Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008442.1 Hibiscus syriacus cultivar Beakdansim tig00111244_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: 816021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:141651 original size:21 final size:21
Alignment explanation
Indices: 141627--141700 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
141617 ACGGATAGCC
141627 CGAAAGACTTATCATATTGCT
1 CGAAAGACTTATCATATTGCT
* *
141648 CGAAAGACTTA-CAGA-TGACC
1 CGAAAGACTTATCATATTG-CT
* *
141668 CGAAGGATTTAATCATCATT-CT
1 CGAAAGACTT-ATCAT-ATTGCT
141690 CGAAAGACTTA
1 CGAAAGACTTA
141701 CTGATAGCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 2 0.05
20 12 0.30
21 13 0.32
22 11 0.28
23 1 0.03
24 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (21 bp):
CGAAAGACTTATCATATTGCT
Found at i:141693 original size:42 final size:42
Alignment explanation
Indices: 141614--141716 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
141604 ACCCGAAGGT
* * *
141614 CTTACGGATAGCCCGAAAGACTT-ATCATATTGCTCGAAAGA
1 CTTACAGATAGCCCGAAGGATTTAATCATATTGCTCGAAAGA
141655 CTTACAGAT-GACCCGAAGGATTTAATCATCATT-CTCGAAAGA
1 CTTACAGATAG-CCCGAAGGATTTAATCAT-ATTGCTCGAAAGA
*
141697 CTTACTGATAGCCCGAAGGA
1 CTTACAGATAGCCCGAAGGA
141717 CTTACAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 1 0.02
41 18 0.33
42 31 0.57
43 4 0.07
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (42 bp):
CTTACAGATAGCCCGAAGGATTTAATCATATTGCTCGAAAGA
Found at i:141718 original size:20 final size:20
Alignment explanation
Indices: 141614--141721 Score: 58
Period size: 20 Copynumber: 5.2 Consensus size: 20
141604 ACCCGAAGGT
*
141614 CTTACGGATAGCCCGAAAGA
1 CTTACTGATAGCCCGAAAGA
* *
141634 CTTATCAT-ATTGCTCGAAAGA
1 CTTA-C-TGATAGCCCGAAAGA
* *
141655 CTTACAGAT-GACCCGAAGGA
1 CTTACTGATAG-CCCGAAAGA
* * * * *
141675 TTTAATCATCATTCTCGAAAGA
1 CTTACTGAT-A-GCCCGAAAGA
*
141697 CTTACTGATAGCCCGAAGGA
1 CTTACTGATAGCCCGAAAGA
141717 CTTAC
1 CTTAC
141722 AAATTTTGGA
Statistics
Matches: 62, Mismatches: 19, Indels: 14
0.65 0.20 0.15
Matches are distributed among these distances:
19 1 0.02
20 31 0.50
21 17 0.27
22 13 0.21
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (20 bp):
CTTACTGATAGCCCGAAAGA
Found at i:141925 original size:41 final size:42
Alignment explanation
Indices: 141860--141964 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 42
141850 ATCCTACACA
* * *
141860 AAAGTCTTACAGATGACCCTAAGGATTCAA-TATCTTGCTCG
1 AAAGACTTACAGATGACCCGAAGGATTCAATTATCATGCTCG
*
141901 AAAGACTTACAGATGACCCGAAGGATTTAATTATCATGCTCG
1 AAAGACTTACAGATGACCCGAAGGATTCAATTATCATGCTCG
* *
141943 AAAGACTTACTGATGGCCCGAA
1 AAAGACTTACAGATGACCCGAA
141965 TGACTTACAA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 27 0.47
42 30 0.53
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (42 bp):
AAAGACTTACAGATGACCCGAAGGATTCAATTATCATGCTCG
Found at i:142484 original size:42 final size:41
Alignment explanation
Indices: 142383--142489 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
142373 ACCCGAAGGT
* * * * *
142383 CTTACAGATGGCCCTAAAGACTTATCATCTTGCTCGAAATA
1 CTTACAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
* ** *
142424 CTTACAGATGACTTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGA
142466 CTTACAGATGGCCCGAAGGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
142490 CAAATTTTGG
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 18 0.35
42 34 0.65
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:142555 original size:259 final size:253
Alignment explanation
Indices: 141343--142608 Score: 1692
Period size: 251 Copynumber: 5.0 Consensus size: 253
141333 TAACAAAAAT
** * *
141343 TGAAAACATCCTACCCGAAGGTCTTATGGATGGCCC-AAAGGACTTATCATCTTGCTCAAAATAC
1 TGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAA-GACTTATCATCTTGCTCGAAAGAC
* * * *
141407 TAACATATGACCCGAATGATTTAATCATCATGCTCGAAAGAATTACTGATGGCCCGAAGGACTTA
65 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
* * *
141472 CAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATTGCTTTCTTACTTTTCAAGAATT
130 CAAATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAATT
** * * * *
141537 TCATTTT-TTTAAATATTAAATAAGAAACTTTAGAAATCGCTTTCTCA---TTTTCATG
195 TCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTTTCATG
* * * * *
141592 TGAAAATATCATACCCGAAGGTCTTACGGATAGCCCGAAAGACTTATCATATTGCTCGAAAGACT
1 TGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACT
* *
141657 TACAGATGACCCGAAGGATTTAATCATCATTCTCGAAAGACTTACTGATAGCCCGAAGGACTTAC
66 TACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
* * *
141722 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTTCAAGAATT
131 AAATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATCGCTTTCTTAC-TTTTCAATAATT
* * *
141787 TTATTTTCTGAAAACATTAAATGAGAAACTTTGGTAATCACTTTCTCA---TTTTCATG
195 TCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTTTCATG
* * * * * *
141843 TGAAAACATCCTACACAAAAGTCTTACAGATGACCCTAAGGA-TTCAAT-ATCTTGCTCGAAAGA
1 TGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAAGACTT--ATCATCTTGCTCGAAAGA
* *
141906 CTTACAGATGACCCGAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTT
64 CTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* *
141971 ACAAATTTTGGAAATAATTTACTAGGTAAGAAACTTTAGTAACCGCTTTCTTACTTTTCAATAAT
129 ACAAATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAAT
*
142036 TTCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATGGCTTTCTCAGTTTTTTTAAAATCAT
194 TTCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCA--TTTTTT----TCAT
142101 G
253 G
* * * *
142102 TGGAAACATTCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTACTCGAAAAGAC
1 TGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAAGACTTATCATCTTGCTCG-AAAGAC
* ** * * *
142167 TTATAGATGAATCAAAGGATTTAAGT-ATCATGCTCAAAAGACTTACTGATGGCCCGAAGAACTT
65 TTACAGATGACCCGAAGGATTTAA-TCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* *
142231 ACAAATTTTGGAAATAATATACTCA-TTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAA
129 ACAAATTTTGGAAATAATTTACT-AGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAA
*
142295 TTTCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATTGCTTTCTCATTTTTTGAAAATCAT
193 TTTCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTT-----TCAT
142360 G
253 G
* * *
142361 TGGAAACATCCTACCCGAAGGTCTTACAGATGGCCCTAAAGACTTATCATCTTGCTCGAAATACT
1 TGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACT
** * *
142426 TACAGATGACTTGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTAC
66 TACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
** *
142491 AAATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATCATTTTTTTTACTTTTCAATAATT
131 AAATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATC-GCTTTCTTACTTTTCAATAATT
*
142556 TCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTT
195 TCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTT
142609 AAAATAACTT
Statistics
Matches: 907, Mismatches: 87, Indels: 36
0.88 0.08 0.03
Matches are distributed among these distances:
249 163 0.18
250 78 0.09
251 198 0.22
252 2 0.00
255 3 0.00
257 1 0.00
258 108 0.12
259 182 0.20
260 170 0.19
261 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (253 bp):
TGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACT
TACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
AAATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAATTT
CATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTTTCATG
Found at i:144925 original size:2 final size:2
Alignment explanation
Indices: 144918--144952 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
144908 TCAATTTTAT
144918 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
144953 TATCTTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:145043 original size:97 final size:97
Alignment explanation
Indices: 144940--145152 Score: 277
Period size: 97 Copynumber: 2.2 Consensus size: 97
144930 TATATATATA
* * *
144940 TATATATATATATTATCTTTATCA-GACTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACC
1 TATATATATATATTATCTTTATCACG-CTAGCTGAATCTTATCCATAAAGCCGGAGCATTTAACC
*
145004 AATTGCTCTAGAGGGACAACTCAAGCTTAATTG
65 AATTACTCTAGAGGGACAACTCAAGCTTAATTG
* * * *
145037 TATATAT-TATAATCACCTTTATCACGCTAGTTGAATCTTATCTATAAAGCCGGAGCATTTAACC
1 TATATATATAT-ATTATCTTTATCACGCTAGCTGAATCTTATCCATAAAGCCGGAGCATTTAACC
** *
145101 AATTACTCTAGAGGGACAGTTCAAGCTTTATTG
65 AATTACTCTAGAGGGACAACTCAAGCTTAATTG
*
145134 TATACATATAATATTATCT
1 TATATATAT-ATATTATCT
145153 GGGTATACGA
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
96 3 0.03
97 86 0.88
98 7 0.07
99 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (97 bp):
TATATATATATATTATCTTTATCACGCTAGCTGAATCTTATCCATAAAGCCGGAGCATTTAACCA
ATTACTCTAGAGGGACAACTCAAGCTTAATTG
Found at i:149880 original size:17 final size:16
Alignment explanation
Indices: 149839--149880 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
149829 AAATATATTT
149839 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
149855 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
149872 TAAAA-AATT
1 TAAAATAATT
149881 GATCTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:151729 original size:3 final size:3
Alignment explanation
Indices: 151723--151769 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
151713 ATTTATTTAT
151723 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
151770 TACAATGTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:153611 original size:20 final size:20
Alignment explanation
Indices: 153576--153613 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
153566 AGGGTTTTAG
* *
153576 TATATATATGTTTATATTAC
1 TATATATATATATATATTAC
153596 TATATATATATATATATT
1 TATATATATATATATATT
153614 TAGCCGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
TATATATATATATATATTAC
Found at i:162594 original size:8 final size:8
Alignment explanation
Indices: 162581--162616 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
162571 AAACACCCAT
162581 GACCCTCA
1 GACCCTCA
162589 GACCCTCA
1 GACCCTCA
162597 GACCCTCA
1 GACCCTCA
162605 GACCCTCA
1 GACCCTCA
162613 GACC
1 GACC
162617 TTACGAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.25, C:0.50, G:0.14, T:0.11
Consensus pattern (8 bp):
GACCCTCA
Found at i:165059 original size:136 final size:136
Alignment explanation
Indices: 164815--165087 Score: 537
Period size: 136 Copynumber: 2.0 Consensus size: 136
164805 TCGCACAAAC
164815 AAGGATGCATCAACTCTCGACTCCTCAAACCCTAATTCCAACAGACACCCTTTGAGCTTGTCATG
1 AAGGATGCATCAACTCTCGACTCCTCAAACCCTAATTCCAACAGACACCCTTTGAGCTTGTCATG
164880 CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
66 CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
164945 CATCTG
131 CATCTG
*
164951 AAGGATGCATCAACTCTTGACTCCTCAAACCCTAATTCCAACAGACACCCTTTGAGCTTGTCATG
1 AAGGATGCATCAACTCTCGACTCCTCAAACCCTAATTCCAACAGACACCCTTTGAGCTTGTCATG
165016 CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
66 CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
