Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007841.1 Hibiscus syriacus cultivar Beakdansim tig00110195_pilon, whole genome shotgun sequence
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: 1873963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:1585 original size:20 final size:19
Alignment explanation
Indices: 1540--1642 Score: 64
Period size: 20 Copynumber: 5.8 Consensus size: 19
1530 TCTTTTGGTT
1540 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1559 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
1580 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
1599 G--A-G--AATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1613 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1627 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1643 TGCGATTTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
14 23 0.34
16 2 0.03
17 2 0.03
19 11 0.16
20 28 0.41
21 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1608 original size:14 final size:14
Alignment explanation
Indices: 1589--1625 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1579 GGAAATGACT
*
1589 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
1603 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1617 ATCGCAACG
1 ATCGCAACG
1626 CGAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.27, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1665 original size:19 final size:19
Alignment explanation
Indices: 1643--1690 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1633 AAAATCGCAA
*
1643 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
1662 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
1682 TGCGATTTT
1 TGCGATTTT
1691 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:2233 original size:20 final size:20
Alignment explanation
Indices: 2208--2319 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
2198 GCTATGTAAA
2208 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
2228 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
2248 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* * ** *
2269 TCGTATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
2289 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
2309 TCGCATTGCGA
1 TCGCATTGCGA
2320 ATTATGAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.74
21 17 0.22
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:2276 original size:21 final size:20
Alignment explanation
Indices: 2226--2319 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
2216 CGATAGTAAG
*
2226 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
2246 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
* *
2266 AATTCGTATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACCT
* * *
2287 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
2307 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2320 ATTATGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:2332 original size:41 final size:41
Alignment explanation
Indices: 2205--2457 Score: 149
Period size: 41 Copynumber: 6.2 Consensus size: 41
2195 GGCGCTATGT
* * * *
2205 AAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATTTACG-
1 AAATCGCATTGCGAT-TTACGTATTCGCATTGCGAATTAGGA
* * * * * * **
2245 TATTCGCATTGCGATTTTCCTAATTCGTATTGCGATTTA-CT
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTAGGA
* * *
2286 TAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
** * * *
2327 AAATCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTAGGA
* * * * ***
2368 AAATTGCATTGCGATAGT-CAGTA-TCGCATTACGATTTTTCA
1 AAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAATTAGGA
* * *
2409 AATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
2450 AAATCGCA
1 AAATCGCA
2458 ACGCGAAATT
Statistics
Matches: 159, Mismatches: 44, Indels: 19
0.72 0.20 0.09
Matches are distributed among these distances:
39 1 0.01
40 36 0.23
41 117 0.74
42 2 0.01
43 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (41 bp):
AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
Found at i:2340 original size:21 final size:21
Alignment explanation
Indices: 2316--2371 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2306 TATTCGCATT
*
2316 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
2337 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
2357 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
2372 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:2380 original size:21 final size:21
Alignment explanation
Indices: 2309--2381 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
2299 ATTTACGTAT
* *
2309 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
2330 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
2350 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
2371 TTGCATTGCGA
1 TCGCAATGCGA
2382 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:2484 original size:21 final size:22
Alignment explanation
Indices: 2432--2484 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2422 ATTTACTTAT
2432 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2453 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2474 TCGCATTGCGA
1 TCGCATTGCGA
2485 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:28951 original size:76 final size:74
Alignment explanation
Indices: 28822--28967 Score: 247
Period size: 76 Copynumber: 1.9 Consensus size: 74
28812 TGGCAAAGCT
*
28822 TTGAATAGGAGTTGTGTTTGTGAACTAACCGCAACTAGTGTTTTGTATCATATATTATTTTTGGT
1 TTGAATAGGAGTTGTGTTTGTGAACTAACCACAACTAGTGTTTTGTATCATATATTATTTTTGGT
28887 TCGTAGCCA
66 TCGTAGCCA
* *
28896 TTGAATAGCGAGTTGTGTTTGTGAACTAGCCACTAATTAGTGTTTTGTATCATATATTATTTTTG
1 TTGAATAG-GAGTTGTGTTTGTGAACTAACCAC-AACTAGTGTTTTGTATCATATATTATTTTTG
28961 GTTCGTA
64 GTTCGTA
28968 TTAATAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 8 0.12
75 22 0.33
76 37 0.55
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (74 bp):
TTGAATAGGAGTTGTGTTTGTGAACTAACCACAACTAGTGTTTTGTATCATATATTATTTTTGGT
TCGTAGCCA
Found at i:34872 original size:116 final size:116
Alignment explanation
Indices: 34668--34900 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
34658 CATAGATGAC
34668 TCTGCACTAGTGAGAGACTAAAGCATGTAGGTTAATATGGAACAAGTGTTCTTACTACCCTGGTA
1 TCTGCACTAGTGAGAGACTAAAGCATGTAGGTTAATATGGAACAAGTGTTCTTACTACCCTGGTA
34733 TATATGTATTGCATGATGTAGGATAATCCTAGCACCATTTACAATCTCCAA
66 TATATGTATTGCATGATGTAGGATAATCCTAGCACCATTTACAATCTCCAA
34784 TCTGCACTAGTGAGAGACTAAAGCATGTAGGTTAATATGGAACAAGTGTTCTTACTACCCTGGTA
1 TCTGCACTAGTGAGAGACTAAAGCATGTAGGTTAATATGGAACAAGTGTTCTTACTACCCTGGTA
34849 TATATGTATTGCATGATGTAGGATAATCCTAGCACCATTTACAATCTCCAA
66 TATATGTATTGCATGATGTAGGATAATCCTAGCACCATTTACAATCTCCAA
34900 T
1 T
34901 GCAGGACATG
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (116 bp):
TCTGCACTAGTGAGAGACTAAAGCATGTAGGTTAATATGGAACAAGTGTTCTTACTACCCTGGTA
TATATGTATTGCATGATGTAGGATAATCCTAGCACCATTTACAATCTCCAA
Found at i:42014 original size:236 final size:233
Alignment explanation
Indices: 41549--42017 Score: 868
Period size: 236 Copynumber: 2.0 Consensus size: 233
41539 TGGTCACCAC
* *
41549 CCAACAAGCCTCAAAGCAGCAACAGCAGCAGTTAAACGTAGACCCAAGAATGTAAAATCCGGCCT
1 CCAACAAGCCTCAAAACAGCAACAGCAGCAGATAAACGTAGACCCAAGAATGTAAAATCCGGCCT
41614 TAACAGTGTTTTTATTTCTGAATTAAAGTTCTGTAAATATGATGATCTCAGGAAGGGTATTGCCA
66 TAACAGTGTTTTTATTTCTGAATTAAAGTTCTGTAAATATGATGATCTCAGGAAGGGTATTGCCA
41679 TCTGTAGGAGTACGATGCCAACCGAATACATATCAAATAGATCAGGACTGTTGAGTTGTAACAAT
131 TCTGTAGGAGTACGATGCCAACCGAATACATATCAAATAGATCAGGACTGTTGAGTTGTAACAAT
41744 AATTACAAATTACATATCGATACATTCATTGCTATAAA
196 AATTACAAATTACATATCGATACATTCATTGCTATAAA
*
41782 CCAACAAGCCTCAAAACAGCAACAGCA-CAGATAAACGTAGACCCAAGATTGTAAAATCCGGCCT
1 CCAACAAGCCTCAAAACAGCAACAGCAGCAGATAAACGTAGACCCAAGAATGTAAAATCCGGCCT
41846 TAACAGTGTTTTTATTTCTGAATTAAAGTTCTGTAAATATGATGATGATCTCAGGAAGGGTATTG
66 TAACAGTGTTTTTATTTCTGAATTAAAGTTCTGT-AA-AT-ATGATGATCTCAGGAAGGGTATTG
41911 CCATCTGTAGGAGTACGATGCCAACTCGAATACATATCAAATAGATCAGGACTGTTGAGTTGTAA
128 CCATCTGTAGGAGTACGATGCCAAC-CGAATACATATCAAATAGATCAGGACTGTTGAGTTGTAA
41976 CAATAATTACAAATTACATATCGATACATTCATTGCTATAAA
192 CAATAATTACAAATTACATATCGATACATTCATTGCTATAAA
42018 GGAAACGAGA
Statistics
Matches: 229, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
232 69 0.30
233 28 0.12
234 2 0.01
235 49 0.21
236 81 0.35
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (233 bp):
CCAACAAGCCTCAAAACAGCAACAGCAGCAGATAAACGTAGACCCAAGAATGTAAAATCCGGCCT
TAACAGTGTTTTTATTTCTGAATTAAAGTTCTGTAAATATGATGATCTCAGGAAGGGTATTGCCA
TCTGTAGGAGTACGATGCCAACCGAATACATATCAAATAGATCAGGACTGTTGAGTTGTAACAAT
AATTACAAATTACATATCGATACATTCATTGCTATAAA
Found at i:58864 original size:4 final size:4
Alignment explanation
Indices: 58855--59857 Score: 1964
Period size: 4 Copynumber: 252.2 Consensus size: 4
