Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 52 of 73
Found at i:12398404 original size:248 final size:248
Alignment explanation
Indices: 12397970--12398871 Score: 1468
Period size: 248 Copynumber: 3.6 Consensus size: 248
12397960 ATGTCGAAGC
**
12397970 ATAGCTTAAGTATAGAAGGGCTATCTGCCAAAGACCCCCGAGTT-GATTACACTCAGCTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
*
12398034 GCATATCATTTACAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACTTTCGAGTTCG
66 GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACTTTCGAGTTCG
*
12398099 ACTACGCTCAGCTCTCAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
131 ACTACGCTCAGCTCCCAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
* * * *
12398164 CAATAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGTAGC
196 CAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGA
* * *
12398217 ATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGAACCCCGAGTTCGATTACAATCAGCTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
* *
12398282 GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAATACTTTCGAGTTCG
66 GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACTTTCGAGTTCG
**
12398347 ACTACGCTCAGCTCTTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
131 ACTACGCTCAGCTCCCAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
* *
12398412 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGTACATCATTTGCAAA
196 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGA
12398465 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
* * * * * *
12398530 GCATATCATTTACAACATAACTTAAGGCTAGAAGGGTTATATGTTACCAAAGACCTTCGAGTTTG
66 GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACTTTCGAGTTCG
*
12398595 ACTACGCTCAGCTCCCAAGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
131 ACTACGCTCAGCTCCCAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
*
12398660 CAAAAGGCCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGA
196 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGA
* * *
12398713 ATAACTTAAGTCGAGGAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
* * *
12398778 GCATATCATTTAAAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTT-GAGTTT
66 GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGA-CTTTCGAGTTC
* *
12398842 GACTACGCTCAGCTCCAAGGCACATCATTT
130 GACTACGCTCAGCTCCCAGGCATATCATTT
12398872 ACAGTATAGC
Statistics
Matches: 607, Mismatches: 45, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
247 43 0.07
248 561 0.92
249 3 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (248 bp):
ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACTTTCGAGTTCG
ACTACGCTCAGCTCCCAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGA
Found at i:12399506 original size:25 final size:25
Alignment explanation
Indices: 12399478--12399537 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
12399468 TTTAGAAAAC
12399478 ATTTTGAAAATATATAAGATATATA
1 ATTTTGAAAATATATAAGATATATA
*
12399503 ATTTTGAAAATATATATGATATATA
1 ATTTTGAAAATATATAAGATATATA
* *
12399528 GTTTTTAAAA
1 ATTTTGAAAA
12399538 CATTTCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43
