Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008495.1 Hibiscus syriacus cultivar Beakdansim tig00111338_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: 5120959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 21
Found at i:208130 original size:27 final size:27
Alignment explanation
Indices: 208082--208137 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
208072 TTCTATCTTA
* *
208082 TATATCATATTAATAAATAATTAAAAT
1 TATATAATATTAATAAAAAATTAAAAT
*
208109 TATATAATAATTAA-AAAAAATTACAAT
1 TATATAAT-ATTAATAAAAAATTAAAAT
208136 TA
1 TA
208138 ACAGGCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (27 bp):
TATATAATATTAATAAAAAATTAAAAT
Found at i:208350 original size:20 final size:21
Alignment explanation
Indices: 208325--208363 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
208315 TTTTTAATTG
208325 TAATTTTTTGGA-TTATTATA
1 TAATTTTTTGGATTTATTATA
208345 TAATTTTTTGGATTTATTA
1 TAATTTTTTGGATTTATTA
208364 ATATGACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
TAATTTTTTGGATTTATTATA
Found at i:210384 original size:75 final size:74
Alignment explanation
Indices: 210256--210464 Score: 237
Period size: 75 Copynumber: 2.8 Consensus size: 74
210246 TTGTGTTTAA
* * *
210256 TATTTTTCTAGACTTAATATTATGGTTTGAGTCTT-AAGATTTAATACTTTAATATTATGATTTG
1 TATTATTCTAGACTTAATATTATGGTTTGAGTCTTGAA-ATTTGACA-TTTAATATTATGATTTG
210320 ATTATGGATTT
64 ATTATGGATTT
* * * * ** *
210331 TATTATTCTAGAGTTAATATTTTGGTTTGAATCTTGAAATTTGACATTTTAATATTGTGGCTTGT
1 TATTATTCTAGACTTAATATTATGGTTTGAGTCTTGAAATTTGACA-TTTAATATTATGATTTGA
210396 TTATGGATTT
65 TTATGGATTT
* * * *
210406 TACTATTCTAAACTTAATATTATGGTGTGAGTCTTGATATTTGAC-TTT-AT-TTATGATTT
1 TATTATTCTAGACTTAATATTATGGTTTGAGTCTTGAAATTTGACATTTAATATTATGATTT
210465 TTTATATATA
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
71 6 0.05
72 2 0.02
73 3 0.03
75 99 0.88
76 2 0.02
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (74 bp):
TATTATTCTAGACTTAATATTATGGTTTGAGTCTTGAAATTTGACATTTAATATTATGATTTGAT
TATGGATTT
Found at i:211901 original size:32 final size:31
Alignment explanation
Indices: 211865--211943 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
211855 TCAATATCGA
* *
211865 ATCGATTGATTTTTGAGTCGGGTTAATACCAT
1 ATCGATTGATTTTTGAGTC-GGTCAATACCAG
* * * *
211897 ATCGATTAGA-TTTCGGGTCTGTCAATATCAG
1 ATCGATT-GATTTTTGAGTCGGTCAATACCAG
211928 ATCGATTGATTTTTGA
1 ATCGATTGATTTTTGA
211944 TTTGAGTCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
30 2 0.05
31 19 0.51
32 14 0.38
33 2 0.05
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.41
Consensus pattern (31 bp):
ATCGATTGATTTTTGAGTCGGTCAATACCAG
Found at i:212347 original size:16 final size:16
Alignment explanation
Indices: 212291--212449 Score: 77
Period size: 16 Copynumber: 9.9 Consensus size: 16
212281 ATTTGATCTT
*
212291 GTTCGGGTTATTTTCG
1 GTTCGGGTTACTTTCG
* * *
212307 GATCTGGTTAAATTT-G
1 GTTCGGGTT-ACTTTCG
** *
212323 GTTTAGGTTGCTTTCG
1 GTTCGGGTTACTTTCG
*
212339 GTTCGGGTTATTTTCG
1 GTTCGGGTTACTTTCG
* * *
212355 GTTTGAGTTATTTTCG
1 GTTCGGGTTACTTTCG
* **
212371 GTTCGGGTTGCTTTAT
1 GTTCGGGTTACTTTCG
* * * * *
212387 ATTTGTGTTAATTTTG
1 GTTCGGGTTACTTTCG
*
212403 GTTCGGGTTTCTTTCG
1 GTTCGGGTTACTTTCG
* * *
212419 GTTCAGGTTAATTTTG
1 GTTCGGGTTACTTTCG
* *
212435 GTTTGAGTTACTTTC
1 GTTCGGGTTACTTTC
212450 AATTCGTGTC
Statistics
Matches: 99, Mismatches: 42, Indels: 4
0.68 0.29 0.03
Matches are distributed among these distances:
15 3 0.03
16 92 0.93
17 4 0.04
ACGTcount: A:0.11, C:0.10, G:0.27, T:0.52
Consensus pattern (16 bp):
GTTCGGGTTACTTTCG
Found at i:212406 original size:32 final size:32
Alignment explanation
Indices: 212356--212416 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
212346 TTATTTTCGG
212356 TTTGAGTTATTTTCGGTTCGGGTTGCTTTATA
1 TTTGAGTTATTTTCGGTTCGGGTTGCTTTATA
* *
212388 TTTGTGTTAATTTT-GGTTCGGGTTTCTTT
1 TTTGAGTT-ATTTTCGGTTCGGGTTGCTTT
212417 CGGTTCAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.10, C:0.08, G:0.25, T:0.57
Consensus pattern (32 bp):
TTTGAGTTATTTTCGGTTCGGGTTGCTTTATA
Found at i:216242 original size:20 final size:20
Alignment explanation
Indices: 216217--216254 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
216207 TTCGATAAGG
216217 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
216237 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
216255 CTTTCACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:224812 original size:64 final size:63
Alignment explanation
Indices: 224685--224841 Score: 228
Period size: 64 Copynumber: 2.5 Consensus size: 63
224675 ATTAGACCCT
*
224685 TAGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCTAAGTGCATCGATGCATGG
1 TAGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCTAAGTGCATCAATGCATGG
* * * *
224748 TCTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCTGAGTGTATCAATGTATG
1 T-AGTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AACAAGCCTAAGTGCATCAATGCATG
224811 G
63 G
224812 TAGTGCATCGATGCATAAAATGCATTCGAT
1 TAGTGCATCGATGCATAAAATGCATTCGAT
224842 AAGGTGAGTG
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 29 0.34
64 51 0.60
65 3 0.04
66 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (63 bp):
TAGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCTAAGTGCATCAATGCATGG
Found at i:225737 original size:138 final size:138
Alignment explanation
Indices: 225495--225927 Score: 428
Period size: 138 Copynumber: 3.1 Consensus size: 138
225485 TCAATTTGAA
* * * * * * *
225495 GATAATTTGGTGACAACACGGTTCGT-ACGTAATGAGGAAGTCTGATTGTCTGTGGATGAAACTG
1 GATAATTTGGAGACAACACGGTTC-TCACGTGATGAGGAAGTCTGGTTATCTGAGGATTAAGCT-
* * * *
225559 GC-CCTATGCGTTGAGGAGATCTGGTTAGTGGATGAGATTGTGACTACGTGATGAGGACGTCTAG
64 GCTCCTATGCGTTGAGGAGATTTGGTCAGTGGATGAAATTGTTACTACGTGATGAGGACGTCTAG
*
225623 ACATATTTAGG
129 TCAT-TTTAGG
*
225634 GATAA-TTGGAGACAACACGGTTCTCACGTGATGAGGAAGTCTGGTTATCTGAGGATTATGCTGC
1 GATAATTTGGAGACAACACGGTTCTCACGTGATGAGGAAGTCTGGTTATCTGAGGATTAAGCTGC
* * ** * * *
225698 TCCTATGTGTTGAGGAGATTTGGTCATTGGGCGAAATTGTTCCTACGTGATGTGGATGTCTAGTC
66 TCCTATGCGTTGAGGAGATTTGGTCAGTGGATGAAATTGTTACTACGTGATGAGGACGTCTAGTC
*
225763 ATCTTTAGA
131 AT-TTTAGG
* ** * * * * *
225772 GATACTTTAAACATAACACAGTTC-CTACGTGATGAGGAAGTTTGGTTATCTGAGGA-T-GGCAA
1 GATAATTTGGAGACAACACGGTTCTC-ACGTGATGAGGAAGTCTGGTTATCTGAGGATTAAGC--
** * * * * *
225834 TGCTCCTACACGTTGAGAAAATTTGGTCAGTGGATGACATTGTTTCTACGTGATGAGGACGTGTA
63 TGCTCCTATGCGTTGAGGAGATTTGGTCAGTGGATGAAATTGTTACTACGTGATGAGGACGTCTA
*
225899 GTCGTTTTAGG
128 GTCATTTTAGG
225910 GATAATTTGGAGACAACA
1 GATAATTTGGAGACAACA
225928 ATCTCAAGTG
Statistics
Matches: 238, Mismatches: 50, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
137 5 0.02
138 130 0.55
139 103 0.43
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (138 bp):
GATAATTTGGAGACAACACGGTTCTCACGTGATGAGGAAGTCTGGTTATCTGAGGATTAAGCTGC
TCCTATGCGTTGAGGAGATTTGGTCAGTGGATGAAATTGTTACTACGTGATGAGGACGTCTAGTC
ATTTTAGG
Found at i:225901 original size:139 final size:138
Alignment explanation
Indices: 225580--225927 Score: 346
Period size: 139 Copynumber: 2.5 Consensus size: 138
225570 TGAGGAGATC
* * * * * *
225580 TGGTTAGTGGATGAGATTGTGACTACGTGATGAGGACGTCTAGACATATTTAGGGATAATTGGAG
1 TGGTCAGTGGATGAAATTGTTACTACGTGATGAGGACGTCTAGTCATATTTAGAGATAATTGGAA
* * ***
225645 ACAACACGGTTCTCACGTGATGAGGAAGTCTGGTTATCTGAGGATTATGCTGCTCCTATGTGTTG
66 ACAACACAGTTCTCACGTGATGAGGAAGTCTGGTTATCTGAGGATTAGGCTGCTCCTACACGTTG
* *
225710 AGGAGATT
131 AGAAAATT
* ** * * * * * *
225718 TGGTCATTGGGCGAAATTGTTCCTACGTGATGTGGATGTCTAGTCATCTTTAGAGATACTT-TAA
1 TGGTCAGTGGATGAAATTGTTACTACGTGATGAGGACGTCTAGTCATATTTAGAGATAATTGGAA
*
225782 ACATAACACAGTTC-CTACGTGATGAGGAAGTTTGGTTATCTGAGGA-T-GGCAATGCTCCTACA
66 AC--AACACAGTTCTC-ACGTGATGAGGAAGTCTGGTTATCTGAGGATTAGGC--TGCTCCTACA
225844 CGTTGAGAAAATT
126 CGTTGAGAAAATT
* * * * *
225857 TGGTCAGTGGATGACATTGTTTCTACGTGATGAGGACGTGTAGTCGT-TTTAGGGATAATTTGGA
1 TGGTCAGTGGATGAAATTGTTACTACGTGATGAGGACGTCTAGTCATATTTAGAGATAA-TTGGA
*
225921 GACAACA
65 AACAACA
225928 ATCTCAAGTG
Statistics
Matches: 167, Mismatches: 36, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
137 5 0.03
138 63 0.38
139 96 0.57
140 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (138 bp):
TGGTCAGTGGATGAAATTGTTACTACGTGATGAGGACGTCTAGTCATATTTAGAGATAATTGGAA
ACAACACAGTTCTCACGTGATGAGGAAGTCTGGTTATCTGAGGATTAGGCTGCTCCTACACGTTG
AGAAAATT
Found at i:226020 original size:30 final size:30
Alignment explanation
Indices: 225986--226172 Score: 108
Period size: 30 Copynumber: 5.8 Consensus size: 30
225976 CACAAAATTT
225986 TGTTTCAAGAGAAACTGTCTCAAAGGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTTA
***
226016 TGTTTCAAGAGAAACTGTCTTACGCAAGACAAAACTT-
1 TGTTTCAAGAGAAACTGTC-T---C---A-AAGGTTTA
* ** *
226053 TGTTTCGAGAGAAACAATCTCAATGGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTTA
* *
226083 TGTTTCAAGATAAACTGTCTCAAGAGAGACAAAACTT-
1 TGTTTCAAGAGAAACTGTCTCAA-AG-G------TTTA
* *
226120 TGTTTTAAGAGAAATTGTCTCAAAGGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTTA
*
226150 TGTTTCAAGAGAAATTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
226173 GCAAGACAAA
Statistics
Matches: 118, Mismatches: 21, Indels: 36
0.67 0.12 0.21
Matches are distributed among these distances:
29 5 0.04
30 61 0.52
31 2 0.02
32 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 3 0.03
37 37 0.31
38 6 0.05
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (30 bp):
TGTTTCAAGAGAAACTGTCTCAAAGGTTTA
Found at i:226064 original size:67 final size:67
Alignment explanation
Indices: 225953--226276 Score: 416
Period size: 67 Copynumber: 4.8 Consensus size: 67
225943 AAATTTTTTA
* * * * *
225953 AAGAGAAAATATCTCAAGCGAGACACAAAATTTTGTTTCAAGAGAAACTGTCTCAAAGGTTTATG
1 AAGAGAAACTGTCTCAAGC-A-AGACAAAACTTTGTTTCAAGAGAAACTATCTCAAAGGTTTATG
226018 TTTC
64 TTTC
* * * * *
226022 AAGAGAAACTGTCTTACGCAAGACAAAACTTTGTTTCGAGAGAAACAATCTCAATGGTTTATGTT
1 AAGAGAAACTGTCTCAAGCAAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAAGGTTTATGTT
226087 TC
66 TC
* * * *
226089 AAGATAAACTGTCTCAAG-AGAGACAAAACTTTGTTTTAAGAGAAATTGTCTCAAAGGTTTATGT
1 AAGAGAAACTGTCTCAAGCA-AGACAAAACTTTGTTTCAAGAGAAACTATCTCAAAGGTTTATGT
226153 TTC
65 TTC
* ** * *
226156 AAGAGAAATTGTCTCAAGCAAGACAAAACTTTGTTTTGAGAGAAACAATCTCAAAGTTTTATGTT
1 AAGAGAAACTGTCTCAAGCAAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAAGGTTTATGTT
226221 TC
66 TC
* * *
226223 AAGAGAAGCTGACTCAAGAAAGACAAAACTTTGTTTCAAGAGAAACTATCTCAA
1 AAGAGAAACTGTCTCAAGCAAGACAAAACTTTGTTTCAAGAGAAACTATCTCAA
226277 GCAAAACGAA
Statistics
Matches: 220, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
66 1 0.00
67 202 0.92
68 2 0.01
69 15 0.07
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (67 bp):
AAGAGAAACTGTCTCAAGCAAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAAGGTTTATGTT
TC
Found at i:226139 original size:37 final size:37
Alignment explanation
Indices: 226083--226200 Score: 101
Period size: 37 Copynumber: 3.4 Consensus size: 37
226073 CAATGGTTTA
* *
226083 TGTTTCAAGATAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
* *
226120 TGTTTTAAGAGAAATTGTCTCAA-AG-G------TTT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
226149 ATGTTTCAAGAGAAATTGTCTCAAGCA-AGACAAAACTT
1 -TGTTTCAAGAGAAATTGTCTCAAG-AGAGACAAAACTT
**
226187 TGTTTTGAGAGAAA
1 TGTTTCAAGAGAAA
226201 CAATCTCAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
29 2 0.03
30 22 0.35
32 2 0.03
35 1 0.02
36 2 0.03
37 32 0.51
38 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (37 bp):
TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
Found at i:226208 original size:37 final size:37