58845 CCTCTTACTC
58855 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58903 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58951 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58999 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59047 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59095 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59143 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59191 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59237 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59283 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59331 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59379 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59427 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59475 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59523 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59571 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59619 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59667 ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59713 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59761 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59809 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
59857 A
1 A
59858 AAAAGTTTTA
Statistics
Matches: 993, Mismatches: 0, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
2 6 0.01
4 987 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:66295 original size:5 final size:5
Alignment explanation
Indices: 66285--66313 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
66275 TTAAACATGC
66285 TTGTA TTGTA TTGTA TTGTA TTGTA TTGT
1 TTGTA TTGTA TTGTA TTGTA TTGTA TTGT
66314 GTCTAAGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.21, T:0.62
Consensus pattern (5 bp):
TTGTA
Found at i:68533 original size:65 final size:65
Alignment explanation
Indices: 68373--68533 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
68363 TTGTTTAAGG
* * * **
68373 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
68436 A
65 A
*
68437 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
68501 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
68534 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:70205 original size:149 final size:148
Alignment explanation
Indices: 69948--70261 Score: 495
Period size: 149 Copynumber: 2.1 Consensus size: 148
69938 GATTCGAGGG
* * * * * *
69948 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* * *
70013 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTAGGGACATTATTAT
70078 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
70096 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
70161 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTAGGGACATTATTA
70226 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
70245 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
70262 TGCAATTATA
Statistics
Matches: 152, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
148 49 0.32
149 103 0.68
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTAGGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:70262 original size:23 final size:23
Alignment explanation
Indices: 70229--70273 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
70219 ATTATTATAT
*
70229 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
70252 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
70274 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:71667 original size:24 final size:24
Alignment explanation
Indices: 71640--71693 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
71630 AGATCTGCAA
71640 TGGATCTGGATATAGTTGCATATT
1 TGGATCTGGATATAGTTGCATATT
71664 TGGATCTGGATATAGTTGCATATT
1 TGGATCTGGATATAGTTGCATATT
71688 TGGATC
1 TGGATC
71694 ATAGTAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (24 bp):
TGGATCTGGATATAGTTGCATATT
Found at i:73770 original size:65 final size:65
Alignment explanation
Indices: 73610--73770 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
73600 TTGTTTAAGG
* * * ** *
73610 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCAAATAGGATTT
73673 A
65 A
*
73674 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCAAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCAAATAGGATTTA
*
73738 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
73771 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCAAATAGGATTTA
Found at i:75449 original size:149 final size:148
Alignment explanation
Indices: 75177--75490 Score: 479
Period size: 149 Copynumber: 2.1 Consensus size: 148
75167 GAGTCGAGGG
* * * * * * * *
75177 TCTACGCGGTCCTTCAGGACATATGTATATTTTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
75242 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGTGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGTGACATTATTAT
75307 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
75325 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
75390 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTA-TGGACATTATT
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGT-GACATTATT
75454 ATATGGCACTACGGTGCAAT
129 ATATGGCACTACGGTGCAAT
75474 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
75491 TGCAATTATA
Statistics
Matches: 151, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
148 48 0.32
149 103 0.68
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGTGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:75491 original size:23 final size:23
Alignment explanation
Indices: 75458--75502 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
75448 ATTATTATAT
*
75458 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
75481 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
75503 AGATGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:76853 original size:31 final size:35
Alignment explanation
Indices: 76781--76861 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 35
76771 ACCCCGATTA
*
76781 TATATATATAATATTTTATATTTTTGTATATTAAT
1 TATATATATAATATTATATATTTTTGTATATTAAT
76816 TATATATAT-ATA-TATATA-TTTT-TATATTAAT
1 TATATATATAATATTATATATTTTTGTATATTAAT
*
76847 TATATATAAAATATT
1 TATATATATAATATT
76862 TTTGGGTTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 17 0.40
32 7 0.17
33 6 0.14
34 3 0.07
35 9 0.21
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (35 bp):
TATATATATAATATTATATATTTTTGTATATTAAT
Found at i:90105 original size:15 final size:15
Alignment explanation
Indices: 90085--90117 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
90075 AACCCGACCC
*
90085 GACCCGTTGATCGTT
1 GACCCGTTGACCGTT
90100 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
90115 GAC
1 GAC
90118 TGGAGTTGAC
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:0.15, C:0.30, G:0.27, T:0.27
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:91252 original size:18 final size:18
Alignment explanation
Indices: 91226--91260 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
91216 TCGAAAGGAC
*
91226 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
91244 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
91261 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:94959 original size:13 final size:13
Alignment explanation
Indices: 94958--94998 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
94948 CCGTTTACCC
94958 GACCCGACCCGTT
1 GACCCGACCCGTT
*
94971 TACCCGACCCGTT
1 GACCCGACCCGTT
94984 GACCCGACCCGTT
1 GACCCGACCCGTT
94997 GA
1 GA
94999 TCGTTGACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.17, C:0.44, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:94994 original size:18 final size:18
Alignment explanation
Indices: 94936--94981 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
94926 ACCGGTCACA
94936 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
94954 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
94972 ACCCGACCCG
1 ACCCGACCCG
94982 TTGACCCGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:95009 original size:15 final size:15
Alignment explanation
Indices: 94976--95021 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
94966 CCGTTTACCC
*
94976 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
*
94989 GACCCGTTGATCGTT
1 GACCCGTTGACCGTT
95004 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
95019 GAC
1 GAC
95022 TGGAGTTGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.39
15 17 0.61
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:96158 original size:18 final size:18
Alignment explanation
Indices: 96132--96166 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96122 TCGAAAGGAC
*
96132 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
