACGAGTT
*
59946 ATGGTTAGGTTGTTACACGTC
1 ATGGTTAGGTTGTTACACGCC
59967 ATGGTTAGGTTGTTACACGCC
1 ATGGTTAGGTTGTTACACGCC
59988 ATG
1 ATG
59991 TTGAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.36
Consensus pattern (21 bp):
ATGGTTAGGTTGTTACACGCC
Found at i:60134 original size:29 final size:27
Alignment explanation
Indices: 60078--60149 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 27
60068 CATGTTGAAA
* * *
60078 AAAAAATATTATTATTGCACGCTGTATT
1 AAAAAATATT-TTGTTGCACGATATATT
*
60106 GAAAAAATATTGTTGTTGCATGATATATT
1 -AAAAAATATT-TTGTTGCACGATATATT
*
60135 TAAAAATATTTTGTT
1 AAAAAATATTTTGTT
60150 ACTCTTTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 5 0.14
28 9 0.24
29 23 0.62
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (27 bp):
AAAAAATATTTTGTTGCACGATATATT
Found at i:82876 original size:30 final size:31
Alignment explanation
Indices: 82816--82885 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
82806 TCATTAGTCT
* * *
82816 TAAAAGTTTATTTGACTTAAAATAAAAAATA
1 TAAAAATTTATTTAACTCAAAATAAAAAATA
82847 TAAAAATTTATTTAACTCAAAAT-AAAAATA
1 TAAAAATTTATTTAACTCAAAATAAAAAATA
*
82877 TAAAGATTT
1 TAAAAATTT
82886 GATTAAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 15 0.43
31 20 0.57
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (31 bp):
TAAAAATTTATTTAACTCAAAATAAAAAATA
Found at i:82900 original size:29 final size:30
Alignment explanation
Indices: 82834--82918 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 30
82824 TATTTGACTT
* *
82834 AAAATAAAAAATATAAAAATTTATTTAACTC
1 AAAAT-AAAAATATAAAGATTTATTTAAATC
82865 AAAATAAAAATATAAAGATTTGA-TTAAAT-
1 AAAATAAAAATATAAAGATTT-ATTTAAATC
* * *
82894 ACAATAAAAGTATAAAGACTTATTT
1 AAAATAAAAATATAAAGATTTATTT
82919 GAATTTTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 1 0.02
29 20 0.43
30 20 0.43
31 6 0.13
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (30 bp):
AAAATAAAAATATAAAGATTTATTTAAATC
Found at i:84608 original size:44 final size:44
Alignment explanation
Indices: 84545--84629 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
84535 AAAGAAAACA
* *
84545 ACTATTTGAAGAGTTATATTATAAAAAGAAACT-AATCTTTTCAT
1 ACTATTTGAAGAGTCATATTAT-AAAAGAAAATAAATCTTTTCAT
84589 ACTATTTGAAGAGTCATATTATAAAAGAAAATAAATCTTTT
1 ACTATTTGAAGAGTCATATTATAAAAGAAAATAAATCTTTT
84630 TATTAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 9 0.24
44 29 0.76
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (44 bp):
ACTATTTGAAGAGTCATATTATAAAAGAAAATAAATCTTTTCAT
Found at i:93035 original size:72 final size:72
Alignment explanation
Indices: 92912--93053 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 72
92902 ACTGTTTATT
* * *
92912 TTTTATACGTATGAGAGTCTAGAAAGAGAGACGATTCAAACCTTGGACTTTGAGTCTTCGATCAT
1 TTTTATACATACGAGAGTCTAGAAAGAGAGACGATTCAAACCTTAGACTTTGAGTCTTCGATCAT
92977 CTTAATC
66 CTTAATC
* ** * * * *
92984 TTTTATACATACGAGAGTCTAGAGAGAGAGGGGGTTCAAATCTTA-AGCTTTGAGTCTTTGGTCA
1 TTTTATACATACGAGAGTCTAGAAAGAGAGACGATTCAAACCTTAGA-CTTTGAGTCTTCGATCA
93048 TCTTAA
65 TCTTAA
93054 AAAGGGGTGG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 1 0.02
72 58 0.98