Consensus pattern (25 bp):
ATTTTGAAAATATATAAGATATATA
Found at i:12399665 original size:38 final size:37
Alignment explanation
Indices: 12399503--12399697 Score: 204
Period size: 38 Copynumber: 5.3 Consensus size: 37
12399493 AAGATATATA
12399503 ATTTTG-AAAATATATATGA-TATATAGTTTTTAAAAC
1 ATTTTGAAAAATATATAT-ATTATATAGTTTTTAAAAC
* * * *
12399539 A-TTTCAAAAATATGTATAATATATGGTTTTTTAAAAC
1 ATTTTGAAAAATATATATATTATATAG-TTTTTAAAAC
* * * * *
12399576 ATTTCG-AAAATATATA-A-TATGTAATGTTTAAAAT
1 ATTTTGAAAAATATATATATTATATAGTTTTTAAAAC
*
12399610 ATTTTTGAAAACGTATATATATTATATAGTTTTTAAAAC
1 A-TTTTGAAAA-ATATATATATTATATAGTTTTTAAAAC
12399649 ATTTTGAAAACATATATATATTATATAGTTTTTAAAAC
1 ATTTTGAAAA-ATATATATATTATATAGTTTTTAAAAC
*
12399687 ATTTTTAAAAA
1 ATTTTGAAAAA
12399698 ACTTAAATAT
Statistics
Matches: 131, Mismatches: 19, Indels: 17
0.78 0.11 0.10
Matches are distributed among these distances:
34 9 0.07
35 12 0.09
36 21 0.16
37 27 0.21
38 48 0.37
39 14 0.11
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
ATTTTGAAAAATATATATATTATATAGTTTTTAAAAC
Found at i:12399799 original size:35 final size:37
Alignment explanation
Indices: 12399746--12399862 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 37
12399736 AAAAAAAACG
* *
12399746 TTTTTGAAAAATATATATAATATATAAGTTTTTAAAACAA
1 TTTTTGAAACATATA-ATATTATAT-AGTTTTTAAAA-AA
* *
12399786 TTTTTGAAA-ATATAA-ATTATATAGTTTTGAAAATTA
1 TTTTTGAAACATATAATATTATATAGTTTTTAAAA-AA
*
12399822 TTTTTTAAACATAT-ATATTATATAG-TTTTAAAAAA
1 TTTTTGAAACATATAATATTATATAGTTTTTAAAAAA
12399857 TGTTTT
1 T-TTTT
12399863 TTATTATATT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
35 2 0.03
36 31 0.46
37 19 0.28
38 1 0.01
39 5 0.07
40 9 0.13
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (37 bp):
TTTTTGAAACATATAATATTATATAGTTTTTAAAAAA
Found at i:12399880 original size:37 final size:37
Alignment explanation
Indices: 12399718--12399865 Score: 124
Period size: 37 Copynumber: 3.9 Consensus size: 37
12399708 ATATATATAT
* * *
12399718 ATATATATTATA-A-TTTTAAAAAAAAACGTTTTTGAAAA
1 ATATATATTATATAGTTTT-AAAAAATA--TTTTTTAAAC
* *
12399756 ATATATATAATATATAAGTTTTTAAAACA-ATTTTTGAAA-
1 ATATATAT--TATAT-AG-TTTTAAAAAATATTTTTTAAAC
* * *
12399795 ATATAAATTATATAGTTTTGAAAATTATTTTTTAAAC
1 ATATATATTATATAGTTTTAAAAAATATTTTTTAAAC
*
12399832 ATATATATTATATAGTTTTAAAAAATGTTTTTTA
1 ATATATATTATATAGTTTTAAAAAATATTTTTTA
12399866 TTATATTATG
Statistics
Matches: 92, Mismatches: 10, Indels: 17
0.77 0.08 0.14
Matches are distributed among these distances:
35 7 0.08
36 11 0.12
37 35 0.38
38 8 0.09
39 7 0.08
40 13 0.14
42 2 0.02
43 5 0.05
44 4 0.04
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (37 bp):
ATATATATTATATAGTTTTAAAAAATATTTTTTAAAC
Found at i:12402573 original size:19 final size:19
Alignment explanation
Indices: 12402549--12402586 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12402539 TAAAAATTAC
12402549 TTAAACTAAAATATTTAAG
1 TTAAACTAAAATATTTAAG
12402568 TTAAACTAAAATATTTAAG
1 TTAAACTAAAATATTTAAG
12402587 CCAACTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (19 bp):
TTAAACTAAAATATTTAAG
Found at i:12411324 original size:152 final size:155