96150 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
96167 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:99860 original size:13 final size:13
Alignment explanation
Indices: 99859--99899 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
99849 CCGTTTACCC
99859 GACCCGACCCGTT
1 GACCCGACCCGTT
*
99872 TACCCGACCCGTT
1 GACCCGACCCGTT
99885 GACCCGACCCGTT
1 GACCCGACCCGTT
99898 GA
1 GA
99900 TCGTTGACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.17, C:0.44, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:99895 original size:18 final size:18
Alignment explanation
Indices: 99837--99882 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
99827 ACCGGTCACA
99837 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
99855 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
99873 ACCCGACCCG
1 ACCCGACCCG
99883 TTGACCCGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:99910 original size:15 final size:15
Alignment explanation
Indices: 99877--99922 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
99867 CCGTTTACCC
*
99877 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
*
99890 GACCCGTTGATCGTT
1 GACCCGTTGACCGTT
99905 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
99920 GAC
1 GAC
99923 TGGAGTTGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.39
15 17 0.61
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:101059 original size:18 final size:18
Alignment explanation
Indices: 101033--101067 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
101023 TCGAAAGGAC
*
101033 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
101051 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
101068 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:105947 original size:36 final size:36
Alignment explanation
Indices: 105888--106032 Score: 200
Period size: 36 Copynumber: 4.0 Consensus size: 36
105878 TCATTTTATT
* * ** *
105888 TAAAATTCAAACTCTATAATTATCTTCAGCAGCTAA
1 TAAAATTCAAATTCCAGCATTATCTTCAGCAACTAA
* * *
105924 TAAATTTCAAATTCCAACCTTATCTTCAGCAACTAA
1 TAAAATTCAAATTCCAGCATTATCTTCAGCAACTAA
* *
105960 TAAAATTCAAATTCCAGTATTATCTTCAGCAGCTAA
1 TAAAATTCAAATTCCAGCATTATCTTCAGCAACTAA
105996 TAAAATTCAAATTCCAGCATTATCTTCAGCAACTAA
1 TAAAATTCAAATTCCAGCATTATCTTCAGCAACTAA
106032 T
1 T
106033 CAATTCCTAA
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (36 bp):
TAAAATTCAAATTCCAGCATTATCTTCAGCAACTAA
Found at i:106005 original size:72 final size:72
Alignment explanation
Indices: 105888--106032 Score: 229
Period size: 72 Copynumber: 2.0 Consensus size: 72
105878 TCATTTTATT
* * *
105888 TAAAATTCAAACTCTATAATTATCTTCAGCAGCTAATAAATTTCAAATTCCAACCTTATCTTCAG
1 TAAAATTCAAACTCCATAATTATCTTCAGCAGCTAATAAAATTCAAATTCCAACATTATCTTCAG
105953 CAACTAA
66 CAACTAA
* *
105960 TAAAATTCAAATTCCAGT-ATTATCTTCAGCAGCTAATAAAATTCAAATTCCAGCATTATCTTCA
1 TAAAATTCAAACTCCA-TAATTATCTTCAGCAGCTAATAAAATTCAAATTCCAACATTATCTTCA
106024 GCAACTAA
65 GCAACTAA
106032 T
1 T
106033 CAATTCCTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
72 66 0.99
73 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (72 bp):
TAAAATTCAAACTCCATAATTATCTTCAGCAGCTAATAAAATTCAAATTCCAACATTATCTTCAG
CAACTAA
Found at i:106493 original size:32 final size:31
Alignment explanation
Indices: 106434--106497 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 31
106424 TCGTATTTTC
106434 AATATTTTTTTATTAATTTTTTTATAATTTA
1 AATATTTTTTTATTAATTTTTTTATAATTTA
106465 AATATTTTATTTA-T-ATTTTTATTAATAATTTA
1 AATATTTT-TTTATTAATTTTT-TT-ATAATTTA
106497 A
1 A
106498 TTTTACACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 6 0.20
31 11 0.37
32 13 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (31 bp):
AATATTTTTTTATTAATTTTTTTATAATTTA
Found at i:122275 original size:13 final size:14
Alignment explanation
Indices: 122256--122288 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
122246 TGGGAATCTA
*
122256 AATTTAATTTAATT
1 AATTTAATATAATT
122270 -ATTTAATATAATT
1 AATTTAATATAATT
122283 AATTTA
1 AATTTA
122289 GGATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATATAATT
Found at i:122767 original size:21 final size:21
Alignment explanation
Indices: 122742--122797 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
122732 AAAGTTAAAT
122742 TTTTAGATAGATTTTCATCGA
1 TTTTAGATAGATTTTCATCGA
* *
122763 TTTTAGATAGATGTTCGTCGA
1 TTTTAGATAGATTTTCATCGA
122784 TTTTA-AGTAGATTT
1 TTTTAGA-TAGATTT
122798 AATTAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (21 bp):
TTTTAGATAGATTTTCATCGA
Found at i:126838 original size:137 final size:137
Alignment explanation
Indices: 126674--127115 Score: 720
Period size: 137 Copynumber: 3.3 Consensus size: 137
126664 TTAGGAAATG
*
126674 AAATAA-GGAA-G-GCGCCCCCGGGAACGCGCCTTCACCACTTTGCCAAATCCCCTCATAAATAA
1 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACCACTTTGCCAAGTCCCCTCATAAATAA
*
126736 TAGGTACTGACATGAATAGTTCTCCGGGGGCATGAGTGACATAATATGGCAATGATAACATATTC
66 TAGGTACTGACATGAATAGTTCTTCGGGGGCATGAGTGACATAATATGGCAATGATAACATATTC
126801 TCTGACA
131 TCTGACA
* * *
126808 AAATAATGGAAGGCACCCCCCCGGGAACGCGCCTTCACCACTTTGCCAAGTCCCCTCAGAAATAA
1 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACCACTTTGCCAAGTCCCCTCATAAATAA
*
126873 TAGGTACTGACATGAATAGTTCTTTGGGGGACATGAGTGACATAATATGGCAATGATAACATATT
66 TAGGTACTGACATGAATAGTTCTTCGGGGG-CATGAGTGACATAATATGGCAATGATAACATATT
126938 CTCTGACA
130 CTCTGACA
126946 AAATAATGGAAGGCGCGCCCCC-GGAACGCGCCTTCACCACTTTGCCAAGTCCCCTCATAAATAA
1 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACCACTTTGCCAAGTCCCCTCATAAATAA
* *
127010 TAGGTACTGACATGAATAGTTTTTC--GGGCATGAGTGACATAATAGGGCAATGATAACATATTC
66 TAGGTACTGACATGAATAGTTCTTCGGGGGCATGAGTGACATAATATGGCAATGATAACATATTC
*
127073 TCTGA-T
131 TCTGACA
* *
127079 AAA-AATGGAAAGCGCGCCCCCGAGAACGCGCCTTCAC
1 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAC
127116 TTGAATAGTA
Statistics
Matches: 288, Mismatches: 15, Indels: 11
0.92 0.05 0.04
Matches are distributed among these distances:
132 17 0.06
133 17 0.06
134 45 0.16
135 7 0.02
136 1 0.00
137 139 0.48
138 62 0.22
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (137 bp):
AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACCACTTTGCCAAGTCCCCTCATAAATAA
TAGGTACTGACATGAATAGTTCTTCGGGGGCATGAGTGACATAATATGGCAATGATAACATATTC
TCTGACA
Found at i:130004 original size:21 final size:21
Alignment explanation
Indices: 129978--130019 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
129968 AATAATTAAT
*
129978 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
129999 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
130020 TAATATTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:133844 original size:12 final size:12
Alignment explanation
Indices: 133827--133893 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 12
133817 TATACAGTTA
133827 AAAATATTATTT
1 AAAATATTATTT
133839 AAAATATTA-TT
1 AAAATATTATTT
*
133850 ---AT-TTTTTT
1 AAAATATTATTT
* * *
133858 AATATTTTATGT
1 AAAATATTATTT
*
133870 AAAACATTATTT
1 AAAATATTATTT
133882 AAAATATTATTT
1 AAAATATTATTT
133894 TTTACCGAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
11 4 0.10
12 32 0.76
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (12 bp):
AAAATATTATTT
Found at i:133858 original size:43 final size:42
Alignment explanation
Indices: 133811--133896 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 42
133801 TGTACCACAA
*
133811 TTTTAATA-TACA-GTTAAAAATATTATTTAAAATATTATTATTT
1 TTTTAATATTACATG-T-AAAACATTATTTAAAATATTATT-TTT
**
133854 TTTTAATATTTTATGTAAAACATTATTTAAAATATTATTTTT
1 TTTTAATATTACATGTAAAACATTATTTAAAATATTATTTTT
133896 T
1 T
133897 ACCGAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 4 0.11
43 30 0.79
44 3 0.08
45 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (42 bp):
TTTTAATATTACATGTAAAACATTATTTAAAATATTATTTTT
Found at i:136026 original size:25 final size:25
Alignment explanation
Indices: 135992--136044 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
135982 AATAAGAAGG
*
135992 TAAATGAATAAGACAGGTAAATGAA
1 TAAATGAATAAGACAGGTAAATAAA
136017 TAAATGAATAAGACAGGTAAATAAA
1 TAAATGAATAAGACAGGTAAATAAA
136042 TAA
1 TAA
136045 GATTTCACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (25 bp):
TAAATGAATAAGACAGGTAAATAAA
Found at i:136038 original size:17 final size:17
Alignment explanation
Indices: 135972--136019 Score: 89
Period size: 16 Copynumber: 2.9 Consensus size: 17
135962 TTTATGATTT
135972 CAGGTAAATGAATAAGA
1 CAGGTAAATGAATAAGA
135989 -AGGTAAATGAATAAGA
1 CAGGTAAATGAATAAGA
136005 CAGGTAAATGAATAA
1 CAGGTAAATGAATAA
136020 ATGAATAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19
Consensus pattern (17 bp):
CAGGTAAATGAATAAGA
Found at i:141577 original size:25 final size:23
Alignment explanation
Indices: 141520--141579 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 23
