Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008693.1 Hibiscus syriacus cultivar Beakdansim tig00111721_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: 2243253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:272272 original size:37 final size:37
Alignment explanation
Indices: 272231--272319 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 37
272221 TCATCGTTTG
272231 TTTTCTTTTTTTTTTTTTTTCTTTTCTCTTTTTTCTT
1 TTTTCTTTTTTTTTTTTTTTCTTTTCTCTTTTTTCTT
* *
272268 TTTTCTTTTTTCTTTTTTTTCTTTTTTCTTTTTTCTT
1 TTTTCTTTTTTTTTTTTTTTCTTTTCTCTTTTTTCTT
*
272305 TTTT-TTCTTTTTTTT
1 TTTTCTTTTTTTTTTT
272320 CTGATGGATG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
36 9 0.19
37 39 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (37 bp):
TTTTCTTTTTTTTTTTTTTTCTTTTCTCTTTTTTCTT
Found at i:272789 original size:11 final size:11
Alignment explanation
Indices: 272773--272801 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
272763 AATCAATCCC
272773 TCTTTTTTTCT
1 TCTTTTTTTCT
272784 TCTTTTTTTCT
1 TCTTTTTTTCT
272795 TCTTTTT
1 TCTTTTT
272802 ACTTTGAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TCTTTTTTTCT
Found at i:278599 original size:261 final size:256
Alignment explanation
Indices: 278094--278605 Score: 846
Period size: 261 Copynumber: 2.0 Consensus size: 256
278084 GATGTTTAAA
278094 TGCTTCTGAAACTTTCTTTTATATTTATTTCTAAAAATATGGGTAGAACCCACTGTTACATCGCT
1 TGCTTCTGAAACTTTCTTTTATATTTATTTCTAAAAATATGGGTAGAACCCACTGTTACATCGCT
* * **
278159 TTGTTCGTTACCACGAAATCCCCCTCCTCGAATGGTTGCCTCTTCATTTGATATTGTTTATTCAT
66 TTGTTCGTTACCACAAAATCCCACTCCTCGAATGGTTGCCTCTTCATTTGATACCGTTTATTCAT
* * *
278224 CACCAAGCACCCCCTGATCGTGAATTTTCTTTGTTGCTCACTGTTGGTCGAATCATTCCCCTTTT
131 CACCAACCACCCCCTGATCGTGAATTTTCTTTGTTGCTCACTGCTAGTCGAATCATTCCCCTTTT
*
278289 TTGTTGTTGAAAACCGAGAGCCCTCACTCTTGTGTTTGTGATATTTTTTTCTGGTTTTTTT
196 TTGTTGTTGAAAACCAAGAGCCCTCACTCTTGTGTTTGTGATATTTTTTTCTGGTTTTTTT
*
278350 TGCTTCTGAAACTTTCTTTTATATTTATTTCTAAAAATATGGGTAGAACCTACTGTTACATCGCT
1 TGCTTCTGAAACTTTCTTTTATATTTATTTCTAAAAATATGGGTAGAACCCACTGTTACATCGCT
* *
278415 TTGTTCGTTACCACAAAATTTCCCTTGATTCCTCGAATGGTTGCCTCTTCATTTGATACCGTTTT
66 TTGTTCGTTACCACAAAA--TCCC---ACTCCTCGAATGGTTGCCTCTTCATTTGATACCGTTTA
*
278480 TTCATCACCAACCACCCCCTGATCGTGAATTTTCTTTGTTGCTCACTGCTAGTCGAATCGTTCCC
126 TTCATCACCAACCACCCCCTGATCGTGAATTTTCTTTGTTGCTCACTGCTAGTCGAATCATTCCC
*
278545 C-TTTTTGTTGTTGAAAACCAAGAGCCCTCGCTCTTGTGTTTGTGATATTTTTTTTCTGGTT
191 CTTTTTTGTTGTTGAAAACCAAGAGCCCTCACTCTTGTGTTTGTGATA-TTTTTTTCTGGTT
278606 CTTTCTTTTC
Statistics
Matches: 237, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
256 81 0.34
258 4 0.02
260 44 0.19
261 108 0.46
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (256 bp):
TGCTTCTGAAACTTTCTTTTATATTTATTTCTAAAAATATGGGTAGAACCCACTGTTACATCGCT
TTGTTCGTTACCACAAAATCCCACTCCTCGAATGGTTGCCTCTTCATTTGATACCGTTTATTCAT
CACCAACCACCCCCTGATCGTGAATTTTCTTTGTTGCTCACTGCTAGTCGAATCATTCCCCTTTT
TTGTTGTTGAAAACCAAGAGCCCTCACTCTTGTGTTTGTGATATTTTTTTCTGGTTTTTTT
Found at i:285468 original size:40 final size:40
Alignment explanation
Indices: 285416--285554 Score: 147
Period size: 40 Copynumber: 3.4 Consensus size: 40
285406 TTGACGCAGC
*
285416 TCCTACGTGATGAGGAGATCTGGTTGGTGGATGACATGGT
1 TCCTACGTGATGAGGAGATCTGGTTGATGGATGACATGGT
* **
285456 TCCTACGTGATGAGGACGAT-TGGTT-ATCTAAGGTTGACATGAC
1 TCCTACGTGATGAGGA-GATCTGGTTGA--T--GGATGACATGGT
* *
285499 TCCTACGTGATGAGGAGATCTGGTCGATGGATGAAATGGT
1 TCCTACGTGATGAGGAGATCTGGTTGATGGATGACATGGT
* *
285539 TCCTTCGCGATGAGGA
1 TCCTACGTGATGAGGA
285555 CGACTGACCA
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
40 43 0.53
41 4 0.05
42 4 0.05
43 29 0.36
44 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGATCTGGTTGATGGATGACATGGT
Found at i:285508 original size:43 final size:42
Alignment explanation
Indices: 285392--285522 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 42
285382 ATGAGGACGG
285392 CTGGTTATCTATGGTTGAC--GCAGCTCCTACGTGATGAGGAGAT
1 CTGGTTATCTA-GGTTGACATG-A-CTCCTACGTGATGAGGAGAT
** * **
285435 CTGGTT-GGT-GGATGACATGGTTCCTACGTGATGAGGACGAT
1 CTGGTTATCTAGGTTGACATGACTCCTACGTGATGAGGA-GAT
285476 -TGGTTATCTAAGGTTGACATGACTCCTACGTGATGAGGAGAT
1 CTGGTTATCT-AGGTTGACATGACTCCTACGTGATGAGGAGAT
285518 CTGGT
1 CTGGT
285523 CGATGGATGA
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
40 27 0.38
41 4 0.06
42 5 0.07
43 35 0.49
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.31
Consensus pattern (42 bp):
CTGGTTATCTAGGTTGACATGACTCCTACGTGATGAGGAGAT
Found at i:285509 original size:83 final size:83
Alignment explanation
Indices: 285382--285560 Score: 254
Period size: 83 Copynumber: 2.2 Consensus size: 83
285372 TTCTTACACA
* * * *
285382 ATGAGGACGGCTGGTTATCTATGGTTGACGCAGCTCCTACGTGATGAGGAGATCTGGTTGGTGGA
1 ATGAGGACGACTGGTTATCTAAGGTTGACGCAGCTCCTACGTGATGAGGAGATCTGGTCGATGGA
* *
285447 TGACATGGTTCCTACGTG
66 TGAAATGGTTCCTACGCG
*
285465 ATGAGGACGATTGGTTATCTAAGGTTGA--CATGACTCCTACGTGATGAGGAGATCTGGTCGATG
1 ATGAGGACGACTGGTTATCTAAGGTTGACGCA-G-CTCCTACGTGATGAGGAGATCTGGTCGATG
*
285528 GATGAAATGGTTCCTTCGCG
64 GATGAAATGGTTCCTACGCG
285548 ATGAGGACGACTG
1 ATGAGGACGACTG
285561 ACCATCTTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 2 0.02
82 1 0.01
83 82 0.96
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (83 bp):
ATGAGGACGACTGGTTATCTAAGGTTGACGCAGCTCCTACGTGATGAGGAGATCTGGTCGATGGA
TGAAATGGTTCCTACGCG
Found at i:285734 original size:67 final size:65
Alignment explanation
Indices: 285580--285744 Score: 213
Period size: 67 Copynumber: 2.5 Consensus size: 65
285570 AGGGATAATG
* ** * *
285580 GTTTCAAGAAAAACCATCTCAAGCGAGACAAAACTTGTTTCAAGGGAAACATACTCAAAGATGAT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAGACTCAAAGATGAT
* * * *
285645 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCTATGGAAACAGACTCAAAGACTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-CTTGTTTCAAGGGAAACAGACTCAAAGA-TG
*
285710 TT
64 AT
*
285712 GTTTCAAGAGACACTGTCTCAAGAGAGACAAAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
285745 AAATTGAGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 29 0.33
66 24 0.28
67 34 0.39
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAGACTCAAAGATGAT
Found at i:285802 original size:38 final size:37
Alignment explanation
Indices: 285754--285871 Score: 132
Period size: 38 Copynumber: 3.1 Consensus size: 37
285744 AAAATTGAGT
* *
285754 AAAAATTGTCTCAAGTGAGACAAAATTTGCTTT-TTAG
1 AAAAATTGTCTCAAGCGAGACAAAATTTG-TTTCTAAG
*
285791 AGAAAATTGTCTCAAGCGAGATAAAATTTGTTTCTAAG
1 A-AAAATTGTCTCAAGCGAGACAAAATTTGTTTCTAAG
* * *
285829 AAAGAATTGTCTCTAGCGAGACAACACTTTGTTT-TGAG
1 AAA-AATTGTCTCAAGCGAGACAA-AATTTGTTTCTAAG
285867 AAAAA
1 AAAAA
285872 CACCCTCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
37 8 0.11
38 54 0.77
39 8 0.11
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (37 bp):
AAAAATTGTCTCAAGCGAGACAAAATTTGTTTCTAAG
Found at i:286172 original size:22 final size:22
Alignment explanation
Indices: 286109--286174 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 22
286099 TCTTTTATTT
*
286109 TCAAAATTTTGAAAATA-TCAA
1 TCAAAAATTTGAAAATATTCAA
* *
286130 TTAATAGAATGTTGAAGAATATTTAA
1 TCAA-A-AAT-TTGAA-AATATTCAA
286156 TCAAAAATTTGAAAATATT
1 TCAAAAATTTGAAAATATT
286175 GCCCCTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
21 3 0.08
22 7 0.19
23 7 0.19
24 8 0.22
25 5 0.14
26 6 0.17
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (22 bp):
TCAAAAATTTGAAAATATTCAA
Found at i:287828 original size:16 final size:16
Alignment explanation
Indices: 287807--287837 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
287797 GGTTGATGAT
*
287807 AGCAACAGGAGCAGAC
1 AGCAACAGCAGCAGAC
287823 AGCAACAGCAGCAGA
1 AGCAACAGCAGCAGA
287838 GACTAGCGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.26, G:0.29, T:0.00
Consensus pattern (16 bp):
AGCAACAGCAGCAGAC
Found at i:288138 original size:9 final size:10
Alignment explanation
Indices: 288126--288162 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
288116 GTAAAATATG
288126 TAATTAA-AA
1 TAATTAATAA
288135 TAATTAATAA
1 TAATTAATAA
288145 TAA-TAATAA
1 TAATTAATAA
288154 TAA-TAATAA
1 TAATTAATAA
288163 ATTTTTAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 22 0.81
10 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAATTAATAA
Found at i:288147 original size:3 final size:3
Alignment explanation
Indices: 288133--288162 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
288123 ATGTAATTAA
288133 AAT AATT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
288163 ATTTTTAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:289477 original size:21 final size:21
Alignment explanation
Indices: 289452--289493 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
289442 ATCCAACAGC
289452 CCATATCAATCCAGATTAGGG
1 CCATATCAATCCAGATTAGGG
289473 CCATATCAATCCAGATTAGGG
1 CCATATCAATCCAGATTAGGG
289494 TTTTTATCAT
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:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
CCATATCAATCCAGATTAGGG
Found at i:290754 original size:10 final size:10
Alignment explanation
Indices: 290735--290778 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