Alignment explanation
Indices: 226150--226313 Score: 114
Period size: 37 Copynumber: 4.6 Consensus size: 37
226140 CAAAGGTTTA
***
226150 TGTTTCAAGAGAAATTGTCTCAAGCAAGACAAAACTT
1 TGTTTCAAGAGAAACAATCTCAAGCAAGACAAAACTT
** **
226187 TGTTTTGAGAGAAACAATCTC-A--AAG-----TTTT
1 TGTTTCAAGAGAAACAATCTCAAGCAAGACAAAACTT
* * *
226216 ATGTTTCAAGAGAAGCTGA-CTCAAGAAAGACAAAACTT
1 -TGTTTCAAGAGAAAC-AATCTCAAGCAAGACAAAACTT
* * *
226254 TGTTTCAAGAGAAACTATCTCAAGCAAAACGAAACTT
1 TGTTTCAAGAGAAACAATCTCAAGCAAGACAAAACTT
226291 TGTTT-AGAGAGAAACAATCTCAA
1 TGTTTCA-AGAGAAACAATCTCAA
226314 CGGTTTATCA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
29 2 0.02
30 15 0.16
31 2 0.02
33 3 0.03
34 3 0.03
36 3 0.03
37 66 0.69
38 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAGAAACAATCTCAAGCAAGACAAAACTT
Found at i:226217 original size:134 final size:134
Alignment explanation
Indices: 225972--226276 Score: 475
Period size: 134 Copynumber: 2.3 Consensus size: 134
225962 TATCTCAAGC
* * *
225972 GAGACACAAAATTTTGTTTCAAGAGAAACTGTCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTT
1 GAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTC
* * * *
226037 ACGCAAGACAAAACTTTGTTTCGAGAGAAACAATCTCAATGGTTTATGTTTCAAGATAAACTGTC
66 AAGCAAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGAC
226102 TCAA
131 TCAA
* * *
226106 GAGAGACAAAACTTTGTTTTAAGAGAAATTGTCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTC
1 GAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTC
* * *
226171 AAGCAAGACAAAACTTTGTTTTGAGAGAAACAATCTCAAAGTTTTATGTTTCAAGAGAAGCTGAC
66 AAGCAAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGAC
226236 TCAA
131 TCAA
* *
226240 GAAAGACAAAACTTTGTTTCAAGAGAAACTATCTCAA
1 GAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAA
226277 GCAAAACGAA
Statistics
Matches: 154, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
134 154 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (134 bp):
GAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTC
AAGCAAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGAC
TCAA
Found at i:226362 original size:104 final size:103
Alignment explanation
Indices: 226254--226459 Score: 245
Period size: 104 Copynumber: 2.0 Consensus size: 103
226244 GACAAAACTT
* * *
226254 TGTTTCAAGAG-AAACTATCTCAAGCAAAACGAAACTTTG-TTTAGAGAGAAACAATCTCAACGG
1 TGTTTCAAGAGAAAACTATCTCAAGCAAAAC-AAAATTTGCTTTA-AGAAAAACAATCTCAAAGG
* *
226317 TTTATCAATTTTGTTTCAAGTGAAACCATTTCTAAATTTTG
64 -TTATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTTG
* * * * * *
226358 TGTTTTAAGGGAAAACTGTCTCAAGCGAGACAAAATTTGTCTTTAAGAAAAACAATCTCAAATGT
1 TGTTTCAAGAGAAAACTATCTCAAGCAAAACAAAATTTG-CTTTAAGAAAAACAATCTCAAAGGT
* *
226423 TATTAATTTTGTTTCAAGTGAAATAATTTCAAAATTT
65 TATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTT
226460 GTATTTCTGG
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
104 50 0.58
105 32 0.37
106 4 0.05
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (103 bp):
TGTTTCAAGAGAAAACTATCTCAAGCAAAACAAAATTTGCTTTAAGAAAAACAATCTCAAAGGTT
ATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTTG
Found at i:226506 original size:103 final size:104
Alignment explanation
Indices: 226293--226526 Score: 283
Period size: 103 Copynumber: 2.2 Consensus size: 104
226283 CGAAACTTTG
* ** * *
226293 TTTAGAGAGAAACAATCTCAACGGTTTATCAATTTTGTTTCAAGTGAAACCATTTCTAAATTTTG
1 TTTA-AGAAAAACAATCTCAAATG-TTATCAATTTTGTTTCAAGTGAAACAATTTCTAAAATTTG
*
226358 TGTTTTAAGGGAAAACTGTCTCAAGCGAGACAAAATTTGTC
64 TATTTTAAGGGAAAACTGTCTCAAGCGAGACAAAATTTGTC
* *
226399 TTTAAGAAAAACAATCTCAAATGTTATTAATTTTGTTTCAAGTGAAATAATTTC-AAAATTTGTA
1 TTTAAGAAAAACAATCTCAAATGTTATCAATTTTGTTTCAAGTGAAACAATTTCTAAAATTTGTA
* * ** * *
226463 TTTCT-GGGGGAAACTGTCTCAAGTTAGGCAAAATTTGTT
66 TTT-TAAGGGAAAACTGTCTCAAGCGAGACAAAATTTGTC
* *
226502 TTTAAGAAAAATAATATCAAATGTT
1 TTTAAGAAAAACAATCTCAAATGTT
226527 CATGCCTTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
103 62 0.56
104 29 0.26
105 16 0.14
106 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (104 bp):
TTTAAGAAAAACAATCTCAAATGTTATCAATTTTGTTTCAAGTGAAACAATTTCTAAAATTTGTA
TTTTAAGGGAAAACTGTCTCAAGCGAGACAAAATTTGTC
Found at i:226586 original size:36 final size:36
Alignment explanation
Indices: 226546--226657 Score: 113
Period size: 36 Copynumber: 3.1 Consensus size: 36
226536 AGGAAGATTA
226546 TCTCAAGTGAAACAAAATATTTTTTAAGAAAAACTG
1 TCTCAAGTGAAACAAAATATTTTTTAAGAAAAACTG
* **
226582 TCTCAAGTGAGACAAAAT-TTGATTTTAAG-AAAACAA
1 TCTCAAGTGAAACAAAATATT--TTTTAAGAAAAACTG
* * * *
226618 TCTCAAGTGAGATC-AATTATGTTTGAAGAAAAACTG
1 TCTCAAGTGA-AACAAAATATTTTTTAAGAAAAACTG
226654 TCTC
1 TCTC
226658 TAGCGAGACA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
35 8 0.13
36 44 0.72
37 9 0.15
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (36 bp):
TCTCAAGTGAAACAAAATATTTTTTAAGAAAAACTG
Found at i:226666 original size:72 final size:73
Alignment explanation
Indices: 226545--226696 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 73
226535 AAGGAAGATT
* * *
226545 ATCTCAAGTGAAACAAAATATTTTTTAAGAAAAACTGTCTCAAGTGAGACAAAA-TTTGATTTTA
1 ATCTCAAGTGAAACAAAATATGTTTGAAGAAAAACTGTCTCAAGCGAGACAAAACTTTG-TTTTA
226609 AGA-AAACA
65 AGAGAAACA
* * * *
226617 ATCTCAAGTGAGATC-AATTATGTTTGAAGAAAAACTGTCTCTAGCGAGACAAAACTTTGTTTTG
1 ATCTCAAGTGA-AACAAAATATGTTTGAAGAAAAACTGTCTCAAGCGAGACAAAACTTTGTTTTA
*
226681 AGAGAAATA
65 AGAGAAACA
226690 ATCTCAA
1 ATCTCAA
226697 AGGTGACAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
72 52 0.75
73 17 0.25
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (73 bp):
ATCTCAAGTGAAACAAAATATGTTTGAAGAAAAACTGTCTCAAGCGAGACAAAACTTTGTTTTAA
GAGAAACA
Found at i:232138 original size:26 final size:24
Alignment explanation
Indices: 232074--232138 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 24
232064 TAAAAATACG
*
232074 TACATAAATAAAATGCATAAAATA
1 TACATATATAAAATGCATAAAATA
* * *
232098 TATAAATATACAAATGCGTAAACATA
1 TACATATATA-AAATGCATAAA-ATA
232124 TACATATATGAAAAT
1 TACATATAT-AAAAT
232139 TTAATATGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 7 0.22
25 10 0.31
26 14 0.44
27 1 0.03
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (24 bp):
TACATATATAAAATGCATAAAATA
Found at i:270687 original size:365 final size:365
Alignment explanation
Indices: 270017--270735 Score: 1233
Period size: 365 Copynumber: 2.0 Consensus size: 365
270007 GGAATACAAC
*
270017 CCCTTGAAACTGTATTGAAAAGTTTATTCTTATTCACTTTACTCTAGCACTATGACCTAATGGAT
1 CCCTTGAAACTATATTGAAAAGTTTATTCTTATTCACTTTACTCTAGCACTATGACCTAATGGAT
* * *
270082 ACCCCTATCATATCACTATCAATGTTTTCTACCTGAATACCTCTATCTTTGACTAATTTCGAGCT
66 ACCCCTATCATATCACTATCAATGTGTTCTACCTCAATACCCCTATCTTTGACTAATTTCGAGCT
* *
270147 AACATAGGAATGCGTAGAACTTGGATCAATCAAAACAAATACATACTCATCATAAAGATAGAAAG
131 AACATAGGAATGAGTAGAACTCGGATCAATCAAAACAAATACATACTCATCATAAAGATAGAAAG
* *
270212 TACATGTTATAATCTCTTCGTTATTACGATCTTCCCAATTATTGGGATCTACTATTGCTTGTATT
196 TACATGTTATAATCTCTTCGTTATCACGATCTTCCCAATTATTAGGATCTACTATTGCTTGTATT
*
270277 TTCTTGGGATCAACTCTGATTCCTTCTGCTGAAATTACATGGCCAAGAAAAGAAAATTATGGTTA
261 TTCTTGGGATCAACTATGATTCCTTCTGCTGAAATTACATGGCCAAGAAAAGAAAATTATGGTTA
**
270342 CCAAAATTCACATTTTGATAGGTTAGCCTTCAACTCTGAT
326 CCAAAATTCACATTTTGATACCTTAGCCTTCAACTCTGAT
*
270382 CCCTTGAAACTATATTGGAAAA-TTTATTCTTATTCACTTTACTCTAGCACTATGATCTAATGGA
1 CCCTTGAAACTATATT-GAAAAGTTTATTCTTATTCACTTTACTCTAGCACTATGACCTAATGGA
*
270446 TACCCCTATCATATCACTATCAATGTGTTCTACCTCAATACCCCTATTTTTGACTAATTTCGAGC
65 TACCCCTATCATATCACTATCAATGTGTTCTACCTCAATACCCCTATCTTTGACTAATTTCGAGC
270511 TAACATAGGAATGAGTAGAACTCGGATCAATCAAAACAAATACATACTCATCATAAAGATAGAAA
130 TAACATAGGAATGAGTAGAACTCGGATCAATCAAAACAAATACATACTCATCATAAAGATAGAAA
* * * * *
270576 GTACCTGTTATAATCTCTTGGTTATCACGATCTTCTCATTTCTTAGGATCTACTATTGCTTGTAT
195 GTACATGTTATAATCTCTTCGTTATCACGATCTTCCCAATTATTAGGATCTACTATTGCTTGTAT
* * *
270641 TTTCTTGGGATCTACTATGATTTCTTCTGCTGAAATTACATGGCCAAGAAAAGAAAATTTTGGTT
260 TTTCTTGGGATCAACTATGATTCCTTCTGCTGAAATTACATGGCCAAGAAAAGAAAATTATGGTT
270706 ACCAAAATTCACATTTTGATACCTTAGCCT
325 ACCAAAATTCACATTTTGATACCTTAGCCT
270736 ACAATTTTTT
Statistics
Matches: 332, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
365 327 0.98
366 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (365 bp):
CCCTTGAAACTATATTGAAAAGTTTATTCTTATTCACTTTACTCTAGCACTATGACCTAATGGAT
ACCCCTATCATATCACTATCAATGTGTTCTACCTCAATACCCCTATCTTTGACTAATTTCGAGCT
AACATAGGAATGAGTAGAACTCGGATCAATCAAAACAAATACATACTCATCATAAAGATAGAAAG
TACATGTTATAATCTCTTCGTTATCACGATCTTCCCAATTATTAGGATCTACTATTGCTTGTATT
TTCTTGGGATCAACTATGATTCCTTCTGCTGAAATTACATGGCCAAGAAAAGAAAATTATGGTTA
CCAAAATTCACATTTTGATACCTTAGCCTTCAACTCTGAT
Found at i:287623 original size:47 final size:47
Alignment explanation
Indices: 287529--287625 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
287519 GAATAAATAT
* * *
287529 ATGCGAACTAGAGATCATGCGGTTATGTTTATTTTTCTCAAATAAGC
1 ATGCGAAATAGAGATCATGCGGTTATGTGTATTTTTCTCAAAAAAGC
*
287576 ATGCGAAATAGATATCATGCGGTTATG-GTATTTTGT-TCAAACAAAGC
1 ATGCGAAATAGAGATCATGCGGTTATGTGTATTTT-TCTCAAA-AAAGC
287623 ATG
1 ATG
287626 GGGGTAGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
46 11 0.25
47 33 0.75
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (47 bp):
ATGCGAAATAGAGATCATGCGGTTATGTGTATTTTTCTCAAAAAAGC
Found at i:289996 original size:99 final size:99
Alignment explanation
Indices: 289869--290058 Score: 281
Period size: 99 Copynumber: 1.9 Consensus size: 99
289859 TTATAATATT
* * * * *
289869 ATATGTATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTAACTTTATGG
1 ATATATATACAATAAAGATTGAGATGTCCCTCTAGAGCAATTGATTAAACGCCCTAACATTATGG
*
289934 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGAGAAAGGTGATTATA
* * **
289968 ATATATATACATTTAAGATTGAGATGTCCCTCTAGAGCAATTGATTAAACGCCCTGGCATTATGG
1 ATATATATACAATAAAGATTGAGATGTCCCTCTAGAGCAATTGATTAAACGCCCTAACATTATGG
*
290033 ATAAGATTTAGCTAGCCTGAGAAAGG
66 ATAAGATTCAGCTAGCCTGAGAAAGG
290059 AAAATTACAA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (99 bp):
ATATATATACAATAAAGATTGAGATGTCCCTCTAGAGCAATTGATTAAACGCCCTAACATTATGG
ATAAGATTCAGCTAGCCTGAGAAAGGTGATTATA
Found at i:292015 original size:37 final size:37
Alignment explanation
Indices: 291931--292044 Score: 160
Period size: 37 Copynumber: 3.1 Consensus size: 37
291921 ACTTCGGGCC
* *
291931 ATCTCAAGCCTTCAC-GATAGAGTAGTGAAG-AAAATA
1 ATCTTAAGCCTTCACGGA-AGAGTAGTGAAGCAAATTA
*
291967 ATCTTAAGCCTTCACGGAAGAGTAGTGAGGCAAATTA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTA
* *
292004 ATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTA
292041 ATCT
1 ATCT
292045 CGAGTATGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
36 25 0.36
37 45 0.64
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTA
Found at i:292602 original size:55 final size:55
Alignment explanation
Indices: 292092--292601 Score: 635
Period size: 55 Copynumber: 9.3 Consensus size: 55
292082 TCATTTTATA
*
292092 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGAGGACACGTTTGCTG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
* ** *
292147 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAACAAACACATTTGCTG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
* * * ** *
292202 AAGATTGTTCGAGTCCTATAATCTCTGAAAGAATAGGGAGCGGATATATTTTCTG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
* * * * * *
292257 ATGATTTTTCAAGTCCTACACTCCCTGAAAGAATAGGGAGCAGACACTTTTGCTG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
* * *
292312 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAGTCACGTTTGCTT
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
* * * * * *