141510 AATCCCAAAT
*
141520 TTAAATATATATACATTTACATT
1 TTAAATATATATACATTTACATA
141543 TGTAAGATATATATACATTATTA-ATAA
1 T-TAA-ATATATATACA-T-TTACAT-A
141570 TTAAATATAT
1 TTAAATATAT
141580 TATAATGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 17 0.55
26 6 0.19
27 4 0.13
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (23 bp):
TTAAATATATATACATTTACATA
Found at i:141961 original size:23 final size:22
Alignment explanation
Indices: 141931--142119 Score: 193
Period size: 23 Copynumber: 8.4 Consensus size: 22
141921 TTCTGAACAA
* *
141931 TTCTTCTTCTATAAACAAGTTTC
1 TTCTTCTTCCATAAACCA-TTTC
141954 TTCTTCTTCCATAAA-CATTTTC
1 TTCTTCTTCCATAAACCA-TTTC
* *
141976 TTCTTCCTCCATAAACGCATTGC
1 TTCTTCTTCCATAAAC-CATTTC
*
141999 TGCTTCTTCCATAAACTCATTTC
1 TTCTTCTTCCATAAAC-CATTTC
* ** *
142022 TTCTT-ATAAATAAACCTCTTTC
1 TTCTTCTTCCATAAACC-ATTTC
*
142044 TTCTTTTTCCATAAACCATTTC
1 TTCTTCTTCCATAAACCATTTC
* *
142066 TTTTTCTTCCATAAACCCGTTTC
1 TTCTTCTTCCATAAA-CCATTTC
142089 TTCTTCTTCCATAAACCTATTTC
1 TTCTTCTTCCATAAACC-ATTTC
142112 TTCTTCTT
1 TTCTTCTT
142120 TCATTAGTCT
Statistics
Matches: 137, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.01
22 54 0.39
23 80 0.58
24 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.03, T:0.47
Consensus pattern (22 bp):
TTCTTCTTCCATAAACCATTTC
Found at i:141990 original size:45 final size:46
Alignment explanation
Indices: 141931--142119 Score: 190
Period size: 45 Copynumber: 4.2 Consensus size: 46
141921 TTCTGAACAA
* *
141931 TTCTTCTTCTATAAACAAGTTTCTTCTTCTTCCATAAACAT-TTTC
1 TTCTTCTTCCATAAACCAGTTTCTTCTTCTTCCATAAACATATTTC
* * *
141976 TTCTTCCTCCATAAACGCA-TTGCTGCTTCTTCCATAAAC-TCATTTC
1 TTCTTCTTCCATAAAC-CAGTTTCTTCTTCTTCCATAAACAT-ATTTC
* ** ** * *
142022 TTCTT-ATAAATAAACCTCTTTCTTCTTTTTCCATAAAC-CATTTC
1 TTCTTCTTCCATAAACCAGTTTCTTCTTCTTCCATAAACATATTTC
* * *
142066 TTTTTCTTCCATAAACCCGTTTCTTCTTCTTCCATAAACCTATTTC
1 TTCTTCTTCCATAAACCAGTTTCTTCTTCTTCCATAAACATATTTC
142112 TTCTTCTT
1 TTCTTCTT
142120 TCATTAGTCT
Statistics
Matches: 116, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
44 11 0.09
45 83 0.72
46 22 0.19
ACGTcount: A:0.22, C:0.28, G:0.03, T:0.47
Consensus pattern (46 bp):
TTCTTCTTCCATAAACCAGTTTCTTCTTCTTCCATAAACATATTTC
Found at i:142095 original size:90 final size:90
Alignment explanation
Indices: 141950--142116 Score: 239
Period size: 90 Copynumber: 1.9 Consensus size: 90
141940 TATAAACAAG
*
141950 TTTCTTCTTCTTCCATAAACATTTTCTTCTTCCTCCATAAACGCATTGCTGCTTCTTCCATAAA-
1 TTTCTTCTTCTTCCATAAACATTTTCTTCTTCCTCCATAAACCCATTGCTGCTTCTTCCATAAAC
142014 CTCATTTCTTCTTATAAATAAACCTC
66 CT-ATTTCTTCTTATAAATAAACCTC
* * * * * *
142040 TTTCTTCTTTTTCCATAAACCA-TTTCTTTTTCTTCCATAAACCCGTTTCTTCTTCTTCCATAAA
1 TTTCTTCTTCTTCCATAAA-CATTTTCTTCTTCCTCCATAAACCCATTGCTGCTTCTTCCATAAA
142104 CCTATTTCTTCTT
65 CCTATTTCTTCTT
142117 CTTTCATTAG
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
90 64 0.94
91 4 0.06
ACGTcount: A:0.22, C:0.29, G:0.02, T:0.47
Consensus pattern (90 bp):
TTTCTTCTTCTTCCATAAACATTTTCTTCTTCCTCCATAAACCCATTGCTGCTTCTTCCATAAAC
CTATTTCTTCTTATAAATAAACCTC
Found at i:148880 original size:18 final size:19
Alignment explanation
Indices: 148839--148881 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
148829 TTGGTTTACG
148839 GAATATAAGATTACCAGTGA
1 GAATATAAGATTACCAG-GA
*
148859 GAATGTAAGATTACCA-GA
1 GAATATAAGATTACCAGGA
148877 GAATA
1 GAATA
148882 GGATTACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (19 bp):
GAATATAAGATTACCAGGA
Found at i:155638 original size:24 final size:24
Alignment explanation
Indices: 155611--155703 Score: 118
Period size: 24 Copynumber: 3.9 Consensus size: 24
155601 CAAGAGTCGA
* *
155611 AAATTCTACGCGGTCCTTCGAGAC
1 AAATTCTACGTGGTCCTTCGGGAC
*
155635 AAATTTCTACGTGGTCCTCCGGGAC
1 AAA-TTCTACGTGGTCCTTCGGGAC
155660 AAATTCTACGTGGTCCTTCGGGAC
1 AAATTCTACGTGGTCCTTCGGGAC
*
155684 AAA-TCTATGTGG-CACTTCGG
1 AAATTCTACGTGGTC-CTTCGG
155704 TGCATATTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.02
23 14 0.23
24 26 0.42
25 21 0.34
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (24 bp):
AAATTCTACGTGGTCCTTCGGGAC
Found at i:155718 original size:24 final size:24
Alignment explanation
Indices: 155689--155739 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
155679 GGGACAAATC
*
155689 TATGTGGCACTTCGGTGCATATTA
1 TATGTGGCACTTCGGTGCAAATTA
155713 TATGTGGCACTTCGGTGCAAATTA
1 TATGTGGCACTTCGGTGCAAATTA
155737 TAT
1 TAT
155740 TAGCAGTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (24 bp):
TATGTGGCACTTCGGTGCAAATTA
Found at i:156829 original size:29 final size:29
Alignment explanation
Indices: 156782--156837 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
156772 GTGTTGGCCA
*
156782 TAGGTCGCCATGCCTTCCGGGCGACCTTG
1 TAGGTCGCCATACCTTCCGGGCGACCTTG
156811 TAGGTCGCCATACAC-TCCGGGCGACCT
1 TAGGTCGCCATAC-CTTCCGGGCGACCT
156838 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.14, C:0.36, G:0.29, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATACCTTCCGGGCGACCTTG
Found at i:156929 original size:29 final size:29
Alignment explanation
Indices: 156896--156951 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
156886 TCCCAACACA
*
156896 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
156925 TAGGTCGCCATGCACTCTGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
156952 ACCATCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:157003 original size:23 final size:23
Alignment explanation
Indices: 156969--157028 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
156959 CTCGGCTGCC
* * *
156969 CTCGGATTCCCTTGCATATCTCG
1 CTCGGATGCCCTCGCATAGCTCG
156992 CTCGGATGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
157015 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
157029 GATGCTCTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.12, C:0.35, G:0.25, T:0.28
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:157041 original size:20 final size:20
Alignment explanation
Indices: 156992--157069 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
156982 GCATATCTCG
* *
156992 CTCGGATGCCCTCGCATAGCT
1 CTCGGATGGCCTCGGAT-GCT
157013 CGTTCGGATGGCCTCGGATGCT
1 C--TCGGATGGCCTCGGATGCT
*
157035 CTCGGATGGCCTCTGATGCT
1 CTCGGATGGCCTCGGATGCT
*
157055 CTCGGATAGCCTCGG
1 CTCGGATGGCCTCGG
157070 TCGGATGGCC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 31 0.62
21 1 0.02
22 4 0.08
23 14 0.28
ACGTcount: A:0.12, C:0.32, G:0.31, T:0.26
Consensus pattern (20 bp):
CTCGGATGGCCTCGGATGCT
Found at i:157086 original size:10 final size:9
Alignment explanation
Indices: 157016--157069 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 9
157006 CATAGCTCGT
157016 TCGGATGGCC
1 TCGGAT-GCC
157026 TCGGATGCTC
1 TCGGATGC-C
157036 TCGGATGGCC
1 TCGGAT-GCC
*
157046 TCTGATGCTC
1 TCGGATGC-C
157056 TCGGATAGCC
1 TCGGAT-GCC
157066 TCGG
1 TCGG
157070 TCGGATGGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.11, C:0.30, G:0.33, T:0.26
Consensus pattern (9 bp):
TCGGATGCC
Found at i:157163 original size:29 final size:29
Alignment explanation
Indices: 157126--157183 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
157116 GCTATCTCTT
**
157126 GTAGCTCGCGGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
*
157155 GTAGGTCGCCCGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
157184 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:158186 original size:23 final size:22
Alignment explanation
Indices: 158129--158192 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
158119 ATTAATTGTA
* *
158129 TATATTTATAAAAGTATATTAAT
1 TATATTTATAATA-TAAATTAAT
*
158152 TATA-ATATAATATAAATTAATT
1 TATATTTATAATATAAATTAA-T
158174 TATATTTATAATATAAATT
1 TATATTTATAATATAAATT
158193 TTAAATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 7 0.20
22 11 0.31
23 17 0.49
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATATTTATAATATAAATTAAT
Found at i:158206 original size:25 final size:23
Alignment explanation
Indices: 158129--158207 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
158119 ATTAATTGTA
* *
158129 TATATTTATAAAAGTATATT-AAT
1 TATATTTATAATA-TAAATTAAAT
* *
158152 TATA-ATATAATATAAATTAATT
1 TATATTTATAATATAAATTAAAT
158174 TATATTTATAATATAAATTTTAAAT
1 TATATTTATAATATAAA--TTAAAT
*
158199 TATTTTTAT
1 TATATTTAT
158208 TTTTAGTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 5 0.11
22 12 0.27
23 15 0.33
25 13 0.29
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
TATATTTATAATATAAATTAAAT
Found at i:161499 original size:13 final size:13
Alignment explanation
Indices: 161481--161569 Score: 61
Period size: 13 Copynumber: 6.1 Consensus size: 13
161471 CACAACCCGA
161481 CCGACCCGTTGAC
1 CCGACCCGTTGAC
*
161494 CCGACCCGACCGTTTAC
1 CCGA--C--CCGTTGAC
*
161511 CTGACCCGTTGACCC