165081 CATCTG
131 CATCTG
165087 A
1 A
165088 GGCATATTCT
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 136 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (136 bp):
AAGGATGCATCAACTCTCGACTCCTCAAACCCTAATTCCAACAGACACCCTTTGAGCTTGTCATG
CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
CATCTG
Found at i:165308 original size:19 final size:19
Alignment explanation
Indices: 165284--165325 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
165274 ACTTGAGAGA
165284 AGCCATTAGTCACAAGCCT
1 AGCCATTAGTCACAAGCCT
*
165303 AGCCATTAGTCACAAGTCT
1 AGCCATTAGTCACAAGCCT
165322 AGCC
1 AGCC
165326 TTGTAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
AGCCATTAGTCACAAGCCT
Found at i:172892 original size:13 final size:13
Alignment explanation
Indices: 172859--172892 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
172849 TTGAAAAAGG
*
172859 AAGAAAAGGAAAT
1 AAGAAAAGGAAAC
172872 AAGAAAAGGAAAC
1 AAGAAAAGGAAAC
*
172885 AAGCAAAG
1 AAGAAAAG
172893 ACATGAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.24, T:0.03
Consensus pattern (13 bp):
AAGAAAAGGAAAC
Found at i:173315 original size:14 final size:15
Alignment explanation
Indices: 173291--173319 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
173281 GTATTTAACT
173291 TGTTCTAATTGATGA
1 TGTTCTAATTGATGA
173306 TGTT-TAATTGATGA
1 TGTTCTAATTGATGA
173320 ATGAATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
TGTTCTAATTGATGA
Found at i:173936 original size:23 final size:22
Alignment explanation
Indices: 173910--173966 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
173900 AAGAATTACC
173910 TTTAGGATTTATTTGTTATT-TAT
1 TTTAGGATTTATTT-TTATTGT-T
*
173933 TTTAGGAATTATATTTTTCTTGTT
1 TTTAGG-ATT-TATTTTTATTGTT
173957 TTTAGGATTT
1 TTTAGGATTT
173967 TGAAGGCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.03
23 9 0.30
24 14 0.47
25 6 0.20
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.63
Consensus pattern (22 bp):
TTTAGGATTTATTTTTATTGTT
Found at i:174707 original size:4 final size:4
Alignment explanation
Indices: 174698--174723 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
174688 TCACTTTAAA
174698 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
174724 TATCATTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:176566 original size:12 final size:12
Alignment explanation
Indices: 176544--176587 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
176534 ACAACTTTTC
176544 AACCA-CTAGCT
1 AACCATCTAGCT
* *
176555 AATCGTCTAGCT
1 AACCATCTAGCT
176567 AACCATCTAGCT
1 AACCATCTAGCT
176579 AACCATCTA
1 AACCATCTA
176588 ACTATAAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 3 0.11
12 25 0.89
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.25
Consensus pattern (12 bp):
AACCATCTAGCT
Found at i:179251 original size:43 final size:43
Alignment explanation
Indices: 179204--179330 Score: 218
Period size: 43 Copynumber: 3.0 Consensus size: 43
179194 GACATATAGT
* *
179204 GGCGTTTGTCTTTACAAACGCCGCTATTGAATGTGTATTTAAC
1 GGCGTTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAAC
*
179247 GGCGTTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAGC
1 GGCGTTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAAC
*
179290 GACGTTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTA
1 GGCGTTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTA
179331 GTGGCATTTG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (43 bp):
GGCGTTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAAC
Found at i:179453 original size:15 final size:15
Alignment explanation
Indices: 179433--179461 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
179423 GCATAAAACA
179433 AAACTATACACATTG
1 AAACTATACACATTG
179448 AAACTATACACATT
1 AAACTATACACATT
179462 AGTTCACCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
AAACTATACACATTG
Found at i:180748 original size:21 final size:21
Alignment explanation
Indices: 180722--180763 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
180712 AAGCTTAAAT
180722 GTGTTATAGCCGGCAGCACCG
1 GTGTTATAGCCGGCAGCACCG
180743 GTGTTATAGCCGGCAGCACCG
1 GTGTTATAGCCGGCAGCACCG
180764 AGCCTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (21 bp):
GTGTTATAGCCGGCAGCACCG
Found at i:182145 original size:10 final size:11
Alignment explanation
Indices: 182122--182164 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
182112 TTTAATGTTT
*
182122 ATTTTATAATA
1 ATTTAATAATA
182133 ATTTAATAA-A
1 ATTTAATAATA
*
182143 ATTTAATAATC
1 ATTTAATAATA
182154 A-TTAATAATA
1 ATTTAATAATA
182164 A
1 A
182165 ATTGATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:182147 original size:20 final size:21
Alignment explanation
Indices: 182122--182200 Score: 56
Period size: 20 Copynumber: 3.8 Consensus size: 21
182112 TTTAATGTTT
*
182122 ATTTTATAATAATTTAATAAA
1 ATTTAATAATAATTTAATAAA
*
182143 ATTTAATAATCA-TTAATAATA
1 ATTTAATAATAATTTAATAA-A
* * *
182164 AATTGAT--TAATTTAAAAAA
1 ATTTAATAATAATTTAATAAA
* *
182183 TATTTGATAATTATTTAA
1 -ATTTAATAATAATTTAA
182201 AGGTATTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
19 3 0.07
20 19 0.42
21 16 0.36
22 7 0.16
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTTAATAATAATTTAATAAA
Found at i:182625 original size:41 final size:41
Alignment explanation
Indices: 182574--183071 Score: 574
Period size: 41 Copynumber: 12.2 Consensus size: 41
182564 TTGTAAACAC
**
182574 AAACGCCACTAAAACACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
182615 AAACGCCACTAAATCATGAGTCTATAGCGACGTTTGTA-AA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* *
182655 AAATGCCACTAAATCACGAGTCTATAGCGGCGTTTGTA-ACA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATA-A
* * * *
182696 AACACGCCACTAAAGTATGAGTCTTTAGCGGCGATTGTATAA
1 AA-ACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
182738 AAACGCCACTAAAGTACGAGTCTTTAGTGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
182779 AAACGCCACTAAATCATGAGTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* *
182820 AAACGCCACTAAAGTACGAGTCTTTAGC-GCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* *
182860 AAACGCCACTAAATCATGAGTCTATAGCGGCGTTTGTATAAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTAT-AA
* * *
182902 AAACGCCACTAAAGTACAAGTCTATAGCGTCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
** * *
182943 AAATACCACTAAATTAC-AGACTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
182983 AAACTCCACTAAATTAC-ATTCTTTAGCGGCATTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * * * * * *
183023 AAACGCCGCTATAGTAGGAGTCTTTAGCAGCGTTTGTTCTAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTG-TATAA
183065 AAACGCC
1 AAACGCC
183072 GCTACAAACG
Statistics
Matches: 395, Mismatches: 55, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
40 140 0.35
41 174 0.44
42 80 0.20
43 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:183941 original size:29 final size:30
Alignment explanation
Indices: 183821--183970 Score: 141
Period size: 29 Copynumber: 5.1 Consensus size: 30
183811 ATTTTTATTG
*
183821 TTTATCCCTTTAAGATTATGTTTTTACTA-
1 TTTATCCCTTTAAGATTTTGTTTTTACTAT
* ** *
183850 TTTAGCCCTTTAAGATTTTGTAATTAATAT
1 TTTATCCCTTTAAGATTTTGTTTTTACTAT
* * *
183880 TTTAGT-CCTTTTAGTTTTTGTTTTTACT-G
1 TTTA-TCCCTTTAAGATTTTGTTTTTACTAT
183909 TTTATCCCTTTAAGATTTTG-TTTTACTAT
1 TTTATCCCTTTAAGATTTTGTTTTTACTAT
* *
183938 TTTAGT-CCTTTGAG-TTTATGTTTTTTCTAT
1 TTTA-TCCCTTTAAGATTT-TGTTTTTACTAT
183968 TTT
1 TTT
183971 GGTCGTTGTA
Statistics
Matches: 97, Mismatches: 17, Indels: 13
0.76 0.13 0.10
Matches are distributed among these distances:
28 11 0.11
29 53 0.55
30 33 0.34
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.59
Consensus pattern (30 bp):
TTTATCCCTTTAAGATTTTGTTTTTACTAT
Found at i:183962 original size:58 final size:59
Alignment explanation
Indices: 183827--183969 Score: 198
Period size: 59 Copynumber: 2.4 Consensus size: 59
183817 ATTGTTTATC
*
183827 CCTTTAAGATTATGTTTTTACTATTTAGCCCTTTAAGATTTTGTAATTAATATTTTAGT
1 CCTTTAAGTTTATGTTTTTACTATTTAGCCCTTTAAGATTTTGTAATTAATATTTTAGT
* * * * * *
183886 CCTTTTAGTTTTTGTTTTTACTGTTTATCCCTTTAAGATTTTGT-TTTACTATTTTAGT
1 CCTTTAAGTTTATGTTTTTACTATTTAGCCCTTTAAGATTTTGTAATTAATATTTTAGT
* *
183944 CCTTTGAGTTTATGTTTTTTCTATTT
1 CCTTTAAGTTTATGTTTTTACTATTT
183970 TGGTCGTTGT
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
58 34 0.47
59 39 0.53
ACGTcount: A:0.20, C:0.11, G:0.10, T:0.59
Consensus pattern (59 bp):
CCTTTAAGTTTATGTTTTTACTATTTAGCCCTTTAAGATTTTGTAATTAATATTTTAGT
Found at i:183970 original size:88 final size:88
Alignment explanation
Indices: 183778--183948 Score: 263
Period size: 88 Copynumber: 1.9 Consensus size: 88
183768 CTCTGGTTTA
* * *
183778 TTTGTAATTATTGTTTTAGTCCTTTTAGTTTCTATTTTTATTGTTTATCCCTTTAAGATTATGTT
1 TTTGTAATTAATATTTTAGTCCTTTTAGTTTCTATTTTTACTGTTTATCCCTTTAAGATTATGTT
183843 TTTACTATTTAGCCCTTTAAGAT
66 TTTACTATTTAGCCCTTTAAGAT
* * *
183866 TTTGTAATTAATATTTTAGTCCTTTTAGTTTTTGTTTTTACTGTTTATCCCTTTAAGATTTTG-T
1 TTTGTAATTAATATTTTAGTCCTTTTAGTTTCTATTTTTACTGTTTATCCCTTTAAGATTATGTT
*
183930 TTTACTATTTTAGTCCTTT
66 TTTACTA-TTTAGCCCTTT
183949 GAGTTTATGT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
87 8 0.11
88 67 0.89
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (88 bp):
TTTGTAATTAATATTTTAGTCCTTTTAGTTTCTATTTTTACTGTTTATCCCTTTAAGATTATGTT
TTTACTATTTAGCCCTTTAAGAT
Found at i:185010 original size:15 final size:15
Alignment explanation
Indices: 184990--185020 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
184980 TATGAGCAAT
184990 TCAAAAGTTAAGTAA
1 TCAAAAGTTAAGTAA
185005 TCAAAAGTTAAGTAA
1 TCAAAAGTTAAGTAA
185020 T
1 T
185021 TAAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (15 bp):
TCAAAAGTTAAGTAA
Found at i:186822 original size:15 final size:15
Alignment explanation
Indices: 186802--186851 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
186792 CAAAGATAAA
186802 AAATCCGATGGGAAG
1 AAATCCGATGGGAAG
186817 AAATCCGATGGGAAG
1 AAATCCGATGGGAAG
*
186832 AAATCCGATGAGAAG
1 AAATCCGATGGGAAG
186847 AAATC
1 AAATC
186852 TGACAAGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.28, T:0.14
Consensus pattern (15 bp):
AAATCCGATGGGAAG
Found at i:187514 original size:27 final size:27
Alignment explanation
Indices: 187476--187530 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
187466 AGTGAACATA
187476 TCAGCGGCATTTTCATCAGTATGTACC
1 TCAGCGGCATTTTCATCAGTATGTACC
187503 TCAGCGGCATTTTCATCAGTATGTACC
1 TCAGCGGCATTTTCATCAGTATGTACC
187530 T
1 T
187531 TCTGAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
TCAGCGGCATTTTCATCAGTATGTACC
Found at i:192767 original size:48 final size:48
Alignment explanation
Indices: 192715--192811 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
192705 AGGTGGTGAA
*
192715 TACGATTCTAAGTTTCTAAAAAATATATGTGAAAAACTTAACATTATT
1 TACGATTCTAACTTTCTAAAAAATATATGTGAAAAACTTAACATTATT
192763 TACGATTCTAACTTTCTAAAAAATATATGTGAAAAACTTAACATTATT
1 TACGATTCTAACTTTCTAAAAAATATATGTGAAAAACTTAACATTATT
192811 T
1 T