292367 AAGATTATTCGAGTCCTATACTCTCTAAAAGAATAAGGAGCAGACACGTTTGCTA
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
* *
292422 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAAGGAGCGAACACGTTTGCTG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
* * * *
292477 AAGATTGTTCGAGTCTTATACTCACTGAAAGAATAGGGAGTGGGC-CTGTTTGCTG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACAC-GTTTGCTG
* * * * * * *
292532 AAGATTGTTTGAGTCTTATATTCCCTGAAAGAATAAGGAGTGGACACGTTTTCCG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
* *
292587 AAGATTTTTCAAGTC
1 AAGATTGTTCGAGTC
292602 TCACTTATCC
Statistics
Matches: 394, Mismatches: 59, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
54 1 0.00
55 392 0.99
56 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (55 bp):
AAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACGTTTGCTG
Found at i:296290 original size:13 final size:13
Alignment explanation
Indices: 296274--296302 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
296264 TTTCCCTAGT
296274 TTATTTATTTAAA
1 TTATTTATTTAAA
296287 TTATTTATTTAAA
1 TTATTTATTTAAA
296300 TTA
1 TTA
296303 GGTTATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTTATTTAAA
Found at i:312120 original size:82 final size:82
Alignment explanation
Indices: 311983--312146 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
311973 ACCTATACAT
311983 GCCATGGGAAGTACATATGCAAAATTACGATAATCTAATACCAAGTAAGGGTAACTCCCCCAAAC
1 GCCATGGGAAGTACATATGCAAAATTACGATAATCTAATACCAAGTAAGGGTAACTCCCCCAAAC
312048 TTGTTGAAGGCATCATC
66 TTGTTGAAGGCATCATC
312065 GCCATGGGAAGTACATATGCAAAATTACGATAATCTAATACCAAGTAAGGGTAACTCCCCCAAAC
1 GCCATGGGAAGTACATATGCAAAATTACGATAATCTAATACCAAGTAAGGGTAACTCCCCCAAAC
312130 TTGTTGAAGGCATCATC
66 TTGTTGAAGGCATCATC
312147 CCCAATGCAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (82 bp):
GCCATGGGAAGTACATATGCAAAATTACGATAATCTAATACCAAGTAAGGGTAACTCCCCCAAAC
TTGTTGAAGGCATCATC
Found at i:314084 original size:22 final size:22
Alignment explanation
Indices: 314056--314102 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
314046 TATTATACTT
*
314056 TTTATTTATT-TTTTTTTCATCA
1 TTTATTT-TTATTATTTTCATCA
*
314078 TTTATTTTTATTATTTTCATTA
1 TTTATTTTTATTATTTTCATCA
314100 TTT
1 TTT
314103 CTAAATCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTTTATTATTTTCATCA
Found at i:318442 original size:99 final size:98
Alignment explanation
Indices: 318267--318463 Score: 385
Period size: 99 Copynumber: 2.0 Consensus size: 98
318257 GTTGTAGAAA
318267 GTGAGTAAATTCTATACTTTAACTTTTGTCATTATTATTCTTGTGGAGGTCGTTTGGGTCCAAAG
1 GTGAGTAAATTCTATACTTTAACTTTTGTCATTATTATTCTTGTGGAGGTCGTTTGGGTCCAAAG
318332 CTAGCTACTATAAAATCTTGGAATATGATTTTT
66 CTAGCTACTATAAAATCTTGGAATATGATTTTT
318365 GTGAGGTAAATTCTATACTTTAACTTTTGTCATTATTATTCTTGTGGAGGTCGTTTGGGTCCAAA
1 GTGA-GTAAATTCTATACTTTAACTTTTGTCATTATTATTCTTGTGGAGGTCGTTTGGGTCCAAA
318430 GCTAGCTACTATAAAATCTTGGAATATGATTTTT
65 GCTAGCTACTATAAAATCTTGGAATATGATTTTT
318464 CTTGCCTAAC
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 4 0.04
99 94 0.96
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (98 bp):
GTGAGTAAATTCTATACTTTAACTTTTGTCATTATTATTCTTGTGGAGGTCGTTTGGGTCCAAAG
CTAGCTACTATAAAATCTTGGAATATGATTTTT
Found at i:318683 original size:95 final size:96
Alignment explanation
Indices: 318574--318756 Score: 359
Period size: 95 Copynumber: 1.9 Consensus size: 96
318564 CAATTCATAT
318574 TTGTGAAATTTTTTATGTTTTGGGAATTGATTATATGAGACCTCTCCTTTCATCTTTTGGGAATT
1 TTGTGAAATTTTTTATGTTTTGGGAATTGATTATATGAGACCTCTCCTTTCATCTTTTGGGAATT
318639 GTTATATAGTGCTTACTG-TGATGTGTCTGA
66 GTTATATAGTGCTTACTGATGATGTGTCTGA
318669 TTGTGAAATTTTTTATGTTTTGGGAATTGATTATATGAGACCTCTCCTTTCATCTTTTGGGAATT
1 TTGTGAAATTTTTTATGTTTTGGGAATTGATTATATGAGACCTCTCCTTTCATCTTTTGGGAATT
318734 GTTATATAGTGCTTACTGATGAT
66 GTTATATAGTGCTTACTGATGAT
318757 TATGTGTCTG
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 83 0.95
96 4 0.05
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (96 bp):
TTGTGAAATTTTTTATGTTTTGGGAATTGATTATATGAGACCTCTCCTTTCATCTTTTGGGAATT
GTTATATAGTGCTTACTGATGATGTGTCTGA
Found at i:320039 original size:95 final size:94
Alignment explanation
Indices: 319873--320055 Score: 294
Period size: 95 Copynumber: 1.9 Consensus size: 94
319863 AATGGTTTGT
* *
319873 TGACAGTCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTCGT
1 TGACAGTCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATATCCTTCGT
**
319938 TGTGAAGTTAAAATTGACTCTGAATGAAAC
66 CATGAAGTT-AAATTGACTCTGAATGAAAC
* *
319968 TGACAGTCAGCCGCTCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGT
1 TGACAGTCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATATCCTTCGT
*
320033 CATGAAGTTAAATTGCCTCTGAA
66 CATGAAGTTAAATTGACTCTGAA
320056 ATTGGAAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 13 0.16
95 68 0.84
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (94 bp):
TGACAGTCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATATCCTTCGT
CATGAAGTTAAATTGACTCTGAATGAAAC
Found at i:320102 original size:200 final size:204
Alignment explanation
Indices: 319834--320466 Score: 740
Period size: 212 Copynumber: 3.0 Consensus size: 204
319824 TTATCCGCTG
** * * * *
319834 TGAAGTTGAAATTGGTTCTGGAACTGG-GAAATGGTTTGTTGACAGTCAGCCGCCCCTTCA-CTG
1 TGAAGTTGAAATTGCCTCTGAAATTGGAAAAAT-GTTTGTTGACAGTCAGCCGCCCCTTTATC-G
* * * * *
319897 TGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTCGTTGTGAAGTTAAAATTGACTCTG-A
64 TGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
* * * *
319961 A-T-GAAACTGACAGTCAGCCGCTCCTTCA-CTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAA
129 ATTGGAAATTGACAGTCAGCCGCCCCTTCATC-GTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAA
320023 TATCCTTCGTCA
193 TATCCTTCGTCA
* * *
320035 TGAAGTT-AAATTGCCTCTGAAATTGGAAAAATGTTTGTTGACAATCAACCGCCCCTTTGTCGTG
1 TGAAGTTGAAATTGCCTCTGAAATTGGAAAAATGTTTGTTGACAGTCAGCCGCCCCTTTATCGTG
* *
320099 AAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAAT
66 AAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
* *
320164 TAGGAAATTGTTTGTTGATAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCATGGG
131 T-GGAAA-------TTGACAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGG
* **
320229 TCAAATATCCTTCGTTG
188 TCCAATATCCTTCGTCA
* * * * *
320246 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAGTCAGCCGCCCCTTCATTGTG
1 TGAAGTTGAAATTGCCTCTGAAATTGGAAAAATGTTTGTTGACAGTCAGCCGCCCCTTTATCGTG
* *
320311 AAGTTGAGCTTGTGTTGTATTGGGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
66 AAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
* *
320376 TGGGAAATTATTTATTGACAGTCAGTCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGG
131 T-GG--A--A---ATTGACAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGG
320441 TCCAATATCCTTCGTCA
188 TCCAATATCCTTCGTCA
320458 TGAAGTTGA
1 TGAAGTTGA
320467 GCCCCGAATG
Statistics
Matches: 365, Mismatches: 45, Indels: 33
0.82 0.10 0.07
Matches are distributed among these distances:
200 95 0.26
201 14 0.04
202 1 0.00
204 4 0.01
211 64 0.18
212 184 0.50
214 1 0.00
216 1 0.00
219 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (204 bp):
TGAAGTTGAAATTGCCTCTGAAATTGGAAAAATGTTTGTTGACAGTCAGCCGCCCCTTTATCGTG
AAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
TGGAAATTGACAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATAT
CCTTCGTCA
Found at i:320210 original size:106 final size:106
Alignment explanation
Indices: 319968--320466 Score: 732
Period size: 106 Copynumber: 4.7 Consensus size: 106
319958 TGAATGAAAC
* * *
319968 TGACAGTCAGCCGCTCCTTCA-CTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
1 TGACAGTCAGCCGCCCCTTCATC-GTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCG
** * * *
320032 TCATGAAGTT-AAATTGCCTCTGAAATTGGAAAAATGTTTGT
65 TTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
* * ** *
320073 TGACAATCAACCGCCCCTTTGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCAT
1 TGACAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGT
* *
320138 TGTGAAGTTGAAATTGGTTCTGAAATTAGGAAATTGTTTGT
66 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
* * *
320179 TGATAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCATGGGTCAAATATCCTTCGT
1 TGACAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGT
320244 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
66 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
* * *
320285 TGACAGTCAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTGTATTGGGTCCAATATCATTCGT
1 TGACAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGT
* *
320350 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTAT
66 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
* *
320391 TGACAGTCAGTCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGT
1 TGACAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGT
**
320456 CATGAAGTTGA
66 TGTGAAGTTGA
320467 GCCCCGAATG
Statistics
Matches: 352, Mismatches: 40, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
105 62 0.18
106 290 0.82
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (106 bp):
TGACAGTCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGT
TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
Found at i:321598 original size:8 final size:7
Alignment explanation
Indices: 321567--321628 Score: 74
Period size: 7 Copynumber: 8.7 Consensus size: 7
321557 CTTATTTTTC
321567 TTTTCTT
1 TTTTCTT
321574 TTTTCTT
1 TTTTCTT
321581 TTGTT-TT
1 TT-TTCTT
*
321588 TGTTCTT
1 TTTTCTT
321595 TTGTTCTT
1 TT-TTCTT
321603 TTTTCTCT
1 TTTTCT-T
321611 TTTTC-T
1 TTTTCTT
321617 TTTTCTT
1 TTTTCTT
321624 TTTTC
1 TTTTC
321629 AATTTAGGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
6 8 0.17
7 25 0.52
8 15 0.31
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:321604 original size:29 final size:29
Alignment explanation
Indices: 321569--321625 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
321559 TATTTTTCTT
321569 TTCTTTTTTCT-TTTGTT-TTTGTTCTTTTG
1 TTCTTTTTTCTCTTT-TTCTTT-TTCTTTTG
321598 TTCTTTTTTCTCTTTTTCTTTTTCTTTT
1 TTCTTTTTTCTCTTTTTCTTTTTCTTTT
321626 TTCAATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (29 bp):
TTCTTTTTTCTCTTTTTCTTTTTCTTTTG
Found at i:331473 original size:158 final size:155
Alignment explanation
Indices: 331169--331481 Score: 599
Period size: 158 Copynumber: 2.0 Consensus size: 155
331159 TTACTCGAAA
331169 TATAATCAAAAGTAAGTAAAAGGATCGAAATATTACTTTAAAATTTAAACTTACCCTTTTCGTTA
1 TATAATCAAAAGTAAGTAAAAGGATCGAAATATTACTTTAAAATTTAAACTTACCCTTTTCGTTA
331234 GAAAGACACTGGAAATTACCTTAGCCGACTCACTTACCTGTGTCCCAGCGGAATCGCCAAGCTGC
66 GAAAGACACTGGAAATTACCTTAGCCGACTCACTTACCTGTGTCCCAGCGGAATCGCCAAGCTGC
331299 CGGAACCGTCCTTCGGTTGGGCCCG
131 CGGAACCGTCCTTCGGTTGGGCCCG
331324 TATAATCAAAAGTAAGTAAAAAGGATCGAAATATTACTTTAAAATTTAAACTTACCCTTTTCGTT
1 TATAATCAAAAGTAAGT-AAAAGGATCGAAATATTACTTTAAAATTTAAACTTACCCTTTTCGTT
331389 AGAAAGACAACTGGAAATTACCTTAGCCTGACTCACTTACCTGTGTCCCAGCGGAATCGCCAAGC
65 AGAAAGAC-ACTGGAAATTACCTTAGCC-GACTCACTTACCTGTGTCCCAGCGGAATCGCCAAGC
331454 TGCCGGAACCGTCCTTCGGTTGGGCCCG
128 TGCCGGAACCGTCCTTCGGTTGGGCCCG
331482 AAATTGGGCT
Statistics
Matches: 155, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
155 17 0.11
156 55 0.35
157 19 0.12
158 64 0.41
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (155 bp):
TATAATCAAAAGTAAGTAAAAGGATCGAAATATTACTTTAAAATTTAAACTTACCCTTTTCGTTA
GAAAGACACTGGAAATTACCTTAGCCGACTCACTTACCTGTGTCCCAGCGGAATCGCCAAGCTGC
CGGAACCGTCCTTCGGTTGGGCCCG
Found at i:332010 original size:13 final size:11
Alignment explanation
Indices: 331986--332052 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 11
331976 AAAAGAAGGA