290725 TTCACCACAC
*
290735 CAAATACTCT
1 CAAATCCTCT
290745 CAAATCCTCT
1 CAAATCCTCT
*
290755 CAAATTCTCT
1 CAAATCCTCT
*
290765 CAAGTCCTCT
1 CAAATCCTCT
290775 CAAA
1 CAAA
290779 AACCAAACCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:290764 original size:20 final size:20
Alignment explanation
Indices: 290735--290778 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
290725 TTCACCACAC
290735 CAAATACTCTCAAATCCTCT
1 CAAATACTCTCAAATCCTCT
* *
290755 CAAATTCTCTCAAGTCCTCT
1 CAAATACTCTCAAATCCTCT
290775 CAAA
1 CAAA
290779 AACCAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (20 bp):
CAAATACTCTCAAATCCTCT
Found at i:290820 original size:5 final size:5
Alignment explanation
Indices: 290810--290838 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
290800 ATTTATAAGG
290810 TATTA TATTA TATTA TATTA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATT
290839 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:290859 original size:21 final size:20
Alignment explanation
Indices: 290809--290905 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
290799 CATTTATAAG
*
290809 GTATTATA-TTATATTATATTA
1 GTATTATATTTA-ATT-TTTTA
290830 -TATTATATTTAATTTTTTTA
1 GTATTATATTTAA-TTTTTTA
* *
290850 GTATTTTATTTAA-TTATT-
1 GTATTATATTTAATTTTTTA
290868 GTA--ATATTTAATTTTTTA
1 GTATTATATTTAATTTTTTA
290886 GTACTT-TATTTAATTATTTT
1 GTA-TTATATTTAATT-TTTT
290906 TTCAGTTATA
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
16 7 0.11
17 4 0.06
18 6 0.10
19 4 0.06
20 21 0.34
21 20 0.32
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (20 bp):
GTATTATATTTAATTTTTTA
Found at i:290866 original size:36 final size:36
Alignment explanation
Indices: 290834--290903 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
290824 ATATTATATT
*
290834 ATATTTAATTTTTTTAGTATTTTATTTAATTATTGTA
1 ATATTTAA-TTTTTTAGTACTTTATTTAATTATTGTA
290871 ATATTTAATTTTTTAGTACTTTATTTAATTATT
1 ATATTTAATTTTTTAGTACTTTATTTAATTATT
290904 TTTTCAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 24 0.75
37 8 0.25
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (36 bp):
ATATTTAATTTTTTAGTACTTTATTTAATTATTGTA
Found at i:295564 original size:21 final size:20
Alignment explanation
Indices: 295526--295564 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
295516 ATGTCATATA
295526 AAGGATAGGATTTTGAGTTT
1 AAGGATAGGATTTTGAGTTT
295546 AAGGA-AGTGATTATTGAGT
1 AAGGATAG-GATT-TTGAGT
295565 AGGAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (20 bp):
AAGGATAGGATTTTGAGTTT
Found at i:296404 original size:21 final size:21
Alignment explanation
Indices: 296378--296440 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
296368 GTCGAGGGTT
296378 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
296399 TCATAGGTCCTTCGGGACATAC
1 TCATAGGTCCTTCGGGACA-AC
* *
296421 TCACAGGTCTTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
296441 ATTTCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:296428 original size:22 final size:21
Alignment explanation
Indices: 296382--296440 Score: 91
Period size: 22 Copynumber: 2.8 Consensus size: 21
296372 AGGGTTTCAT
*
296382 AGGTCCTTCGGGACAACTCAT
1 AGGTCCTTCGGGACAACTCAC
296403 AGGTCCTTCGGGACATACTCAC
1 AGGTCCTTCGGGACA-ACTCAC
*
296425 AGGTCTTTCGGGACAA
1 AGGTCCTTCGGGACAA
296441 ATTTCATATG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (21 bp):
AGGTCCTTCGGGACAACTCAC
Found at i:302884 original size:22 final size:21
Alignment explanation
Indices: 302832--302890 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
302822 AGGGTTTCAT
*
302832 AAGTCTTTCGGGACAACTCAT
1 AAGTCTTTCGGGACAACTCAC
* * * *
302853 AGGTCCTTCGGGATATACTCGC
1 AAGTCTTTCGGGACA-ACTCAC
302875 AAGTCTTTCGGGACAA
1 AAGTCTTTCGGGACAA
302891 ATTTCATATG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
AAGTCTTTCGGGACAACTCAC
Found at i:308460 original size:21 final size:20
Alignment explanation
Indices: 308423--308461 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
308413 ATGTCATATA
308423 AAGGATAGTATTTTGAGTTT
1 AAGGATAGTATTTTGAGTTT
308443 AAGGA-AGTGATTATTGAGT
1 AAGGATAGT-ATT-TTGAGT
308462 AGGAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 8 0.47
21 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (20 bp):
AAGGATAGTATTTTGAGTTT
Found at i:313780 original size:37 final size:37
Alignment explanation
Indices: 313698--313799 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
313688 GTGCTTGTGG
* * * * *
313698 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAATTTGAATCCTAGCAAAACTCT
* * * *
313735 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAATTTGAATCCTAGCAAAACTCT
313772 ATCCTATTTTTAGGAATTTGAATCCTAG
1 ATCCTATTTTTAGGAATTTGAATCCTAG
313800 TAAGACGAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAATTTGAATCCTAGCAAAACTCT
Found at i:314639 original size:105 final size:105
Alignment explanation
Indices: 314345--314974 Score: 862
Period size: 105 Copynumber: 6.0 Consensus size: 105
314335 GCATTGTTCC
* * * ** *
314345 GAGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * * *
314409 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTTTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
314451 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-ACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
314510 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
314550 GAGTCCAATATCCTTCGTTCTGAAGTAGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
314615 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
314655 GAGCCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
314720 CAGCTGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
314760 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
314825 AAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
314865 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
314930 CCACCCGTCCCTTCGTTC-TGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
314971 GAGT
1 GAGT
314975 GTCATGATAT
Statistics
Matches: 475, Mismatches: 40, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
99 75 0.16
100 6 0.01
101 7 0.01
102 1 0.00
104 6 0.01
105 303 0.64
106 75 0.16
107 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:315221 original size:36 final size:36
Alignment explanation
Indices: 315174--315249 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
315164 TGTTTGGAGA
* * *
315174 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
315210 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
315246 GAAA
1 GAAA
315250 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:315424 original size:39 final size:39
Alignment explanation
Indices: 315370--315444 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
315360 TCAATGTTTA
* *
315370 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
315409 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
315445 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:315483 original size:105 final size:104
Alignment explanation
Indices: 315149--315464 Score: 521
Period size: 105 Copynumber: 3.1 Consensus size: 104
315139 TTCGTTAAAT
* ** *
315149 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
315211 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
315250 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
315315 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
315355 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
315420 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
315459 TGTTTT
1 TGTTTT
315465 TAAGAGAAAC
Statistics
Matches: 201, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
101 46 0.23
103 3 0.01
104 51 0.25
105 101 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:315666 original size:72 final size:74
Alignment explanation
Indices: 315552--315712 Score: 204
Period size: 72 Copynumber: 2.2 Consensus size: 74
315542 AAAAAATAGC
** * *
315552 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAACGGTCTCAAGCGAGACAAA-TCTTGTTTTA
1 CTTGAGTGAAAT-AAAT-CCTTCTTTCGAGAAAAACAGTCTCAAGCGAGACAAAGT-ATGTTTTA
315616 AGAAAAAC-AAT
63 AGAAAAACAAAT
* *
315627 CTTGAGTGAAATAAAT-CTTCTTTCGAGAAAAATAGTCTCAAGTGAGACAAAGTATGTTTTAAGA
1 CTTGAGTGAAATAAATCCTTCTTTCGAGAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAGA
315691 AAAACAAAT
66 AAAACAAAT
*
315700 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
315713 TCATCTGCAT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
72 57 0.74
73 4 0.05
74 4 0.05
75 12 0.16
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (74 bp):
CTTGAGTGAAATAAATCCTTCTTTCGAGAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAGA
AAAACAAAT
Found at i:317171 original size:183 final size:183
Alignment explanation
Indices: 316859--317385 Score: 948
Period size: 183 Copynumber: 2.9 Consensus size: 183
316849 ATCAGGTTTA
316859 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * **
316924 GCCAAGTGTCCGAGCAATGTCATTGTTTGAATGTAATCTATTCATAAAGACC-GGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAG-CCAGGGCTTTCGAGT
316988 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * **
317042 ACTTAAGGGTTTATCTCATCGTAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
317107 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGTTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
317172 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
317225 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGACTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
317290 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
317355 TCCTCTATAACCAATTGCCTTAGTGGAATAG
131 TCCTCTATAACCAATTGCCTTAGTGGAATAG
317386 TTTAACTTTA
Statistics
Matches: 328, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 2 0.01
183 326 0.99
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:322087 original size:37 final size:36
Alignment explanation
Indices: 322046--322119 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
322036 GGATAAAGAT
*
322046 AAAAAGAAAATAG-ATAAATAAATGAGTAAAATATATA
1 AAAAAGAAAA-AGCATAAATAAATAAGTAAAATA-ATA
* * *
322083 AAAAAGTAAAAGCATATATATATAAGTAAAATAATA
1 AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
322119 A
1 A
322120 TAATAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.23
Consensus pattern (36 bp):
AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
Found at i:322101 original size:20 final size:20
Alignment explanation
Indices: 322076--322113 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
322066 AATGAGTAAA
322076 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
322096 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
322114 TAATAATAAT
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:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:322550 original size:21 final size:22
Alignment explanation
Indices: 322507--322550 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
322497 GTTTACAATA
*
322507 GCTTTGCCTTTGTATTTTCTGT
1 GCTTTGCCTCTGTATTTTCTGT
* *
322529 GCTTT-CCTCTGTGTTTTGTGT
1 GCTTTGCCTCTGTATTTTCTGT
322550 G
1 G
322551 TAAATCGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.02, C:0.18, G:0.23, T:0.57
Consensus pattern (22 bp):
GCTTTGCCTCTGTATTTTCTGT
Found at i:322653 original size:37 final size:37
Alignment explanation
Indices: 322603--322707 Score: 113
Period size: 37 Copynumber: 2.8 Consensus size: 37
322593 GTGCTTGTGG
* *
322603 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAATTTGAATCTTAGTAGAACTCT
* * * * *
322640 ATCCTATTTTTAGGAGTTTGAATCCTT-GCAAAATTTT
1 ATCCTATTTTTAGGAATTTGAAT-CTTAGTAGAACTCT
* *
322677 GTCCTATTTTTAGGAATTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAATTTGAATCTTAGTAG
322708 GACGAAAATG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
36 2 0.04
37 49 0.91
38 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAATTTGAATCTTAGTAGAACTCT
Found at i:325713 original size:20 final size:21
Alignment explanation
Indices: 325690--325749 Score: 95
Period size: 22 Copynumber: 2.9 Consensus size: 21
325680 CGAGGGTTTC
*
325690 ATAGGTCCTTCGAGACAAC-T
1 ATAGGTCCTTCGGGACAACTT
325710 ATAGGTCCTTCGGGACATACTT
1 ATAGGTCCTTCGGGACA-ACTT
325732 ATAGGTCCTTCGGGACAA
1 ATAGGTCCTTCGGGACAA
325750 ATTTCATATG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 16 0.43
21 3 0.08
22 18 0.49
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
ATAGGTCCTTCGGGACAACTT
Found at i:328616 original size:21 final size:21
Alignment explanation
Indices: 328590--328634 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
328580 TTCCAGATTC
328590 GCAACGCGAACTTCGACTATT
1 GCAACGCGAACTTCGACTATT
*
328611 GCAACGCGAACTTTGACTATT
1 GCAACGCGAACTTCGACTATT
328632 GCA
1 GCA
328635 TTGCGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
GCAACGCGAACTTCGACTATT
Found at i:328640 original size:21 final size:21
Alignment explanation
Indices: 328595--328660 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
328585 GATTCGCAAC
* **
328595 GCGAACTTCGACTATTGCAAC
1 GCGAACTTTGACTATTGCATT
328616 GCGAACTTTGACTATTGCATT
1 GCGAACTTTGACTATTGCATT
328637 GCG-A-TTT-ACATATTCGCATT
1 GCGAACTTTGAC-TATT-GCATT
328657 GCGA
1 GCGA
328661 CTGTCCAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.05
19 7 0.18
20 9 0.23
21 21 0.54
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (21 bp):
GCGAACTTTGACTATTGCATT
Found at i:328679 original size:21 final size:21
Alignment explanation
Indices: 328649--328939 Score: 185
Period size: 21 Copynumber: 14.0 Consensus size: 21
328639 GATTTACATA
*
328649 TTCGCATTGCGACT-GTCCAAG
1 TTCGCGTTGCGA-TAGTCCAAG
*
328670 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
328691 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
328712 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
328731 TTCGCGTTGCAATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
328754 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
328773 TTCGAGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
328796 TT-G-GTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
328815 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
328838 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
328857 TTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
328880 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
328899 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
328922 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
328940 AATCGCAACG
Statistics
Matches: 207, Mismatches: 42, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
19 55 0.27
20 2 0.01
21 108 0.52
22 1 0.00
23 41 0.20
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:328701 original size:42 final size:42
Alignment explanation
Indices: 328674--328939 Score: 428
Period size: 42 Copynumber: 6.4 Consensus size: 42
328664 TCCAAGTTCG
*
328674 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
328714 CGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
328756 TGTTGCGATAGTCCAAGTTCGAGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
328798 GGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
328840 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
328882 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
328924 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
328940 AATCGCAACG
Statistics
Matches: 207, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
40 27 0.13
41 2 0.01
42 178 0.86
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:329040 original size:6 final size:6
Alignment explanation
Indices: 329029--329053 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
329019 GACACGTATT
329029 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
329054 TGACGAGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:329695 original size:6 final size:6
Alignment explanation
Indices: 329687--329725 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
329677 GTCCGTCTCG
*
329687 GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
329726 AATACGTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.15, G:0.54, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:329873 original size:35 final size:35
Alignment explanation
Indices: 329823--329895 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
329813 TTTTGGACTA
*
329823 TCGCAACGAATTTGGAATAAATCGCAACGCGAACT
1 TCGCAACGAACTTGGAATAAATCGCAACGCGAACT
329858 TCGCAACGAACTTGGAATAAATCGCAACGCGAACT
1 TCGCAACGAACTTGGAATAAATCGCAACGCGAACT
329893 TCG
1 TCG
329896 ACTATCGCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (35 bp):
TCGCAACGAACTTGGAATAAATCGCAACGCGAACT
Found at i:329884 original size:21 final size:19
Alignment explanation
Indices: 329858--329955 Score: 115
Period size: 21 Copynumber: 4.8 Consensus size: 19
329848 AACGCGAACT
*
329858 TCGCAACGAACTTGGAATAAA
1 TCGCAACGAACTTGGACT--A
*
329879 TCGCAACGCGAACTTCGACTA
1 TCGCAA--CGAACTTGGACTA
329900 TCGCAACGAACTTGGACTA
1 TCGCAACGAACTTGGACTA
329919 TCGCAATGCGAACTTGGACTA
1 TCGCAA--CGAACTTGGACTA
*
329940 TCGCAACGAATTTGGA
1 TCGCAACGAACTTGGA
329956 AAATAACATT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
19 27 0.39
21 32 0.46
23 10 0.14
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (19 bp):
TCGCAACGAACTTGGACTA
Found at i:329933 original size:40 final size:41
Alignment explanation
Indices: 329858--329956 Score: 146
Period size: 40 Copynumber: 2.4 Consensus size: 41
329848 AACGCGAACT
329858 TCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTA
* * *
329900 TCGCAACGAACTTGGACT-ATCGCAATGCGAACTTGGACTA
1 TCGCAACGAACTTGGAATAATCGCAACGCGAACTTCGACTA
*
329940 TCGCAACGAATTTGGAA
1 TCGCAACGAACTTGGAA
329957 AATAACATTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 35 0.67
42 17 0.33
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (41 bp):
TCGCAACGAACTTGGAATAATCGCAACGCGAACTTCGACTA
Found at i:329969 original size:40 final size:40
Alignment explanation
Indices: 329815--329963 Score: 119
Period size: 40 Copynumber: 3.8 Consensus size: 40
329805 TGTTGCGATT
* *
329815 TTGGACTATCGCAACGAATTTGG--AATAA-ATCGC-AAC
1 TTGGACTATCGCAACGAACTTGGAAAATAACAACGCGAAC
** * **
329851 GCGAACT-TCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGG-A-AAATAACAACGCGAAC
* ** ** *
329892 TTCGACTATCGCAACGAACTTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAAATAACAACGCGAAC
*
329932 TTGGACTATCGCAACGAATTTGGAAAATAACA
1 TTGGACTATCGCAACGAACTTGGAAAATAACA
329964 TTGCGATAGT
Statistics
Matches: 86, Mismatches: 20, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
35 14 0.16
36 4 0.05
39 3 0.03
40 43 0.50
41 7 0.08
42 15 0.17
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (40 bp):
TTGGACTATCGCAACGAACTTGGAAAATAACAACGCGAAC
Found at i:330611 original size:138 final size:138
Alignment explanation
Indices: 330463--330850 Score: 388
Period size: 138 Copynumber: 2.8 Consensus size: 138
330453 TCATTTCAAT
* ** *
330463 TATTCAATTCAATAATTGTCACAATTAATCAGGATAAATAATTAGAGT-CTGTATTTTAGTTTTA
1 TATTCAATTCAATAATTGTCAAAATTAATCAGG-TAAATAATTAGA-TCCTCCATTTTAATTTTA
* ** * *
330527 ATTTCACTGTAGT-CTTTAATTTAGGAGAATTTTCAATTTGGTCCTCGCTTTCAAGGTCGATGTT
64 ATTTCACTGTAGTCCTTTAATTTAGAAGAATTTTCAATTTGGTCCTCGCTTTCAAGCCCAAGGTT
330591 CCATTTTGAC
129 CCATTTTGAC
* * * ** * * *
330601 TATTCGATTCATTAATTTGTTAAAATTGGTTAGGTTAATATTTAGATCCTCCATTTTAATTTTAA
1 TATTCAATTCAATAA-TTGTCAAAATTAATCAGGTAAATAATTAGATCCTCCATTTTAATTTTAA
** *
330666 TTTCACTGTAGTCCTTTAATTTAGAAGAATTTTTTATTTGGTCCTCGCTTTCATGCCCAAGGTTC
65 TTTCACTGTAGTCCTTTAATTTAGAAGAATTTTCAATTTGGTCCTCGCTTTCAAGCCCAAGGTTC
330731 CATTTTGAC
130 CATTTTGAC
* * *** * * * *
330740 TATTCAATTCAGTAATTGGTTAGAAATCGGTTAGGTTAATATTTAGAGCCTCCATTTT--TTTTA
1 TATTCAATTCAATAATT-GTCA-AAATTAATCAGGTAAATAATTAGATCCTCCATTTTAATTTTA
* * * ** *
330803 ATTCCATTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTTCTCG
64 ATTTCACTGTAGTCCTTTAATTTAGAAGAATTTTCAATTTGGTCCTCG
330851 TTTTTCTGCT
Statistics
Matches: 217, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
137 1 0.00
138 100 0.46
139 83 0.38
140 33 0.15
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (138 bp):
TATTCAATTCAATAATTGTCAAAATTAATCAGGTAAATAATTAGATCCTCCATTTTAATTTTAAT
TTCACTGTAGTCCTTTAATTTAGAAGAATTTTCAATTTGGTCCTCGCTTTCAAGCCCAAGGTTCC
ATTTTGAC
Found at i:330734 original size:139 final size:139
Alignment explanation
Indices: 330515--330850 Score: 489
Period size: 139 Copynumber: 2.4 Consensus size: 139
330505 TAGAGTCTGT
**
330515 ATTTTAGTTTTAATTTCACTGTAGT-CTTTAATTTAGGAGAATTTTCAATTTGGTCCTCGCTTTC
1 ATTTTA-TTTTAATTTCACTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTC
** * * * * * *
330579 AAGGTCGATGTTCCATTTTGACTATTCGATTCATTAATTTGTTA-AAATTGGTTAGGTTAATATT
65 AAGCCCAAGGTTCCATTTTGACTATTCAATTCAGTAATTGGTTAGAAATCGGTTAGGTTAATATT
*
330643 TAGATCCTCC
130 TAGAGCCTCC
*
330653 ATTTTAATTTTAATTTCACTGTAGTCCTTTAATTTAGAAGAATTTTTTATTTGGTCCTCGCTTTC
1 ATTTT-ATTTTAATTTCACTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTC
*
330718 ATGCCCAAGGTTCCATTTTGACTATTCAATTCAGTAATTGGTTAGAAATCGGTTAGGTTAATATT
65 AAGCCCAAGGTTCCATTTTGACTATTCAATTCAGTAATTGGTTAGAAATCGGTTAGGTTAATATT
330783 TAGAGCCTCC
130 TAGAGCCTCC
* * *
330793 ATTTT-TTTTAATTCCATTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTTCTCG
1 ATTTTATTTTAATTTCACTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCG
330851 TTTTTCTGCT
Statistics
Matches: 178, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
138 72 0.40
139 73 0.41
140 33 0.19
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (139 bp):
ATTTTATTTTAATTTCACTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTCA
AGCCCAAGGTTCCATTTTGACTATTCAATTCAGTAATTGGTTAGAAATCGGTTAGGTTAATATTT
AGAGCCTCC
Found at i:330920 original size:138 final size:138
Alignment explanation
Indices: 330515--330904 Score: 498
Period size: 138 Copynumber: 2.8 Consensus size: 138
330505 TAGAGTCTGT
**
330515 ATTTTAGTTTTAATTTCACTGTAGT-CTTTAATTTAGGAGAATTTTCAATTTGGTCCTCGCTTTC
1 ATTTTA-TTTTAATTTCACTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTC
* * * * *
330579 AAGGTCGATGTTCCATTTTGACTATTCGATTCATTAATTTGTTAAAATTGGTTAGGTTAATATTT
65 ATGCTCGAGGTTCCATTTTGACTATTCGATTCAATAATTTGTTAAAAATGGTTAGGTTAATATTT
*
330644 AGATCCTCC
130 AGAGCCTCC
*
330653 ATTTTAATTTTAATTTCACTGTAGTCCTTTAATTTAGAAGAATTTTTTATTTGGTCCTCGCTTTC
1 ATTTT-ATTTTAATTTCACTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTC
* * * * * *
330718 ATGCCCAAGGTTCCATTTTGACTATTCAATTCAGTAATTGGTTAGAAATCGGTTAGGTTAATATT
65 ATGCTCGAGGTTCCATTTTGACTATTCGATTCAATAATTTGTTAAAAAT-GGTTAGGTTAATATT
330783 TAGAGCCTCC
129 TAGAGCCTCC
* * * *
330793 ATTTT-TTTTAATTCCATTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTTCTCGTTTTTC
1 ATTTTATTTTAATTTCACTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCG-CTTTC
* * * * * *
330857 -TGCTTGAGGTTTCATTTTGATTGTTCGACTCAATAATTTATTAAAAAT
65 ATGCTCGAGGTTCCATTTTGACTATTCGATTCAATAATTTGTTAAAAAT
330905 AATTTGGATT
Statistics
Matches: 217, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
138 108 0.50
139 80 0.37
140 29 0.13
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.47
Consensus pattern (138 bp):
ATTTTATTTTAATTTCACTGTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTCA
TGCTCGAGGTTCCATTTTGACTATTCGATTCAATAATTTGTTAAAAATGGTTAGGTTAATATTTA
GAGCCTCC
Found at i:333027 original size:13 final size:14
Alignment explanation
Indices: 333003--333032 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
332993 ATTTTTAAAA
333003 ATTATAAAATTTTT
1 ATTATAAAATTTTT
333017 ATTAT-AAATTTTT
1 ATTATAAAATTTTT
333030 ATT
1 ATT
333033 TAATTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATAAAATTTTT
Found at i:334805 original size:15 final size:15
Alignment explanation
Indices: 334785--334866 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
334775 TTCCGGAAAA
*
334785 TGAATTACTAGAATT
1 TGAATTACTGGAATT
334800 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
334815 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
334830 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
334845 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
334859 TGAATTAC
1 TGAATTAC
334867 ATTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:334844 original size:45 final size:44
Alignment explanation
Indices: 334779--334866 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
334769 TTGGTTTTCC
**
334779 GGAAAATGAATTACTAGAATTTGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTAGAATTTGAATT-CTGGAAAATGAATTACT
*
334824 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GGAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTAC
334867 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (44 bp):
GGAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTACT
Found at i:334864 original size:29 final size:30
Alignment explanation
Indices: 334785--334866 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
334775 TTCCGGAAAA
* **
334785 TGAATTACTAGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
334815 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
334845 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
334867 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:335094 original size:19 final size:19
Alignment explanation
Indices: 335032--335095 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
335022 TTAAATATAA
*
335032 TAAATAATATTATTTATCA-
1 TAAATAAT-TTATTTATTAT
*
335051 TAAA-ACTTT-TTTATTAT
1 TAAATAATTTATTTATTAT
335068 TAAAAAATAATTTATTTATTAT
1 T---AAATAATTTATTTATTAT
335090 TAAATA
1 TAAATA
335096 GTATTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
16 6 0.17
17 3 0.08
18 2 0.06
19 9 0.25
20 3 0.08
21 4 0.11
22 9 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAATAATTTATTTATTAT
Found at i:335131 original size:29 final size:32
Alignment explanation
Indices: 335091--335161 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 32
335081 ATTTATTATT
* *
335091 AAATAGTATTTTTATA-ATTTTA-T-TAATAA
1 AAATATTATTTTTATATATTTTAGTGAAATAA
*
335120 AAATATTATTTTTTGTATATTTTAGTGAAATAA
1 AAATATTA-TTTTTATATATTTTAGTGAAATAA
335153 AAATATTAT
1 AAATATTAT
335162 AAATATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 7 0.20
30 7 0.20
31 6 0.17
32 2 0.06
33 13 0.37
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.51
Consensus pattern (32 bp):
AAATATTATTTTTATATATTTTAGTGAAATAA
Found at i:335300 original size:31 final size:31
Alignment explanation
Indices: 335248--335327 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 31
335238 CTTTATTAAA
335248 ATATTATTTAAATATAT-AAAAATTATATTAT
1 ATATTA-TTAAATATATAAAAAATTATATTAT
*
335279 -TCATTATTAAATATATAAAAAATTTTATTAT
1 AT-ATTATTAAATATATAAAAAATTATATTAT
335310 ATATTATTAAA-ATA-AAAA
1 ATATTATTAAATATATAAAA
335328 TATAGTATCT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
29 4 0.09
30 14 0.31
31 26 0.58
32 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
ATATTATTAAATATATAAAAAATTATATTAT
Found at i:335306 original size:28 final size:28
Alignment explanation
Indices: 335249--335340 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 28
335239 TTTATTAAAA
335249 TATTATTTAAATATATAAAAATTATATTAT
1 TATTA-TTAAATATATAAAAA-TATATTAT
*
335279 TCATTATTAAATATATAAAAA-ATTTTAT
1 T-ATTATTAAATATATAAAAATATATTAT
*
335307 TATATATTATTAA-A-ATAAAAATATAGTAT
1 TAT-TATTA--AATATATAAAAATATATTAT
335336 CTATT
1 -TATT
335341 TGTTTGCCGT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
27 2 0.04
28 19 0.36
29 7 0.13
30 21 0.40
31 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (28 bp):