1 CCGACCCGTTGA--C
161526 GACCCGACCCGTTGAC
1 --CC-GACCCGTTGAC
161542 CCGACCCGTTGAC
1 CCGACCCGTTGAC
*
161555 CGTGACCCGTTGAC
1 C-CGACCCGTTGAC
161569 C
1 C
161570 ATTGACCGGA
Statistics
Matches: 61, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
13 22 0.36
14 14 0.23
15 3 0.05
16 1 0.02
17 11 0.18
18 10 0.16
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:161504 original size:18 final size:18
Alignment explanation
Indices: 161475--161549 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
161465 GACGGTCACA
161475 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
161492 ACCCGACCCGA-CCGTT-
1 ACCCGACCCGACCCGTTG
* *
161508 ----TACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
161522 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
161540 ACCCGACCCG
1 ACCCGACCCG
161550 TTGACCGTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
17 11 0.23
18 26 0.55
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:161519 original size:30 final size:31
Alignment explanation
Indices: 161481--161555 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 31
161471 CACAACCCGA
*
161481 CCGACCCGTTGACCCGACCCGA-CCGTTTAC
1 CCGACCCGTTGACCCGACCCGACCCGTTGAC
*
161511 CTGACCCGTTGACCCGACCCGACCCGTTGAC
1 CCGACCCGTTGACCCGACCCGACCCGTTGAC
161542 CCGACCCGTTGACC
1 CCGACCCGTTGACC
161556 GTGACCCGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 21 0.51
31 20 0.49
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (31 bp):
CCGACCCGTTGACCCGACCCGACCCGTTGAC
Found at i:161563 original size:14 final size:13
Alignment explanation
Indices: 161526--161569 Score: 70
Period size: 13 Copynumber: 3.3 Consensus size: 13
161516 CCGTTGACCC
161526 GACCCGACCCGTT
1 GACCCGACCCGTT
161539 GACCCGACCCGTT
1 GACCCGACCCGTT
*
161552 GACCGTGACCCGTT
1 GACC-CGACCCGTT
161566 GACC
1 GACC
161570 ATTGACCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.16, C:0.43, G:0.25, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:162874 original size:18 final size:18
Alignment explanation
Indices: 162848--162882 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
162838 TCGAAAGGAC
*
162848 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
162866 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
162883 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:191339 original size:114 final size:114
Alignment explanation
Indices: 191136--191357 Score: 345
Period size: 114 Copynumber: 1.9 Consensus size: 114
191126 TCCGTAAGCT
* * * * *
191136 GCCTTACCTTCCATCCCTACCAAGTCTTGCTAGCAGCCGGTGCCGCCGATGCCTGTGTTTCTATC
1 GCCTTACCTTCCATCCCTACCAAGTCTTACTAGCAGACAGTGACACCGATGCCTGTGTTTCTATC
* *
191201 TATGCTGATGACAACTCTCGTACAAGATGAATGTTTGAATTCTTTCACG
66 TATGCTGATGACAACTCTCATACAAGATGAATGCTTGAATTCTTTCACG
* * * *
191250 GCCTTGCCTTCCATCCCTACCAAGTCTTACTAGCTGACAGTGACACTGATGCCTGTGTTTCTTTC
1 GCCTTACCTTCCATCCCTACCAAGTCTTACTAGCAGACAGTGACACCGATGCCTGTGTTTCTATC
191315 TATGCTGATGACAACTCTCATACAAGATGAATGCTTGAATTCT
66 TATGCTGATGACAACTCTCATACAAGATGAATGCTTGAATTCT
191358 AGCAGCACAC
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (114 bp):
GCCTTACCTTCCATCCCTACCAAGTCTTACTAGCAGACAGTGACACCGATGCCTGTGTTTCTATC
TATGCTGATGACAACTCTCATACAAGATGAATGCTTGAATTCTTTCACG
Found at i:200715 original size:4 final size:4
Alignment explanation
Indices: 200682--200708 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
200672 TATATACATA
200682 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
200709 ATATATACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:206790 original size:17 final size:18
Alignment explanation
Indices: 206768--206803 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
206758 TTAATTTCAT
206768 ATTTTAATTTTC-ATTTC
1 ATTTTAATTTTCAATTTC
*
206785 ATTTTATTTTTCAATTTC
1 ATTTTAATTTTCAATTTC
206803 A
1 A
206804 ATTATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTAATTTTCAATTTC
Found at i:221973 original size:2 final size:2
Alignment explanation
Indices: 221968--222004 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
221958 CAAACTAAGT
221968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
222005 CATTTTGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:230446 original size:27 final size:27
Alignment explanation
Indices: 230416--230474 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
230406 TTTAAAATTT
230416 TAAATTTTATTATAAATGAAATTTATC
1 TAAATTTTATTATAAATGAAATTTATC
*
230443 TAAATTTTATTATAAATGAATTTTATC
1 TAAATTTTATTATAAATGAAATTTATC
230470 TAAAT
1 TAAAT
230475 AAAATTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (27 bp):
TAAATTTTATTATAAATGAAATTTATC
Found at i:237838 original size:14 final size:14
Alignment explanation
Indices: 237819--237861 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
237809 TATTCCTTTT
237819 TTATTTATATTATA
1 TTATTTATATTATA
*
237833 TTATTTTTATTATA
1 TTATTTATATTATA
*
237847 -TATATATCATTATA
1 TTATTTAT-ATTATA
237861 T
1 T
237862 ATATATAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:237839 original size:20 final size:20
Alignment explanation
Indices: 237770--237859 Score: 64
Period size: 20 Copynumber: 4.4 Consensus size: 20
237760 TTGTCCCCTA
*
237770 TATATATATTTTTAATTATAT
1 TATAT-TATTTTTATTTATAT
*
237791 T-TATT-TATTTATTTACTA-
1 TATATTATTTTTATTTA-TAT
237809 TAT-TCCT-TTTTTATTTATAT
1 TATAT--TATTTTTATTTATAT
237829 TATATTATTTTTATTATATAT
1 TATATTATTTTTATT-TATAT
237850 ATATCATTAT
1 -TAT-ATTAT
237860 ATATATATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
18 10 0.18
19 7 0.12
20 24 0.43
21 7 0.12
22 3 0.05
23 5 0.09
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATTATTTTTATTTATAT
Found at i:237862 original size:14 final size:14
Alignment explanation
Indices: 237841--237867 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
237831 TATTATTTTT
237841 ATTATATATATATC
1 ATTATATATATATC
237855 ATTATATATATAT
1 ATTATATATATAT
237868 AGATGTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATATATATATC
Found at i:237922 original size:16 final size:16
Alignment explanation
Indices: 237901--237961 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
237891 ACTATTTATA
237901 TATATTTTCTTAATAT
1 TATATTTTCTTAATAT
**
237917 TATATTTTATACGTTTTTAT
1 TATA-TTT-T-C-TTAATAT
237937 ATATATTTTCTTAATAT
1 -TATATTTTCTTAATAT
*
237954 TCTATTTT
1 TATATTTT
237962 TGTTTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
16 11 0.31
17 8 0.23
18 2 0.06
19 2 0.06
20 8 0.23
21 4 0.11
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.64
Consensus pattern (16 bp):
TATATTTTCTTAATAT
Found at i:238008 original size:17 final size:17
Alignment explanation
Indices: 237964--238019 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
237954 TCTATTTTTG
*
237964 TTTTATTTATTTA-TATA
1 TTTTATTT-TTTACTTTA
*
237981 TATTATATTTTTACTTTA
1 TTTTAT-TTTTTACTTTA
237999 TTTTATTTTTT-CTATTA
1 TTTTATTTTTTACT-TTA
238016 TTTT
1 TTTT
238020 TTTAATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 21 0.64
18 10 0.30
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTACTTTA
Found at i:238017 original size:43 final size:44
Alignment explanation
Indices: 237960--238093 Score: 116
Period size: 43 Copynumber: 3.0 Consensus size: 44
237950 ATATTCTATT
*
237960 TTTGTTTTATTTATTTATATATATTATATTTTTACTTTATTTTA
1 TTTGTTTTACTTATTTATATATATTATATTTTTACTTTATTTTA
* * * * *
238004 TTT-TTTCTA-TTATTTTTTTAATATTATGTATAT-CTTTATTTTTTA
1 TTTGTTT-TACTTATTTATAT-ATATTATATTTTTACTTTA--TTTTA
238049 TTTGTTTTACTTAGTATTATATAT-TTATTATTTTTA-TTTATTTTA
1 TTTGTTTTACTTA-T-TTATATATATTA-TATTTTTACTTTATTTTA
238094 GTAAATACTA
Statistics
Matches: 70, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
43 16 0.23
44 15 0.21
45 15 0.21
46 9 0.13
47 11 0.16
48 4 0.06
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (44 bp):
TTTGTTTTACTTATTTATATATATTATATTTTTACTTTATTTTA
Found at i:238047 original size:55 final size:54
Alignment explanation
Indices: 237953--238057 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 54
237943 TTTCTTAATA
*
237953 TTCTATTTTTGTTTTATTTATTTATATATATTATATTTTTACTTTATTTTATTTT
1 TTCTATTTTTGTTTTATTTATGTATATATATTATATTTTTA-TTTATTTTATTTT
* *
238008 TTCTATTATTT-TTTTAATATTATGTATATCT-TTAT-TTTTTATTTGTTTTA
1 TTCTATT-TTTGTTTT-AT-TTATGTATATATATTATATTTTTATTTATTTTA
238058 CTTAGTATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
54 8 0.18
55 17 0.39
56 9 0.20
57 10 0.23
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (54 bp):
TTCTATTTTTGTTTTATTTATGTATATATATTATATTTTTATTTATTTTATTTT
Found at i:238252 original size:26 final size:26
Alignment explanation
Indices: 238217--238279 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
238207 ATTTTATTCA
**
238217 TTTTGTTTATTTTTTATTTTTTACGTG
1 TTTTGTTTATTTTCCATTTTTT-CGTG
*
238244 TTTTG-TTATTTTCCATTTTTTCTTG