331986 AAAAATAAAAT
1 AAAAATAAAAT
331997 AAAAATAGAGAAT
1 AAAAATA-A-AAT
332010 AAAAATAAAA-
1 AAAAATAAAAT
332020 AGAAAATAGATAAAT
1 A-AAAAT--A-AAAT
332035 AAATAAATAAAAT
1 -AA-AAATAAAAT
332048 AAAAA
1 AAAAA
332053 AAAGGTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
10 1 0.02
11 17 0.36
12 4 0.09
13 15 0.32
14 4 0.09
15 1 0.02
16 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:332017 original size:24 final size:26
Alignment explanation
Indices: 331985--332052 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 26
331975 TAAAAGAAGG
*
331985 AAAAAATAAAATAAAAATAGA-GAAT
1 AAAAAATAAAATAAAAATAGATAAAT
332010 -AAAAATAAAA-AGAAAATAGATAAAT
1 AAAAAATAAAATA-AAAATAGATAAAT
332035 AAATAAATAAAATAAAAA
1 AAA-AAATAAAATAAAAA
332053 AAAGGTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 1 0.03
24 18 0.49
25 3 0.08
26 2 0.05
27 12 0.32
28 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (26 bp):
AAAAAATAAAATAAAAATAGATAAAT
Found at i:332277 original size:18 final size:18
Alignment explanation
Indices: 332256--332291 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
332246 TATATATAAC
332256 AAAAAATAATAAATAAAT
1 AAAAAATAATAAATAAAT
**
332274 AAAATTTAATAAATAAAT
1 AAAAAATAATAAATAAAT
332292 TTAAGTTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATAATAAATAAAT
Found at i:334259 original size:31 final size:31
Alignment explanation
Indices: 334161--334259 Score: 73
Period size: 31 Copynumber: 3.3 Consensus size: 31
334151 GATTTAAACA
*
334161 TTTAAGGACTAATTTAGAAA-GAGGTTCATAG
1 TTTAAGGACTAATTTA-AAATGAGATTCATAG
* * * * *
334192 TTTAGGGA-TGCAA-TTAGAAT--GTTTGAAAG
1 TTTAAGGACT--AATTTAAAATGAGATTCATAG
*
334221 TTGAAGGACTAATTTAAAATGAGATTCATAG
1 TTTAAGGACTAATTTAAAATGAGATTCATAG
334252 TTTAAGGA
1 TTTAAGGA
334260 TGAAATTGAA
Statistics
Matches: 49, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
28 2 0.04
29 18 0.37
30 4 0.08
31 23 0.47
32 2 0.04
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (31 bp):
TTTAAGGACTAATTTAAAATGAGATTCATAG
Found at i:334312 original size:60 final size:60
Alignment explanation
Indices: 334132--334314 Score: 200
Period size: 60 Copynumber: 3.0 Consensus size: 60
334122 TTTGGATGGA
*
334132 TTTAGGGATGAAATTTGAAG-ATTTAAACA-TTTAAGGACTAATTTAGAAA-GAGGTTCATAG
1 TTTAGGGATGAAA-TTGAAGTA-TTAAAAAGTTTAAGGACTAATTTA-AAATGAGGTTCATAG
* * * *
334192 TTTAGGGATGCAATTAGAATGT-TT-GAAAGTTGAAGGACTAATTTAAAATGAGATTCATAG
1 TTTAGGGATGAAATT-GAA-GTATTAAAAAGTTTAAGGACTAATTTAAAATGAGGTTCATAG
*
334252 TTTAAGGATGAAATTGAAGTATTAAAAAGTTTAAGGA-TCAATTTAAAATGAGGGTT-ATAG
1 TTTAGGGATGAAATTGAAGTATTAAAAAGTTTAAGGACT-AATTTAAAATGA-GGTTCATAG
334312 TTT
1 TTT
334315 GAGAACATAT
Statistics
Matches: 104, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
58 2 0.02
59 13 0.12
60 85 0.82
61 4 0.04
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (60 bp):
TTTAGGGATGAAATTGAAGTATTAAAAAGTTTAAGGACTAATTTAAAATGAGGTTCATAG
Found at i:343105 original size:25 final size:25
Alignment explanation
Indices: 343071--343121 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
343061 ATATTAAGAA
343071 ATGATATAACATCTTTAAGGCAAGC
1 ATGATATAACATCTTTAAGGCAAGC
343096 ATGATATAACATCTTTAAGGCAAGC
1 ATGATATAACATCTTTAAGGCAAGC
343121 A
1 A
343122 GAAGACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (25 bp):
ATGATATAACATCTTTAAGGCAAGC
Found at i:346339 original size:26 final size:26
Alignment explanation
Indices: 346291--346375 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 26
346281 GAGAAAAGAA
*
346291 TAATAAAAAATAT-TAATATAATAATAT
1 TAATAAAAAA-ATGAAATA-AATAATAT
346318 TAATAAAAAAATGAAATAAATAAATAT
1 TAATAAAAAAATGAAATAAAT-AATAT
346345 ATAATAATGTAAAAA-GAAATAAA-AATAT
1 -TAATAA---AAAAATGAAATAAATAATAT
346373 TAA
1 TAA
346376 AATTAAGAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
26 5 0.10
27 22 0.43
28 11 0.22
30 8 0.16
31 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (26 bp):
TAATAAAAAAATGAAATAAATAATAT
Found at i:346414 original size:26 final size:25
Alignment explanation
Indices: 346335--346419 Score: 77
Period size: 26 Copynumber: 3.4 Consensus size: 25
346325 AAAATGAAAT
* *
346335 AAATAAATATATA-ATAATGTAAAAAG
1 AAATAAAAATATATATAAAGT--AAAG
*
346361 AAATAAAAATAT-TA-AAATTAAGAG
1 AAATAAAAATATATATAAAGTAA-AG
*
346385 AAATGAAAAATATATATAAAGTAAAT
1 AAAT-AAAAATATATATAAAGTAAAG
346411 AAATAAAAA
1 AAATAAAAA
346420 ATGAAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.04
24 6 0.12
25 16 0.33
26 19 0.39
27 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (25 bp):
AAATAAAAATATATATAAAGTAAAG
Found at i:346421 original size:26 final size:26
Alignment explanation
Indices: 346326--346421 Score: 72
Period size: 26 Copynumber: 3.6 Consensus size: 26
346316 ATTAATAAAA
*
346326 AAATGAAATAAATAAATATATAATAATGT
1 AAAT-AAATAAA-AAATATAT-ATAAAGT
* *
346355 AAA-AAGAAATAAAAATAT-TA-AAATT
1 AAATAA-ATA-AAAAATATATATAAAGT
* *
346380 AAGAGAAATGAAAAATATATATAAAGT
1 AA-ATAAATAAAAAATATATATAAAGT
346407 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
346422 GAAATAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
25 13 0.25
26 16 0.30
27 11 0.21
28 8 0.15
29 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (26 bp):
AAATAAATAAAAAATATATATAAAGT
Found at i:346740 original size:33 final size:33
Alignment explanation
Indices: 346703--346780 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
346693 AGTCATACTT
*
346703 GGACTCAAATGC-TTCAGTTTTAGTGTTTCAATA
1 GGACTCAAATACATT-AGTTTTAGTGTTTCAATA
*
346736 GGACTCAAATACATTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACATTAGTTTTAGTGTTTCAATA
346769 GGACTCAAATAC
1 GGACTCAAATAC
346781 GTTGATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 40 0.95
34 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (33 bp):
GGACTCAAATACATTAGTTTTAGTGTTTCAATA
Found at i:346855 original size:10 final size:9
Alignment explanation
Indices: 346835--346869 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
346825 TGGGGCCTGT
346835 AAAATAAAA
1 AAAATAAAA
346844 AAAATAAAA
1 AAAATAAAA
*
346853 AAAATAATA
1 AAAATAAAA
*
346862 ATAATAAA
1 AAAATAAA
346870 TATAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAATAAAA
Found at i:347361 original size:32 final size:32
Alignment explanation
Indices: 347324--347386 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
347314 GATTTGATGT
*
347324 TTCAAGAGAAACATTTTCAAAGGTTTTTTTTC
1 TTCAAGAGAAACAATTTCAAAGGTTTTTTTTC
* * *
347356 TTCAAGAGAAATAATTTCGAGGGTTTTTTTT
1 TTCAAGAGAAACAATTTCAAAGGTTTTTTTT
347387 TTGTTTCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (32 bp):
TTCAAGAGAAACAATTTCAAAGGTTTTTTTTC
Found at i:347412 original size:15 final size:15
Alignment explanation
Indices: 347392--347443 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
347382 TTTTTTTGTT
347392 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
*
347407 TCAAGAAAAACTTAGT-
1 TCAAGAGAAAC-T-GTC
*
347423 TCTAAAAGAAACTGTC
1 TC-AAGAGAAACTGTC
347439 TCAAG
1 TCAAG
347444 GGAGACAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 14 0.48
16 6 0.21
17 9 0.31
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:347534 original size:37 final size:37
Alignment explanation
Indices: 347481--347553 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
347471 ATATTAAAAG
* *
347481 ATTTTGTTTCATGGGAAACTGTCTCAAGAGAGACAAT
1 ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAT
347518 ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
1 ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
347554 AACTTGGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (37 bp):
ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAT
Found at i:348843 original size:31 final size:32
Alignment explanation
Indices: 348766--348859 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 32
348756 ATTCCCAAAG
* *
348766 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCCAAAATTTGATGTTGAATCTCAAAAA
*
348798 ATGCCCCAAAATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAAAATTTGATGTTGAATCTCAAAAA
* **
348830 ATG-TCCAGCATTTGATGTTGAATCTTCAAA
1 ATGCCCCAAAATTTGATGTTGAATC-TCAAA
348860 TATGCCCTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 17 0.31
32 37 0.69
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (32 bp):
ATGCCCCAAAATTTGATGTTGAATCTCAAAAA
Found at i:349951 original size:14 final size:13
Alignment explanation
Indices: 349918--349959 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
349908 TCAATTTTCC
349918 TTTTTTTCTCTTT
1 TTTTTTTCTCTTT
*
349931 TTATTTTCTCTTT
1 TTTTTTTCTCTTT
349944 GTTTTTTTCTCTTT
1 -TTTTTTTCTCTTT
349958 TT
1 TT
349960 GTTCTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTTTTCTCTTT
Found at i:351862 original size:5 final size:5
Alignment explanation
Indices: 351852--351886 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
351842 GCAAGTGATG
351852 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
351887 AGAGTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:353403 original size:33 final size:31
Alignment explanation
Indices: 353366--353441 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 31
353356 AGTCCTACTT
353366 GGACTCAAATGCTTCAGTTTTAGTGTTTCAATA
1 GGACTCAAATG-TT-AGTTTTAGTGTTTCAATA
*
353399 GGACTCAAATATGTTGGTTTTAGTGTTTCAATA
1 GGACTC-AA-ATGTTAGTTTTAGTGTTTCAATA
353432 GGACTCAAAT
1 GGACTCAAAT
353442 ACGTTGATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 2 0.05
32 2 0.05
33 29 0.73
34 4 0.10
35 3 0.08
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (31 bp):
GGACTCAAATGTTAGTTTTAGTGTTTCAATA
Found at i:353442 original size:33 final size:33
Alignment explanation
Indices: 353382--353447 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
353372 AAATGCTTCA
*
353382 GTTTTAGTGTTTCAATAGGACTCAAATATGTTG
1 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
353415 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
353448 ATTTATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (33 bp):
GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
Found at i:353553 original size:5 final size:5
Alignment explanation
Indices: 353527--353567 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
353517 AATATTTTTA
353527 ATAAT AATAAT A-AAT A-AAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
353568 TTTTTAGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 8 0.24
5 21 0.62
6 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:353675 original size:21 final size:21
Alignment explanation
Indices: 353641--353682 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
353631 TGTCAGAATA
*
353641 TGGAAATTTTAGAA-TTGAAG
1 TGGAAATGTTAGAAGTTGAAG
353661 TGGAAATGGTTAGAAGTTGAAG
1 TGGAAAT-GTTAGAAGTTGAAG
353683 AGTAATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (21 bp):
TGGAAATGTTAGAAGTTGAAG
Found at i:354765 original size:48 final size:48
Alignment explanation
Indices: 354723--354823 Score: 148
Period size: 48 Copynumber: 2.1 Consensus size: 48
354713 ATATGTTTAT
*
354723 AGCATGTAACCTGTCATCTGTGTGATGGTGGTGATATTATATGTACTG
1 AGCATGTAACCTGACATCTGTGTGATGGTGGTGATATTATATGTACTG
* * * *
354771 AGCATGTAACCTGACGTTTGTGTGATGGTGGTGCTATTATATGATACTA
1 AGCATGTAACCTGACATCTGTGTGATGGTGGTGATATTATATG-TACTG
354820 AGCA
1 AGCA
354824 CATAATCTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 39 0.83
49 8 0.17
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.36
Consensus pattern (48 bp):
AGCATGTAACCTGACATCTGTGTGATGGTGGTGATATTATATGTACTG
Found at i:354851 original size:49 final size:48
Alignment explanation
Indices: 354741--354898 Score: 155
Period size: 49 Copynumber: 3.4 Consensus size: 48