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (72 bp):
TTTTATACATACGAGAGTCTAGAAAGAGAGACGATTCAAACCTTAGACTTTGAGTCTTCGATCAT
CTTAATC
Found at i:95836 original size:26 final size:26
Alignment explanation
Indices: 95779--95829 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
95769 CGTTTACTTA
*
95779 ATCGTGTTGTCATGTTTAAACGTGTT
1 ATCGTGTTGTCATGTTTAAACATGTT
*
95805 ATCGTGTTGTCGTGTTTAAACATGT
1 ATCGTGTTGTCATGTTTAAACATGT
95830 ATACGTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.45
Consensus pattern (26 bp):
ATCGTGTTGTCATGTTTAAACATGTT
Found at i:96081 original size:15 final size:13
Alignment explanation
Indices: 96070--96117 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
96060 TTTATATTAA
96070 ATTTTATTATATTT
1 ATTTTATTATA-TT
*
96084 GATGTTATTATTATT
1 -ATTTTATTA-TATT
96099 ATTTTATTATAATT
1 ATTTTATTAT-ATT
96113 ATTTT
1 ATTTT
96118 TATAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 1 0.03
14 16 0.55
15 10 0.34
16 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (13 bp):
ATTTTATTATATT
Found at i:96120 original size:29 final size:30
Alignment explanation
Indices: 96070--96134 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
96060 TTTATATTAA
* *
96070 ATTTTATTATATTTGATGTTATTATTATT-
1 ATTTTATTATAATTGATGTTATAATTATTG
*
96099 ATTTTATTATAATT-ATTTTTATAATTATTG
1 ATTTTATTATAATTGA-TGTTATAATTATTG
96129 ATTTTA
1 ATTTTA
96135 AATTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.77
30 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (30 bp):
ATTTTATTATAATTGATGTTATAATTATTG
Found at i:96266 original size:39 final size:41
Alignment explanation
Indices: 96189--96268 Score: 112
Period size: 39 Copynumber: 2.0 Consensus size: 41
96179 AATCGTGTTA
96189 TTAATCGTGTCGTATCGTATATTGACACATTTAATAAACGTG
1 TTAATCGTGTCG-ATCGTATATTGACACATTTAATAAACGTG
*
96231 TTAATCGTGTC-AT-GTCATATT-ACACATTTATTAAACGT
1 TTAATCGTGTCGATCGT-ATATTGACACATTTAATAAACGT
96269 ATATGTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 18 0.50
40 7 0.19
42 11 0.31
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (41 bp):
TTAATCGTGTCGATCGTATATTGACACATTTAATAAACGTG
Found at i:101666 original size:33 final size:35
Alignment explanation
Indices: 101611--101703 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 35
101601 TCTCAGCCGA
* *
101611 CCGTCTTCCTCTCCTCTATCAGCCA-C-CCTTCCC
1 CCGTCTTCATCTCCTCTCTCAGCCAGCACCTTCCC
* *
101644 CCGTGTTCATCTCCTCTCTCAGCCAGTCATCCTTCCT
1 CCGTCTTCATCTCCTCTCTCAGCCAG-CA-CCTTCCC
*
101681 CCTTCTTCATCTCCTCTCTCAGC
1 CCGTCTTCATCTCCTCTCTCAGC
101704 TGGTCATCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 22 0.44
35 1 0.02
37 27 0.54
ACGTcount: A:0.10, C:0.48, G:0.08, T:0.34
Consensus pattern (35 bp):
CCGTCTTCATCTCCTCTCTCAGCCAGCACCTTCCC
Found at i:101803 original size:23 final size:25
Alignment explanation
Indices: 101754--101809 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
101744 CTCTCAACCG
*
101754 CTCTCAGCCGTGGGTTTGCCTCTCT
1 CTCTCAGCCGTGGGTCTGCCTCTCT
*
101779 CTCTCAGCCGTGGGTCTGCCCCTCT
1 CTCTCAGCCGTGGGTCTGCCTCTCT
101804 CTCTCA
1 CTCTCA
101810 ACCGCTCACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.05, C:0.41, G:0.21, T:0.32