TATTATTAAATATATAAAAATATATTAT
Found at i:335677 original size:31 final size:31
Alignment explanation
Indices: 335642--335758 Score: 86
Period size: 31 Copynumber: 3.8 Consensus size: 31
335632 AAATATTATT
335642 TATTA-ATTTATTAATATT-TATAATAATATAA
1 TATTATATTT-TTAATATTATATAA-AATATAA
*
335673 TATTATATTTTTAATATTATATAAAATAATCA
1 TATTATATTTTTAATATTATATAAAAT-ATAA
* * *
335705 -ATTATA-TTATAATA--ATATAAGATATTA
1 TATTATATTTTTAATATTATATAAAATATAA
* *
335732 TATT-TTTATTTTAATAATATAATAAAA
1 TATTATAT-TTTTAATATTAT-ATAAAA
335759 ATTTATATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
27 4 0.06
28 11 0.16
29 7 0.10
30 7 0.10
31 24 0.34
32 17 0.24
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
TATTATATTTTTAATATTATATAAAATATAA
Found at i:335680 original size:22 final size:23
Alignment explanation
Indices: 335650--335693 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
335640 TTTATTAATT
335650 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
335673 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
335694 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:335785 original size:19 final size:19
Alignment explanation
Indices: 335763--335815 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
335753 ATAAAAATTT
*
335763 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
335782 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
335804 ATAT-TTTAATAA
1 ATATATTTAATAA
335816 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:335836 original size:23 final size:23
Alignment explanation
Indices: 335810--335854 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
335800 AATAATATTT
335810 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
335833 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
335855 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:336213 original size:20 final size:20
Alignment explanation
Indices: 336176--336214 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
336166 CCGGAAAACG
**
336176 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
336196 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
336215 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:336224 original size:15 final size:15
Alignment explanation
Indices: 336188--336245 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
336178 TTCCAGAAAT
336188 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
336203 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
336217 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
336232 GTAATTCATTTTCC
1 GTAATTCATTTTCC
336246 GAAAAATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 12 0.32
15 26 0.68
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:336317 original size:31 final size:33
Alignment explanation
Indices: 336279--336348 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 33
336269 AACAGATTAT
*
336279 AATATAATTGATTATTTTA-TAT-AATATTAA-A
1 AATATAATT-ATTATATTATTATAAATATTAATA
336310 AATATAA-TATTATATTATTATAAATATTAATA
1 AATATAATTATTATATTATTATAAATATTAATA
336342 AAT-TAAT
1 AATATAAT
336349 AAATAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 8 0.24
30 4 0.12
31 18 0.53
32 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
AATATAATTATTATATTATTATAAATATTAATA
Found at i:336323 original size:22 final size:23
Alignment explanation
Indices: 336298--336341 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
336288 GATTATTTTA
336298 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
336320 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
336342 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:337543 original size:13 final size:13
Alignment explanation
Indices: 337522--337576 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
337512 AAGTTCGATA
*
337522 AATTCAAATACTT
1 AATTGAAATACTT
337535 AATTGAAATACTT
1 AATTGAAATACTT
*
337548 AATT-AAATCAACAT
1 AATTGAAAT--ACTT
337562 AATTGAAATACTT
1 AATTGAAATACTT
337575 AA
1 AA
337577 ATACTTCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.11
13 21 0.58
14 7 0.19
15 4 0.11
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:337658 original size:32 final size:33
Alignment explanation
Indices: 337562--337660 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
337552 AAATCAACAT
* * *
337562 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
337595 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
337628 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
337660 A
1 A
337661 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:337679 original size:21 final size:21
Alignment explanation
Indices: 337655--337694 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
337645 ACTTCAAGTT
337655 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
337676 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
337695 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:340011 original size:11 final size:12
Alignment explanation
Indices: 339990--340035 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
339980 TCCGGATAAA
339990 AACCGGTTTTTT
1 AACCGGTTTTTT
340002 AACCGGTTTTTTT
1 AACCGG-TTTTTT
340015 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
340029 ATCCGGT
1 AACCGGT
340036 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:340020 original size:15 final size:14
Alignment explanation
Indices: 339989--340028 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
339979 TTCCGGATAA
339989 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
340002 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
340015 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
340029 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:341670 original size:28 final size:29
Alignment explanation
Indices: 341611--341671 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
341601 GTATCAAATC
341611 ATGTGACAAGGTTCAACCAAAACTTTTGA
1 ATGTGACAAGGTTCAACCAAAACTTTTGA
*
341640 ATGTGACAAGGTTCAACC-AAACTTTTTA
1 ATGTGACAAGGTTCAACCAAAACTTTTGA
341668 ATGT
1 ATGT
341672 ACAGCTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (29 bp):
ATGTGACAAGGTTCAACCAAAACTTTTGA
Found at i:343842 original size:18 final size:19
Alignment explanation
Indices: 343819--343859 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
343809 ACAACACAAC
343819 AGTTTAACCAG-ACTACCT
1 AGTTTAACCAGAACTACCT
343837 AGTTTAACCAGAACTACCT
1 AGTTTAACCAGAACTACCT
343856 AGTT
1 AGTT
343860 AAATACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (19 bp):
AGTTTAACCAGAACTACCT
Found at i:349894 original size:21 final size:20
Alignment explanation
Indices: 349870--350002 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 20
349860 CAGTTCCCAG
349870 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
349890 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
349911 AATTCGCATTGCGATTTTCTAG
1 AA-TCGCAACGCGATTAT-GAA
* *
349933 AATCGCAAAGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
349953 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
349973 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
349993 TATCGCAACG
1 AATCGCAACG
350003 AGTATCCGTA
Statistics
Matches: 86, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
19 2 0.02
20 45 0.52
21 35 0.41
22 3 0.03
23 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:350042 original size:20 final size:20
Alignment explanation
Indices: 349994--350164 Score: 209
Period size: 20 Copynumber: 8.4 Consensus size: 20
349984 GATTCTGACT
*
349994 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
350015 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
350035 ATCACAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
350056 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
350076 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
350096 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
*
350116 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
350136 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
350156 ATCACAACG
1 ATCGCAACG
350165 ACAATACGTA
Statistics
Matches: 127, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
20 94 0.74
21 33 0.26
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:350109 original size:40 final size:41
Alignment explanation
Indices: 349994--350184 Score: 278
Period size: 40 Copynumber: 4.7 Consensus size: 41
349984 GATTCTGACT
* *
349994 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
350035 ATCACAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
350076 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
350116 ATCGCAACGAGTATCCGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
350156 ATCACAACGACAATACGTAAAATCGCAAC
1 ATCGCAACGAGAATACGTAAAATCGCAAC
350185 ACGATTTTTA
Statistics
Matches: 133, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 71 0.53
41 62 0.47
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:350174 original size:20 final size:20
Alignment explanation
Indices: 349994--350184 Score: 122
Period size: 20 Copynumber: 9.4 Consensus size: 20
349984 GATTCTGACT
** *
349994 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGACAATACGT-AA