192812 GTGAGTTTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.38
Consensus pattern (48 bp):
TACGATTCTAACTTTCTAAAAAATATATGTGAAAAACTTAACATTATT
Found at i:196436 original size:18 final size:18
Alignment explanation
Indices: 196413--196456 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
196403 TTTTATTATT
*
196413 TGGTCACGGGTGGAGACA
1 TGGTCACGGCTGGAGACA
196431 TGGTCACGGCTGGAGACA
1 TGGTCACGGCTGGAGACA
*
196449 TGGGCACG
1 TGGTCACG
196457 ACACGGTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.16
Consensus pattern (18 bp):
TGGTCACGGCTGGAGACA
Found at i:206039 original size:11 final size:11
Alignment explanation
Indices: 206017--206047 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
206007 AAGTTGTTCG
206017 AAAGAAAGAAAA
1 AAAGAAA-AAAA
206029 AAAGAAAAAAA
1 AAAGAAAAAAA
206040 AAAGAAAA
1 AAAGAAAA
206048 CGAAACAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:211833 original size:25 final size:26
Alignment explanation
Indices: 211806--211887 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 26
211796 AAAATGCATA
211806 AAATAAAAGAACAATAGCTAAATC--
1 AAATAAAAGAACAATAGCTAAATCAG
* *
211830 AAA-AATA-AACAAT-GACTAAAATGCAT
1 AAATAAAAGAACAATAG-CT-AAAT-CAG
*
211856 AAATAAAAGAACAATAGC-AAATAAG
1 AAATAAAAGAACAATAGCTAAATCAG
211881 AAATAAA
1 AAATAAA
211888 TAGTGACCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
21 1 0.02
22 8 0.17
23 7 0.15
24 4 0.09
25 8 0.17
26 7 0.15
27 3 0.07
28 7 0.15
29 1 0.02
ACGTcount: A:0.66, C:0.10, G:0.09, T:0.16
Consensus pattern (26 bp):
AAATAAAAGAACAATAGCTAAATCAG
Found at i:211836 original size:51 final size:50
Alignment explanation
Indices: 211773--211907 Score: 202
Period size: 51 Copynumber: 2.7 Consensus size: 50
211763 AAATAGTACC
*
211773 CAAATCAGAAATAAATAGTGACTAAAATGCATAAAATAAAAGAACAATAG
1 CAAATCAAAAATAAATAGTGACTAAAATGCATAAAATAAAAGAACAATAG
* *
211823 CTAAATCAAAAATAAACAATGACTAAAATGCAT-AAATAAAAGAACAATAG
1 C-AAATCAAAAATAAATAGTGACTAAAATGCATAAAATAAAAGAACAATAG
*
211873 CAAAT-AAGAAATAAATAGTGACCAAAATGCATAAA
1 CAAATCAA-AAATAAATAGTGACTAAAATGCATAAA
211908 TTGAAAGTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
48 2 0.03
49 25 0.33
50 21 0.28
51 28 0.37
ACGTcount: A:0.61, C:0.11, G:0.10, T:0.18
Consensus pattern (50 bp):
CAAATCAAAAATAAATAGTGACTAAAATGCATAAAATAAAAGAACAATAG
Found at i:211862 original size:50 final size:49
Alignment explanation
Indices: 211773--211908 Score: 202
Period size: 49 Copynumber: 2.7 Consensus size: 49
211763 AAATAGTACC
*
211773 CAAATCAGAAATAAATAGTGACTAAAATGCATAAAATAAAAGAACAATAG
1 CAAATCAAAAATAAATAGTGACTAAAATGCAT-AAATAAAAGAACAATAG
* *
211823 CTAAATCAAAAATAAACAATGACTAAAATGCATAAATAAAAGAACAATAG
1 C-AAATCAAAAATAAATAGTGACTAAAATGCATAAATAAAAGAACAATAG
*
211873 CAAAT-AAGAAATAAATAGTGACCAAAATGCATAAAT
1 CAAATCAA-AAATAAATAGTGACTAAAATGCATAAAT
211909 TGAAAGTATC
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
48 2 0.03
49 29 0.37
50 19 0.24
51 28 0.36
ACGTcount: A:0.60, C:0.11, G:0.10, T:0.18
Consensus pattern (49 bp):
CAAATCAAAAATAAATAGTGACTAAAATGCATAAATAAAAGAACAATAG
Found at i:213485 original size:40 final size:39
Alignment explanation
Indices: 213441--213557 Score: 153
Period size: 40 Copynumber: 2.9 Consensus size: 39
213431 GATGGTTATC
*
213441 CCAAGGAGATGCTAATCCAACTCCTTATGTGATGGACAAG
1 CCAA-GAGATGCTGATCCAACTCCTTATGTGATGGACAAG
* *
213481 CCAAGATGATGATGATCCAACTCCTTATGTGATGCACAAG
1 CCAAGA-GATGCTGATCCAACTCCTTATGTGATGGACAAG
* * *
213521 CAAAAGTGATGCTGATCCAACTCCTTTTGTGATGGAC
1 C-CAAGAGATGCTGATCCAACTCCTTATGTGATGGAC
213558 GAGTGAAATG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.03
40 62 0.93
41 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (39 bp):
CCAAGAGATGCTGATCCAACTCCTTATGTGATGGACAAG
Found at i:214177 original size:203 final size:200
Alignment explanation
Indices: 213527--214180 Score: 810
Period size: 203 Copynumber: 3.2 Consensus size: 200
213517 CAAGCAAAAG
* * * * * * * *
213527 TGATGCTGATCCAACTCCTTTTGTGATGGACGAGTGAAA-TGATGGTGTTGTTGCAACTCCTTAT
1 TGATGTTGATCCAACTCCATATGTGATGGATGAG-CAAAGTGTTTGTGTTGTTCCAACTCCTTAT
** *
213591 ACGATGAAATCTAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGAT
65 GTGATGAAAT-GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGAT
* * * * *
213656 GAGTTATTCTCATTATGAGCTCCCCATCAGAAATGTTGATCCACCTCCTTCTTTGATGAAATCGA
129 GAGTTCTTCTCATTATGAACTCTCCAT-AGAAATGTTGATCCA-CTCCTTCTGTGATGGAATC-A
213721 A-CAAAGTGA
191 ATCAAAGTGA
** * * **
213730 TGATGTTGATCCAACTCCATATGTGATGGATGAGCCTAGTATTGGTAATGTTCCAACTCCTTATG
1 TGATGTTGATCCAACTCCATATGTGATGGATGAGCAAAGTGTTTGTGTTGTTCCAACTCCTTATG
* ** * **
213795 TGATTGAAACGATATAAGTTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAAATG
66 TGA-TGAAATGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATG
* * * *
213860 AGTTCTTCTCATTATGAACTCTCCAGTAGAAATATTGATCCATCTCTTTCTGTGATAGAATCGAT
130 AGTTCTTCTCATTATGAACTCTCCA-TAGAAATGTTGATCCA-CTCCTTCTGTGATGGAATCAAT
213925 CAAAGTGA
193 CAAAGTGA
* *
213933 TGATGCTGATCCAACTCCATATGTGATGGATGAGTAAAGTGTTTGTGTTGTTCCAACTCCTTATG
1 TGATGTTGATCCAACTCCATATGTGATGGATGAGCAAAGTGTTTGTGTTGTTCCAACTCCTTATG
* *
213998 TGATGAAAATGAGCTAAGGTTGAACAAGTACTTCTCATTATGAACTTCTTCTCCCTCATCGGACG
66 TGATG-AAATGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATG
*
214063 AGTTCTTCTCATTATGAACTCTCCACT-GAAAATGTTGATCCACATCCTTCCGTGATGGAATCAA
130 AGTTCTTCTCATTATGAACTCTCCA-TAG-AAATGTTGATCCAC-TCCTTCTGTGATGGAATCAA
*
214127 TCAAAGTAA
192 TCAAAGTGA
** *
214136 TGACATTGATCCAACTCCATATGCGATGGATGAGCAAAGTGTTTG
1 TGATGTTGATCCAACTCCATATGTGATGGATGAGCAAAGTGTTTG
214181 AATAATTTTT
Statistics
Matches: 385, Mismatches: 59, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
202 6 0.02
203 373 0.97
204 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (200 bp):
TGATGTTGATCCAACTCCATATGTGATGGATGAGCAAAGTGTTTGTGTTGTTCCAACTCCTTATG
TGATGAAATGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGA
GTTCTTCTCATTATGAACTCTCCATAGAAATGTTGATCCACTCCTTCTGTGATGGAATCAATCAA
AGTGA
Found at i:214201 original size:161 final size:161
Alignment explanation
Indices: 214029--214336 Score: 483
Period size: 161 Copynumber: 1.9 Consensus size: 161
214019 GAACAAGTAC
214029 TTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTATGAACTCTCCACTGAAA
1 TTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTATGAACTCTCCACTGAAA
*
214094 ATGTTGATCCACATCCTTCCGTGATGGAATC-AATCAAAGTAATGACATTGATCCAACTCCATAT
66 ATATTGATCCACATCCTTCCGTGATGGAATCGAA-CAAAGTAATGACATTGATCCAACTCCATAT
*
214158 GCGATGGATGAGCAAAGTGTTTGAATAATTTT
130 GCAATGGATGAGCAAAGTGTTTGAATAATTTT
* *
214190 TTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
1 TTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTATGAACTCTCCACTGAAA
* * * * ** **
214255 ATATTGATCCACCTTCTTCTGTGATGTAATCGAACAAAGTGGTGATGTTGATCCAACTCCATATG
66 ATATTGATCCACATCCTTCCGTGATGGAATCGAACAAAGTAATGACATTGATCCAACTCCATATG
*
214320 CAATGGATGAGCCAAGT
131 CAATGGATGAGCAAAGT
214337 ATTGGTGCTG
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
161 131 0.98
162 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (161 bp):
TTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTATGAACTCTCCACTGAAA
ATATTGATCCACATCCTTCCGTGATGGAATCGAACAAAGTAATGACATTGATCCAACTCCATATG
CAATGGATGAGCAAAGTGTTTGAATAATTTT
Found at i:214530 original size:182 final size:182
Alignment explanation
Indices: 214223--214581 Score: 558
Period size: 182 Copynumber: 2.0 Consensus size: 182
214213 CTCATCGGAT
* *
214223 GAGTTCTTCTCATTATGAACTCTCCACTGGAAATATTGATCCACCTTCTTCTGTGATGTAATCGA
1 GAGTTCTTCTCATTATGAACTCTCCACTGGAAATATTGATCCACCTACTTCTGTGATGGAATCGA
* * *
214288 ACAAAGTGGTGATGTTGATCCAACTCCATATGCAATGGATGAGCCAAGTATTGGTGCTGTTTCAA
66 ACAAAGTGATGATGTTGATCCAACTCCATATGCAATGGATGAGCAAAGTATTGGTGCTGTTCCAA
214353 CTCCTTA-TATGATGAAAACGAGCAAAGGTTGAACAAATTCTTCTAATCGGGC
131 CTCCTTACT-TGATGAAAACGAGCAAAGGTTGAACAAATTCTTCTAATCGGGC
* *
214405 GAGTTCTTCTCATTATGAACTCTCTACTGGAAATGTTGATCCACCTACTTCTGTGATGGAATCGA
1 GAGTTCTTCTCATTATGAACTCTCCACTGGAAATATTGATCCACCTACTTCTGTGATGGAATCGA
* * * * *
214470 TCAAAGTGATGATGTTGTTCCAACTCCATATGCGATGGATGAGCAAAGTGTTTGTGCTGTTCCAA
66 ACAAAGTGATGATGTTGATCCAACTCCATATGCAATGGATGAGCAAAGTATTGGTGCTGTTCCAA
* * * *
214535 CTCCTTACTTGATGGAAATGAGCTAAGGTTGAACAAGTTCTTCTAAT
131 CTCCTTACTTGATGAAAACGAGCAAAGGTTGAACAAATTCTTCTAAT
214582 TACAAACTTA
Statistics
Matches: 160, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
182 159 0.99
183 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (182 bp):
GAGTTCTTCTCATTATGAACTCTCCACTGGAAATATTGATCCACCTACTTCTGTGATGGAATCGA
ACAAAGTGATGATGTTGATCCAACTCCATATGCAATGGATGAGCAAAGTATTGGTGCTGTTCCAA
CTCCTTACTTGATGAAAACGAGCAAAGGTTGAACAAATTCTTCTAATCGGGC
Found at i:214833 original size:17 final size:17
Alignment explanation
Indices: 214811--214852 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
214801 GTTGAACAAG
214811 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
214828 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
214845 TTCTTCTC
1 TTCTTCTC
214853 CCTCGTCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.26, G:0.05, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:219356 original size:24 final size:24
Alignment explanation
Indices: 219341--219479 Score: 190
Period size: 24 Copynumber: 5.8 Consensus size: 24
219331 CAAAATTCAC
* * *
219341 GTCAAGTATCTTATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAA
*
219365 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
* *
219389 GTCAAGTATTAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
*
219413 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAA
*
219437 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAA
219461 GTCAAGTATCATATCAGAA
1 GTCAAGTATCATATCAGAA
219480 ATCAAATAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
23 2 0.02
24 101 0.96
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:219453 original size:12 final size:12
Alignment explanation
Indices: 219419--219483 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
219409 CCAAGTCAAG
219419 TATCATATCAGA
1 TATCATATCAGA
*
219431 -ATCCATGTCAGA
1 TAT-CATATCAGA
219443 TATCATATCAGA
1 TATCATATCAGA
*
219455 -ATCCATGTCA-A
1 TAT-CATATCAGA
219466 GTATCATATCAGA
1 -TATCATATCAGA
*
219479 AATCA
1 TATCA
219484 AATAAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
11 5 0.12
12 32 0.76
13 5 0.12
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (12 bp):
TATCATATCAGA
Found at i:219496 original size:72 final size:72
Alignment explanation
Indices: 219352--219496 Score: 168
Period size: 72 Copynumber: 2.0 Consensus size: 72
219342 TCAAGTATCT
* * *
219352 TATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATTAGATCAGAATCCAAGTCA
1 TATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATAA
**
219417 AGTATCA
66 AAAATCA
* * * * *
219424 TATCAGAATCCATGTC-AGATATCATATCAGAATCCATGTCAAGTATCATATCAGAAAT-CAAAT
1 TATCAAAATCCAGGTCAAG-TATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAAAT
219487 AAAAAATCA
64 AAAAAATCA
219496 T
1 T
219497 GTAAAATATT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