354731 ACCTGTCATC
* * **
354741 TGTGTGATGGTGGTGATATTATATGTACTGAGCATGTAACCTGACGTT
1 TGTGTGATGGTGGTGCTATTATATGTACTAAGCACATAACCTGACGTT
* *
354789 TGTGTGATGGTGGTGCTATTATATGATACTAAGCACATAATCTGATGTT
1 TGTGTGATGGTGGTGCTATTATATG-TACTAAGCACATAACCTGACGTT
* * * * * * *
354838 TGTGTGAGGGTGGTGC--GT-T-GGTACTCAGCACGTAACCTGATGTA
1 TGTGTGATGGTGGTGCTATTATATGTACTAAGCACATAACCTGACGTT
354882 TGTGTGATGGT-GTGCTA
1 TGTGTGATGGTGGTGCTA
354899 AAGTATTGGG
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
43 4 0.04
44 29 0.31
45 1 0.01
46 1 0.01
47 1 0.01
48 24 0.26
49 33 0.35
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.36
Consensus pattern (48 bp):
TGTGTGATGGTGGTGCTATTATATGTACTAAGCACATAACCTGACGTT
Found at i:359186 original size:32 final size:32
Alignment explanation
Indices: 359150--359217 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
359140 CGATTGTATC
*
359150 ATCTCCATATTTAATTCTTTAACTTCCCAATA
1 ATCTCCATATTGAATTCTTTAACTTCCCAATA
* *
359182 ATCTCCGTGTTGAATTCTTTAACTTCCCAATA
1 ATCTCCATATTGAATTCTTTAACTTCCCAATA
359214 ATCT
1 ATCT
359218 TAATGTTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.04, T:0.43
Consensus pattern (32 bp):
ATCTCCATATTGAATTCTTTAACTTCCCAATA
Found at i:364776 original size:19 final size:20
Alignment explanation
Indices: 364733--364772 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
364723 GAAAAGTTCT
*
364733 AATAAAATAACTAATTCATA
1 AATAAAATAACTAATTAATA
364753 AATAAAATAA-TAA-TAATA
1 AATAAAATAACTAATTAATA
364771 AA
1 AA
364773 ATAATCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAAAATAACTAATTAATA
Found at i:366009 original size:54 final size:54
Alignment explanation
Indices: 365904--366010 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
365894 ATAAGCGGAT
* * ** *
365904 ATTATATCGTTAACCCTAAAATTTTGTCATTGCCTTAATGGTTTTAGAACTGAG
1 ATTATATCGTTAACCCTAAAAATTTGACATTGCCTTAATGAATTTAAAACTGAG
365958 ATTATATCGTTAACCCTAAAAATTTGACATTGCCTTAATGAATTTAAAACTGA
1 ATTATATCGTTAACCCTAAAAATTTGACATTGCCTTAATGAATTTAAAACTGA
366011 TGGAATGCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (54 bp):
ATTATATCGTTAACCCTAAAAATTTGACATTGCCTTAATGAATTTAAAACTGAG
Found at i:366547 original size:208 final size:208
Alignment explanation
Indices: 366312--366721 Score: 802
Period size: 208 Copynumber: 2.0 Consensus size: 208
366302 TAATCATAAG
366312 TTAATTTTAAAATTTTAATAATTAGTCGAATAATTAAAATAGAACATCAAGCAAAAGTGGGGACT
1 TTAATTTTAAAATTTTAATAATTAGTCGAATAATTAAAATAGAACATCAAGCAAAAGTGGGGACT
366377 AATTTAAATTACTCCCTAATTAATCTAAATGAGTACCTAAATAAAAAATAAAACTTAAGGGGTCT
66 AATTTAAATTACTCCCTAATTAATCTAAATGAGTACCTAAATAAAAAATAAAACTTAAGGGGTCT
*
366442 CATCTAAAATCAAGAACTTAAATCTAAGATTCAAACAAGCAAATGCAAAACTAAATATCAAAATT
131 CATCTAAAATCAAGAACTTAAATCTAAGATTCAAACAAACAAATGCAAAACTAAATATCAAAATT
366507 AAAAATATTATGA
196 AAAAATATTATGA
366520 TTAATTTTAAAATTTTAATAATTAGTCGAATAATTAAAATAGAACATCAAGCAAAAGTGGGGACT
1 TTAATTTTAAAATTTTAATAATTAGTCGAATAATTAAAATAGAACATCAAGCAAAAGTGGGGACT
*
366585 AATTTAAATTACTCCCTAATTAATCTAAATGAGTACCTAAATGAAAAATAAAACTTAAGGGGTCT
66 AATTTAAATTACTCCCTAATTAATCTAAATGAGTACCTAAATAAAAAATAAAACTTAAGGGGTCT
366650 CATCTAAAATCAAGAACTTAAATCTAAGATTCAAACAAACAAATGCAAAACTAAATATCAAAATT
131 CATCTAAAATCAAGAACTTAAATCTAAGATTCAAACAAACAAATGCAAAACTAAATATCAAAATT
366715 AAAAATA
196 AAAAATA
366722 ATTAAAATGT
Statistics
Matches: 200, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
208 200 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (208 bp):
TTAATTTTAAAATTTTAATAATTAGTCGAATAATTAAAATAGAACATCAAGCAAAAGTGGGGACT
AATTTAAATTACTCCCTAATTAATCTAAATGAGTACCTAAATAAAAAATAAAACTTAAGGGGTCT
CATCTAAAATCAAGAACTTAAATCTAAGATTCAAACAAACAAATGCAAAACTAAATATCAAAATT
AAAAATATTATGA
Found at i:369621 original size:24 final size:25
Alignment explanation
Indices: 369541--369622 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 25
369531 AAATATACAA
369541 ATATAATATATATAATA-ATAACTAT
1 ATATAATATATATAATACAT-ACTAT
* * * *
369566 TTCTTAATATATA-AA-ACGTAATAT
1 AT-ATAATATATATAATACATACTAT
369590 ATAGTAATATATATAATACATACTA-
1 ATA-TAATATATATAATACATACTAT
369615 ATATAATA
1 ATATAATA
369623 CAAACGTGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 20 0.45
25 9 0.20
26 15 0.34
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATAATATATATAATACATACTAT
Found at i:369652 original size:7 final size:7
Alignment explanation
Indices: 369640--369705 Score: 53
Period size: 7 Copynumber: 8.7 Consensus size: 7
369630 GCAGAAACAT
369640 ATAAATA
1 ATAAATA
369647 ATAAATA
1 ATAAATA
369654 ATAAATTA
1 ATAAA-TA
369662 ATATAATA
1 ATA-AATA
*
369670 GAAAAATTA
1 -ATAAA-TA
*
369679 AT-AACA
1 ATAAATA
369685 ATGATAATA
1 AT-A-AATA
369694 ATAAATA
1 ATAAATA
369701 ATAAA
1 ATAAA
369706 AATTTAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
6 3 0.06
7 23 0.48
8 11 0.23
9 11 0.23
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (7 bp):
ATAAATA
Found at i:373908 original size:20 final size:20
Alignment explanation
Indices: 373883--373923 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
373873 TTCGTTTATA
*
373883 TTCGTTCGTTTGTGTTCGTT
1 TTCGTTCGTTTATGTTCGTT
373903 TTCGTTCGTTTATGTTCGTT
1 TTCGTTCGTTTATGTTCGTT
373923 T
1 T
373924 ATCATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.15, G:0.22, T:0.61
Consensus pattern (20 bp):
TTCGTTCGTTTATGTTCGTT
Found at i:373922 original size:14 final size:14
Alignment explanation
Indices: 373863--373902 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
373853 TGTTTTTTGT
373863 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
* *
373876 GTTTATATTCGTTC
1 GTTTGTGTTCGTTC
373890 GTTTGTGTTCGTT
1 GTTTGTGTTCGTT
373903 TTCGTTCGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.05, C:0.10, G:0.25, T:0.60
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:373924 original size:10 final size:10
Alignment explanation
Indices: 373886--373925 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
373876 GTTTATATTC
*
373886 GTTCGTTTGT
1 GTTCGTTTAT
373896 GTTCGTTT-T
1 GTTCGTTTAT
373905 CGTTCGTTTAT
1 -GTTCGTTTAT
373916 GTTCGTTTAT
1 GTTCGTTTAT
373926 CATTTAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.04
10 26 0.93
11 1 0.04
ACGTcount: A:0.05, C:0.12, G:0.23, T:0.60
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:374859 original size:31 final size:31
Alignment explanation
Indices: 374768--374859 Score: 77
Period size: 31 Copynumber: 3.0 Consensus size: 31
374758 TTAATTTTTA
*
374768 ATTTT-ACCCCTAAACTTTAGA-AAGAATA-C
1 ATTTTAACCCTTAAACTTTAGATAA-AATATC
* * * *
374797 -TATTTAGA-CCTTAAACTCTACATGAAGTATC
1 AT-TTTA-ACCCTTAAACTTTAGATAAAATATC
374828 ATTTTAACCCTTAAACTTTAGATAAAATATC
1 ATTTTAACCCTTAAACTTTAGATAAAATATC
374859 A
1 A
374860 AATTGACCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
28 1 0.02
29 3 0.06
30 15 0.32
31 27 0.57
32 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (31 bp):
ATTTTAACCCTTAAACTTTAGATAAAATATC
Found at i:375469 original size:33 final size:33
Alignment explanation
Indices: 375421--375496 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
375411 AGTACCTAAA
* *
375421 ATATTTTTGTGGTCAAAGTAAGTACCAAAAATT
1 ATATTTTTTTTGTCAAAGTAAGTACCAAAAATT
* * *
375454 ATATTTTTTTTGTCAAATTAAGTACCTAAAGTT
1 ATATTTTTTTTGTCAAAGTAAGTACCAAAAATT
375487 A-ATTTTTTTT
1 ATATTTTTTTT
375497 CAAAAATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
32 9 0.24
33 29 0.76
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (33 bp):
ATATTTTTTTTGTCAAAGTAAGTACCAAAAATT
Found at i:375515 original size:31 final size:31
Alignment explanation
Indices: 375409--375516 Score: 87
Period size: 31 Copynumber: 3.5 Consensus size: 31
375399 CTTTTCTATC
* * *
375409 TAAGTACCTAAA-AT-ATTTTTGTGGTCAAAG
1 TAAGTACCTAAAGTTAATTTTT-TTGTCAAAA
* * *
375439 TAAGTACCAAAAATTATATTTTTTTTGTCAAAT
1 TAAGTACCTAAAGTTA-A-TTTTTTTGTCAAAA
375472 TAAGTACCTAAAGTTAATTTTTTT-TCAAAAA
1 TAAGTACCTAAAGTTAATTTTTTTGTC-AAAA
* *
375503 TATGTACTTAAAGT
1 TAAGTACCTAAAGT
375517 ATTCAATCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
30 13 0.20
31 23 0.36
32 1 0.02
33 22 0.34
34 5 0.08
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (31 bp):
TAAGTACCTAAAGTTAATTTTTTTGTCAAAA
Found at i:376208 original size:21 final size:21
Alignment explanation
Indices: 376147--376201 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
376137 AATTCTCTTC
376147 ATGAAAAGATTAAATCCTTTT
1 ATGAAAAGATTAAATCCTTTT
376168 ATGAAAAGATTAAATCCTTTT
1 ATGAAAAGATTAAATCCTTTT
*
376189 ATGAAAAGGTTAA
1 ATGAAAAGATTAA
376202 GCCCTTTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGAAAAGATTAAATCCTTTT
Found at i:376238 original size:21 final size:21
Alignment explanation
Indices: 376193--376239 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
376183 CCTTTTATGA
*
376193 AAAGGTTAAGCCCTTTACATC
1 AAAGGTTAAGCCATTTACATC
*
376214 AAAGGTTAAGTCATTT-CATC
1 AAAGGTTAAGCCATTTACATC
376234 GAAAGG
1 -AAAGG
376240 GCTTAACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (21 bp):
AAAGGTTAAGCCATTTACATC
Found at i:378973 original size:113 final size:113
Alignment explanation
Indices: 378843--379079 Score: 465
Period size: 113 Copynumber: 2.1 Consensus size: 113
378833 TGATTAGAAG
378843 TTGATATTGTTTGAAGCTTGAATCCTAAGAAAAATGTGAAGGGACCATTTCAACTATTAAAGAAA
1 TTGATATTGTTTGAAGCTTGAATCCTAAGAAAAATGTGAAGGGACCATTTCAACTATTAAAGAAA
378908 ATATTTGGATAATTTTTGAAAGAATGCTTTTTAAAGTGTTTAAATGTT
66 ATATTTGGATAATTTTTGAAAGAATGCTTTTTAAAGTGTTTAAATGTT
378956 TTGATATTGTTTGAAGCTTGAATCCTAAGAAAAATGTGAAGGGACCATTTCAACTATTAAAGAAA
1 TTGATATTGTTTGAAGCTTGAATCCTAAGAAAAATGTGAAGGGACCATTTCAACTATTAAAGAAA
379021 ATATTTGGATAATTTTTGAAAGAATGCTTTTTAAAGTGTTTAAATGTT
66 ATATTTGGATAATTTTTGAAAGAATGCTTTTTAAAGTGTTTAAATGTT
*
379069 TTGTTATTGTT
1 TTGATATTGTT
379080 CAAGTTTCAT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 123 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (113 bp):
TTGATATTGTTTGAAGCTTGAATCCTAAGAAAAATGTGAAGGGACCATTTCAACTATTAAAGAAA
ATATTTGGATAATTTTTGAAAGAATGCTTTTTAAAGTGTTTAAATGTT
Found at i:386196 original size:3 final size:3
Alignment explanation
Indices: 386188--386225 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
386178 CGCTATTATC
* *
386188 TTA TTA TTA -TA TTA TTA TTA TTA TTA ATA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
386226 ATAAATACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:387754 original size:11 final size:11
Alignment explanation
Indices: 387740--387767 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
387730 ATTTTAATTT
387740 TTGCATGTTGA
1 TTGCATGTTGA
387751 TTGCATGTTGA
1 TTGCATGTTGA
387762 TTGCAT
1 TTGCAT
387768 ATTAGTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.46
Consensus pattern (11 bp):
TTGCATGTTGA
Found at i:388560 original size:131 final size:130
Alignment explanation
Indices: 388209--388575 Score: 384
Period size: 130 Copynumber: 2.8 Consensus size: 130
388199 CGATATTGAG
* * *
388209 AATAATAATATCT-TTTCATTTCGTTCGGAGTAATAAATGACTGCTTTAAGACATGAGAGGTCAT
1 AATAATAATATCTCTTT-ATTTCATTAGGTGTAATAAATGACTGCTTTAAG-CATGAGAGGTCAT
* * * * * * * * *
388273 TTATTCTTGATTGGTAATAATTTGATATTTTCATTTTCTCTCAAATTAATATCGATTTTTAAGAT
64 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATCAAATTTTAAGAT
388338 GA
129 GA
* * * * * *
388340 AATAATGATATCTCTTT-TTTCGATTAGAT-CAACAAATGACCGCTTTAAGGTATGAGAGGTCAT
1 AATAATAATATCTCTTTATTTC-ATTAGGTGTAATAAATGACTGCTTTAA-GCATGAGAGGTCAT
* * ** * *
388403 TTATTCTCGTTTGGAAATCATTAGATATTATCGTTTTCACTTGAATCGATATTAAATTTTAAGAT
64 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATCAAATTTTAAGAT
388468 GA
129 GA
* * * *
388470 AATAATAATATCTCTTTATTTCAATT-GGTGTAATAAATGATTG-TTGCAATGCATGAAAGGTGA