* *
350015 ATCGCAACG-CGTATCCGTAA
1 ATCGCAACGAC-AATACGTAA
*
350035 ATCACAACGACAATACGTAAA
1 ATCGCAACGACAATACGT-AA
* *
350056 ATCGCAACG-CGTATCCGTAA
1 ATCGCAACGAC-AATACGTAA
*
350076 ATCGCAACGAGAATACGTAA
1 ATCGCAACGACAATACGTAA
*
350096 ATCGCAACG-C-GTATCTGTAA
1 ATCGCAACGACAATA-C-GTAA
** *
350116 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGACAATACGTAA
* * *
350136 ATCGCAATG-CGTATCCGTAA
1 ATCGCAACGAC-AATACGTAA
*
350156 ATCACAACGACAATACGTAAA
1 ATCGCAACGACAATACGT-AA
350177 ATCGCAAC
1 ATCGCAAC
350185 ACGATTTTTA
Statistics
Matches: 136, Mismatches: 22, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.01
19 1 0.01
20 89 0.65
21 43 0.32
22 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGACAATACGTAA
Found at i:350805 original size:21 final size:21
Alignment explanation
Indices: 350744--350822 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
350734 TTTTAAACTT
350744 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
350764 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
350784 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
350805 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
350823 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:350826 original size:14 final size:14
Alignment explanation
Indices: 350804--350868 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
350794 CGAGAGAAAT
350804 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
350818 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
350836 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
350851 GATAATCGCAACGC
1 GAAAATCGCAACGA
350865 GAAA
1 GAAA
350869 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:350840 original size:33 final size:33
Alignment explanation
Indices: 350799--350879 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
350789 CGCAACGAGA
350799 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
350832 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
350865 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
350880 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:350897 original size:19 final size:19
Alignment explanation
Indices: 350875--351037 Score: 129
Period size: 20 Copynumber: 8.6 Consensus size: 19
350865 GAAACCAAAA
* *
350875 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATATTCATT
* *
350894 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATATTCATT
*
350913 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATATTCATT
350932 TCGCGTTGCG--ATTC---
1 TCGCGTTGCGATATTCATT
* *
350946 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATATTCATT
* *
350965 TCCGCATTGCGATAGTCATT
1 T-CGCGTTGCGATATTCATT
* *
350985 CTCTCGTTGCGATAGTCATT
1 -TCGCGTTGCGATATTCATT
* *
351005 TCCGCATTGCGATAGTCATT
1 T-CGCGTTGCGATATTCATT
*
351025 CTCTCGTTGCGAT
1 -TCGCGTTGCGAT
351038 TTTTATTTCA
Statistics
Matches: 121, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
14 9 0.07
16 3 0.02
17 3 0.02
19 47 0.39
20 57 0.47
21 2 0.02
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATATTCATT
Found at i:351046 original size:40 final size:40
Alignment explanation
Indices: 350942--351037 Score: 192
Period size: 40 Copynumber: 2.4 Consensus size: 40
350932 TCGCGTTGCG
350942 ATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATAGTC
350982 ATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATAGTC
351022 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
351038 TTTTATTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.39
Consensus pattern (40 bp):
ATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATAGTC
Found at i:352897 original size:94 final size:94
Alignment explanation
Indices: 352736--353115 Score: 665
Period size: 94 Copynumber: 4.1 Consensus size: 94
352726 TAGATTGCTT
* *
352736 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
352801 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
352830 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
352895 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
352924 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
352989 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
353018 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
353083 ATTTGCCTTTGTTTTGTCTTTTGGTT-AA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
353111 AGTAA
1 AGTAA
353116 TGCAATCCAT
Statistics
Matches: 277, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 251 0.91
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:353237 original size:14 final size:14
Alignment explanation
Indices: 353218--353275 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 14
353208 AACGCGAAAT
353218 GAATCGCAACGAGA
1 GAATCGCAACGAGA
353232 GAATCGCAACGAGAAA
1 GAATCGCAACGAG--A
353248 TGAAAATCGCAACGAGA
1 -G--AATCGCAACGAGA
353265 GAATCGCAACG
1 GAATCGCAACG
353276 CGAAACAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 23 0.59
16 2 0.05
17 2 0.05
19 12 0.31
ACGTcount: A:0.45, C:0.21, G:0.26, T:0.09
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:353257 original size:19 final size:19
Alignment explanation
Indices: 353170--353330 Score: 87
Period size: 19 Copynumber: 9.1 Consensus size: 19
353160 CTTTCGCAAC
*
353170 ACGA-AAATTAAAATCGCA
1 ACGAGAAATGAAAATCGCA
* **
353188 ACGTGAAAAATGACTATCGCA
1 AC--GAGAAATGAAAATCGCA
*
353209 ACGCGAAATG--AATCGCA
1 ACGAGAAATGAAAATCGCA
353226 ACGAG--A-G--AATCGCA
1 ACGAGAAATGAAAATCGCA
353240 ACGAGAAATGAAAATCGCA
1 ACGAGAAATGAAAATCGCA
353259 ACGAG--A-G--AATCGCA
1 ACGAGAAATGAAAATCGCA
* **
353273 ACGCGAAACAAAAATCGCA
1 ACGAGAAATGAAAATCGCA
* **
353292 ACGCGAAACAAAAATCGCA
1 ACGAGAAATGAAAATCGCA
* **
353311 ACGCGAAACAAAAATCGCA
1 ACGAGAAATGAAAATCGCA
353330 A
1 A
353331 TGCGAAACTA
Statistics
Matches: 121, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
14 24 0.20
15 1 0.01
16 3 0.02
17 12 0.10
18 2 0.02
19 64 0.53
20 2 0.02
21 13 0.11
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (19 bp):
ACGAGAAATGAAAATCGCA
Found at i:353261 original size:33 final size:33
Alignment explanation
Indices: 353203--353294 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
353193 AAAAATGACT
353203 ATCGCAACGCGAAATG--AATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
353234 ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
**
353267 ATCGCAACGCGAAACAAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
353295 CGAAACAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 15 0.27
33 40 0.73
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:353317 original size:38 final size:38
Alignment explanation
Indices: 353266--353347 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
353256 GCAACGAGAG
353266 AATCGCAACGCGAAACAAAAATCGCAACGCGAAACAAA
1 AATCGCAACGCGAAACAAAAATCGCAACGCGAAACAAA
* * *
353304 AATCGCAACGCGAAACAAAAATCGCAATGCGAAACTAT
1 AATCGCAACGCGAAACAAAAATCGCAACGCGAAACAAA
353342 AATCGC
1 AATCGC
353348 GTTGCGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.10
Consensus pattern (38 bp):
AATCGCAACGCGAAACAAAAATCGCAACGCGAAACAAA
Found at i:353347 original size:19 final size:19
Alignment explanation
Indices: 353266--353338 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
353256 GCAACGAGAG
353266 AATCGCAACGCGAAACAAA
1 AATCGCAACGCGAAACAAA
353285 AATCGCAACGCGAAACAAA
1 AATCGCAACGCGAAACAAA
353304 AATCGCAACGCGAAACAAA
1 AATCGCAACGCGAAACAAA
*
353323 AATCGCAATGCGAAAC
1 AATCGCAACGCGAAAC
353339 TATAATCGCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.51, C:0.26, G:0.16, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:353407 original size:20 final size:20
Alignment explanation
Indices: 353382--353465 Score: 141
Period size: 20 Copynumber: 4.2 Consensus size: 20
353372 GATTCTCTCG
**
353382 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
353402 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
353422 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
353442 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
353462 TTGC
1 TTGC
353466 AATTTTAAGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:353993 original size:18 final size:19
Alignment explanation
Indices: 353954--353995 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
353944 CTCACCTGTC
353954 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
353975 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
353993 ATC
1 ATC
353996 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:354049 original size:42 final size:42
Alignment explanation
Indices: 353979--354070 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
353969 TCCCCTATCG
* *
353979 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAACA
* ** *
354021 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
*
354063 TTCTAGAG
1 TTCAAGAG
354071 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
Found at i:355608 original size:33 final size:33
Alignment explanation
Indices: 355551--355648 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
355541 AAAATAGACT
* **
355551 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
355585 ATTGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