Alignment explanation
Indices: 12411041--12411353 Score: 454
Period size: 152 Copynumber: 2.0 Consensus size: 155
12411031 TACATGCTTA
* *
12411041 CACAATGAATGACATTCTTTCCTTTTATATATGGTGCTATTAAGCATGAGAAACAAATTAAAGTT
1 CACAATGAATGACATTCTTTCCTTTTATAAATGGTGCTATCAAGCATGAGAAACAAATTAAAGTT
* *
12411106 ATTGGTCAATTTTGGCACCCCATAAACTTTGACGTATATTGAAAAAATTTCACCTTCAAGTCATC
66 ATTGGTCAATTTTGGCA-CCCAGAAACTATGACGTATATTGAAAAAATTTCACCTTCAAGTCATC
* * *
12411171 AATCATAGTTAACAAATACCGTCCTC
130 AAACAAAGTTAACAAATACCATCCTC
* * *
12411197 CACAATGAATTACATTCTTTCCTTTTATAAATTGTGTTA-CAAGCATGAGAAACAAATTAAAGTT
1 CACAATGAATGACATTCTTTCCTTTTATAAATGGTGCTATCAAGCATGAGAAACAAATTAAAGTT
* * * *
12411261 ATCT-GTCAATTTTGGCA-CC-GAAACTATGACGTCTATTGCAACATTTTCACCTTCAAGTCATC
66 AT-TGGTCAATTTTGGCACCCAGAAACTATGACGTATATTGAAAAAATTTCACCTTCAAGTCATC
12411323 AAACAAAGTTAACAAATACCATCCTC
130 AAACAAAGTTAACAAATACCATCCTC
12411349 CACAA
1 CACAA
12411354 GAAGCGAATC
Statistics
Matches: 142, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
152 65 0.46
153 2 0.01
155 39 0.27
156 36 0.25
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.32
Consensus pattern (155 bp):
CACAATGAATGACATTCTTTCCTTTTATAAATGGTGCTATCAAGCATGAGAAACAAATTAAAGTT
ATTGGTCAATTTTGGCACCCAGAAACTATGACGTATATTGAAAAAATTTCACCTTCAAGTCATCA
AACAAAGTTAACAAATACCATCCTC
Found at i:12415340 original size:21 final size:21
Alignment explanation
Indices: 12415314--12415358 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12415304 TATTTTTTTA
12415314 AAAAATA-AAAATTATATTATT
1 AAAAATATAAAATTA-ATTATT
* *
12415335 AAAAATATTATATTAATTATT
1 AAAAATATAAAATTAATTATT
12415356 AAA
1 AAA
12415359 CATACGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATATAAAATTAATTATT
Found at i:12415450 original size:15 final size:16
Alignment explanation
Indices: 12415409--12415454 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
12415399 TTAGTTTAAT
12415409 TTAATATGTAAAATTA
1 TTAATATGTAAAATTA
*
12415425 TTAATACATGTAATATTA
1 TTAAT--ATGTAAAATTA
12415443 -TAATATGTAAAA
1 TTAATATGTAAAA
12415455 ACTAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.27
16 5 0.19
17 4 0.15
18 10 0.38
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (16 bp):
TTAATATGTAAAATTA
Found at i:12433896 original size:188 final size:194
Alignment explanation
Indices: 12433666--12434051 Score: 678
Period size: 188 Copynumber: 2.0 Consensus size: 194
12433656 ATAAAAGATG
12433666 GAGTAATGTATTTATTGACCAAATAAGGTGGTGATACATTATAATATTCTCTCTTTAGAAATATT
1 GAGTAATGTATTTATTGACCAAATAAGGTGGTGATACATTATAATATTCTCTCTTTAGAAATATT
12433731 AAGTTATTAAATATGTGATATATTGATTCAATTATAGTTAAATATTATAC-G-TA-GTCACATCA
66 AAGTTATTAAATATGTGATATATTGATTCAATTATAGTTAAATATTATACAGATATGTCACATCA
12433793 AGTATAGATAATCTT-AAG-T-TAACTTCAATGTAAAATTTAAAATTCTATGAAACAAATTAAAA
131 AGTATAGATAATCTTAAAGTTATAACTTCAATGTAAAATTTAAAATTCTATG-AACAAATTAAAA
12433855 GAGTAATGTATTTATTGACC-AATAAGGTGGTGATACATTATAATATTCTCTCTTTAGAAATATT
1 GAGTAATGTATTTATTGACCAAATAAGGTGGTGATACATTATAATATTCTCTCTTTAGAAATATT
12433919 AAGTTATTAAATATGTGATATATTGATTCAATTATAGTTAAATATTATACGTAGATATGTCACAT
66 AAGTTATTAAATATGTGATATATTGATTCAATTATAGTTAAATATTATAC--AGATATGTCACAT