71 2 0.03
72 56 0.92
73 3 0.05
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (72 bp):
TATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATAA
AAAATCA
Found at i:224176 original size:24 final size:24
Alignment explanation
Indices: 224149--224241 Score: 125
Period size: 24 Copynumber: 3.9 Consensus size: 24
224139 ATTATATCAA
*
224149 AATCCAGGTCAAGTATCAGATTAG
1 AATCCATGTCAAGTATCAGATTAG
*
224173 AATCCAAGTCAAGTATCAGATTAG
1 AATCCATGTCAAGTATCAGATTAG
*
224197 AATCCATGTC-AGATATCAGATCAG
1 AATCCATGTCAAG-TATCAGATTAG
* *
224221 AATTCATATCAAGTATCAGAT
1 AATCCATGTCAAGTATCAGAT
224242 CATAAATCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
23 2 0.03
24 58 0.94
25 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (24 bp):
AATCCATGTCAAGTATCAGATTAG
Found at i:224242 original size:24 final size:24
Alignment explanation
Indices: 224133--224243 Score: 109
Period size: 24 Copynumber: 4.6 Consensus size: 24
224123 ATAATTCACG
* * * **
224133 TCAAGTATTATATCAAAATCCAGG
1 TCAAGTATCAGATCAGAATCCATA
*
224157 TCAAGTATCAGATTAGAATCCA-A
1 TCAAGTATCAGATCAGAATCCATA
* *
224180 GTCAAGTATCAGATTAGAATCCATG
1 -TCAAGTATCAGATCAGAATCCATA
*
224205 TC-AGATATCAGATCAGAATTCATA
1 TCAAG-TATCAGATCAGAATCCATA
224229 TCAAGTATCAGATCA
1 TCAAGTATCAGATCA
224244 TAAATCAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
23 2 0.03
24 70 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (24 bp):
TCAAGTATCAGATCAGAATCCATA
Found at i:224255 original size:24 final size:24
Alignment explanation
Indices: 224157--224256 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
224147 AAAATCCAGG
* *
224157 TCAAGTATCAGATTAG-AATCCAAG
1 TCAAGTATCAGATCAGAAAT-CAAA
* **
224181 TCAAGTATCAGATTAG-AATCCATG
1 TCAAGTATCAGATCAGAAAT-CAAA
* *
224205 TC-AGATATCAGATCAGAATTCATA
1 TCAAG-TATCAGATCAGAAATCAAA
*
224229 TCAAGTATCAGATCATAAATCAAA
1 TCAAGTATCAGATCAGAAATCAAA
224253 TCAA
1 TCAA
224257 AAATCATGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
23 2 0.03
24 60 0.91
25 4 0.06
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (24 bp):
TCAAGTATCAGATCAGAAATCAAA
Found at i:224262 original size:24 final size:24
Alignment explanation
Indices: 224211--224262 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
224201 CATGTCAGAT
* * **
224211 ATCAGATCAGAATTCATATCAAGT
1 ATCAGATCAGAAATCAAATCAAAA
*
224235 ATCAGATCATAAATCAAATCAAAA
1 ATCAGATCAGAAATCAAATCAAAA
224259 ATCA
1 ATCA
224263 TGTAAAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.25
Consensus pattern (24 bp):
ATCAGATCAGAAATCAAATCAAAA
Found at i:231238 original size:14 final size:14
Alignment explanation
Indices: 231221--231259 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
231211 TTAAAGTTCT
*
231221 AAAAAATAAAGGAC
1 AAAAAATAAAGAAC
231235 -AAAAATAAAGAAC
1 AAAAAATAAAGAAC
231248 AAAAAATTAAAG
1 AAAAAA-TAAAG
231260 CAATGAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 5 0.23
15 5 0.23
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.10
Consensus pattern (14 bp):
AAAAAATAAAGAAC
Found at i:231696 original size:51 final size:51
Alignment explanation
Indices: 231605--231760 Score: 206
Period size: 51 Copynumber: 3.0 Consensus size: 51
231595 AGACTAAATG
* * * * *
231605 AAATAAAAAAAATAGTAGCCAAATCAAAAATAAATAGTGACTAAAAT-TAATA
1 AAAT-AAAAGAATAATAGCTAAATCAGAAATAAACAGTGACTAAAATGT-ATA
*
231657 AAATAGAAGAATAATAGCTAAATCAGAAATAAACAGTGACTAAAATGTATA
1 AAATAAAAGAATAATAGCTAAATCAGAAATAAACAGTGACTAAAATGTATA
* * *
231708 AAATAAAAGAACAATAGCTAAATCAGAAATAAACAGTGACCAAAATGCATA
1 AAATAAAAGAATAATAGCTAAATCAGAAATAAACAGTGACTAAAATGTATA
231759 AA
1 AA
231761 TTGAAAGTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
51 88 0.95
52 5 0.05
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (51 bp):
AAATAAAAGAATAATAGCTAAATCAGAAATAAACAGTGACTAAAATGTATA
Found at i:232590 original size:12 final size:12
Alignment explanation
Indices: 232575--232599 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
232565 CCTCTTTTTC
232575 TCTCTCTCTCTA
1 TCTCTCTCTCTA
232587 TCTCTCTCTCTA
1 TCTCTCTCTCTA
232599 T
1 T
232600 TTTACCTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (12 bp):
TCTCTCTCTCTA
Found at i:234039 original size:51 final size:51
Alignment explanation
Indices: 233984--234102 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
233974 ATACTTTCAA
* * * *
233984 TTTATGAATTCTGGTCACTGCTTATTTTTTATTTAGCTAATGTTATTTTAT
1 TTTATGAATTCTAGTCACTGCTTATTTGTGATTTAGCTAATGTTAATTTAT
* * * * *
234035 TTTATGCATTTTAGTCATTGTTTATTTGTGATTTAGCTACTGTTAATTTAT
1 TTTATGAATTCTAGTCACTGCTTATTTGTGATTTAGCTAATGTTAATTTAT
* *
234086 TTTATGCATTTTAGTCA
1 TTTATGAATTCTAGTCA
234103 GTTTTTATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (51 bp):
TTTATGAATTCTAGTCACTGCTTATTTGTGATTTAGCTAATGTTAATTTAT
Found at i:234058 original size:25 final size:22
Alignment explanation
Indices: 234029--234120 Score: 60
Period size: 24 Copynumber: 3.7 Consensus size: 22
234019 GCTAATGTTA
234029 TTTTATTTTATGCATTTTAGTCAT
1 TTTTA-TTTATG-ATTTTAGTCAT
* *
234053 TGTTTATTTGTGA-TTTAGCTACTGT
1 T-TTTATTTATGATTTTAG-T-C-AT
234078 TAATTTATTTTATGCATTTTAGTCAGT
1 T--TTTA-TTTATG-ATTTTAGTCA-T
234105 TTTTATTTATGATTTT
1 TTTTATTTATGATTTT
234121 GGCTATGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 19
0.69 0.06 0.24
Matches are distributed among these distances:
22 5 0.09
23 7 0.13
24 13 0.24
25 10 0.19
26 4 0.07
27 8 0.15
28 2 0.04
29 5 0.09
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.61
Consensus pattern (22 bp):
TTTTATTTATGATTTTAGTCAT
Found at i:234140 original size:51 final size:50
Alignment explanation
Indices: 234005--234152 Score: 174
Period size: 51 Copynumber: 2.9 Consensus size: 50
233995 TGGTCACTGC
* *
234005 TTATTTTTTATTTAGCTAATGTTATTTTATTTTATGCATTTTAGTCATTGT
1 TTATTTATGATTTAGCT-ATGTTATTTTATTTTATGCATTTTAGTCATTGT
* *
234056 TTATTTGTGATTTAGCTACTGTTAATTTATTTTATGCATTTTAGTCAGTT-T
1 TTATTTATGATTTAGCTA-TGTTATTTTATTTTATGCATTTTAGTCA-TTGT
* *
234107 TTATTTATGATTTTGGCTATGTT-TTTTATTTTTATTTCATTTTAGT
1 TTATTTATGA-TTTAGCTATGTTATTTTA-TTTTA-TGCATTTTAGT
234153 ATTTGTTGTT
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
50 5 0.06
51 61 0.72
52 19 0.22
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.62
Consensus pattern (50 bp):
TTATTTATGATTTAGCTATGTTATTTTATTTTATGCATTTTAGTCATTGT
Found at i:236596 original size:251 final size:245
Alignment explanation
Indices: 236159--236655 Score: 789
Period size: 251 Copynumber: 2.0 Consensus size: 245
236149 CCAAGAATCG
* * ** *
236159 TTTGAATTGAATAGTTATTTGGAATTTTGGGATCAAATGTGATCATATCTTGTCAATATGTTATA
1 TTTGAATTGAATAGTCATTTGGAATTTTGAGATCAAATGTGATCATATCCAGTCAAAATGTTATA
* * ** *
236224 TGTCCGAATCCGAATGATTGATGTTTTTGGAGGTACAAGAAAGGTGTTAAGTTTTAAACATATGC
66 TGTCCGAATCCGAATGATTGATGTTTTTGAAGGTACAACAAACATGATAAGTTTTAAACATATGC
*
236289 CTCTAGTTAAAATAAGGATTCTTTTATCCTAAATAGTCCAGAGAATTATTACAAATATACCCTTA
131 CTCTAGTTAAAATAAGGATTCTTTTATCCTAAACAGTCCAGAGAATTATTACAAATATACCCTTA
236354 TATAATATAGTTAGGGTTTTTAAAATTTTATCCACTTTTCCTCTATATCT
196 TATAATATAGTTAGGGTTTTTAAAATTTTATCCACTTTTCCTCTATATCT
*
236404 TTTGAATTGTATAGTCATTTGGAATTTTGAGATCAAATGTGATCATATCCAGTCAAAATGTTATA
1 TTTGAATTGAATAGTCATTTGGAATTTTGAGATCAAATGTGATCATATCCAGTCAAAATG-T-TA
* *
236469 TATCCGAATCCGAATCCGAATGATTTATGTTTCTT-AAGGTACAACAAACATGATAAGTTTTCAA
64 TAT--G--TCCGAATCCGAATGATTGATGTTT-TTGAAGGTACAACAAACATGATAAGTTTTAAA
236533 CATATGCCTCTAGTTAAAATAAGGATTCTTTTATCCTAAACAGTCCAGAGAATTATTACAAATAT
124 CATATGCCTCTAGTTAAAATAAGGATTCTTTTATCCTAAACAGTCCAGAGAATTATTACAAATAT
*
236598 ACCCTTATATAATATAGTTAGGGTTTTTAAAATTTTCTCCACTTTTCCTCTATATCT
189 ACCCTTATATAATATAGTTAGGGTTTTTAAAATTTTATCCACTTTTCCTCTATATCT
236655 T
1 T
236656 AATTTTACTT
Statistics
Matches: 230, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
245 54 0.23
246 1 0.00
247 5 0.02
249 1 0.00
251 167 0.73
252 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (245 bp):
TTTGAATTGAATAGTCATTTGGAATTTTGAGATCAAATGTGATCATATCCAGTCAAAATGTTATA
TGTCCGAATCCGAATGATTGATGTTTTTGAAGGTACAACAAACATGATAAGTTTTAAACATATGC
CTCTAGTTAAAATAAGGATTCTTTTATCCTAAACAGTCCAGAGAATTATTACAAATATACCCTTA
TATAATATAGTTAGGGTTTTTAAAATTTTATCCACTTTTCCTCTATATCT
Found at i:238723 original size:12 final size:12
Alignment explanation
Indices: 238706--238738 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
238696 CTACTTCTCA
238706 ACACAACTTCAC
1 ACACAACTTCAC
*
238718 ACACAACGTCAC
1 ACACAACTTCAC
238730 ACACAACTT
1 ACACAACTT
238739 TGCACGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.39, G:0.03, T:0.15
Consensus pattern (12 bp):
ACACAACTTCAC
Found at i:243098 original size:24 final size:24
Alignment explanation
Indices: 243070--243117 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
243060 GAGCAATAAT
*
243070 CATCCATGCACGAGCACTAGCAAC
1 CATCCATGCACGAGCACAAGCAAC
243094 CATCCATGCACGAGCACAAGCAAC
1 CATCCATGCACGAGCACAAGCAAC
243118 TGCATGCACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.38, G:0.17, T:0.10
Consensus pattern (24 bp):
CATCCATGCACGAGCACAAGCAAC
Found at i:244889 original size:16 final size:16
Alignment explanation
Indices: 244868--244900 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
244858 TAATTTCAAA
*
244868 TTGAATCATTTTGAGT
1 TTGAATAATTTTGAGT
244884 TTGAATAATTTTGAGT
1 TTGAATAATTTTGAGT
244900 T
1 T
244901 ATCATCTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (16 bp):
TTGAATAATTTTGAGT
Found at i:253476 original size:12 final size:12
Alignment explanation
Indices: 253459--253483 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
253449 ATACGCGCCT
253459 ACTATATATAAA
1 ACTATATATAAA
253471 ACTATATATAAA
1 ACTATATATAAA
253483 A
1 A
253484 TGTTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
ACTATATATAAA
Found at i:255716 original size:260 final size:262
Alignment explanation
Indices: 255240--255729 Score: 650
Period size: 260 Copynumber: 1.9 Consensus size: 262
255230 ATCAAATTTG
* * *
255240 AAAAAAAGTATATGCTCTGCTACTCTTCAGGGTAGATCATATATGAAAACTTCGATTCACTTCAC
1 AAAAAAAGTATATGCTCCGCTACTCTTCAAGGTAGATCAGATATGAAAACTTCGATTCACTT-AC
* * ** * **
255305 TATTTTCAGGGAAGATTGAATCGAGATAGATTTGTTCTACTTCTCTTCAGGGAATATTAAATTTG
65 -ATCTTCAGGGAAGATTAAATCGAGATAGATTTGTTCTACTGATATTCAAAGAATATTAAATTTG
* * * * * *
255370 AAAAAAGGGATCTATTCTGCTGCTTTTCAGGGTAGATCAGATTTGGAGACTTTGATTCACTTTAC
129 AAAAAAGGGATATATTATGCTGCTCTTCAGGGTAGATCAGATCTGGAAACTTTGATTCACTTCAC
* *
255435 TGCTCTTTAGGGAAAATTGAATCGGTGGTTGATTTGCTTCACTGCTCGTCATGGAAGATTAAATT
194 TGCTCTTCAGGGAAAATTGAATC-GAGGTTGATTTGCTTCACTGCTCGTCATGGAAGATTAAATT
255500 TAGAA
258 TAGAA
* * *
255505 AAAAAAAG-ATATGCTCCGTTACTCTTCAAGGTAGATCAGATCTGGAAACATT-GATTCACTT-C
1 AAAAAAAGTATATGCTCCGCTACTCTTCAAGGTAGATCAGATATGAAAAC-TTCGATTCACTTAC
* * * *
255567 -TCTTCAGGGAAGATTAAATCGGGGTTGATTTGCTT-TACTGATATTTAAAGAATATTAAATTTG
65 ATCTTCAGGGAAGATTAAATCGAGATAGATTTG-TTCTACTGATATTCAAAGAATATTAAATTTG
255630 AAAAAAGGGATATGA-TATGCTGCTCTTCAGGGTAGATCAGATCTGGAAACTTTGATTCACTTCA
129 AAAAAAGGGATAT-ATTATGCTGCTCTTCAGGGTAGATCAGATCTGGAAACTTTGATTCACTTCA
*
255694 CTGCTCTTCAGGGAAGATTGAATCGAGGTTGATTTG