1 TTTTGTTTATTTTCCATTTTTTCGTG
*
238269 TTTTATTTATT
1 TTTTGTTTATT
238280 ATTCTCACGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 7 0.23
26 19 0.61
27 5 0.16
ACGTcount: A:0.11, C:0.06, G:0.08, T:0.75
Consensus pattern (26 bp):
TTTTGTTTATTTTCCATTTTTTCGTG
Found at i:241395 original size:12 final size:13
Alignment explanation
Indices: 241360--241397 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
241350 CAATCAGAAC
241360 AAAAAGAGAAAAT
1 AAAAAGAGAAAAT
241373 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
241385 AACAAAG-GAAAAT
1 AA-AAAGAGAAAAT
241398 TGAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:241587 original size:69 final size:69
Alignment explanation
Indices: 241469--241606 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
241459 GATTCAAAAT
* * *
241469 ATGAGATTGATCAAGCACAATCTTTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGAACAATCATTTCCGAATCACTGAACCACTGCACTCGAAGATCATAGAGCA
241534 TCAA
66 TCAA
* *
241538 ATGAGATTGATCAAGAACAATCATTTCTGAATCACTGAATCACTGCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGAACAATCATTTCCGAATCACTGAACCACTGCACTCGAAGATCATAGAGCA
241603 TCAA
66 TCAA
241607 GAGAGAGACA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGAACAATCATTTCCGAATCACTGAACCACTGCACTCGAAGATCATAGAGCA
TCAA
Found at i:243126 original size:37 final size:38
Alignment explanation
Indices: 243071--243145 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
243061 AAAGATTTTA
* * *
243071 TCTCGCTTGAGATAGTTTCCCTTGAAACA-AAATATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
*
243108 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
243146 AAAACATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (38 bp):
TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
Found at i:243219 original size:37 final size:37
Alignment explanation
Indices: 243152--243238 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
243142 ATTGAAAACA
* * * *
243152 TTTCCCTTGAAAC-GAATTTTGTCTCTCTTGAGATAG
1 TTTCCTTTGAAACAAAATTTTGTCTCACTTGAGACAG
243188 TTTCCTTTGAAACAAAATTTTGTCTCACTTGAGACAG
1 TTTCCTTTGAAACAAAATTTTGTCTCACTTGAGACAG
243225 TTT-CTCTTGAAACA
1 TTTCCT-TTGAAACA
243239 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 14 0.31
37 31 0.69
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCTTTGAAACAAAATTTTGTCTCACTTGAGACAG
Found at i:243241 original size:102 final size:102
Alignment explanation
Indices: 243065--243286 Score: 381
Period size: 102 Copynumber: 2.2 Consensus size: 102
243055 TAAAAAAAAG
* * *
243065 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCACTTGAGACAGTTTCTCT
*
243130 TGAAACATAAACATTGAAAACATTTCCCTTGAAACGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
* *
243167 ATTTTGTCTCTCTTGAGATAGTTTCCTTTGAAACAAAATTTTGTCTCACTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCACTTGAGACAGTTTCTCT
*
243232 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
243269 ATTTTGTCTCTCTTGAGA
1 ATTTTGTCTCTCTTGAGA
243287 CAAATTTTGT
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 113 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCACTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
Found at i:243291 original size:21 final size:21
Alignment explanation
Indices: 243267--243309 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
243257 CCCTTGAAAT
243267 AAATTTTGTCTCTCTTGAGAC
1 AAATTTTGTCTCTCTTGAGAC
243288 AAATTTTGTCTCTCTTGAGAC
1 AAATTTTGTCTCTCTTGAGAC
243309 A
1 A
243310 GTTTCCCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (21 bp):
AAATTTTGTCTCTCTTGAGAC
Found at i:243327 original size:36 final size:36
Alignment explanation
Indices: 243280--243464 Score: 145
Period size: 36 Copynumber: 5.3 Consensus size: 36
243270 TTTTGTCTCT
* *
243280 CTTGAGACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCC
* * **
243316 CTTGAAACAAA-----T-TAT-TTGA-ATATGTTTTA
1 CTTGAAACAAATTTCGTCTCTCTTGAGACA-GTTTCC
* * * *
243345 TTTGAAACAAATTTCATCTC-CTTTAAGACAGTTTCT
1 CTTGAAACAAATTTCGTCTCTC-TTGAGACAGTTTCC
* * * * *
243381 TTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAAC-AAATTTCGTCTCTCTTGAGACAGTTTCC
243418 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCC
243454 CTTGAAACAAA
1 CTTGAAACAAA
243465 ATCTTTGAAT
Statistics
Matches: 116, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.02
29 18 0.16
30 2 0.02
31 1 0.01
34 1 0.01
35 1 0.01
36 60 0.52
37 30 0.26
38 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (36 bp):
CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCC
Found at i:243374 original size:86 final size:86
Alignment explanation
Indices: 243202--243374 Score: 188
Period size: 86 Copynumber: 2.0 Consensus size: 86
243192 CTTTGAAACA
* * *
243202 AAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAACATTTCACTTGAAAC
** *
243267 AAATTTTGTCTCTCTTGAGAC
66 AAATTTCATCTCTCTTAAGAC
* ** * ** * *
243288 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AATTATTTGAATATGTTTTATTTGAAA
1 AAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACATAAACA-TTGAAAACATTTCACTTGAAA
243352 CAAATTTCATCTC-CTTTAAGAC
65 CAAATTTCATCTCTC-TTAAGAC
243374 A
1 A
243375 GTTTCTTTTG
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
85 4 0.06
86 67 0.94
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (86 bp):
AAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAACATTTCACTTGAAAC
AAATTTCATCTCTCTTAAGAC
Found at i:243592 original size:67 final size:67
Alignment explanation
Indices: 243426--243597 Score: 208
Period size: 67 Copynumber: 2.6 Consensus size: 67
243416 CTCTTGAAAC
* * * * **
243426 AAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC--AAAATCTTTGAATTTATTTCCCTTAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACAAAAAATCTTCAAATTTATTTCCCTTAAA
243489 AA
66 AA
* **
243491 ATATTTTGTCTCCCTTGAGACAGTTTCTTTTGAAACAAAAAATCTTCAAATTTATTTCCCTTAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACAAAAAATCTTCAAATTTATTTCCCTTAAA
243556 ACA
66 A-A
*
243559 AAATTTTGTTTCCCTTGAGACCA-TTT-TCATGAAACAAAA
1 AAATTTTGTCTCCCTTGAGA-CAGTTTCTCATGAAACAAAA
243598 GATATCTTTG
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 31 0.34
67 37 0.40
68 22 0.24
69 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (67 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACAAAAAATCTTCAAATTTATTTCCCTTAAA
AA
Found at i:244475 original size:110 final size:110
Alignment explanation
Indices: 244277--244534 Score: 301
Period size: 110 Copynumber: 2.4 Consensus size: 110
244267 GCTTCCCAGT
* * ** *
244277 TTCAGAGCCAATTTTAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAACGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * *
244342 CAATGAAGGGGCGACTGATTGTCAACAGACAACTTTTCAGTCTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTCTCA
* *
244387 TTCAGAGTCAATTTCAACTTCACAACGAACGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAACGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * * *
244452 CAGCGAAGGGGCGGCTGGCTGTCAACAAACAA-TTTCCCAGT-TC-
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTT-TCAGTCTCA
* * * * *
244495 --CAGAGCTAATTTCAACTTCACGACGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAACGAACGATATTGAACTC
244535 GGAACAATAC
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
106 34 0.27
109 5 0.04
110 88 0.69
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAACGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTCTCA
Found at i:245920 original size:19 final size:20
Alignment explanation
Indices: 245875--245920 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
245865 TTTTTAATTA
245875 TATTTTTTTATTCACTATAT
1 TATTTTTTTATTCACTATAT
* *
245895 TCCTTTTTTT-TT-ATTATAT
1 T-ATTTTTTTATTCACTATAT
245914 TATTTTT
1 TATTTTT
245921 ATATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 5 0.23
19 7 0.32
20 3 0.14
21 7 0.32
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTTTTATTCACTATAT
Found at i:245925 original size:2 final size:2
Alignment explanation
Indices: 245920--245990 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
245910 ATATTATTTT
245920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
245962 TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
245991 GTATTATTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:246089 original size:38 final size:38
Alignment explanation
Indices: 246047--246125 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
246037 TTTTTAAACG
* * * *
246047 TTTATATATATATTTCT-TAATATTCTATTTTTATTTTA
1 TTTATATATATATATATAT-ATATTATATTTTTACTTTA
246085 TTTATATATATATATATATATATTATATTTTTACTTTA
1 TTTATATATATATATATATATATTATATTTTTACTTTA
246123 TTT
1 TTT
246126 TATTTTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 35 0.97
39 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (38 bp):
TTTATATATATATATATATATATTATATTTTTACTTTA