355618 ATCGCAATGCGAAATGAAAATCGCAACGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA
355649 AACTAATTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 49 0.86
34 8 0.14
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:355641 original size:19 final size:19
Alignment explanation
Indices: 355588--355643 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
355578 CGAGAGAATT
355588 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
355607 GCAA--CG-AGTG--AATC
1 GCAATGCGAAATGAAAATC
355621 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
355640 GCAA
1 GCAA
355644 CGAGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 8 0.27
16 5 0.17
17 5 0.17
19 12 0.40
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Found at i:355650 original size:19 final size:19
Alignment explanation
Indices: 355595--355650 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
355585 ATTGCAATGC
355595 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
355614 G---TG--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
355628 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
355647 GAAA
1 GAAA
355651 CTAATTTCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
14 10 0.36
16 2 0.07
17 2 0.07
19 14 0.50
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:355717 original size:33 final size:34
Alignment explanation
Indices: 355662--355755 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 34
355652 TAATTTCGCC
355662 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
*
355696 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
** *
355729 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
355756 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
Found at i:355821 original size:19 final size:19
Alignment explanation
Indices: 355799--355886 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
355789 CGAGAAACTA
*
355799 ATTTCGCCTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
355818 ATTTTCACATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
355836 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
355852 ATTTCGCATTGCGATTTTT
1 ATTTCGCATTGCGATTTTC
355871 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
355887 CTCTCGTTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
14 6 0.11
16 6 0.11
17 3 0.05
18 4 0.07
19 27 0.47
20 11 0.19
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:355893 original size:52 final size:53
Alignment explanation
Indices: 355799--355919 Score: 154
Period size: 52 Copynumber: 2.3 Consensus size: 53
355789 CGAGAAACTA
* **
355799 ATTTCGCCTTGCGATTTTCATTTTCACATTGCGATTCACTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTTCACATTGCGATTCACTCGTTGCGATAGTC
* * * *
355852 ATTTCGCATTGCGATTTTTA-TTTCGCATTGCGATTCTCTCGTTGCTATAGTC
1 ATTTCGCATTGCGATTTTCATTTTCACATTGCGATTCACTCGTTGCGATAGTC
*
355904 ATTTCCGCGTTGCGAT
1 ATTT-CGCATTGCGAT
355920 AGTCATATTC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
52 31 0.53
53 28 0.47
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (53 bp):
ATTTCGCATTGCGATTTTCATTTTCACATTGCGATTCACTCGTTGCGATAGTC
Found at i:355916 original size:20 final size:20
Alignment explanation
Indices: 355891--355944 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
355881 GCGATTCTCT
*
355891 CGTTGCTATAGTCAT-TTCCG
1 CGTTGCGATAGTCATATT-CG
355911 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATATTCG
*
355931 CTTTGCGATAGTCA
1 CGTTGCGATAGTCA
355945 AATGAATGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCG
Found at i:356269 original size:20 final size:20
Alignment explanation
Indices: 356244--356480 Score: 230
Period size: 20 Copynumber: 11.7 Consensus size: 20
356234 AATTATCGAT
356244 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
356264 CGCGTTGCAATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
356284 TGTCGTTGCAATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
356305 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
356325 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
356345 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
356365 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
356385 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
356405 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
356426 CGCGTTGTGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
* *
356447 CTCGTTGCGATAGTTA-GAAT-
1 CGCGTTGCGAT--TTACGGATA
356467 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
356481 TATGTTCGCG
Statistics
Matches: 177, Mismatches: 31, Indels: 20
0.78 0.14 0.09
Matches are distributed among these distances:
18 3 0.02
20 116 0.66
21 55 0.31
22 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:356330 original size:40 final size:41
Alignment explanation
Indices: 356246--356518 Score: 333
Period size: 40 Copynumber: 6.7 Consensus size: 41
356236 TTATCGATCG
* *
356246 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
356287 CGTTGCAATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
356327 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
356367 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
356408 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
356449 CGTTGCGATAGTTA-GAAT-CGCGTTGCGATTTATA--TGTTCG
1 CGTTGCGAT--TTACGGATACGCGTTGCGATTT-TACGTATTCT
* ** *
356489 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATT
356519 CTGGAAAATC
Statistics
Matches: 204, Mismatches: 22, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 98 0.48
41 94 0.46
42 5 0.02
43 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:356400 original size:81 final size:82
Alignment explanation
Indices: 356246--356518 Score: 333
Period size: 81 Copynumber: 3.4 Consensus size: 82
356236 TTATCGATCG
* * * * *
356246 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGTCGTTGCAATTTACGGATACGCATT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
356311 GCGA-TTTACGTATTCT
66 GCGATTTTACGTATTCT
356327 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
*
356391 GCGATTTTACGTATTGT
66 GCGATTTTACGTATTCT
* * * * *
356408 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGGATACTCGTTGCGATAGTTA-GAAT-CGCG
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT--TTACGGATACGCG
* *
356471 TTGCGATTTATA--TGTTCG
64 TTGCGATTT-TACGTATTCT
* * *
356489 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
356519 CTGGAAAATC
Statistics
Matches: 168, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
80 37 0.22
81 91 0.54
82 32 0.19
83 5 0.03
84 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (82 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
GCGATTTTACGTATTCT
Found at i:356489 original size:20 final size:20
Alignment explanation
Indices: 356466--356518 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
356456 ATAGTTAGAA
*
356466 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
356486 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
356506 TCGCGTTGCGATT
1 TCGCGTTGCGATT
356519 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:356579 original size:42 final size:42
Alignment explanation
Indices: 356486--356579 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
356476 ATTTATATGT
* *
356486 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
356527 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
356569 TCGCGTTGCGA
1 TCGCGTTGCGA
356580 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:356617 original size:20 final size:19
Alignment explanation
Indices: 356568--356621 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
356558 ATTCTTCATA
356568 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
356587 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
356608 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
356622 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:356983 original size:60 final size:60
Alignment explanation
Indices: 356933--357119 Score: 261
Period size: 59 Copynumber: 3.1 Consensus size: 60
356923 TTCTAACTTT
* * * *
356933 ATCCTCAAACTATGACTTTTATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTC
1 ATCCTCAAAATATGACTCTTATTCTAAATTGGTCCTCAAACTTTTGAATATTTCAATTTC
* * * *
356993 ATCC-CAAAATATGACTCTCATTCTAAATCGGTCATCAAACTTTTGAATCTTTCAATTTC
1 ATCCTCAAAATATGACTCTTATTCTAAATTGGTCCTCAAACTTTTGAATATTTCAATTTC
* *
357052 ATCCT-AAAATATGACTCCTATTCTAAATTGGTCCTCAAACTTTTGAATCTTTCAATTTC
1 ATCCTCAAAATATGACTCTTATTCTAAATTGGTCCTCAAACTTTTGAATATTTCAATTTC
*
357111 ATCCCCAAA
1 ATCCTCAAA
357120 GTCACCCAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 105 0.94
60 7 0.06
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
ATCCTCAAAATATGACTCTTATTCTAAATTGGTCCTCAAACTTTTGAATATTTCAATTTC
Found at i:358212 original size:31 final size:32
Alignment explanation
Indices: 358177--358260 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 32
358167 GATTATCTTG
358177 GGGCCTGC-GAGCCTACCCAAGAA-AATTCTCA
1 GGGCCTGCAGAGCCTACCCAAGAACAA-TCTCA
*
358208 GGGCC-ACAGAGGCCTACCCAAGAACAATCTCA
1 GGGCCTGCAGA-GCCTACCCAAGAACAATCTCA
358240 GGG-CTGCAGAGCCTACCCAAG
1 GGGCCTGCAGAGCCTACCCAAG