193 CTGCTCTTCAGGGAAAATTGAATCGAGGTTGATTTG
255730 TTCCATTGCT
Statistics
Matches: 196, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
259 11 0.06
260 127 0.65
261 3 0.02
262 1 0.01
264 44 0.22
265 10 0.05
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (262 bp):
AAAAAAAGTATATGCTCCGCTACTCTTCAAGGTAGATCAGATATGAAAACTTCGATTCACTTACA
TCTTCAGGGAAGATTAAATCGAGATAGATTTGTTCTACTGATATTCAAAGAATATTAAATTTGAA
AAAAGGGATATATTATGCTGCTCTTCAGGGTAGATCAGATCTGGAAACTTTGATTCACTTCACTG
CTCTTCAGGGAAAATTGAATCGAGGTTGATTTGCTTCACTGCTCGTCATGGAAGATTAAATTTAG
AA
Found at i:256255 original size:38 final size:39
Alignment explanation
Indices: 256203--256383 Score: 147
Period size: 38 Copynumber: 4.7 Consensus size: 39
256193 AAATAAAGTT
* * **
256203 GGTTTCTAGAGAAACAATCTTATGAAAGA-CAAGGCTGA
1 GGTTTCTAGGGAAACAATCTTAAGAAAGACCAAGATTGA
* * *
256241 GGTTTCTAGGGAAACGATCTTAAGAAA-ATCAAGAATGA
1 GGTTTCTAGGGAAACAATCTTAAGAAAGACCAAGATTGA
* * * *
256279 CGTTCCTTGGGAAACAATCTTTAGAAAGACCAA-ATTGA
1 GGTTTCTAGGGAAACAATCTTAAGAAAGACCAAGATTGA
* * * * ** * *
256317 GTTTTCT-CGGATACAAGTCCTAAG-AAGGTCATGGTTGA
1 GGTTTCTAGGGAAACAA-TCTTAAGAAAGACCAAGATTGA
256355 GGTTTCTAGGGAAACAATCTTAAGAAAGA
1 GGTTTCTAGGGAAACAATCTTAAGAAAGA
256384 TAAAATGATT
Statistics
Matches: 109, Mismatches: 28, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
37 13 0.12
38 82 0.75
39 14 0.13
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (39 bp):
GGTTTCTAGGGAAACAATCTTAAGAAAGACCAAGATTGA
Found at i:256906 original size:45 final size:45
Alignment explanation
Indices: 256841--257430 Score: 589
Period size: 45 Copynumber: 13.2 Consensus size: 45
256831 CGAGAAATTT
* * *
256841 AAGTCAAGAATGACATCACTAAAAGGTTGACTCCTTTTCGTGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* * * * * *
256886 AAGTCAAGAAGGACAACACTAAAAGATCGACTTCTCTTCACGATA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* * *
256931 AAGTCAAGAATAACATCACTAAAAGGTTGACTTCTCTTCATGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* * * *
256976 AAGTCAAGAAGGACAACACTAAAA-GATCAGCT-CT-TT-GTGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGA-CTCCTCTTCATGAGA
* * * *
257018 AAGTCAATAATAACATCACTAAAAGGTTGACTCCTCTTCGTGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* * * * * **
257063 AAGTCAAGCATCACATCACTAAAAGGTTAATTCCTCTTTGTGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* * * * * * *
257108 AAGTTAAGTAGGACAACACTAAATGATGGACTCCTCTTCACGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* * * *
257153 AAATCAAGAATGACAACACTAAATGATTGACTCATCTTCATGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* * * *
257198 AAGTCAATAATGACAACACTAAAAGATTTAACTCCTCTTCATGAAA
1 AAGTCAAGAATGACAACACTAAAAG-GTTGACTCCTCTTCATGAGA
* * * * *
257244 AATTCAAGAATGAAAACAC-CAAAGATTGACTCCTCTTCACGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* *
257288 AAGTC-AGAAAGAACAACACTAAAAGGTTGACTCCTCTTCACGAGA
1 AAGTCAAGAATG-ACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* *
257333 AAGTCAAGAATGACAACACTAAAAGGCTGACTCATCTTCATGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
* * * ** *
257378 AAGTCAAGAATAACATCACTAAAAGATTGACTATTCTTCACGAGA
1 AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
*
257423 AAGCCAAG
1 AAGTCAAG
257431 TTGAGGTTTT
Statistics
Matches: 450, Mismatches: 86, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
42 27 0.06
43 12 0.03
44 33 0.07
45 341 0.76
46 37 0.08
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (45 bp):
AAGTCAAGAATGACAACACTAAAAGGTTGACTCCTCTTCATGAGA
Found at i:257675 original size:19 final size:20
Alignment explanation
Indices: 257639--257676 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
257629 AAAATTTATC
257639 ATGTATGTATGAAATGATGA
1 ATGTATGTATGAAATGATGA
*
257659 ATGTATG-ATGCAATGATG
1 ATGTATGTATGAAATGATG
257677 CAAATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (20 bp):
ATGTATGTATGAAATGATGA
Found at i:258941 original size:3 final size:3
Alignment explanation
Indices: 258933--258961 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
258923 TATGCTCTCT
258933 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
258962 TTTTCTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:258970 original size:12 final size:13
Alignment explanation
Indices: 258930--259011 Score: 62
Period size: 13 Copynumber: 6.1 Consensus size: 13
258920 TGATATGCTC
*
258930 TCTTTCTTCTTCT
1 TCTTTTTTCTTCT
258943 TCTTCTTCTTCTTCT
1 TCTT-TT-TTCTTCT
258958 TCTTTTTTC-TCT
1 TCTTTTTTCTTCT
258970 T-TATTTTT-TTCT
1 TCT-TTTTTCTTCT
* *
258982 CTTTTTCTTTCTTTT
1 -TCTTT-TTTCTTCT
258997 TCTTTTTTCTATCT
1 TCTTTTTTCT-TCT
259011 T
1 T
259012 TTCTCTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
11 1 0.02
12 12 0.21
13 15 0.27
14 14 0.25
15 14 0.25
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (13 bp):
TCTTTTTTCTTCT
Found at i:258992 original size:26 final size:27
Alignment explanation
Indices: 258951--259019 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
258941 CTTCTTCTTC
258951 TTCT-TCTTCTTT-TTTCTCTTTATTTT
1 TTCTATCTT-TTTCTTTCTCTTTATTTT
* * *
258977 TT-TCTCTTTTTCTTTCTTTTTCTTTT
1 TTCTATCTTTTTCTTTCTCTTTATTTT
259003 TTCTATCTTTTCTCTTT
1 TTCTATCTTTT-TCTTT
259020 TTTTCTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 4 0.11
26 20 0.56
27 7 0.19
28 5 0.14
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (27 bp):
TTCTATCTTTTTCTTTCTCTTTATTTT
Found at i:268460 original size:234 final size:233
Alignment explanation
Indices: 268045--268656 Score: 868
Period size: 234 Copynumber: 2.6 Consensus size: 233
268035 GGGCCATCAA
*
268045 TAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTT
1 TAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTT
* *
268110 CACATGTCTCTCGAAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAATTGTTGAAAAA
66 CACATGTCTCTCAAAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAATTTTTG-AAAA
* * * * * *
268175 GTAAGGAAAGTTTCTTATCTAGTAAACTATTTCCAAAATTAGTACGTCCTTCGGGCCATTAGTAA
130 GTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGTAAGTCCTTCAGGCCATCAGCAA
268240 GTCTTTCGAGCATGATGCTTAAATCCTTCGGGTAATCTG
195 GTCTTTCGAGCATGATGCTTAAATCCTTCGGGTAATCTG
* * * *
268279 TAAGTCTTTCGAGCAATATGATAAGTCTTTCGGGCCATCGATATGACCTTCGGGTAGGATGTTTT
1 TAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTT
* * * *
268344 CACATATCTCTCAAAAAATGTGAAAATTTTCTCATTTAAAGCTGAAAATTGAAATTTTTGAAAAG
66 CACATGTCTCTCAAAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAG
*
268409 TAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAAGTCCTTCAGGCCATCAGCAA
131 TAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGT-AAGTCCTTCAGGCCATCAGCAA
* * *
268474 GTCTTTTGAGCATGATGCTTAAATCCTTTGGGTCATCTG
195 GTCTTTCGAGCATGATGCTTAAATCCTTCGGGTAATCTG
* *
268513 TAAGTCTTTCGAGCAAGATGATAAGT-TCTTCGGGCCATCCACAAGACCTTTGGGCAGGATGTTT
1 TAAGTCTTTCGAGCAAGATGATAAGTCT-TTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTT
* *** * * *
268577 TCACATGTTTAAAAAAAAAAAGGAGAAAAGTTTCTCATTTTAAATCTGGAAATTGAAATTTTT-A
65 TCACATGTCT--CTCAAAAAATGAGAAAAATTTCTCA-TTTAAATCTGAAAATTGAAATTTTTGA
268641 AAATGGTAAGAAAAGT
127 AAA--GTAAGAAAAGT
268657 AAGTCCTTCG
Statistics
Matches: 334, Mismatches: 37, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
233 45 0.13
234 232 0.69
236 23 0.07
237 23 0.07
238 11 0.03
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (233 bp):
TAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTT
CACATGTCTCTCAAAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAG
TAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGTAAGTCCTTCAGGCCATCAGCAAG
TCTTTCGAGCATGATGCTTAAATCCTTCGGGTAATCTG
Found at i:268721 original size:42 final size:42
Alignment explanation
Indices: 268654--268752 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
268644 TGGTAAGAAA
*
268654 AGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCAAGCATGATG
1 AGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCAAGCAAGATG
* * *
268696 AGTAAATCCTTCGGGTCATCT-GTAAGTCTTTCGAGCAAGATG
1 AGTAAGTCCTTCGGGCCAT-TAGTAAGTCTTTCAAGCAAGATG
*
268738 A-TAAGTCATTCGGGC
1 AGTAAGTCCTTCGGGC
268753 TATCCATAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 11 0.22
42 37 0.76
43 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
AGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCAAGCAAGATG
Found at i:269189 original size:42 final size:41
Alignment explanation
Indices: 269142--269222 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 41
269132 GGGCCATCAA
* *
269142 TAAGTCTTTCGAGCATGATGAGTAAATCCCTCTGGTCATCTG
1 TAAGTCTTTCGAGCAAGATGA-TAAATCCCTCGGGTCATCTG
* *
269184 TAAGTCTTTCGAGCAAGATGATAATTCCTTCGGGTCATC
1 TAAGTCTTTCGAGCAAGATGATAAATCCCTCGGGTCATC
269223 CATAAGACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 15 0.43
42 20 0.57
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (41 bp):
TAAGTCTTTCGAGCAAGATGATAAATCCCTCGGGTCATCTG
Found at i:269354 original size:234 final size:234
Alignment explanation
Indices: 268657--270261 Score: 1938
Period size: 234 Copynumber: 6.9 Consensus size: 234
268647 TAAGAAAAGT
* * *
268657 AAGTCCTTCGGGCCATTAGTAAGTCTTTCAAGCATGATGAGTAAATCCTTCGGGTCATCTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCTGGTCATCTGTAAG
* * *
268722 TCTTTCGAGCAAGATGATAAGTCATTCGGGCTATCCATAAGACCTTCGGACATGATGTTTTCACA
66 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCACA
* * *
268787 TGTCTCTCGAAAAATGAGAAAAGTTTCTCATTTAATTCTGAAACTTGAAATTTTTACAAAAGTAA
131 TGTCTCTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGC-AAAGTAA
* *
268852 GAAAAGTTTC-TACCTGGTACACTATTTCCAAAATTGGTA
195 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
* * * * ** *
268891 AAGTCCTTCAGGCTATCAATAAGTCTTTCGTGCATGATGCTTAAATTCTT-TAGGTCATCTGTAA
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCT-GGTCATCTGTAA
* * ** * * *
268955 GTCTTTCGAGCAAGATGATAAGTCATTCGGGCCTTCCGCAAGACCTTC-TAGAGGATTTTTTCAC
65 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCAC
* *
269019 ATGTATCTCG-AAAATGAGAAAAGTTTCTCATTTAAATATGAAAATTGAAATTTTTGCAAAGTAA
130 ATGTCTCTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGCAAAGTAA
* * *
269083 GAAAAGTTTCTTACGTTGTAAACTTTTTCCAAAATTGGTA
195 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
* * *
269123 AAGTCTTTCGGGCCATCAATAAGTCTTTCGAGCATGATGAGTAAATCCCTCTGGTCATCTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCTGGTCATCTGTAAG
* * * * * *
269188 TCTTTCGAGCAAGATGATAATTCCTTCGGGTCATCCATAAGACCTTCAGACATGATATTTTCATA
66 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCACA
* *
269253 TGTCTCTCGAAAAATGAGAAAAGTTTCTCATTTAAATATGAAAATTGAATTTTTTGCAAAGTAAG
131 TGTCTCTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGCAAAGTAAG
*
269318 AAAAGCTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
196 AAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
** * * * ** *
269357 AAGTTTTTCAGGCCATCAGTAAGTATTTCAAGTGTGAAGAGTAAATCCTT-TGGTCATCTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCTGGTCATCTGTAAG
* * * *