12433984 CAAGTATAGATAATCTTAAAGTTAAATAACTTCAATGTAAAATTTAAAATTCTATGAACAAATTA
129 CAAGTATAGATAATCTTAAAGTT--ATAACTTCAATGTAAAATTTAAAATTCTATGAACAAATTA
12434049 AAA
192 AAA
12434052 ATAGTTTAAA
Statistics
Matches: 187, Mismatches: 0, Indels: 12
0.94 0.00 0.06
Matches are distributed among these distances:
188 94 0.50
189 20 0.11
191 1 0.01
192 2 0.01
193 24 0.13
194 3 0.02
195 1 0.01
197 12 0.06
198 30 0.16
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (194 bp):
GAGTAATGTATTTATTGACCAAATAAGGTGGTGATACATTATAATATTCTCTCTTTAGAAATATT
AAGTTATTAAATATGTGATATATTGATTCAATTATAGTTAAATATTATACAGATATGTCACATCA
AGTATAGATAATCTTAAAGTTATAACTTCAATGTAAAATTTAAAATTCTATGAACAAATTAAAA
Found at i:12434376 original size:21 final size:21
Alignment explanation
Indices: 12434350--12434390 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
12434340 GCATAAGAAT
12434350 GGAAAGATGGTTATCGACAAC
1 GGAAAGATGGTTATCGACAAC
*
12434371 GGAAAGATGGTTGTCGACAA
1 GGAAAGATGGTTATCGACAA
12434391 TGACAATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.20
Consensus pattern (21 bp):
GGAAAGATGGTTATCGACAAC
Found at i:12442102 original size:20 final size:20
Alignment explanation
Indices: 12442057--12442108 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
12442047 AAAAATGTCT
*
12442057 TAGTATTGATACCCCTACTC
1 TAGTATTGATACCCCTACCC
*
12442077 TAAGTATTGATA-CTCTACCCC
1 T-AGTATTGATACCCCTA-CCC
*
12442098 TAGTATCGATA
1 TAGTATTGATA
12442109 ATCCCATGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.35
Consensus pattern (20 bp):
TAGTATTGATACCCCTACCC
Found at i:12444254 original size:16 final size:16
Alignment explanation
Indices: 12444222--12444253 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12444212 TTACTATTCA
12444222 TATGAATAGTGAATTT
1 TATGAATAGTGAATTT
12444238 TATGAATAGT-AATTT
1 TATGAATAGTGAATTT
12444253 T
1 T
12444254 TTTTCGGCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (16 bp):
TATGAATAGTGAATTT
Found at i:12449883 original size:30 final size:30
Alignment explanation
Indices: 12449838--12449909 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
12449828 GGTTCTTCGG
* * *
12449838 GACCTATGGACAGTTACTAAGGATCTTTAT
1 GACCTCTGGATAGTTACCAAGGATCTTTAT
*
12449868 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCAAGGATCTTTAT
12449898 GACCTCTGGATA
1 GACCTCTGGATA
12449910 TGTCCTTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCAAGGATCTTTAT
Found at i:12451773 original size:5 final size:5
Alignment explanation
Indices: 12451739--12451773 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
12451729 TTAAATTTTA
* *
12451739 TTTCA TTTCA TTTCG TTTCG TTTCG TTTCG TTTCG
1 TTTCG TTTCG TTTCG TTTCG TTTCG TTTCG TTTCG
12451774 ATACTCTGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.06, C:0.20, G:0.14, T:0.60
Consensus pattern (5 bp):
TTTCG
Found at i:12457059 original size:21 final size:21
Alignment explanation
Indices: 12457013--12457075 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
12457003 ATCTTACATA
**
12457013 GGGGTATCAGG-ACCCTCTTAA
1 GGGGTATC-GGTACCCTCTTGG
*
12457034 AGGGTATCGGTACCCTCTTGG