1 AATAATAATATCTCTTTATTTC-ATTAGGTGTAATAAATGACTGCTT-TAA-GCATGAGAGGTCA
388533 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTC
63 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTC
388576 TTAAAATTAT
Statistics
Matches: 191, Mismatches: 39, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
130 104 0.54
131 84 0.44
132 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (130 bp):
AATAATAATATCTCTTTATTTCATTAGGTGTAATAAATGACTGCTTTAAGCATGAGAGGTCATTT
ATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATCAAATTTTAAGATGA
Found at i:399212 original size:25 final size:24
Alignment explanation
Indices: 399173--399280 Score: 98
Period size: 25 Copynumber: 4.4 Consensus size: 24
399163 AAAAGGAAAG
399173 AAAGAAA-AAGAAAAAATATAGAGAA
1 AAAGAAAGAAGAAAAAA-A-AGAGAA
*
399198 AAAGAAAGAAGAAAAAAAATGAAAA
1 AAAGAAAGAAGAAAAAAAA-GAGAA
399223 AAAGAAAGAA-AAAAGAAAA-AGAA
1 AAAGAAAGAAGAAAA-AAAAGAGAA
** *
399246 TTGAGAAA-AAGAAAAAGAAAAAGAA
1 -AAAGAAAGAAGAAAAA-AAAGAGAA
399271 AAAGAAAGAA
1 AAAGAAAGAA
399281 AAGAAGAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
23 6 0.09
24 22 0.32
25 32 0.46
26 9 0.13
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.05
Consensus pattern (24 bp):
AAAGAAAGAAGAAAAAAAAGAGAA
Found at i:399229 original size:18 final size:17
Alignment explanation
Indices: 399169--399297 Score: 80
Period size: 19 Copynumber: 6.9 Consensus size: 17
399159 CTAAAAAAGG
399169 AAAGAAAGAAAAAGAAAA
1 AAAGAAA-AAAAAGAAAA
* *
399187 AATATAGAGAAAAAG-AAA
1 AA-AGA-AAAAAAAGAAAA
*
399205 GAAGAAAAAAAATGAAAA
1 AAAGAAAAAAAA-GAAAA
399223 AAAGAAAGAAAAAAGAAAA
1 AAAG-AA-AAAAAAGAAAA
*
399242 AGAATTGAGAAAAAGAAAAAGAA
1 A-AA--GA-AAAAA-AAGAA-AA
399265 AAAGAAAAAGAAAGAAAA
1 AAAGAAAAA-AAAGAAAA
* *
399283 GAAGAAAATAAAGAA
1 AAAGAAAAAAAAGAA
399298 TAAACAAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 27
0.70 0.08 0.22
Matches are distributed among these distances:
16 6 0.07
17 9 0.10
18 21 0.24
19 24 0.27
20 12 0.14
21 5 0.06
22 8 0.09
23 3 0.03
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.05
Consensus pattern (17 bp):
AAAGAAAAAAAAGAAAA
Found at i:399295 original size:12 final size:12
Alignment explanation
Indices: 399170--399308 Score: 88
Period size: 12 Copynumber: 11.0 Consensus size: 12
399160 TAAAAAAGGA
399170 AAGAAAGAAAAAG
1 AAGAAA-AAAAAG
* *
399183 AA-AAAATATAG
1 AAGAAAAAAAAG
399194 -AGAAAAAGAAAG
1 AAGAAAAA-AAAG
399206 AAGAAAAAAAATG
1 AAGAAAAAAAA-G
399219 AA-AAAAAGAAAG
1 AAGAAAAA-AAAG
*
399231 AAAAAAGAAAAAG
1 AAGAAA-AAAAAG
*
399244 AATTGAGAAAAAGAAA
1 AA--GA-AAAAA-AAG
399260 AAGAAAAAGAAA-
1 AAGAAAAA-AAAG
*
399272 AAGAAAGAAAAG
1 AAGAAAAAAAAG
*
399284 AAGAAAATAAAG
1 AAGAAAAAAAAG
*
399296 AATAAACAAAAAG
1 AAGAAA-AAAAAG
399309 GAGGGTTCAA
Statistics
Matches: 101, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
10 1 0.01
11 11 0.11
12 39 0.39
13 35 0.35
14 5 0.05
15 4 0.04
16 6 0.06
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:400794 original size:133 final size:133
Alignment explanation
Indices: 400519--401092 Score: 652
Period size: 133 Copynumber: 4.3 Consensus size: 133
400509 GCAAATCAAA
* * * * * *
400519 CTCGATTGAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGAAAGTGGAATGAATCAACATCCTCAGATCTAATTTTCCCTCA
* * *
400584 AGAAAAAG-AGAAACATATCCTTATTTTTCAAGATTTGATATTCCCTGAGTAACAGTTGAACAAG
66 AGAAAAAGTAG-AACATATCCTTCTTTCT-AAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
400648 TCTGC
129 TATGC
* * * * * * **
400653 CTCGATTCAATCTTCACTAAGTGACAGTGGAATGAATCAGCATCCTTAGATCCAATTTTACCTTT
1 CTCGATTCAATCTTCCCTAAGTGAAAGTGGAATGAATCAACATCCTCAGATCTAATTTTCCCTCA
* *
400718 AGAAAAAGT-GAAC-TGATCCCTCTCTTCTAAGATTTGATATTCCCTGAGTAACAGAGGAACAAG
66 AGAAAAAGTAGAACAT-ATCCTTCT-TTCTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
400781 TATGC
129 TATGC
* * * * *
400786 CTTGATTCAATCTTCCCTGAGTTAAAATGGAATGAATCAACGTCCTCAGATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGAAAGTGGAATGAATCAACATCCTCAGATCTAATTTTCCCTCA
* * ** *
400851 AGAAGAAGTACAACATATCCTTCTTT-TCAAGATTTGATATTCCCTGAGTATTAGTGGAATAAGT
66 AGAAAAAGTAGAACATATCCTTCTTTCT-AAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
* *
400915 CTAC
130 ATGC
* * * * * * * * *
400919 CTTGATTCGATCTCCCCTAAGTGATAGTTGAATGAATCAACATCCCCAAATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGAAAGTGGAATGAATCAACATCCTCAGATCTAATTTTCCCTCA
* * *
400984 AGAAAAAGTGGAACATATCCTTCTTTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAAGT
66 AGAAAAAGTAGAACATATCCTTCTTTCT-AAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
401049 ATGC
130 ATGC
* *
401053 CTCGATTTAATCTTCCCTGAGTGAAAGTGGAATGAATCAA
1 CTCGATTCAATCTTCCCTAAGTGAAAGTGGAATGAATCAA
401093 TGTCTCCAGA
Statistics
Matches: 365, Mismatches: 68, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
132 2 0.01
133 218 0.60
134 144 0.39
135 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTAAGTGAAAGTGGAATGAATCAACATCCTCAGATCTAATTTTCCCTCA
AGAAAAAGTAGAACATATCCTTCTTTCTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTA
TGC
Found at i:401025 original size:267 final size:267
Alignment explanation
Indices: 400519--401125 Score: 765
Period size: 267 Copynumber: 2.3 Consensus size: 267
400509 GCAAATCAAA
* * * * *
400519 CTCGATTGAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGAAAGTGGAATGAATCAACGTCCTCAGATCTGATTTTCCCTCA
* * *
400584 AGAAAAAGAGAAACATATCCTTATTTTTCAAGATTTGATATTCCCTGAGTAACAGTTGAACAAGT
66 AGAAGAAGAGAAACATATCCTTACTTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
* * * ** * *
400649 CTGCCTCGATTCAATCTTCACTAAGTGACAGTGGAATGAATCAGCATCCTTAGATCCAATTTTAC
131 CTACCTCGATTCAATCTCCACTAAGTGACAGTGGAATGAATCAACATCCCCAAATACAATTTTAC
** *
400714 CTTTAGAAAAAGTGAACTGATCCCTCTCTTCTAAGATTTGATATTCCCTGAGTAACAGAGGAACA
196 CTCAAGAAAAAGTGAACTGATCCCTCTCTTCTAAGATTTGATATTCCATGAGTAACAGAGGAACA
400779 AGTATGC
261 AGTATGC
* * * *
400786 CTTGATTCAATCTTCCCTGAGTTAAAATGGAATGAATCAACGTCCTCAGATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGAAAGTGGAATGAATCAACGTCCTCAGATCTGATTTTCCCTCA
* ** *
400851 AGAAGAAGTA-CAACATATCCTT-CTTTTCAAGATTTGATATTCCCTGAGTATTAGTGGAATAAG
66 AGAAGAAG-AGAAACATATCCTTACTTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
* * * * * ** *
400914 TCTACCTTGATTCGATCTCCCCTAAGTGATAGTTGAATGAATCAACATCCCCAAATATGATTTTC
130 TCTACCTCGATTCAATCTCCACTAAGTGACAGTGGAATGAATCAACATCCCCAAATACAATTTTA
* * *
400979 CCTCAAGAAAAAGTGGAACAT-ATCCTTCT-TTTTCAAGATTTGATATTCCATGAGTAACAGTGG
195 CCTCAAGAAAAAGT-GAAC-TGATCCCTCTCTTCT-AAGATTTGATATTCCATGAGTAACAGAGG
401042 AACAAGTATGC
257 AACAAGTATGC
* * * *
401053 CTCGATTTAATCTTCCCTGAGTGAAAGTGGAATGAATCAATGT-CTCCAGATTTGATTTTCCATC
1 CTCGATTCAATCTTCCCTGAGTGAAAGTGGAATGAATCAACGTCCT-CAGATCTGATTTTCCCTC
401117 AAGAAGAAG
65 AAGAAGAAG
401126 CGGAACAAAT
Statistics
Matches: 290, Mismatches: 45, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
266 103 0.36
267 185 0.64
268 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (267 bp):
CTCGATTCAATCTTCCCTGAGTGAAAGTGGAATGAATCAACGTCCTCAGATCTGATTTTCCCTCA
AGAAGAAGAGAAACATATCCTTACTTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTACCTCGATTCAATCTCCACTAAGTGACAGTGGAATGAATCAACATCCCCAAATACAATTTTAC
CTCAAGAAAAAGTGAACTGATCCCTCTCTTCTAAGATTTGATATTCCATGAGTAACAGAGGAACA
AGTATGC
Found at i:403741 original size:130 final size:129
Alignment explanation
Indices: 403438--403779 Score: 411
Period size: 130 Copynumber: 2.6 Consensus size: 129
403428 CACTTCGGTC
* * * *
403438 GGAGTAATAAATGACTGTTTTAAGGCATGAGAGGGCATTTATTCCCGATTGGAAATAATTTGATA
1 GGAGTAATAAATGACTG-TTTAA-GCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATA
** * * * * *
403503 TTGCCGTTTTCTCTCTAATTAATATCGATTTTTAAGATGGAATAGTGATATATCTTCATTTCGAT
64 TTATCGTTTTCACTCTAATCAATATCGAATTTTAAGATGAAATAGTAATATATCTTCATTTCGAT
403568 T
129 T
* * * *
403569 TGAGCAATAAATGACTGCTATAAGATATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATA
1 GGAGTAATAAATGACTG-TTTAAG-CATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATA
* * *
403634 TTATCGTTTTCACT-TGAATCAAT-TTGAATTTTAAGATGAAATAGTAATATCTCTTTATTT-GA
64 TTATCGTTTTCACTCT-AATCAATATCGAATTTTAAGATGAAATAGTAATATATCTTCATTTCG-
403696 ATT
127 ATT
* *
403699 GGAGTAATAAATGAATGTTTCAATGCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAAATA
1 GGAGTAATAAATGACTGTTT-AA-GCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATA
403764 TTATCGTTTTCACTCT
64 TTATCGTTTTCACTCT
403780 TAAAATTATT
Statistics
Matches: 180, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
129 3 0.02
130 104 0.58
131 73 0.41
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (129 bp):
GGAGTAATAAATGACTGTTTAAGCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATT
ATCGTTTTCACTCTAATCAATATCGAATTTTAAGATGAAATAGTAATATATCTTCATTTCGATT
Found at i:414153 original size:19 final size:18
Alignment explanation
Indices: 414118--414231 Score: 70
Period size: 19 Copynumber: 6.0 Consensus size: 18
414108 ATTAAAAGAG
414118 AAAAAGAAATAAA-GAAAA
1 AAAAAGAAA-AAAGGAAAA
414136 AAAAAGAAAAAAGTGAAAA
1 AAAAAGAAAAAAG-GAAAA
* **
414155 AAAGATAGAACAACTGAAAA
1 AAA-A-AGAAAAAAGGAAAA
**
414175 AAGAAA-AGAAAATTGAAAA
1 AA-AAAGA-AAAAAGGAAAA
* * *
414194 AGAAAGACAGAAAGAAAAA
1 AAAAAGA-AAAAAGGAAAA
414213 AAAAAGAAAAGAAGGAAAA
1 AAAAAGAAAA-AAGGAAAA
414232 GGAGAATAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
17 3 0.04
18 15 0.20
19 40 0.54
20 9 0.12
21 7 0.09
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAAAGGAAAA
Found at i:414232 original size:37 final size:37
Alignment explanation
Indices: 414128--414232 Score: 99
Period size: 41 Copynumber: 2.8 Consensus size: 37
414118 AAAAAGAAAT
*
414128 AAAG-AAAAAAAAAGAAAAAAGTGAAAA-AAAGATAGA
1 AAAGAAAAAAAAAAGAAAAAAG-GAAAAGAAAGACAGA
** *
414164 ACAACTGAAAAAAGAAAAGAAAATTGAAAAAGAAAGACAG-
1 A-AA--GAAAAAA-AAAAGAAAAAAGGAAAAGAAAGACAGA
414204 AAAGAAAAAAAAAAGAAAAGAAGGAAAAG
1 AAAGAAAAAAAAAAGAAAA-AAGGAAAAG
414233 GAGAATAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
36 10 0.18
37 15 0.27
39 3 0.05
40 10 0.18
41 17 0.31
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (37 bp):
AAAGAAAAAAAAAAGAAAAAAGGAAAAGAAAGACAGA
Found at i:415639 original size:134 final size:134
Alignment explanation
Indices: 415437--415948 Score: 555
Period size: 134 Copynumber: 3.8 Consensus size: 134
415427 GAGAAAAGTG
* * * * * * * *
415437 GAATGAATCAACATCCCCAAATATGATTTTTCCCTCAAGAAGATGCGTAACATATCATTCTCTTT
1 GAATGAATCAACATCCCCAGATCT-AATTTTCCCTCAAAAAGAAGCGGAACAAATCCTTCTCTTT
* * * * *
415502 CAAGATTTGATATTCTCTGAGTAACAGTGGAACAAGTATGCCTTGATTAAATCTTCCCTAAGGAA
65 CAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTATGCCTCGATTCAATCTTCCCTAAGTAA
* *
415567 CAATC
130 CAGTA
** * *
415572 GAATGAATCAATGTCCCCAGATAC-GATTTTCCCTCAAAAAGAAGTGGAACAAATCCTTCTCTTT
1 GAATGAATCAACATCCCCAGAT-CTAATTTTCCCTCAAAAAGAAGCGGAACAAATCCTTCTCTTT
* * * *
415636 CAAGATTTGATATTCCCTAAGTAATAGTGTAACAAGTATGCATCGATTCAATCTTTCCTAAGTAA
65 CAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTATGCCTCGATTCAATCTTCCCTAAGTAA
415701 CAGTA
130 CAGTA
* * **
415706 GAATGAATCAACGTCCCCAGATCTAATTTCCCCTCAAGAAA-AAATGGAACAAATCCTTCTCTTT
1 GAATGAATCAACATCCCCAGATCTAATTTTCCCTCAA-AAAGAAGCGGAACAAATCCTTCTCTTT
* * * * * *
415770 CAAGATTTGATATTCCCTAAGTAATAGTGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTCA
65 CAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTATGCCTCGATTCAATCTTCCCTAAGTAA
*
415835 CAGTG
130 CAGTA
* * * * * * **
415840 GAATGATTCAACATCCTC-GATCTAATTTT-CCTCAAGAAGAAGCAGAATATATCCCCCTCTTTC
1 GAATGAATCAACATCCCCAGATCTAATTTTCCCTCAAAAAGAAGCGGAACAAATCCTTCTCTTTC
* * * *
415903 TAGATTTGACATTCCCTTAGTAACAGTGGAACAAGTCTGCCTCGAT