Consensus pattern (25 bp):
CTCTCAGCCGTGGGTCTGCCTCTCT
Found at i:101823 original size:58 final size:59
Alignment explanation
Indices: 101714--101847 Score: 198
Period size: 60 Copynumber: 2.3 Consensus size: 59
101704 TGGTCATCTT
* * *
101714 CCTCTCTCTCAGCCGTGGGTCTTCCCCTCGCTCTCAACCGCTCTCAGCCGTGGGTTTGCC
1 CCTCTCTCTCAGCCGTGGGTCTGCCCCTCGCTCTCAACCGC-CTCACCCGTGGGTCTGCC
* *
101774 TCTCTCTCTCAGCCGTGGGTCTGCCCCTCTCTCTCAACCG-CTCACCCGTGGGTCTGCC
1 CCTCTCTCTCAGCCGTGGGTCTGCCCCTCGCTCTCAACCGCCTCACCCGTGGGTCTGCC
*
101832 CCTCTCTCTCCGCCGT
1 CCTCTCTCTCAGCCGT
101848 CCACAGTGGA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 30 0.45
60 37 0.55
ACGTcount: A:0.06, C:0.46, G:0.20, T:0.28
Consensus pattern (59 bp):
CCTCTCTCTCAGCCGTGGGTCTGCCCCTCGCTCTCAACCGCCTCACCCGTGGGTCTGCC
Found at i:102168 original size:20 final size:19
Alignment explanation
Indices: 102145--102184 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
102135 TAAGTGAGTA
*
102145 ATATGAGAAATATAAAAAAT
1 ATATGAAAAATA-AAAAAAT
*
102165 ATATTAAAAATAAAAAAAT
1 ATATGAAAAATAAAAAAAT
102184 A
1 A
102185 AGATTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
ATATGAAAAATAAAAAAAT
Found at i:102190 original size:20 final size:20
Alignment explanation
Indices: 102152--102190 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
102142 GTAATATGAG
*
102152 AAATATAAAAAATATATTAA
1 AAATATAAAAAATAGATTAA
102172 AAATA-AAAAAATAAGATTA
1 AAATATAAAAAAT-AGATTA
102191 TAATAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATATAAAAAATAGATTAA
Found at i:108364 original size:16 final size:16
Alignment explanation
Indices: 108343--108374 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
108333 ATGTAATACA
108343 TATTTTATTCTATTCC
1 TATTTTATTCTATTCC
108359 TATTTTATTCTATTCC
1 TATTTTATTCTATTCC
108375 CACAGAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTATTCTATTCC
Found at i:111962 original size:7 final size:7
Alignment explanation
Indices: 111945--112004 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
111935 TGTTATTTGC
111945 TATTTTAT
1 TATTTT-T
111953 TATTTTT
1 TATTTTT
111960 TATCTTTT
1 TAT-TTTT
*
111968 TATTATT
1 TATTTTT
*
111975 T-TTATT
1 TATTTTT
111981 TATTATTT
1 TATT-TTT
* *
111989 CATTTTA
1 TATTTTT
111996 TATTTTT
1 TATTTTT
112003 TA
1 TA
112005 AACAATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
6 6 0.14
7 19 0.44
8 18 0.42
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (7 bp):
TATTTTT
Found at i:111999 original size:28 final size:26
Alignment explanation
Indices: 111947--112003 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
111937 TTATTTGCTA
* *
111947 TTTTATTATTTTTTATCTTTTTATTAT
1 TTTTATTATTTTTCATCTTTATATT-T
111974 TTTTATTTATTATTTCAT-TTTATATTT
1 TTTTA-TTATT-TTTCATCTTTATATTT
112001 TTT
1 TTT
112004 AAACAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 9 0.35
28 12 0.46
29 5 0.19
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTATTATTTTTCATCTTTATATTT
Found at i:112192 original size:30 final size:28
Alignment explanation
Indices: 112158--112217 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 28
112148 AAAATGTATA
112158 TTTTATTATT-TATTTATTATTTCTATTTCT