269421 TCTTCCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAATACCTTCGGGCGGGATGTTTTCACA
66 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCACA
** *
269486 TGTCTCTCGAAAAATGAGAAAAAAATTCTCATTTAAATCTGAAAAATGAAATTTTTGCAAAGTAA
131 TGTCTCTCGAAAAATGAG-AAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGCAAAGTAA
* ** *
269551 TAAAAGTTTCTTATATAGTAAACTATTTCCAAAATTGTTA
195 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
* ** *
269591 AAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCATTC-GAGTCATCTGTAA
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCTG-GTCATCTGTAA
* * * * * *
269655 GTCTTTCGAGCAAGATAATATGTCCTTCGGGCCATCAACAAGACATT-TGAGCAGGATGTTTTCA
65 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGA-CAGGATGTTTTCA
* * * *
269719 CATGTCTATCGAAAAAAGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTGTTGAAAAGTA
129 CATGTCTCTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGCAAAGTA
* * * *
269784 AGAAAAGTTTTTTACATAGTAAACTATTTCTAAAGTTGGTA
194 AGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
* * * * *
269825 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGTATGATG-CTCAAATCATTCAGGT-ATATGTAA
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGT-AAATCCTTCTGGTCATCTGTAA
* * ** * * * *
269888 GTCTTTCAAGCAAGATTATAAGTCCTTTAGGCCATCCACAATACCTTTGGGCAGGATGTTTTCAC
65 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCAC
* * * *
269953 ATGTCTCTCGAAAAAAAAATGAAAAAAGTTTCTCATTTAAATCTGAAAAATTGAACTTTTGGAAA
130 ATGTCTCTCG----AAAAATGAGAAAAGTTTCTCATTTAAATCTG-AAAATTGAAATTTTTGCAA
*
270018 AGTAAGAAAAGTTTCTTACCTAGTAAACTATTTTCAAAATTGGT-
190 AGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
* * * * * *
270062 AAGTCCTTAGGGCTATCAATAAGTCTTTTGAGCATGATGAGTAAATCCTTCGGGTCATCTATAAG
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCTGGTCATCTGTAAG
* * * * * *
270127 CCTTTTGAGCAAGATGATAAGTCTTTC-AGCCCTCCATAAGACCTTCGGGCAGGATGCTTTT-AC
66 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATG-TTTTCAC
* * ** * * * *
270190 ATGTTTTTTTCGAAAAATGAGAAATTTTTTTTATTTAAATCTGAAAATTAAAATTTTTGAAAAGT
130 ATG--TCTCTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGCAAAGT
*
270255 AAAAAAA
193 AAGAAAA
270262 TGATTTCCAA
Statistics
Matches: 1178, Mismatches: 171, Indels: 44
0.85 0.12 0.03
Matches are distributed among these distances:
231 17 0.01
232 164 0.14
233 199 0.17
234 494 0.42
235 108 0.09
237 103 0.09
238 88 0.07
239 5 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (234 bp):
AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCTGGTCATCTGTAAG
TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCACA
TGTCTCTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGCAAAGTAAG
AAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
Found at i:271111 original size:75 final size:75
Alignment explanation
Indices: 270988--271136 Score: 271
Period size: 75 Copynumber: 2.0 Consensus size: 75
270978 ACCAGGAGCC
* * *
270988 CAATTACAATAGGCCCAATCAGGCCACCAATCTGACCTGGCCCAATTACAAGCAATCTTAACCCA
1 CAATTACAACAGGCCCAATCAGGCCACCAATCGGACCTGGCCCAATTACAAGCAATCCTAACCCA
271053 AATTAAAGCT
66 AATTAAAGCT
271063 CAATTACAACAGGCCCAATCAGGCCACCAATCGGACCTGGCCCAATTACAAGCAATCCTAACCCA
1 CAATTACAACAGGCCCAATCAGGCCACCAATCGGACCTGGCCCAATTACAAGCAATCCTAACCCA
271128 AATTAAAGC
66 AATTAAAGC
271137 CCAAACCCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.38, C:0.32, G:0.13, T:0.17
Consensus pattern (75 bp):
CAATTACAACAGGCCCAATCAGGCCACCAATCGGACCTGGCCCAATTACAAGCAATCCTAACCCA
AATTAAAGCT
Found at i:273090 original size:20 final size:21
Alignment explanation
Indices: 273065--273157 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
273055 TTTTCCCAAT
*
273065 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
273085 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
273106 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
273126 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
273147 TCGCAATGCGA
1 TCGCAATGCGA
273158 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:273110 original size:41 final size:41
Alignment explanation
Indices: 273065--273157 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
273055 TTTTCCCAAT
273065 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
273106 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
273147 TCGCAATGCGA
1 TCGCAATGCGA
273158 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:273170 original size:41 final size:41
Alignment explanation
Indices: 273084--273218 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
273074 GAATAAGTAA
** *
273084 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
273125 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
273166 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
273207 TTCGCAACGCGA
1 ATCGCAACGCGA
273219 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:273171 original size:20 final size:20
Alignment explanation
Indices: 273146--273239 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
273136 AATTGGGAAA
*
273146 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
273166 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
273187 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
273207 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
273227 TTCGCAACGCGAT
1 ATCGCAACGCGAT
273240 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:273455 original size:22 final size:22
Alignment explanation
Indices: 273427--273470 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
273417 CACTCTCTCA
273427 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
273449 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
273471 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:275027 original size:18 final size:18
Alignment explanation
Indices: 275006--275050 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
274996 TCCACTTCGG
* *
275006 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
275024 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
275042 GAGCCATCA
1 GAGCCATCA
275051 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:275557 original size:20 final size:19
Alignment explanation
Indices: 275523--275588 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
275513 TAGTTTACTT
*
275523 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGACTA
*
275542 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
275562 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
275581 TCGCAACG
1 TCGCAACG
275589 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:276228 original size:20 final size:20
Alignment explanation
Indices: 276181--276273 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
276171 CGCTATGTAA
* *
276181 ATCGCGTAGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
276201 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
* ** *
276221 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--AAGTAAGT
* *
276242 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
276262 ATCGCATTGCGA
1 ATCGCGTTGCGA
276274 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 43 0.72
21 12 0.20
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:276292 original size:21 final size:21
Alignment explanation
Indices: 276263--276355 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
276253 ATAGTAAGTA
276263 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
276284 TCGCTTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
276304 TCGCATTGTGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
276325 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
276345 TCGCATTGCGA
1 TCGCATTGCGA
276356 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:276293 original size:41 final size:41
Alignment explanation
Indices: 276202--276336 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
276192 AAAGTCAGTA
* * * ** *
276202 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
276242 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* * ** *
276284 TCGCTTTGCGAT-TTACTTATTCGCATTGTGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
276325 TCGCGTTGCGAT
1 TCGCGTTGCGAT
276337 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:276337 original size:41 final size:41
Alignment explanation
Indices: 276263--276355 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
276253 ATAGTAAGTA
*
276263 TCGCATTGCGATTTTCCCAATTCGCTTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
276304 TCGCATTGTGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
276345 TCGCATTGCGA
1 TCGCATTGCGA
276356 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:276913 original size:131 final size:131
Alignment explanation
Indices: 276721--277080 Score: 508
Period size: 131 Copynumber: 2.7 Consensus size: 131
276711 GAGAATAATA
* * * * *
276721 ATATCTTTTCATTTC-AGTTGGGGTAATAAATGATTGCTTTAAGGCATAAGAGGCCATTTATTTT
1 ATATCTCTTCATTTCGA-TTGGAGCAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTTT
* *
276785 CGATTGAAAATAATTCGATATTA-CTGTTTTCTCTCGAATCAATATTGATTTTTGAGAAGGAATA
65 CGATTGAAAATAATTCGATATTATC-GTTTTCTCTCAAATCAATATTGATTTTTAAGAAGGAATA
276849 GTG
129 GTG
*
276852 ATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTTTC
1 ATATCTCTTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTTTC
* *
276917 GATTGAAAATAATTCGATATTATCGTTTTCTCTCAAATTAATATTGATTTTTAAGATGGAATAGT
66 GATTGAAAATAATTCGATATTATCGTTTTCTCTCAAATCAATATTGATTTTTAAGAAGGAATAGT
276982 G
131 G
* * * * * *
276983 ATATCTCTTCATTTCGATTGGAACAATAAATTATTGCTTTAAGGTACGAAAGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTTTC
* * * *
277048 GATCGGAAATAATTAGATATTATCGTTCTCTCT
66 GATTGAAAATAATTCGATATTATCGTTTTCTCT
277081 TAAAATTATT
Statistics
Matches: 206, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
131 204 0.99
132 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (131 bp):
ATATCTCTTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTTTC
GATTGAAAATAATTCGATATTATCGTTTTCTCTCAAATCAATATTGATTTTTAAGAAGGAATAGT
G
Found at i:279086 original size:18 final size:18
Alignment explanation
Indices: 279065--279100 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
279055 ACTCAAATCG
279065 AATAAATAAATTAAATTA
1 AATAAATAAATTAAATTA
* *
279083 AATATATAAATTTAATTA
1 AATAAATAAATTAAATTA
279101 GTTTGATATT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATAAATTAAATTA
Found at i:280743 original size:2 final size:2
Alignment explanation
Indices: 280736--280788 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
280726 GCATTGCCTT
280736 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
280778 TA TA TA TA TA T
1 TA TA TA TA TA T
280789 GACCCTATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:281073 original size:18 final size:18
Alignment explanation
Indices: 281050--281087 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
281040 TAATTTGAGG
*
281050 ATCAATATATAATTAAAA
1 ATCAATAAATAATTAAAA
*
281068 ATCAATAAATAATTTAAA
1 ATCAATAAATAATTAAAA
281086 AT
1 AT
281088 AGAGGTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