66 AAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTATGCCTCGAT
415949 CTGATCTACC
Statistics
Matches: 319, Mismatches: 54, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
131 2 0.01
132 63 0.20
133 11 0.03
134 221 0.69
135 22 0.07
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (134 bp):
GAATGAATCAACATCCCCAGATCTAATTTTCCCTCAAAAAGAAGCGGAACAAATCCTTCTCTTTC
AAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTATGCCTCGATTCAATCTTCCCTAAGTAAC
AGTA
Found at i:424878 original size:54 final size:52
Alignment explanation
Indices: 424819--424924 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 52
424809 AGAAAAAAGG
424819 GGAGAAATATTAT-AGTAAATAGGAGTATTTTTTCAAAGGAATCTTAAATTTTTT
1 GGAGAAATATT-TGAGTAAATAGGAGTA-TTTTTCAAAGGAATCTT-AATTTTTT
*
424873 GGAGAAATGTTTGAGTAAATAGGAGTATTTTTCAAAGGAATCTTAATTTTTT
1 GGAGAAATATTTGAGTAAATAGGAGTATTTTTCAAAGGAATCTTAATTTTTT
424925 CAACGTTTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
52 8 0.16
53 18 0.36
54 24 0.48
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (52 bp):
GGAGAAATATTTGAGTAAATAGGAGTATTTTTCAAAGGAATCTTAATTTTTT
Found at i:425598 original size:302 final size:298
Alignment explanation
Indices: 425126--425727 Score: 823
Period size: 302 Copynumber: 2.0 Consensus size: 298
425116 AACAAAATTT
* * *
425126 TCTAAGGATTTCAATCTTTAATCGAGTTAAAAATGTTTTTACAGAATTATAGTATCCATACTATA
1 TCTAAGGATTTCAATCTTTAATCGAGTTAAAAATGATTTTACAGAATGATAGTATCAATACTATA
* * **
425191 AGAACAATACATACACTTTTCATATGGTATTGATGTAGTATCAATTCTACATCTTTAAAATCACC
66 AGAACAATACATACACTTTGCATATGGTATCGACATAGTATCAATTCTACATCTTTAAAATCACC
* *
425256 AAGTAGTACTTATACTACACTAGGTAGAACTGAAACAACCTATTGTTTTGAGAAAACAAAATAAA
131 AAGCAGTACTTATACTACACTAGGTAGAACCGAAACAACCTATTGTTTTGA-AAAA-AAAAT--A
* * * * *
425321 AAAAATGGTAATGATACTCTATATAGTATATATACTACTTATAATAGTAGTAACGATACTTCCCT
192 AAAAATGGCAATGATACTCCATATAGTATAGATACTACTTATAACAATAGTAACGATACTTCCCT
* * *
425386 AATGTTTTAAAATTCAACATATTGCAGTATATATAAATGGCA
257 AATGTATTAAAATTCAACATATTACAATATATATAAATGGCA
** *
425428 TCTAAGGATTTCGAA-CTTTAATCGAGTCT-AAAATGATTTTACATCATGATAGTATCAATATTA
1 TCTAAGGATTTC-AATCTTTAATCGAGT-TAAAAATGATTTTACAGAATGATAGTATCAATACTA
* * *
425491 TAAGAACAATATATATA-TTGTGCATATGGTATCGACATAGTATCCATTCTACATCTTTAAAATC
64 TAAGAACAATACATACACTT-TGCATATGGTATCGACATAGTATCAATTCTACATCTTTAAAATC
* * * * * *
425555 ACCACGCAGTACTTATACTGCACTAGGTAGTACCGATACAACCTATTGTTTTTACAAAAAAATAA
128 ACCAAGCAGTACTTATACTACACTAGGTAGAACCGAAACAACCTATTGTTTTGAAAAAAAAATAA
* * *
425620 AAAATGGCAATGATACTCCATATAGTATCGATACTACTTATAACAATAGTATCGATACTTCCCTT
193 AAAATGGCAATGATACTCCATATAGTATAGATACTACTTATAACAATAGTAACGATACTTCCCTA
*
425685 ATGTATTAAAATTCAACATATTACAATATGTATAAATGGCA
258 ATGTATTAAAATTCAACATATTACAATATATATAAATGGCA
425726 TC
1 TC
425728 GATACTATCA
Statistics
Matches: 264, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
298 98 0.37
300 5 0.02
301 5 0.02
302 153 0.58
303 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (298 bp):
TCTAAGGATTTCAATCTTTAATCGAGTTAAAAATGATTTTACAGAATGATAGTATCAATACTATA
AGAACAATACATACACTTTGCATATGGTATCGACATAGTATCAATTCTACATCTTTAAAATCACC
AAGCAGTACTTATACTACACTAGGTAGAACCGAAACAACCTATTGTTTTGAAAAAAAAATAAAAA
ATGGCAATGATACTCCATATAGTATAGATACTACTTATAACAATAGTAACGATACTTCCCTAATG
TATTAAAATTCAACATATTACAATATATATAAATGGCA
Found at i:432308 original size:21 final size:21
Alignment explanation
Indices: 432261--432310 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
432251 TCGACTTTGG
* * *
432261 AACTTTTCCTGGGATGGAACT
1 AACTTTTCCTAGGACGGAACC
* *
432282 AGCTTTTCCTAGGACGTAACC
1 AACTTTTCCTAGGACGGAACC
432303 AACTTTTC
1 AACTTTTC
432311 TTATGAAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (21 bp):
AACTTTTCCTAGGACGGAACC
Found at i:432327 original size:21 final size:21
Alignment explanation
Indices: 432303--432350 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
432293 GGACGTAACC
432303 AACTTTTCTTATGAAATTGCT
1 AACTTTTCTTATGAAATTGCT
* *
432324 AACTTTTCTTGTGAAATTTCT
1 AACTTTTCTTATGAAATTGCT
432345 AACTTT
1 AACTTT
432351 CCTATGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (21 bp):
AACTTTTCTTATGAAATTGCT
Found at i:433791 original size:18 final size:18
Alignment explanation
Indices: 433738--433791 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
433728 ATAAAAAGGG
433738 AAAGATAATAATAA-AAT
1 AAAGATAATAATAATAAT
* **
433755 -AATA-AATAATAATTTT
1 AAAGATAATAATAATAAT
*
433771 AAAGATAATAATAATGAT
1 AAAGATAATAATAATAAT
433789 AAA
1 AAA
433792 AAAAGGGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 3 0.11
18 13 0.46
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (18 bp):
AAAGATAATAATAATAAT
Found at i:434061 original size:147 final size:150
Alignment explanation
Indices: 433783--434083 Score: 554
Period size: 147 Copynumber: 2.0 Consensus size: 150
433773 AGATAATAAT
433783 AATGATAAAAAAAGGGTTTTTAAATTATTTAAAGAAATAAAAAATAAAGATTAAATAAACAATTA
1 AATGATAAAAAAAGGGTTTTTAAATTATTTAAAGAAATAAAAAATAAAGATTAAATAAACAATT-
*
433848 AATAAATAAAATAAATTATAATAAAGAAAACTTATGGTAAAAGCAGTCTCAGACTTCAGCTTTGC
65 -ATAAATAAAATAAATTATAATAAAGAAAACTTATGGTAAAAGCAGTCTCAGACATCAGCTTTGC
433913 CTCAAATTCCTCGAATTATCGA
129 CTCAAATTCCTCGAATTATCGA
433935 AATGAT-AAAAAAGGGTTTTTAAATTATTTAAAGAAATAAAAAATAAAGATTAAATAAACAA-T-
1 AATGATAAAAAAAGGGTTTTTAAATTATTTAAAGAAATAAAAAATAAAGATTAAATAAACAATTA
433997 TAAATAAAATAAATTATAATAAAGAAAACTTATGGTAAAAGCAGTCTCAGACATCAGCTTTGCCT
66 TAAATAAAATAAATTATAATAAAGAAAACTTATGGTAAAAGCAGTCTCAGACATCAGCTTTGCCT
434062 CAAATTCCTCGAATTATCGA
131 CAAATTCCTCGAATTATCGA
434082 AA
1 AA
434084 CAAATCTTTA
Statistics
Matches: 148, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
147 86 0.58
150 1 0.01
151 55 0.37
152 6 0.04
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (150 bp):
AATGATAAAAAAAGGGTTTTTAAATTATTTAAAGAAATAAAAAATAAAGATTAAATAAACAATTA
TAAATAAAATAAATTATAATAAAGAAAACTTATGGTAAAAGCAGTCTCAGACATCAGCTTTGCCT
CAAATTCCTCGAATTATCGA
Found at i:435800 original size:24 final size:23
Alignment explanation
Indices: 435746--435790 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
435736 ATCCGTAATC
* *
435746 ACCATTATCATATATCAGTGAAT
1 ACCATAATCATATATCAGTCAAT
435769 ACCAATAATCATATATCAGTCA
1 ACC-ATAATCATATATCAGTCA
435791 TTGTCCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (23 bp):
ACCATAATCATATATCAGTCAAT
Found at i:436478 original size:17 final size:18
Alignment explanation
Indices: 436447--436481 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
436437 CAAAGTCAAC
436447 GGTCAACGAGTCGGGTCG
1 GGTCAACGAGTCGGGTCG
436465 GGTCAACG-GTCGGGTCG
1 GGTCAACGAGTCGGGTCG
436482 AACAGTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACGAGTCGGGTCG
Found at i:442005 original size:24 final size:23
Alignment explanation
Indices: 441951--441995 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
441941 ATCCGTAATC
* *
441951 ACCATTATCATATATCAGTGAAT
1 ACCATAATCATATATCAGTCAAT
441974 ACCAATAATCATATATCAGTCA
1 ACC-ATAATCATATATCAGTCA
441996 TTGTCCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (23 bp):
ACCATAATCATATATCAGTCAAT
Found at i:443657 original size:157 final size:157
Alignment explanation
Indices: 443370--443680 Score: 613
Period size: 157 Copynumber: 2.0 Consensus size: 157
443360 CCTATAAGTT
443370 TTCAAAACTTTTAATTAAACCCCCAAATTTCACCAAATTACACCAATATAAATATATATTTTTCT
1 TTCAAAACTTTTAATTAAACCCCCAAATTTCACCAAATTACACCAATATAAATATATATTTTTCT
443435 CTTATTTCCGGTTTGTTACACCAACCGTGACTAAATAATAATAAAAAATTGCAGAATATGCCCGT
66 CTTATTTCCGGTTTGTTACACCAACCGTGACTAAATAATAATAAAAAATTGCAGAATATGCCCGT
443500 TTTACTACTAATTCTGGAGAGTAACCA
131 TTTACTACTAATTCTGGAGAGTAACCA
443527 TTCAAAACTTTTAATTAAACCCCCAAATTTCACCAAATTACACCAATATAAATATATATTTTTCT
1 TTCAAAACTTTTAATTAAACCCCCAAATTTCACCAAATTACACCAATATAAATATATATTTTTCT
*
443592 CTTATTTCCGGTTTGTTACACCAACCGTGACTAAATAATAATAAAAAATTGCAGAATATGTCCGT
66 CTTATTTCCGGTTTGTTACACCAACCGTGACTAAATAATAATAAAAAATTGCAGAATATGCCCGT
443657 TTTACTACTAATTCTGGAGAGTAA
131 TTTACTACTAATTCTGGAGAGTAA
443681 AACATGCACG
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (157 bp):
TTCAAAACTTTTAATTAAACCCCCAAATTTCACCAAATTACACCAATATAAATATATATTTTTCT
CTTATTTCCGGTTTGTTACACCAACCGTGACTAAATAATAATAAAAAATTGCAGAATATGCCCGT
TTTACTACTAATTCTGGAGAGTAACCA
Found at i:447202 original size:18 final size:17
Alignment explanation
Indices: 447179--447223 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
447169 TTGATGGAGA
*
447179 TCAATTTCATTTGTTTAG
1 TCAATTTCAATT-TTTAG
447197 TCAA-TTCAATTTTTAG
1 TCAATTTCAATTTTTAG
447213 TCAA-TTCAATT
1 TCAATTTCAATT
447224 GGGCATCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 16 0.62
17 6 0.23
18 4 0.15
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (17 bp):
TCAATTTCAATTTTTAG
Found at i:447213 original size:16 final size:16
Alignment explanation
Indices: 447192--447223 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
447182 ATTTCATTTG
447192 TTTAGTCAATTCAATT
1 TTTAGTCAATTCAATT
447208 TTTAGTCAATTCAATT
1 TTTAGTCAATTCAATT
447224 GGGCATCGAG
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:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTAGTCAATTCAATT
Found at i:448165 original size:22 final size:23
Alignment explanation
Indices: 448139--448181 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
448129 CATGATATCC
*
448139 TAAAA-ATTTCAGGGCATGTTTA
1 TAAAATATTTCAAGGCATGTTTA
*
448161 TAAAATATTTCAATGCATGTT
1 TAAAATATTTCAAGGCATGTT
448182 GTTCCAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (23 bp):
TAAAATATTTCAAGGCATGTTTA
Found at i:452803 original size:33 final size:33
Alignment explanation
Indices: 452761--452827 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
452751 CAGTTCATTC
452761 GGTATGGATACCAGTATTTCAGCATGAATACCA
1 GGTATGGATACCAGTATTTCAGCATGAATACCA
* * * *
452794 GGTATGGATACCAGTCTTTCGGTATGGATACCA
1 GGTATGGATACCAGTATTTCAGCATGAATACCA
452827 G
1 G
452828 TCTTTCGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (33 bp):
GGTATGGATACCAGTATTTCAGCATGAATACCA
Found at i:452819 original size:20 final size:20
Alignment explanation
Indices: 452701--452846 Score: 101
Period size: 20 Copynumber: 7.6 Consensus size: 20
452691 TATCGATATT
* **
452701 GTATGGATACAAAACTTTCG
1 GTATGGATACCAGTCTTTCG
* * *
452721 ATATAGATACCAAG-CCTTCG
1 GTATGGATACC-AGTCTTTCG
* *
452741 ATATGGATACCAGTTCATTCG
1 GTATGGATACCAG-TCTTTCG
* *
452762 GTATGGATACCAGTATTTCA
1 GTATGGATACCAGTCTTTCG
* *
452782 GCATGAATACCA-------G
1 GTATGGATACCAGTCTTTCG
452795 GTATGGATACCAGTCTTTCG
1 GTATGGATACCAGTCTTTCG
452815 GTATGGATACCAGTCTTTCG
1 GTATGGATACCAGTCTTTCG
*
452835 GTATAGATACCA
1 GTATGGATACCA
452847 AGAATTCAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
13 10 0.10
19 2 0.02
20 69 0.70
21 18 0.18
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (20 bp):
GTATGGATACCAGTCTTTCG
Found at i:458942 original size:39 final size:38
Alignment explanation
Indices: 458852--458942 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
458842 TAAAAACCTG
*
458852 CGGTAAGGACTTACCCTGAGCACAAACCTGAGGAGCCT
1 CGGTAAGGACTTACCCTGAGAACAAACCTGAGGAGCCT
* * *
458890 GGGTAAGGACTTACCTTGAGAACAATGCC-GAGGAGCCT
1 CGGTAAGGACTTACCCTGAGAACAA-ACCTGAGGAGCCT
458928 ACGGTAAGGACTTAC
1 -CGGTAAGGACTTAC
458943 AAGTCATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 31 0.67
39 15 0.33
ACGTcount: A:0.30, C:0.24, G:0.29, T:0.18
Consensus pattern (38 bp):
CGGTAAGGACTTACCCTGAGAACAAACCTGAGGAGCCT
Found at i:470305 original size:85 final size:83
Alignment explanation
Indices: 470158--470355 Score: 229
Period size: 85 Copynumber: 2.4 Consensus size: 83
470148 ATATAACACG
* * *
470158 CAATGTAAGTCATACATGTATGTCATAAATTTATGACACACAAATGTATGTCAAGTAGATTTATG