1 TTTTATTATTGTATTT-TTA-TT-TATTTCT
112188 TTTTATTATTGTATTTTTATTTATTTCT
1 TTTTATTATTGTATTTTTATTTATTTCT
112216 TT
1 TT
112218 ATTCTTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 9 0.31
29 2 0.07
30 13 0.45
31 5 0.17
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTTATTATTGTATTTTTATTTATTTCT
Found at i:112315 original size:10 final size:9
Alignment explanation
Indices: 112158--112315 Score: 63
Period size: 10 Copynumber: 16.7 Consensus size: 9
112148 AAAATGTATA
112158 TTTTATTATT
1 TTTTATTA-T
112168 TATTTATTAT
1 T-TTTATTAT
* *
112178 TTCTATTTCT
1 TTTTA-TTAT
112188 TTTTATTA-
1 TTTTATTAT
* *
112196 TTGTATTTT
1 TTTTATTAT
112205 TATTTATT-T
1 T-TTTATTAT
* *
112214 CTTTATTCT
1 TTTTATTAT
* *
112223 TCTTCATAAT
1 T-TTTATTAT
*
112233 TTATTTTTACT
1 TT-TTATTA-T
**
112244 TTTTACAAT
1 TTTTATTAT
112253 TTTTA-TAT
1 TTTTATTAT
*
112261 TTGTATTAT
1 TTTTATTAT
*
112270 GTTTTAATTTTT
1 -TTTT-A-TTAT
112282 TTTTATTA-
1 TTTTATTAT
112290 TTTTATTAT
1 TTTTATTAT
112299 TATTTATTAT
1 T-TTTATTAT
112309 TTCTTAT
1 TT-TTAT
112316 CTTTTAATAC
Statistics
Matches: 110, Mismatches: 23, Indels: 30
0.67 0.14 0.18
Matches are distributed among these distances:
8 26 0.24
9 22 0.20
10 44 0.40
11 15 0.14
12 3 0.03
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTATTAT
Found at i:112384 original size:58 final size:57
Alignment explanation
Indices: 112312--112427 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 57
112302 TTATTATTTC
112312 TTATCTTTTAATACTAAAATCAGCATAAAAAAAAATTCAAATTTTTTTTATAACTTT
1 TTATCTTTTAATACTAAAATCAGCATAAAAAAAAATTCAAATTTTTTTTATAACTTT
112369 TNTATCTTTTAATACTAAAATCAGCATAAAAAAAAATTCAAATTTTTTTTATAACTTT
1 T-TATCTTTTAATACTAAAATCAGCATAAAAAAAAATTCAAATTTTTTTTATAACTTT
112427 T
1 T
112428 CCTAAAATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 1 0.02
58 57 0.98
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (57 bp):
TTATCTTTTAATACTAAAATCAGCATAAAAAAAAATTCAAATTTTTTTTATAACTTT
Found at i:112652 original size:7 final size:7
Alignment explanation
Indices: 112640--112687 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
112630 AACCTTTTCC
112640 TTCTTTT
1 TTCTTTT
112647 TTCTTTT
1 TTCTTTT
112654 TTCTTTT
1 TTCTTTT
112661 CTT-TTCTT
1 -TTCTT-TT
*
112669 TTCCTTT
1 TTCTTTT
*
112676 TTCTTTC
1 TTCTTTT
112683 TTCTT
1 TTCTT
112688 CTCTCCCAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
7 30 0.86
8 5 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TTCTTTT
Found at i:112676 original size:22 final size:22
Alignment explanation
Indices: 112639--112689 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
112629 AAACCTTTTC
*
112639 CTTCTT-TTTTCTTTTTTCTTTT
1 CTTCTTCTTTTCCTTTTTC-TTT
112661 CTT-TTCTTTTCCTTTTTCTTT
1 CTTCTTCTTTTCCTTTTTCTTT
112682 CTTCTTCT
1 CTTCTTCT
112690 CTCCCAGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (22 bp):
CTTCTTCTTTTCCTTTTTCTTT
Found at i:112677 original size:17 final size:17
Alignment explanation
Indices: 112633--112681 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
112623 GACCCAAAAC
*
112633 CTTTTCCTTCTT-TTTT
1 CTTTTCCTTTTTCTTTT
*
112649 CTTTT-TTCTTTTCTTTT
1 CTTTTCCT-TTTTCTTTT