Found at i:246133 original size:18 final size:18
Alignment explanation
Indices: 246107--246144 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
246097 TATATATATA
246107 TTATATTTTTACT-TTATT
1 TTATATTTTT-CTATTATT
*
246125 TTATTTTTTTCTATTATT
1 TTATATTTTTCTATTATT
246143 TT
1 TT
246145 TTTCTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATATTTTTCTATTATT
Found at i:246141 original size:13 final size:13
Alignment explanation
Indices: 246125--246149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
246115 TTACTTTATT
246125 TTATTTTTTTCTA
1 TTATTTTTTTCTA
246138 TTATTTTTTTCT
1 TTATTTTTTTCT
246150 TAATATCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:246178 original size:36 final size:36
Alignment explanation
Indices: 246138--246221 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 36
246128 TTTTTTTCTA
*
246138 TTATTT-TTTT-CTTAATATCATGTATATTT-TTATTTT
1 TTATTTATTTTACTTAATAT--TATATATTTATTA-TTT
* *
246174 TTATTTGTTTTACTTAGTATTATATATTTATTATTT
1 TTATTTATTTTACTTAATATTATATATTTATTATTT
246210 TTATTTATTTTA
1 TTATTTATTTTA
246222 GTAAATACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 28 0.67
37 7 0.17
38 7 0.17
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (36 bp):
TTATTTATTTTACTTAATATTATATATTTATTATTT
Found at i:249290 original size:141 final size:141
Alignment explanation
Indices: 249036--249318 Score: 505
Period size: 141 Copynumber: 2.0 Consensus size: 141
249026 AATATTCTAT
249036 AGTGTTGATCAGGTCAAAACTCGTCGAACTCTGTCAAATACCCATCCCTAATTGCGGTAGGATTG
1 AGTGTTGATCAGGTCAAAACTCGTCGAACTCTGTCAAATACCCATCCCTAATTGCGGTAGGATTG
249101 GTATAGTAGAGAGCAGTAGAAAGGGTAAAAAATAAAAGTGTTGCTCCAATTGATAATAAAAATAA
66 GTATAGTAGAGAGCAGTAGAAAGGGTAAAAAATAAAAGTGTTGCTCCAATTGATAATAAAAATAA
249166 TAAAACATAAA
131 TAAAACATAAA
* * *
249177 AGTGTTGATCAGGTCAAAACTCGTCGAGCTCTGAT-AAATGCTCATCCCTAATTGCGGTAGGATT
1 AGTGTTGATCAGGTCAAAACTCGTCGAACTCTG-TCAAATACCCATCCCTAATTGCGGTAGGATT
* *
249241 GGTATAGTAGAGAGCAGTAGATAGGGTAAAAAATAAAAGTGTTGCTCCAATTGATAATAACAATA
65 GGTATAGTAGAGAGCAGTAGAAAGGGTAAAAAATAAAAGTGTTGCTCCAATTGATAATAAAAATA
249306 ATAAAACATAAA
130 ATAAAACATAAA
249318 A
1 A
249319 ACTTAAAAGG
Statistics
Matches: 136, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
141 135 0.99
142 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (141 bp):
AGTGTTGATCAGGTCAAAACTCGTCGAACTCTGTCAAATACCCATCCCTAATTGCGGTAGGATTG
GTATAGTAGAGAGCAGTAGAAAGGGTAAAAAATAAAAGTGTTGCTCCAATTGATAATAAAAATAA
TAAAACATAAA
Found at i:252186 original size:12 final size:12
Alignment explanation
Indices: 252169--252193 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
252159 TATTTTGAGT
252169 GCTGTGGTGGCA
1 GCTGTGGTGGCA
252181 GCTGTGGTGGCA
1 GCTGTGGTGGCA
252193 G
1 G
252194 GAGTGGTGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.52, T:0.24
Consensus pattern (12 bp):
GCTGTGGTGGCA
Found at i:255829 original size:210 final size:209
Alignment explanation
Indices: 255261--255832 Score: 560
Period size: 210 Copynumber: 2.7 Consensus size: 209
255251 TTTCGATGTG
* * * * * * **
255261 AAAAGTTGAGCAAGATAGGAGATGGCCTGTTTACCTCCACTTGTCTCGAAGAAATAAAGCTATCC
1 AAAAGTTAAACAAGATAGGAGACGGACTGTCTACCTCCACTTGTCTCAAAGAAATAAAGCTATAT
* * * * *
255326 GGTTGTCCTAATTTGAT-TTCCATTCCAGATTTGGAAGGGTTGTCCTCTCTT-AGAGTATTACAT
66 GGATGTCCTAATTT-ATGTTCCATTCCGGATTTGGAAGGATT-TCCTCTCTTCAGAAT-TTAGAT
* * ** * * *
255389 ATATATGGGTGTGACAAACTGGAAATTGTTCCAATAACAGGTAGATGTTCATCACTTGAAGAGCT
128 ATATCTGGGTGCGACAAACTGGAAATCATTCCAATAACAGGAAAATGTTCATCACTTGAAAAGCT
* *
255454 TCACATTTTCCAGTGTC
193 TAAAATTTTCCAGTGTC
* * * * * * * * * *
255471 AAAAGTTAAGCAAGGTAGGAGACGGACTGTCTTCTTCTAATTCTCTCATAGAATTAAAGCTACAT
1 AAAAGTTAAACAAGATAGGAGACGGACTGTCTACCTCCACTTGTCTCAAAGAAATAAAGCTATAT
* * * * *
255536 GTATGTCCTAATTTAAGTTCCATTCCGGATTTGGAAGGATTTTCGTCTCTTCGGAATTTGGATAT
66 GGATGTCCTAATTTATGTTCCATTCCGGATTTGGAAGGA-TTTCCTCTCTTCAGAATTTAGATAT
* **
255601 ATAC-GGGTGCCACAAACTGGAAATCATTCCAATAACAGGAAAATGTTCATTGCTTGAAAAGCTT
130 AT-CTGGGTGCGACAAACTGGAAATCATTCCAATAACAGGAAAATGTTCATCACTTGAAAAGCTT
*
255665 AAAATTTTCTATTGTGT-
194 AAAATTTTCCA--GTGTC
* * * * * *
255682 GAAA-TTAAACAAGATAGGAGACGGGCTGTCTACCTCCACTTGTCTTAAAGAAGTCAAGCTATTT
1 AAAAGTTAAACAAGATAGGAGACGGACTGTCTACCTCCACTTGTCTCAAAGAAATAAAGCTATAT
* * *
255746 GGATGTCCTAATTTATGTTCCATTCCGGATTTGGAAGGATTTCCCTTTGTTCAGAATTTAGTTAT
66 GGATGTCCTAATTTATGTTCCATTCCGGATTTGGAAGGATTT-CCTCTCTTCAGAATTTAGATAT
** *
255811 ATCTGACTGCGGCAAACTGGAA
130 ATCTGGGTGCGACAAACTGGAA
255833 GCAAGAACCC
Statistics
Matches: 288, Mismatches: 66, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
209 5 0.02
210 271 0.94
211 8 0.03
212 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (209 bp):
AAAAGTTAAACAAGATAGGAGACGGACTGTCTACCTCCACTTGTCTCAAAGAAATAAAGCTATAT
GGATGTCCTAATTTATGTTCCATTCCGGATTTGGAAGGATTTCCTCTCTTCAGAATTTAGATATA
TCTGGGTGCGACAAACTGGAAATCATTCCAATAACAGGAAAATGTTCATCACTTGAAAAGCTTAA
AATTTTCCAGTGTC
Found at i:256573 original size:38 final size:38
Alignment explanation
Indices: 256522--256594 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
256512 AACATACTTG
256522 TCATGCATCTCCTCATTACTTATCCTTGATAATCATTA
1 TCATGCATCTCCTCATTACTTATCCTTGATAATCATTA
* *
256560 TCATGCATCTCCTCATTATTTATCCTTGATCATCA
1 TCATGCATCTCCTCATTACTTATCCTTGATAATCA
256595 ATAATGAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.05, T:0.42
Consensus pattern (38 bp):
TCATGCATCTCCTCATTACTTATCCTTGATAATCATTA
Found at i:257495 original size:18 final size:19
Alignment explanation
Indices: 257472--257512 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
257462 TTTATGATGA
257472 TAGAAA-CGTATATATTTG
1 TAGAAATCGTATATATTTG
* *
257490 TAGAAATCTTATTTATTTG
1 TAGAAATCGTATATATTTG
257509 TAGA
1 TAGA
257513 TCCATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TAGAAATCGTATATATTTG
Found at i:257536 original size:2 final size:2
Alignment explanation
Indices: 257529--257574 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
257519 TTATTTTTAA
257529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
257570 AT AT A
1 AT AT A
257575 ATGAGGTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:267599 original size:119 final size:119
Alignment explanation
Indices: 267388--267625 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
267378 ATAGATTTGT
267388 TTCATTGCTGAATGTGTCACAGTCCTTGAGTTTCATTTCCTCTTGTAAAGTGATTTCATTAAGGT
1 TTCATTGCTGAATGTGTCACAGTCCTTGAGTTTCATTTCCTCTTGTAAAGTGATTTCATTAAGGT
267453 TAACCCTTTTTTAACAGTTTTTCCTATTGTTCCATAGGTGCAAATCATGGCGAG
66 TAACCCTTTTTTAACAGTTTTTCCTATTGTTCCATAGGTGCAAATCATGGCGAG
267507 TTCATTGCTGAATGTGTCACAGTCCTTGAGTTTCATTTCCTCTTGTAAAGTGATTTCATTAAGGT
1 TTCATTGCTGAATGTGTCACAGTCCTTGAGTTTCATTTCCTCTTGTAAAGTGATTTCATTAAGGT
267572 TAACCCTTTTTTAACAGTTTTTCCTATTGTTCCATAGGTGCAAATCATGGCGAG
66 TAACCCTTTTTTAACAGTTTTTCCTATTGTTCCATAGGTGCAAATCATGGCGAG
267626 CAAGAAACTA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (119 bp):
TTCATTGCTGAATGTGTCACAGTCCTTGAGTTTCATTTCCTCTTGTAAAGTGATTTCATTAAGGT
TAACCCTTTTTTAACAGTTTTTCCTATTGTTCCATAGGTGCAAATCATGGCGAG
Found at i:269522 original size:125 final size:125
Alignment explanation
Indices: 269300--269551 Score: 486
Period size: 125 Copynumber: 2.0 Consensus size: 125
269290 TGTGTTGAGG
269300 TTGAAGATGATGGGTGTTTAGGTAGTGAAATGGTTTTGTTGAGGGACTTCGTATCTCTTTTAGAA
1 TTGAAGATGATGGGTGTTTAGGTAGTGAAATGGTTTTGTTGAGGGACTTCGTATCTCTTTTAGAA
*
269365 AAAGTTTTAAAGTGTCGTCCGTTAAATAAGATTATAACTTTCATTGATGGATATGGTGTT
66 AAAGTTTTAAAGTGTCGTCCGTTAAATAAGATTATAACTTTCATCGATGGATATGGTGTT
269425 TTGAAGATGATGGGTGTTTAGGTAGTGAAATGGTTTTGTTGAGGGACTTCGTATCTCTTTTAGAA
1 TTGAAGATGATGGGTGTTTAGGTAGTGAAATGGTTTTGTTGAGGGACTTCGTATCTCTTTTAGAA
*
269490 AAAGTTTTAAAGTGTCGTCCGTTAAATAAGATTATAACTTTCATCGATGGTTATGGTGTT
66 AAAGTTTTAAAGTGTCGTCCGTTAAATAAGATTATAACTTTCATCGATGGATATGGTGTT
269550 TT
1 TT
269552 TAAGGTTTAT
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (125 bp):
TTGAAGATGATGGGTGTTTAGGTAGTGAAATGGTTTTGTTGAGGGACTTCGTATCTCTTTTAGAA
AAAGTTTTAAAGTGTCGTCCGTTAAATAAGATTATAACTTTCATCGATGGATATGGTGTT
Found at i:269734 original size:47 final size:48
Alignment explanation
Indices: 269654--269759 Score: 162
Period size: 47 Copynumber: 2.2 Consensus size: 48
269644 TTGTTTCACT
*
269654 GAAAACAGTTTCCGGAAAATGAAATATGAAAAATGAATTATATTTATG
1 GAAAACATTTTCCGGAAAATGAAATATGAAAAATGAATTATATTTATG
* *
269702 G-AAACATTTTCCGGAAAATTAAATCT-ATAAAATGAATTATATTTATG
1 GAAAACATTTTCCGGAAAATGAAATATGA-AAAATGAATTATATTTATG
269749 GAAAACATTTT
1 GAAAACATTTT
269760 TTAGAAATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 1 0.02
47 42 0.79
48 10 0.19
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (48 bp):
GAAAACATTTTCCGGAAAATGAAATATGAAAAATGAATTATATTTATG
Found at i:270179 original size:15 final size:15
Alignment explanation