ATCAATAAATAATTAAAA
Found at i:281456 original size:18 final size:18
Alignment explanation
Indices: 281416--281457 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
281406 CCTCTTGAAA
*
281416 ATTTTAAATTTTCTAATAT
1 ATTTT-AATTTTCTAACAT
*
281435 -TTTTAATTTTTTAACAT
1 ATTTTAATTTTCTAACAT
281452 ATTTTA
1 ATTTTA
281458 TATTGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAATTTTCTAACAT
Found at i:281801 original size:60 final size:59
Alignment explanation
Indices: 281625--281802 Score: 139
Period size: 60 Copynumber: 3.0 Consensus size: 59
281615 CCCTTCAATC
* * *
281625 ATGACTCTT-ATTCTAAATTGGTCCCTAAA-TTTTTAAACATTCCAAATTCATACCTAAACT
1 ATGA-TCTTCATTCTAAATTGGT-CCTAAACTTTTTAAACATTTCAATTTCAT-CCCAAACT
* ** * * * * * *
281685 ATAAAT-AGCATTCTAGATTAGTCCTCAAAC-TTTTGAACATTTTAGTTTCAACCCCAAACT
1 AT-GATCTTCATTCTAAATTGGTCCT-AAACTTTTTAAACATTTCAATTTC-ATCCCAAACT
* *
281745 ATGATCTTCATTCTAAATTGGTCGATAAACTTTTTTAACATTTCAATTTCATCCCAAA
1 ATGATCTTCATTCTAAATTGGTC-CTAAACTTTTTAAACATTTCAATTTCATCCCAAA
281803 TTATATGCAC
Statistics
Matches: 88, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
59 5 0.06
60 64 0.73
61 19 0.22
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (59 bp):
ATGATCTTCATTCTAAATTGGTCCTAAACTTTTTAAACATTTCAATTTCATCCCAAACT
Found at i:287139 original size:3 final size:3
Alignment explanation
Indices: 287131--287179 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
287121 CTTTTATGAG
*
287131 GAA GAA GAA GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
287179 G
1 G
287180 GTGAATTAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:297790 original size:2 final size:2
Alignment explanation
Indices: 297783--297823 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
297773 CACAACACAA
297783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
297824 ACATACATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:299044 original size:2 final size:2
Alignment explanation
Indices: 299037--299083 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
299027 CTGTTTATCC
299037 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
299078 AT AT AT
1 AT AT AT
299084 TGCATGAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:302158 original size:11 final size:11
Alignment explanation
Indices: 302144--302168 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
302134 ATTAAAGGCA
302144 GGTTAATATAC
1 GGTTAATATAC
302155 GGTTAATATAC
1 GGTTAATATAC
302166 GGT
1 GGT
302169 GTTACCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:302558 original size:20 final size:19
Alignment explanation
Indices: 302535--302581 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
302525 CGATATACCA
302535 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
302555 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
302575 GGTAAAA
1 GGTAAAA
302582 CGTTACTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:302742 original size:175 final size:180
Alignment explanation
Indices: 302322--302787 Score: 622
Period size: 183 Copynumber: 2.6 Consensus size: 180
302312 GATCCAAATT
* * * * * **
302322 AAAAATGTGTCGATCCAAAACGATATAACATGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATATATCGATCCAAAACG--ATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
302387 AAACCGGTAAAGCGCTACCAGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
64 AAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
302452 GTGAATTTAAAAGAGAAACAGTTTTAAATCCTACAAAATGTCGATACTTTTAA
129 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTA-AAAATGTCGATACTTTTAA
*
302505 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATA-A-CAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* ** *
302570 AAACCGGTAAAACGTTACTGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
64 AAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* ** *
302634 GTGAATTTAAAAGAGAAGCA-TTTTAGCGCCT-ATAATGTCGATAC-TTT-A
129 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTAAAAATGTCGATACTTTTAA
* *
302682 AAAAATATATCGATCCACAATGATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT-AA
1 AAAAATATATCGATCCAAAACGATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAA
302746 ACCGGT-AAACGATACCAGATATATTGAAAGTGTCGATACTTT
66 ACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTT
302788 CGTAAGTACG
Statistics
Matches: 256, Mismatches: 25, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
173 33 0.13
174 8 0.03
175 36 0.14
176 1 0.00
177 23 0.09
178 3 0.01
179 12 0.05
181 11 0.04
182 38 0.15
183 91 0.36
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (180 bp):
AAAAATATATCGATCCAAAACGATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAA
ACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGT
GAATTTAAAAGAGAAACAGTTTTAAAGCCTAAAAATGTCGATACTTTTAA
Found at i:304944 original size:19 final size:19
Alignment explanation
Indices: 304918--304978 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
304908 CAAACAATCA
304918 AGAGTCGAAGAGAAACTTG
1 AGAGTCGAAGAGAAACTTG
*
304937 ATAGTCGAAGAGAAACTTG
1 AGAGTCGAAGAGAAACTTG
* * *
304956 AGAGTCTAAGATACACTTG
1 AGAGTCGAAGAGAAACTTG
304975 AGAG
1 AGAG
304979 GCATAAGGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (19 bp):
AGAGTCGAAGAGAAACTTG
Found at i:305073 original size:30 final size:32
Alignment explanation
Indices: 305012--305073 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
305002 AAATACATGG
*
305012 AGTGGTAAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTAAAAGAAGTAGAGGTGTTAAGGGTGA
* *
305044 AGTGGTGAAAGAAGTTG-GG-GTTAAGGGTGA
1 AGTGGTAAAAGAAGTAGAGGTGTTAAGGGTGA
305074 TATTAAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 10 0.37
31 2 0.07
32 15 0.56
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (32 bp):
AGTGGTAAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:306571 original size:117 final size:116
Alignment explanation
Indices: 306365--306597 Score: 432
Period size: 117 Copynumber: 2.0 Consensus size: 116
306355 GATCTCTAGG
306365 AAGTATCCCTTGAAAACTTTCAAATTTGTGAGCATAAGAAGATAAGCAATTGAATGGGTATGAGA
1 AAGTATCCCTTGAAAACTTTCAAATTTGTGAGCATAAGAAGATAAGCAATTGAATGGGTAT-AGA
306430 TGTTATCACAAATAAAAGCTTAATTTATGCAGTATTCATCATAATGACATGA
65 TGTTATCACAAATAAAAGCTTAATTTATGCAGTATTCATCATAATGACATGA
306482 AAGTATCCCTTGAAAACTTTCAAATTTGTGAGCATAAGAAGAATAAGCAATTGAATGGGTAT-GA
1 AAGTATCCCTTGAAAACTTTCAAATTTGTGAGCATAAGAAG-ATAAGCAATTGAATGGGTATAGA
306546 TGTTATCACAAATAGAAAGCTTAATTTATGCAGTATTCATCATAATGACATG
65 TGTTATCACAAATA-AAAGCTTAATTTATGCAGTATTCATCATAATGACATG
306598 TGTGGTTTTC
Statistics
Matches: 114, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
116 16 0.14
117 78 0.68
118 20 0.18
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (116 bp):
AAGTATCCCTTGAAAACTTTCAAATTTGTGAGCATAAGAAGATAAGCAATTGAATGGGTATAGAT
GTTATCACAAATAAAAGCTTAATTTATGCAGTATTCATCATAATGACATGA
Found at i:306957 original size:18 final size:18
Alignment explanation
Indices: 306925--306970 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
306915 AAATGTAGGT
306925 TAATTT-TATAAGATTTA
1 TAATTTGTATAAGATTTA
*
306942 TAATTTGTATACGATTTA
1 TAATTTGTATAAGATTTA
306960 TAATTTTGTAT
1 TAA-TTTGTAT
306971 GTGAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 6 0.23
18 13 0.50
19 7 0.27
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (18 bp):
TAATTTGTATAAGATTTA
Found at i:307575 original size:196 final size:200
Alignment explanation
Indices: 307199--308140 Score: 1445
Period size: 197 Copynumber: 4.8 Consensus size: 200
307189 AATTTACAAT
* * *
307199 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCGTATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
307264 CGAAACCCAAAAGTATAATGTAATAGGT-A-TTTTTCAATCTAATCGGTACAAGTATACCGGTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTTCAATCTAACCGGTACAAGTATACCGGTTT
307327 TATGAGAGAATAGGTCTAAAAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 TATGAGAGAATAGGTCTAAAAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
307392 -ATGA
196 AATGA
*
307396 ATGGC-AACAGGGTGGCAACAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCGATAAACA
1 ATGGCAAACAGGGT-GCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACA
*
307459 TCGAAACCCATAAGTATAATGT-ATAGGTAATTTTTTCAATCTAACCGATACAAGTATACCGGTT
65 TCGAAACCCATAAGTATAATGTAATAGGTAATTTTTTCAATCTAACCGGTACAAGTATACCGGTT
307523 TTATGAGAGAATAGGTCT-AAAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
130 TTATGAGAGAATAGGTCTAAAAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
307587 -AATGA
195 GAATGA
307592 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
307657 CGAAACCCATAAGTATAATGTAATA-GTAA--TTTTCAATCTAACCGGTACAAGTATACCGGTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTTCAATCTAACCGGTACAAGTATACCGGTTT
*
307719 TAT-AGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
131 TATGAGAGAATAGGTCTAAA-AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
307783 GAATGA
195 GAATGA
*
307789 ATGGCAAACCAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCTATAAACA
1 ATGGCAAA-CAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACA
307854 TCGAAACCCATAAGTATAATGTAATAGGTAATTTTTT-AA--T-ACCGGTACAAGTATACC-GTT
65 TCGAAACCCATAAGTATAATGTAATAGGTAATTTTTTCAATCTAACCGGTACAAGTATACCGGTT
*
307914 TTATGAGAGAATAGGTCTAAATAATGTGTCG--ACTTTTGTAG-TT-TGTCGATATTTTTGGTCC
130 TTATGAGAGAATAGGTCTAAA-AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCC
307975 AGAATGA
194 AGAATGA
* *
307982 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAA-AGT-G-TCCCAT-AACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * *
308043 CGAAAACCCAAAAGTAT-ATGTATTAGGT-ATTTTTTCAATCTAACCGATATAAGTATACCGGTT
66 CG-AAACCCATAAGTATAATGTAATAGGTAATTTTTTCAATCTAACCGGTACAAGTATACCGG-T
* * * * *
308106 TTTATGGGAGAATTGGTAT-AATATGTATTGACACT
129 TTTATGAGAGAATAGGTCTAAAAATGTATCGACACT
308141 GTTTAATGTT
Statistics
Matches: 697, Mismatches: 24, Indels: 52
0.90 0.03 0.07
Matches are distributed among these distances:
187 7 0.01
188 19 0.03
189 18 0.03
190 2 0.00
191 23 0.03
192 40 0.06
193 53 0.08
194 15 0.02
195 53 0.08
196 182 0.26
197 190 0.27
198 85 0.12
199 4 0.01
200 2 0.00
201 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTTCAATCTAACCGGTACAAGTATACCGGTTT
TATGAGAGAATAGGTCTAAAAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:307851 original size:18 final size:19
Alignment explanation
Indices: 307812--307851 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
307802 GTGCAACAAT
307812 AAAGTGTCGATCCATATATAA
1 AAAGTGTCGATCC--ATATAA
307833 AAAGTGTCGATCC-TATAA
1 AAAGTGTCGATCCATATAA
307851 A
1 A
307852 CATCGAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
AAAGTGTCGATCCATATAA
Found at i:312975 original size:23 final size:23
Alignment explanation
Indices: 312949--313014 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 23
312939 AAAGAAGACA
312949 AAAAATGTGTCACAAAGGTAAAG
1 AAAAATGTGTCACAAAGGTAAAG
** ** ** * *
312972 AAAAACATACCTTAAAGGCAGAG
1 AAAAATGTGTCACAAAGGTAAAG
312995 AAAAATGTGTCACAAAGGTA
1 AAAAATGTGTCACAAAGGTA