1 CAATGTAAGTCATACATGCACGTCATAAATTTATGACACACAAATGTATGTCAACTAGATTTATG
*
470223 ACGGGGGCTTTAATGACGTT
66 A-GGGGGC-TTAATGACGCT
* * * * **
470243 CAATGTAAGTAATACATGCGA-GTCATAAATTTCTGACACACAAATGTGTGTCATCTTTATTTAT
1 CAATGTAAGTCATACATGC-ACGTCATAAATTTATGACACACAAATGTATGTCAACTAGATTTAT
* *
470307 GATGGGGCTTCATGACGCT
65 GAGGGGGCTTAATGACGCT
*
470326 CAATG-AACGTCATAAATGCACGTCATAAAT
1 CAATGTAA-GTCATACATGCACGTCATAAAT
470356 GTGTGTCATA
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
82 3 0.03
83 32 0.33
84 5 0.05
85 56 0.58
86 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (83 bp):
CAATGTAAGTCATACATGCACGTCATAAATTTATGACACACAAATGTATGTCAACTAGATTTATG
AGGGGGCTTAATGACGCT
Found at i:470348 original size:13 final size:13
Alignment explanation
Indices: 470327--470370 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
470317 CATGACGCTC
*
470327 AATGAACGTCATA
1 AATGCACGTCATA
470340 AATGCACGTCATA
1 AATGCACGTCATA
***
470353 AATGTGTGTCATA
1 AATGCACGTCATA
470366 AATGC
1 AATGC
470371 GTGTCATAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (13 bp):
AATGCACGTCATA
Found at i:470374 original size:13 final size:13
Alignment explanation
Indices: 470334--470378 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
470324 CTCAATGAAC
**
470334 GTCATAAATGCAC
1 GTCATAAATGCGT
*
470347 GTCATAAATGTGT
1 GTCATAAATGCGT
470360 GTCATAAATGCGT
1 GTCATAAATGCGT
470373 GTCATA
1 GTCATA
470379 GATTTATGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:471701 original size:18 final size:15
Alignment explanation
Indices: 471638--471733 Score: 67
Period size: 15 Copynumber: 6.3 Consensus size: 15
471628 CGAACCCTCG
471638 TTTTTC-TTTTCATT
1 TTTTTCATTTTCATT
*
471652 TTATTTCTTATTTC--T
1 TT-TTTCAT-TTTCATT
*
471667 TATTTCATTTTCATT
1 TTTTTCATTTTCATT
471682 TTTTTCATTTTCCATCTT
1 TTTTTCATTTT-CA--TT
*
471700 TTTTTCATTTT--TC
1 TTTTTCATTTTCATT
471713 TTTTTCACTTTTTCATT
1 TTTTTCA--TTTTCATT
471730 TTTT
1 TTTT
471734 CTTGTTTAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
13 12 0.18
14 7 0.11
15 21 0.32
16 3 0.05
17 9 0.14
18 13 0.20
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTCATTTTCATT
Found at i:471714 original size:15 final size:15
Alignment explanation
Indices: 471669--471734 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 15
471659 TTATTTCTTA
471669 TTTCA-TTTTCATTTT
1 TTTCATTTTTC-TTTT
471684 TTTCATTTTCCATCTTTT
1 TTTCATTTT---TCTTTT
471702 TTTCATTTTTC--TT
1 TTTCATTTTTCTTTT
*
471715 TTTCACTTTTTCATTT
1 TTTCA-TTTTTCTTTT
471731 TTTC
1 TTTC
471735 TTGTTTAAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 7 0.16
14 6 0.14
15 7 0.16
16 9 0.20
18 13 0.30
19 2 0.05
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCATTTTTCTTTT
Found at i:487020 original size:3 final size:3
Alignment explanation
Indices: 487012--487055 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
487002 TTTGTATGGG
*
487012 TTA TTA TTA TTA TTA TTTA ATA TTA TTA TTA TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
487056 TACGTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:487037 original size:16 final size:14
Alignment explanation
Indices: 487015--487055 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 14
487005 GTATGGGTTA
487015 TTATTATTATTATT
1 TTATTATTATTATT
487029 TAATATTATTATTATT
1 T--TATTATTATTATT
487045 TTATTATTATT
1 TTATTATTATT
487056 TACGTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:491652 original size:24 final size:24
Alignment explanation
Indices: 491610--491656 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
491600 TGCTTTGGCC
*
491610 AAAAGAAAAGAGATTTATGTAAAAG
1 AAAAGAAAAGAGATATATG-AAAAG
*
491635 AAAAG-AAAGAGCTATATGAAAA
1 AAAAGAAAAGAGATATATGAAAA
491657 CAATCATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (24 bp):
AAAAGAAAAGAGATATATGAAAAG
Found at i:497266 original size:42 final size:41
Alignment explanation
Indices: 497197--497301 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 41
497187 TTACTTAGTT
*
497197 AATCCTTCGGGCCATC-AGTAAGGCTTTCGAA-CATGATGATTA
1 AATCCTTCGGGCCATCTA-TAAGGCTTTC-AAGCAAGATGA-TA
* * * *
497239 AATCCTTCGGGTCATCTATCAGTCTTTCAAGTAAGATGATA
1 AATCCTTCGGGCCATCTATAAGGCTTTCAAGCAAGATGATA
*
497280 AGTCCTTCGGGCCATCTATAAG
1 AATCCTTCGGGCCATCTATAAG
497302 ACCTTCAGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
41 23 0.43
42 29 0.55
43 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (41 bp):
AATCCTTCGGGCCATCTATAAGGCTTTCAAGCAAGATGATA
Found at i:497536 original size:42 final size:42
Alignment explanation
Indices: 497458--497554 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 42
497448 AATTGATAAG
* * * *
497458 TCCTTTGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAA
1 TCCTTTGGGCCATCAGCAAGTCTTTCGAACAAGATGATTAAA
* * * *
497500 TCCTTTGGGTCATCTGCCAGTCTTTCGAACAAGATGA-TAAG
1 TCCTTTGGGCCATCAGCAAGTCTTTCGAACAAGATGATTAAA
* *
497541 TTCTTCGGGCCATC
1 TCCTTTGGGCCATC
497555 TATAAGACTT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 14 0.32
42 30 0.68
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
TCCTTTGGGCCATCAGCAAGTCTTTCGAACAAGATGATTAAA
Found at i:497938 original size:256 final size:255
Alignment explanation
Indices: 497199--498026 Score: 1119
Period size: 259 Copynumber: 3.2 Consensus size: 255
497189 ACTTAGTTAA
* *
497199 TCCTTCGGGCCATCAGTAAGGCTTTCGAACATGATGATTAAATCCTTCGGGTCATCTATCAGTCT
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGTCT
* * *
497264 TTCAAGTAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGTAGGATGTTTTTACATGA
66 TTCACGTAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAGGATGTTTTCACATGA
* * * * * * *
497329 TTTTTGAAAAATAAGAAAGCCATTTCCAAATTTTTTTATTTAATATTTTCAAAAAAATTGAATTT
131 TTTTCGAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAATATTTTC--AAAAA-TGAAATT
*
497394 TTTGAAAAGTAAGAAATTATTTTCCAAAGTTTCTTACCTAG-AAACTATTTCCAAAA-TTGATAA
193 TTTGAAAAGTAAGAAAGTA-TTTCCAAAGTTTCTTACCTAGTAAACT-TTTCCAAAATTTG-TAA
497457 G
255 G
* * * **
497458 TCCTTTGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTTGGGTCATCTGCCAGTCT
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGTCT
* *
497523 TTCGAAC--AAGATGATAAGTTCTTCGGGCCATCTATAAGACTTTCAGGCAGGATGTTTTCACAT
66 TTC--ACGTAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAGGATGTTTTCACAT
* * *
497586 GATTTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCTTTTAATATTTTTAGAAAATGAAATT
129 GATTTTCGAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAATATTTTCA-AAAATGAAATT
**
497651 TTTGAAAAGTAAGAAAGTATTTCCAAAGTTTCTTACCTAGTAATTTGTTTCCAAAATTTGTAAG
193 TTTGAAAAGTAAGAAAGTATTTCCAAAGTTTCTTACCTAGTAAACT-TTTCCAAAATTTGTAAG
* * * * *
497715 TCCTTCTGGCCATCAGTAAATCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTATCAGTCT
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGTCT
* * *
497780 TTCACGTAAGATGATAAGTCCTTCGGGCCATCT-T-AGACCTTCGGGCAAAGATATTTTCACATG
66 TTCACGTAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGC-AGGATGTTTTCACATG
* * * *
497843 ATTTTCCAAAAATGAGAAAACAATTTCCAAAGTTTCTCATTTAGTAGTTTCAAAAATGAAATTTT
130 ATTTTCGAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAATATTTTCAAAAATGAAATTTT
* * * *
497908 TGAAAATTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTCCAAAATTAGTAAG
195 TGAAAAGTAAGAAAG-TATTTCCAAAGTTTCTTACCTAGTAAACTTTTCCAAAATTTGTAAG
* *
497970 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTTATCT
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCT
498027 GCCAGTCACA
Statistics
Matches: 501, Mismatches: 59, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
255 105 0.21
256 107 0.21
257 124 0.25
258 7 0.01
259 157 0.31
261 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (255 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGTCT
TTCACGTAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAGGATGTTTTCACATGA
TTTTCGAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAATATTTTCAAAAATGAAATTTTT
GAAAAGTAAGAAAGTATTTCCAAAGTTTCTTACCTAGTAAACTTTTCCAAAATTTGTAAG
Found at i:498164 original size:3 final size:3
Alignment explanation
Indices: 498156--498222 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
498146 TTTGTCCAGG
* * * * * * *
498156 TTA TTA TTA TTA TTA TTG TTG TTG TTG TTG TTA TTG TTA TTTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
498202 TTA TTA TTA TTTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TT
498223 TATAATTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:498211 original size:16 final size:16
Alignment explanation
Indices: 498186--498236 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
498176 GTTGTTGTTG
*
498186 TTATTGTTATTTAATA
1 TTATTATTATTTAATA
*
498202 TTATTATTATTTATTA
1 TTATTATTATTTAATA
*
498218 TTATTTATAATTTTAATA
1 TTA-TTATTA-TTTAATA
498236 T
1 T
498237 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 17 0.59
17 5 0.17
18 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTATTATTTAATA
Found at i:499131 original size:3 final size:3
Alignment explanation
Indices: 499123--499177 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
499113 TATTAATTTA
* * * *
499123 ATT ATT ATT AATT ATT AGT ATT TTT ATT -TT ATT GTT ATT ATT ATC
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
499168 ATT ATT -TT AT
1 ATT ATT ATT AT
499178 ATTTATAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:500318 original size:107 final size:107
Alignment explanation
Indices: 500123--500320 Score: 263
Period size: 107 Copynumber: 1.9 Consensus size: 107
500113 ATACTCATAG
* * * *
500123 GTCCCCTATAATTTAGCGCATTTTTGAATGTTGGTCACCTACGAGGACCAAAGTTGTTATTTACC
1 GTCCCCCATAATTTAGCGCATTTTTGAATGCTGGTAACCTAAGAGGACCAAAGTTGTTATTTACC
** *
500188 CGTTTTCATGCATATTTTATATTTTTGGGATGTTTTTGTTTA
66 AATTTTCATGCATATTATATATTTTTGGGATGTTTTTGTTTA
* ** *
500230 GTCCCCCATAGTTTAGCGTGTTTTTGTATGCTGGTAACCTATAG-GGACCAAAGTTGTTATTTAC
1 GTCCCCCATAATTTAGCGCATTTTTGAATGCTGGTAACCTA-AGAGGACCAAAGTTGTTATTTAC
* *
500294 CAATTTTCATGCATGTTATGTATTTTT
65 CAATTTTCATGCATATTATATATTTTT
500321 TGGAATATTT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
107 76 0.99
108 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (107 bp):
GTCCCCCATAATTTAGCGCATTTTTGAATGCTGGTAACCTAAGAGGACCAAAGTTGTTATTTACC
AATTTTCATGCATATTATATATTTTTGGGATGTTTTTGTTTA
Found at i:504958 original size:20 final size:20
Alignment explanation
Indices: 504942--504986 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
504932 GTGCATTTTT
504942 ATTTTCTACATTGCATTTAC
1 ATTTTCTACATTGCATTTAC
**
504962 ATTTTCTGTATTGCATTTAC
1 ATTTTCTACATTGCATTTAC
504982 -TTTTC
1 ATTTTC
504987 GCACTACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.18, G:0.07, T:0.56
Consensus pattern (20 bp):
ATTTTCTACATTGCATTTAC
Found at i:512039 original size:6 final size:6
Alignment explanation
Indices: 512020--512074 Score: 55
Period size: 5 Copynumber: 9.5 Consensus size: 6
512010 TCACATGAAG
*
512020 AAAGAA AAACGAA AAAG-A AAAG-G AAAGAA AAATGAA AAAG-A AAA-AA
1 AAAGAA AAA-GAA AAAGAA AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA
512066 AAAGAA AAA
1 AAAGAA AAA
512075 AATAAATATC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 17 0.40
6 13 0.31
7 12 0.29
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:512049 original size:23 final size:23
Alignment explanation
Indices: 512017--512074 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
512007 ACTTCACATG
512017 AAGAAAGAAAAACGAAAAAGAAA
1 AAGAAAGAAAAACGAAAAAGAAA
* *
512040 AGGAAAGAAAAATGAAAAAGAAA
1 AAGAAAGAAAAACGAAAAAGAAA
*
512063 AAAAAAGAAAAA
1 AAGAAAGAAAAA
512075 AATAAATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (23 bp):
AAGAAAGAAAAACGAAAAAGAAA
Done.