Indices: 270161--270198 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
270151 AATTATAATC
270161 ATAATTAATATATT-A
1 ATAATTAAT-TATTAA
270176 ATAAATTAATTATTAA
1 AT-AATTAATTATTAA
270192 ATAATTA
1 ATAATTA
270199 TAATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAATTATTAA
Found at i:283243 original size:17 final size:17
Alignment explanation
Indices: 283221--283254 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
283211 TGATCTTTCA
*
283221 AATTTAGTTAATTAAAT
1 AATTTAATTAATTAAAT
*
283238 AATTTAATTATTTAAAT
1 AATTTAATTAATTAAAT
283255 GATGTCAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AATTTAATTAATTAAAT
Found at i:299904 original size:2 final size:2
Alignment explanation
Indices: 299897--299963 Score: 118
Period size: 2 Copynumber: 33.5 Consensus size: 2
299887 TTATTCGATA
299897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
299939 AT AT AT AT AT AT AT AT CAT AT -T AT A
1 AT AT AT AT AT AT AT AT -AT AT AT AT A
299964 AATGACATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 60 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:314513 original size:4 final size:4
Alignment explanation
Indices: 314488--314529 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
314478 GGATAAAAGC
* * *
314488 ATAT ATAC ATAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
314530 TATGGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:314521 original size:10 final size:10
Alignment explanation
Indices: 314488--314529 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
314478 GGATAAAAGC
314488 ATATATACAT
1 ATATATACAT
*
314498 ATACATACAT
1 ATATATACAT
*
314508 ATATATATAT
1 ATATATACAT
*
314518 ATATATATAT
1 ATATATACAT
314528 AT
1 AT
314530 TATGGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATACAT
Found at i:314529 original size:6 final size:6
Alignment explanation
Indices: 314488--314529 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
314478 GGATAAAAGC
* * *
314488 ATATAT ACATAT ACATAC ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
314530 TATGGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:322004 original size:59 final size:60
Alignment explanation
Indices: 321932--322051 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
321922 TGAGTGATTT
* * * **
321932 TTTTGTAACTTTTAATTATTGGAG-ACTCAACAAAATAGTATCT-TATAATCAAAAAATTA
1 TTTTATAACTTTTAATAATTAGAGTACTCAACAAAATAACAT-TATATAATCAAAAAATTA
* *
321991 TTTTATAATTTTTAATAATTAGAGTACTCAACAAAATAACATTATATAATCAAAGAATTA
1 TTTTATAACTTTTAATAATTAGAGTACTCAACAAAATAACATTATATAATCAAAAAATTA
322051 T
1 T
322052 ATGTATGCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 21 0.40
60 31 0.60
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (60 bp):
TTTTATAACTTTTAATAATTAGAGTACTCAACAAAATAACATTATATAATCAAAAAATTA
Found at i:336197 original size:31 final size:31
Alignment explanation
Indices: 336159--336219 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
336149 AACGGCTCTA
336159 TGTTCATTTACGCCTCTTATTTGACGAACAT
1 TGTTCATTTACGCCTCTTATTTGACGAACAT
*
336190 TGTTCATTTACGTCTCTTATTTGACGAACA
1 TGTTCATTTACGCCTCTTATTTGACGAACA
336220 ACAGGTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (31 bp):
TGTTCATTTACGCCTCTTATTTGACGAACAT
Found at i:340399 original size:30 final size:31
Alignment explanation
Indices: 340335--340414 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
340325 TCAACTGTTG
* * *
340335 ATTATTT-AATTTTGTCAATTAAATTATTAA
1 ATTATTTAAATTTTATTAATTAAATCATTAA
*
340365 ATTATTTAAATTTTATTAATTAAATCATT-T
1 ATTATTTAAATTTTATTAATTAAATCATTAA
*
340395 ATTA-TTAATATTTGATTAAT
1 ATTATTTAA-ATTTTATTAAT
340415 GAATTGATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 4 0.09
30 21 0.49
31 18 0.42
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTATTTAAATTTTATTAATTAAATCATTAA
Found at i:341434 original size:25 final size:25
Alignment explanation
Indices: 341397--341455 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
341387 TTGAGTTATT
*
341397 TTTATTATGATAATATTTTTT-TAA
1 TTTATTATAATAATATTTTTTATAA
341421 TATTATTATAATAATATTTTTTATAA
1 T-TTATTATAATAATATTTTTTATAA
*
341447 TTTAATATA
1 TTTATTATA
341456 TTTAAAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 1 0.03
25 26 0.84
26 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTATTATAATAATATTTTTTATAA
Found at i:346354 original size:38 final size:36
Alignment explanation
Indices: 346304--346383 Score: 106
Period size: 38 Copynumber: 2.2 Consensus size: 36
346294 ATAATTATTT
*
346304 TATATGTATATAATATTAATAAATTTAATTAAAATTAA
1 TATATATATATAATATTAATAAATTTAATTAAAA-T-A
* * *
346342 TATATATATATAATATTTATATATTTAATTTAAATA
1 TATATATATATAATATTAATAAATTTAATTAAAATA
346378 TATATA
1 TATATA
346384 CCCGGCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 7 0.18
37 1 0.03
38 30 0.79
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (36 bp):
TATATATATATAATATTAATAAATTTAATTAAAATA
Found at i:346364 original size:15 final size:15
Alignment explanation
Indices: 346342--346383 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
346332 TTAAAATTAA
346342 TATATATATATAATAT
1 TATATATATATAAT-T
*
346358 T-TATATATTTAATT
1 TATATATATATAATT
*
346372 TAAATATATATA
1 TATATATATATA
346384 CCCGGCTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:346365 original size:19 final size:19
Alignment explanation
Indices: 346304--346383 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 19
346294 ATAATTATTT
*
346304 TATATGTATATAATATTAA
1 TATATATATATAATATTAA
* * *
346323 TAAATTTA-ATTAAAATTAA
1 TATATATATA-TAATATTAA
346342 TATATATATATAATATT--
1 TATATATATATAATATTAA
346359 TATATAT-T-TAAT-TTAA
1 TATATATATATAATATTAA
346375 -ATATATATA
1 TATATATATA
346384 CCCGGCTCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 2 0.04
15 10 0.20
16 2 0.04
17 7 0.14
18 1 0.02
19 26 0.53
20 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
TATATATATATAATATTAA
Found at i:346526 original size:24 final size:25
Alignment explanation
Indices: 346480--346528 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
346470 TCCCCACTAT
*
346480 TTTTTAAGCGTGAACGGGTATGAGG
1 TTTTTAAACGTGAACGGGTATGAGG
346505 TTTTTAAACG-GAGACGGG-ATGAGG
1 TTTTTAAACGTGA-ACGGGTATGAGG
346529 GAACCAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.27, C:0.08, G:0.37, T:0.29
Consensus pattern (25 bp):
TTTTTAAACGTGAACGGGTATGAGG
Found at i:354096 original size:29 final size:29
Alignment explanation
Indices: 354063--354145 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
354053 AAGGAGACAA
* *
354063 GGTCGCCGGGCGTGCATGGCGACCTCCTT
1 GGTCGCCCGGAGTGCATGGCGACCTCCTT
*
354092 GGTCGCCCGAAGTGCATGGCGACCTCCTT
1 GGTCGCCCGGAGTGCATGGCGACCTCCTT
354121 GGTCGCCCGGAGTGCATGGCGACCT
1 GGTCGCCCGGAGTGCATGGCGACCT
354146 ATGGGTTGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.11, C:0.34, G:0.36, T:0.19
Consensus pattern (29 bp):
GGTCGCCCGGAGTGCATGGCGACCTCCTT
Found at i:357465 original size:21 final size:21
Alignment explanation
Indices: 357439--357495 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
357429 ATTTACCGTG
*
357439 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGACGCT
* *
357460 ATTGCGGTCGTCGCGGATGCT
1 ATTGCGGCCGTCGCGGACGCT
357481 ATTGCGGCCGTCGCG
1 ATTGCGGCCGTCGCG
357496 TGTAACTCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:366143 original size:15 final size:16
Alignment explanation
Indices: 366111--366143 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
366101 AAAATCTTTC
366111 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
366127 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
366142 TT
1 TT
366144 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:366919 original size:16 final size:17
Alignment explanation
Indices: 366892--366926 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
366882 TATCGCCGAC
366892 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
366909 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
366925 CG
1 CG
366927 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:371204 original size:75 final size:76
Alignment explanation
Indices: 371063--371213 Score: 214
Period size: 75 Copynumber: 2.0 Consensus size: 76
371053 CTTTCAGAAA
* * * * *
371063 GAAATTATTAACTATCATGTTGAAGAGGAACAACTTGAAGTGCTTGAGGAATTCACCAATCTGCC
1 GAAATTATAAACTATCAAGTTGAAGAGAAACAACTTCAAATGCTTGAGGAATTCACCAATCTGCC
371128 TCTGTAAATGT
66 TCTGTAAATGT
* * *
371139 GAAATTATAAACTATCAAGTTGAAGAGAAACTAC-TCAAATGCTTGATGAATTCACTAATCTGCC
1 GAAATTATAAACTATCAAGTTGAAGAGAAACAACTTCAAATGCTTGAGGAATTCACCAATCTGCC
*
371203 TCTTTAAATGT
66 TCTGTAAATGT
371214 CTTTCCATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 36 0.55
76 30 0.45
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (76 bp):
GAAATTATAAACTATCAAGTTGAAGAGAAACAACTTCAAATGCTTGAGGAATTCACCAATCTGCC
TCTGTAAATGT
Done.