112666 CTTTTCCTTTTTCTTT
1 CTTTTCCTTTTTCTTT
112682 CTTCTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 1 0.04
16 8 0.30
17 17 0.63
18 1 0.04
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
CTTTTCCTTTTTCTTTT
Found at i:112771 original size:14 final size:14
Alignment explanation
Indices: 112750--112790 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
112740 CCTTTTTTCC
112750 CTCTTTCTT-TTTT
1 CTCTTTCTTCTTTT
112763 -T-TTTCTTCTTTT
1 CTCTTTCTTCTTTT
112775 CTCTTTCTTCTTTT
1 CTCTTTCTTCTTTT
112789 CT
1 CT
112791 TTCTCCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.24
12 5 0.20
13 1 0.04
14 13 0.52
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTCTTTCTTCTTTT
Found at i:112779 original size:25 final size:26
Alignment explanation
Indices: 112750--112800 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
112740 CCTTTTTTCC
* *
112750 CTCTTTCTT-TTTTTTTTCTTCTTTT
1 CTCTTTCTTCTTTTCTTTCTCCTTTT
112775 CTCTTTCTTCTTTTCTTTCTCCTTTT
1 CTCTTTCTTCTTTTCTTTCTCCTTTT
112801 TCCTCTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (26 bp):
CTCTTTCTTCTTTTCTTTCTCCTTTT
Found at i:112986 original size:22 final size:22
Alignment explanation
Indices: 112939--112986 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
112929 TGTTGTTTGA
** *
112939 TTGTGGCTTTTTGGTTGGTGTT
1 TTGTGGCTTTTTGGTTAATGTG
112961 TTGTGGCTTTTTGGATTAAT-TG
1 TTGTGGCTTTTTGG-TTAATGTG
112983 TTGT
1 TTGT
112987 TGTTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.06, C:0.04, G:0.31, T:0.58
Consensus pattern (22 bp):
TTGTGGCTTTTTGGTTAATGTG
Found at i:113241 original size:5 final size:5
Alignment explanation
Indices: 113209--113269 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
113199 GCCATTCCTC
* * *
113209 TTTTT TTTTA TTATTA -TATA TATTA TTTTA TTTTA TATTATA TTTTA
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA T-TT-TA TTTTA
*
113256 TTTTA TTATA TTTT
1 TTTTA TTTTA TTTT
113270 TTTATTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
4 2 0.04
5 33 0.73
6 7 0.16
7 3 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:113244 original size:22 final size:23
Alignment explanation
Indices: 113209--113267 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
113199 GCCATTCCTC
*
113209 TTTTTTTTTATTATTATATATATTA
1 TTTTATTTTATTA-T-TATATATTA
*
113234 TTTTATTTTA-TATTATATTTTA
1 TTTTATTTTATTATTATATATTA
*
113256 TTTTATTATATT
1 TTTTATTTTATT
113268 TTTTTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 17 0.57
23 2 0.07
24 2 0.07
25 9 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTATTTTATTATTATATATTA
Found at i:113279 original size:17 final size:18
Alignment explanation
Indices: 113211--113276 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 18
113201 CATTCCTCTT
113211 TTTTTTTATTATTATATATA
1 TTTTTTTATT-TTAT-TATA
*
113231 TTATTTTATTTTA-TAT-
1 TTTTTTTATTTTATTATA
*
113247 TATATTTTATTTTATTATA
1 T-TTTTTTATTTTATTATA
113266 TTTTTTTATTT
1 TTTTTTTATTT
113277 ATTGAGGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.02
17 15 0.37
18 12 0.29
19 4 0.10
20 9 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTATTTTATTATA
Done.