313015 GAATTATTCT
Statistics
Matches: 28, Mismatches: 15, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.52, C:0.12, G:0.20, T:0.17
Consensus pattern (23 bp):
AAAAATGTGTCACAAAGGTAAAG
Found at i:314007 original size:3 final size:3
Alignment explanation
Indices: 313999--314024 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
313989 GTTTTGATTG
313999 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
314025 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:316272 original size:167 final size:168
Alignment explanation
Indices: 315979--316314 Score: 624
Period size: 167 Copynumber: 2.0 Consensus size: 168
315969 TCTAACTTCA
315979 TCTCATTCAAAATTTGAAGTGGCGGGATTTTAACCTCCACTGGTAAGACCGCCTGCATCTCGTAG
1 TCTCATTCAAAATTTGAAGTGGCGGGATTTTAACCTCCACTGGTAAGACCGCCTGCATCTCGTAG
*
316044 ACTAAAAAAAGGTGTTCCCATGCTGAAGTTCACACTGTAGTTCGATATGCATACAAAAAAAATAA
66 ACTAAAAAAAGGTGTTCCCATGCTGAAGTTCACACTGTAGTTCGATATGCATACAAAAAAAACAA
316109 TTTTTCATGCCAAT-CCTGTATGTATCATTGGTCATTG
131 TTTTTCATGCCAATCCCTGTATGTATCATTGGTCATTG
316146 TCTCATTCAAAATTTTGAAGTGGCGGGA-TTTAACCTCCACTGGTAAGACCGCCTGCATCTCGTA
1 TCTCATTCAAAA-TTTGAAGTGGCGGGATTTTAACCTCCACTGGTAAGACCGCCTGCATCTCGTA
316210 GACTAAAAAAAGGTGTTACCCATGCTGAAGTTCACACTGTAGTTCGATATGCATAC-AAAAAAAC
65 GACTAAAAAAAGGTGTT-CCCATGCTGAAGTTCACACTGTAGTTCGATATGCATACAAAAAAAAC
316274 AATTTTTCATGCCAATCCCTGTATGTATCATTGGTCATTG
129 AATTTTTCATGCCAATCCCTGTATGTATCATTGGTCATTG
316314 T
1 T
316315 GATAATTCTT
Statistics
Matches: 165, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
167 88 0.53
168 77 0.47
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (168 bp):
TCTCATTCAAAATTTGAAGTGGCGGGATTTTAACCTCCACTGGTAAGACCGCCTGCATCTCGTAG
ACTAAAAAAAGGTGTTCCCATGCTGAAGTTCACACTGTAGTTCGATATGCATACAAAAAAAACAA
TTTTTCATGCCAATCCCTGTATGTATCATTGGTCATTG
Found at i:326923 original size:136 final size:137
Alignment explanation
Indices: 326609--326928 Score: 371
Period size: 139 Copynumber: 2.3 Consensus size: 137
326599 TCGAACTGTC
* *
326609 AAAATGGAACCTCGAGCATAAGCGAGGA-CAAATTCAAAAATTCTCCTAAATTAAAGGATTAGTT
1 AAAATGGAACCTCGAGCA-AAGCGAGGACCAAATT-AAAAATTCCCCTAAATTAAAGGATAAGTT
* * * * *
326673 ATGAAATTATACCTAATATGAAGGCTCTACTTATTAACCTGGTCAATTTTAACCAATTATTTTAT
64 ATGAAATTAAACATAATATGAAGGCTCTAATTATTAACCTAGT-AATTTTAACCAATTATTTGAT
326738 TCGAATAATT
128 TCGAATAATT
* * * *
326748 AAAATGGAACCTCGAGAAAAAGTGAGAACCAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTT
1 AAAATGGAACCTCGAG-CAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTAAAGGA-TAAGTT
** ** *
326813 -TGAAATTAAACATGAA-ATGGTGGCTCTAATTATTAACCTAGT-A-TTTGGCCAATTATTTGGT
64 ATGAAATTAAACAT-AATATGAAGGCTCTAATTATTAACCTAGTAATTTTAACCAATTATTTGAT
*
326874 TTGAATAATT
128 TCGAATAATT
* *
326884 AAAATGGAACATCGAGCAAGAGCGGGGACCAAATTAAAAATTCCC
1 AAAATGGAACCTCGAGCAA-AGCGAGGACCAAATTAAAAATTCCC
326929 TTAACGAAAT
Statistics
Matches: 154, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
135 2 0.01
136 60 0.39
137 1 0.01
139 77 0.50
140 14 0.09
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (137 bp):
AAAATGGAACCTCGAGCAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTAAAGGATAAGTTAT
GAAATTAAACATAATATGAAGGCTCTAATTATTAACCTAGTAATTTTAACCAATTATTTGATTCG
AATAATT
Found at i:327860 original size:21 final size:21
Alignment explanation
Indices: 327831--327883 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
327821 ATTCTGATTA
327831 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
327852 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
327873 TCGCAATGCGA
1 TCGCATTGCGA
327884 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:327898 original size:20 final size:20
Alignment explanation
Indices: 327873--327959 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
327863 TTTTCCTAAT
327873 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
327893 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
327914 TCGCAATGTGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
327934 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
327954 TCGCAA
1 TCGCAA
327960 CACGAATCTG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 40 0.74
21 14 0.26
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:327976 original size:20 final size:20
Alignment explanation
Indices: 327953--327999 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
327943 GAATACGTAA
327953 ATCGCAAC-ACGAATCTGACT
1 ATCGCAACGA-GAATCTGACT
*
327973 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
327993 ATCGCAA
1 ATCGCAA
328000 TACTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:331348 original size:33 final size:34
Alignment explanation
Indices: 331287--331382 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
331277 TCATTTGACT
* **
331287 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* *
331321 ATCGCAATGCG-AAATGAAAATCTCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
331354 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
331383 CGAAATTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:331584 original size:14 final size:14
Alignment explanation
Indices: 331565--331601 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
331555 CATCAATTAA
331565 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
331579 ACAAATCATCTTTT
1 ACAAATCAACATTT
331593 ACAAATCAA
1 ACAAATCAA
331602 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:339098 original size:21 final size:21
Alignment explanation
Indices: 339072--339111 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
339062 CCCCCTTTGA
*
339072 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
339093 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
339112 TGGGGGTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:342578 original size:21 final size:18
Alignment explanation
Indices: 342554--342598 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
342544 GAACAGTGGG
342554 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGA---ATGAT
*
342575 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
342593 AGGGGA
1 AGGGGA
342599 GGCCTCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:343182 original size:20 final size:20
Alignment explanation
Indices: 343159--343228 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
343149 AAACAACAAA
343159 ATCGCAACGTC-AAAATGACT
1 ATCGCAACG-CGAAAATGACT
*
343179 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
343199 ATCGCAATGCGAATTTGGACT
1 ATCGCAACGCGAAAAT-GACT
343220 ATCGCAACG
1 ATCGCAACG
343229 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.02
20 31 0.70
21 12 0.27
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:343221 original size:21 final size:20
Alignment explanation
Indices: 343170--343226 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
343160 TCGCAACGTC
343170 AAAATGACTATCGCAATGCG
1 AAAATGACTATCGCAATGCG
343190 AAAATGACTATCGCAATGCG
1 AAAATGACTATCGCAATGCG
**
343210 AATTTGGACTATCGCAA
1 AAAAT-GACTATCGCAA
343227 CGAGAGAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 23 0.68
21 11 0.32
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
AAAATGACTATCGCAATGCG
Found at i:343298 original size:20 final size:20
Alignment explanation
Indices: 343273--343449 Score: 166
Period size: 20 Copynumber: 9.5 Consensus size: 20
343263 GATTCTTTCG
**
343273 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
343293 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
343313 TTGCGATAGTCATTTTAGCA
1 TTGCGATAGTCATTTTCGCA
*
343333 ATGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
343353 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
343367 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
343386 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
343400 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
343420 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
343440 TTGCGATAGT
1 TTGCGATAGT
343450 AACTATCTTC
Statistics
Matches: 133, Mismatches: 10, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
14 14 0.11
16 12 0.09
17 6 0.05
18 5 0.04
19 7 0.05
20 89 0.67
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:343388 original size:33 final size:34
Alignment explanation
Indices: 343293--343426 Score: 126
Period size: 33 Copynumber: 3.8 Consensus size: 34
343283 CAAATTCGCA
* *
343293 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTAGCA
1 TTGCGATAGTCATTTTCGCATTGCGAT--TC--TCT--CG
* * * *
343333 ATGCGATAGTCATTTTCGCATTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
**
343367 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
*
343400 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
343427 AGTCATTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
33 28 0.35
34 22 0.28
36 2 0.03
38 1 0.01
40 26 0.33
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.43
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:345329 original size:20 final size:20
Alignment explanation
Indices: 345282--345355 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
345272 GAAACTTTAA
* **
345282 ATCGTAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
345302 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
345322 ATCACAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
345342 ATCGCAACGCGAAA
1 ATCGCAACACGAAA
345356 TGAAAATAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:345745 original size:22 final size:22
Alignment explanation
Indices: 345683--345748 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
345673 CTGACGTGAA
* *
345683 TGATTTCACCGGAGATGGAGAC
1 TGATTTCATCGGAGATGGGGAC
* * *
345705 TGATATCGTCGGTGATGGGGAC
1 TGATTTCATCGGAGATGGGGAC
345727 TGATTTCATCGGAGATGGGGAC
1 TGATTTCATCGGAGATGGGGAC
345749 AGATATCGCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (22 bp):
TGATTTCATCGGAGATGGGGAC
Found at i:345967 original size:20 final size:20
Alignment explanation
Indices: 345944--346075 Score: 192
Period size: 20 Copynumber: 6.5 Consensus size: 20
345934 CGATAGTCAG
345944 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
345964 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
345984 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
346004 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
346024 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* * *
346045 ATTCTCGTTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
346065 ATTCGCATTGC
1 ATTCGCATTGC
346076 AAATTAGGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
20 84 0.86
21 14 0.14
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:346101 original size:21 final size:21
Alignment explanation
Indices: 346077--346119 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
346067 TCGCATTGCA
346077 AATTAGGAAAATCGCAACGCG
1 AATTAGGAAAATCGCAACGCG
* * *
346098 AATTTGGGAAATCGCAATGCG
1 AATTAGGAAAATCGCAACGCG
346119 A
1 A
346120 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.19
Consensus pattern (21 bp):
AATTAGGAAAATCGCAACGCG
Done.