358261 GATCACCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
30 1 0.02
31 19 0.40
32 25 0.53
33 2 0.04
ACGTcount: A:0.30, C:0.33, G:0.25, T:0.12
Consensus pattern (32 bp):
GGGCCTGCAGAGCCTACCCAAGAACAATCTCA
Found at i:358423 original size:12 final size:12
Alignment explanation
Indices: 358406--358461 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
358396 GAGATATCAA
358406 AAATCAGAACAG
1 AAATCAGAACAG
*
358418 AAATCAGAGCAG
1 AAATCAGAACAG
*
358430 AAATCATAACAG
1 AAATCAGAACAG
* *
358442 AATTCAGAGCAG
1 AAATCAGAACAG
358454 AAATCAGA
1 AAATCAGA
358462 TAAAATATTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (12 bp):
AAATCAGAACAG
Found at i:358435 original size:24 final size:24
Alignment explanation
Indices: 358406--358461 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
358396 GAGATATCAA
358406 AAATCAGAACAGAAATCAGAGCAG
1 AAATCAGAACAGAAATCAGAGCAG
* *
358430 AAATCATAACAGAATTCAGAGCAG
1 AAATCAGAACAGAAATCAGAGCAG
358454 AAATCAGA
1 AAATCAGA
358462 TAAAATATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (24 bp):
AAATCAGAACAGAAATCAGAGCAG
Found at i:359287 original size:19 final size:19
Alignment explanation
Indices: 359249--359287 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
359239 ACCAACAAAA
* *
359249 TCGCAACACGATCTCGAAT
1 TCGCAACACGAACTCCAAT
*
359268 TCGCAACGCGAACTCCAAT
1 TCGCAACACGAACTCCAAT
359287 T
1 T
359288 TCGTAACTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (19 bp):
TCGCAACACGAACTCCAAT
Found at i:359329 original size:21 final size:21
Alignment explanation
Indices: 359304--359416 Score: 106
Period size: 20 Copynumber: 5.5 Consensus size: 21
359294 CTCAGTTTCC
**
359304 AAAATCGCAGTATGAATAGTA
1 AAAATCGCAACATGAATAGTA
*
359325 AAAATCGCAACGTGAATAGTA
1 AAAATCGCAACATGAATAGTA
* *
359346 AAAATCGTAACGTGAATAGT-
1 AAAATCGCAACATGAATAGTA
* *
359366 AAAATAGCAACGTGAATAGT-
1 AAAATCGCAACATGAATAGTA
* ** *
359386 AAAATCACAACGCGAATTG-A
1 AAAATCGCAACATGAATAGTA
359406 AAAATCGCAAC
1 AAAATCGCAAC
359417 GCGAATTTAG
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
20 43 0.54
21 37 0.46
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (21 bp):
AAAATCGCAACATGAATAGTA
Found at i:359377 original size:20 final size:20
Alignment explanation
Indices: 359316--359436 Score: 136
Period size: 20 Copynumber: 5.9 Consensus size: 20
359306 AATCGCAGTA
359316 TGAATAGTAAAAATCGCAACG
1 TGAATAGT-AAAATCGCAACG
*
359337 TGAATAGTAAAAATCGTAACG
1 TGAATAGT-AAAATCGCAACG
*
359358 TGAATAGTAAAATAGCAACG
1 TGAATAGTAAAATCGCAACG
*
359378 TGAATAGTAAAATCACAACG
1 TGAATAGTAAAATCGCAACG
* * *
359398 CGAATTGAAAAATCGCAACG
1 TGAATAGTAAAATCGCAACG
*
359418 CGAATTTAG-AAAATCGCAA
1 TGAA--TAGTAAAATCGCAA
359437 AATCGCGTTG
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
20 48 0.55
21 38 0.43
22 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (20 bp):
TGAATAGTAAAATCGCAACG
Found at i:359845 original size:22 final size:20
Alignment explanation
Indices: 359786--359855 Score: 95
Period size: 20 Copynumber: 3.4 Consensus size: 20
359776 CATATAGATT
359786 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
** *
359806 ATTTGCGATTTTAATATTCA
1 CGTTGCGATTTTACTATTCA
359826 CGTTGCGATTTTTTACTATTCA
1 CGTTGCGA--TTTTACTATTCA
359848 CGTTGCGA
1 CGTTGCGA
359856 ATTTGACTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 23 0.55
22 19 0.45
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:359874 original size:20 final size:20
Alignment explanation
Indices: 359849--359915 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
359839 TACTATTCAC
359849 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
359869 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
* *
359889 GTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTGACTTTTGT
359909 GTTGCGA
1 GTTGCGA
359916 TTTACAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:359929 original size:40 final size:41
Alignment explanation
Indices: 359843--359984 Score: 123
Period size: 40 Copynumber: 3.5 Consensus size: 41
359833 ATTTTTTACT
* * * *
359843 ATTCACGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACT
1 ATTCGCGTTGCGAATTTGACTTCTATGTTGCGAATTTGACA
359884 A-TCGCGTTGCGAATTTGACTTCTATGTTGCG-ATTT-ACAA
1 ATTCGCGTTGCGAATTTGACTTCTATGTTGCGAATTTGAC-A
* * * * * *
359923 ATTCGCGTTACGAATATGGAC-ACTAGGTTGCGAAATTG-GA
1 ATTCGCGTTGCGAAT-TTGACTTCTATGTTGCGAATTTGACA
* *
359963 GTTCGCATTGCGAATTTGACTT
1 ATTCGCGTTGCGAATTTGACTT
359985 TCGCGTTGCG
Statistics
Matches: 80, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
38 2 0.03
39 9 0.11
40 61 0.76
41 8 0.10
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (41 bp):
ATTCGCGTTGCGAATTTGACTTCTATGTTGCGAATTTGACA
Found at i:363170 original size:31 final size:31
Alignment explanation
Indices: 363098--363173 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 31
363088 TGGGGCCTGC
* *
363098 GAGCCTACCCAAGAAAATTCTTAGGGCCACA
1 GAGCCTACCCAAGAAAATTCTCAAGGCCACA
363129 GAGGCCTACCCAAGAATAA-TCTCAAGGCCACA
1 GA-GCCTACCCAAGAA-AATTCTCAAGGCCACA
363161 GAGCCTACCCAAG
1 GAGCCTACCCAAG
363174 GGTCACCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 13 0.32
32 26 0.63
33 2 0.05
ACGTcount: A:0.36, C:0.32, G:0.20, T:0.13
Consensus pattern (31 bp):
GAGCCTACCCAAGAAAATTCTCAAGGCCACA
Found at i:363343 original size:12 final size:12
Alignment explanation
Indices: 363317--363410 Score: 91
Period size: 12 Copynumber: 7.8 Consensus size: 12
363307 CAGAGATATA
* *
363317 AGAAATCATAAC
1 AGAAATCAGAGC
*
363329 AGAATTCAGAGC
1 AGAAATCAGAGC
* *
363341 AGAAATCATAGT
1 AGAAATCAGAGC
363353 A-AAATTCAGAGC
1 AGAAA-TCAGAGC
*
363365 AGAAATCAGAAC
1 AGAAATCAGAGC
*
363377 AGAATTCAGAGC
1 AGAAATCAGAGC
*
363389 AGAAATCAGAAC
1 AGAAATCAGAGC
*
363401 ATAAATCAGA
1 AGAAATCAGA
363411 TAAAATATTC
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
11 3 0.05
12 60 0.91
13 3 0.05
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.16
Consensus pattern (12 bp):
AGAAATCAGAGC
Found at i:363347 original size:24 final size:24
Alignment explanation
Indices: 363317--363410 Score: 125
Period size: 24 Copynumber: 3.9 Consensus size: 24
363307 CAGAGATATA
*
363317 AGAAATCATAACAGAATTCAGAGC
1 AGAAATCAGAACAGAATTCAGAGC
* ** *
363341 AGAAATCATAGTAAAATTCAGAGC
1 AGAAATCAGAACAGAATTCAGAGC
363365 AGAAATCAGAACAGAATTCAGAGC
1 AGAAATCAGAACAGAATTCAGAGC
* *
363389 AGAAATCAGAACATAAATCAGA
1 AGAAATCAGAACAGAATTCAGA
363411 TAAAATATTC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.16
Consensus pattern (24 bp):
AGAAATCAGAACAGAATTCAGAGC
Found at i:366023 original size:14 final size:14
Alignment explanation
Indices: 366006--366035 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
365996 TAATAATTTT
366006 ATTTTAATATTATA
1 ATTTTAATATTATA
*
366020 ATTTTCATATTATA
1 ATTTTAATATTATA
366034 AT
1 AT
366036 AAAAATCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTAATATTATA
Found at i:366251 original size:24 final size:26
Alignment explanation
Indices: 366207--366277 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
366197 AATATAATAT
366207 TAAATAA-ATTATTTCAA-TATTT-TAA
1 TAAATAATATTA-TT-AATTATTTGTAA
*
366232 -AAATAATTTTATTAATTATTTTGTAA
1 TAAATAATATTATTAATTA-TTTGTAA
*
366258 TAAATAATATTATTTATTAT
1 TAAATAATATTATTAATTAT
366278 ACTTGATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 2 0.05
24 10 0.26
25 6 0.16
26 4 0.11
27 16 0.42
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TAAATAATATTATTAATTATTTGTAA
Found at i:370970 original size:45 final size:45
Alignment explanation
Indices: 370925--371110 Score: 282
Period size: 45 Copynumber: 4.1 Consensus size: 45
370915 CATTATTTTT
* * * * *
370925 ATTTATGGCATCCTTTTATGCCTTTATTGCACAGTTGTGCATTTT
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
* ** *
370970 ATTTATGGCGTTATTTCATGCCTTTAATGCATCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
*
371015 ATTTATGGCATCTTTTCATGCCTTTAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
371060 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
371105 ATTTAT
1 ATTTAT
371111 ATAATAAAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 127 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (45 bp):
ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
Found at i:371005 original size:24 final size:24
Alignment explanation
Indices: 370978--371052 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
370968 TTATTTATGG
370978 CGTTATTTCATGCCTTTAATGCAT
1 CGTTATTTCATGCCTTTAATGCAT
* * *
371002 CGTTA-TGCATTTCATTT-ATGGCAT
1 CGTTATTTCA-TGCCTTTAAT-GCAT
*
371026 C--T-TTTCATGCCTTTAATGCAC
1 CGTTATTTCATGCCTTTAATGCAT
371047 CGTTAT
1 CGTTAT
371053 GCATTTCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
21 9 0.24
22 6 0.16
23 6 0.16
24 16 0.43
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.45
Consensus pattern (24 bp):
CGTTATTTCATGCCTTTAATGCAT
Found at i:373953 original size:12 final size:12
Alignment explanation
Indices: 373936--373963 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
373926 TTGAATTCAT
373936 TTTTCATTTTTC
1 TTTTCATTTTTC
373948 TTTTCATTTTTC
1 TTTTCATTTTTC
373960 TTTT
1 TTTT
373964 TTTCTTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCATTTTTC
Done.