1 GGGGTATCGGTACCCTCTTGG
12457055 GGGGTATCGGTACCCT-TTGG
1 GGGGTATCGGTACCCTCTTGG
12457075 G
1 G
12457076 CAATCTGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 7 0.19
21 30 0.81
ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27
Consensus pattern (21 bp):
GGGGTATCGGTACCCTCTTGG
Found at i:12457379 original size:13 final size:14
Alignment explanation
Indices: 12457361--12457392 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12457351 GATTTTCTAA
12457361 TTGAAAATCAT-TT
1 TTGAAAATCATGTT
12457374 TTG-AAATCATGTT
1 TTGAAAATCATGTT
12457387 TTGAAA
1 TTGAAA
12457393 TTACTCCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 8 0.47
14 2 0.12
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (14 bp):
TTGAAAATCATGTT
Found at i:12457382 original size:12 final size:13
Alignment explanation
Indices: 12457365--12457393 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12457355 TTCTAATTGA
12457365 AAATCAT-TTTTG
1 AAATCATGTTTTG
12457377 AAATCATGTTTTG
1 AAATCATGTTTTG
12457390 AAAT
1 AAAT
12457394 TACTCCCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (13 bp):
AAATCATGTTTTG
Found at i:12459743 original size:23 final size:23
Alignment explanation
Indices: 12459711--12459771 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
12459701 ACCCTCATGT
* *
12459711 GGGGGTATCGATATCCATTC-AA
1 GGGGGTATCGATACCCATGCAAA
*
12459733 GGAGGGTATCGGTACCCATGCAAA
1 GG-GGGTATCGATACCCATGCAAA
*
12459757 TGGGGTATCGATACC
1 GGGGGTATCGATACC
12459772 TCCTGCACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 2 0.06
23 27 0.84
24 3 0.09
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (23 bp):
GGGGGTATCGATACCCATGCAAA
Found at i:12459922 original size:17 final size:17
Alignment explanation
Indices: 12459900--12459939 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
12459890 TCTTTAAACA
12459900 TAATTTGAACATATAAT
1 TAATTTGAACATATAAT
12459917 TAATTTGAACATATAAT
1 TAATTTGAACATATAAT
12459934 TAATTT
1 TAATTT
12459940 TCACTAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (17 bp):
TAATTTGAACATATAAT
Found at i:12463631 original size:21 final size:20
Alignment explanation
Indices: 12463607--12463648 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
12463597 GACTATTTTC
12463607 ATTTTTCAATTTTGAAATATA
1 ATTTTTCAATTTTGAAA-ATA
**
12463628 ATTTTTGTATTTTGAAAATA
1 ATTTTTCAATTTTGAAAATA
12463648 A
1 A
12463649 AGTCTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTTCAATTTTGAAAATA
Found at i:12465655 original size:20 final size:21
Alignment explanation
Indices: 12465630--12465688 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
12465620 ATCTTACATA
*
12465630 GGGGTATTGGTACCCTCTT-G
1 GGGGTATCGGTACCCTCTTGG
12465650 GGGGTATCGGTACCCTCTTGG
1 GGGGTATCGGTACCCTCTTGG
12465671 GGGGTATCGGTACCCTCT
1 GGGGTATCGGTACCCTCT
12465689 GAGCAATCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.10, C:0.24, G:0.36, T:0.31
Consensus pattern (21 bp):
GGGGTATCGGTACCCTCTTGG
Found at i:12466015 original size:6 final size:6
Alignment explanation
Indices: 12466004--12466031 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12465994 ATCAACACTT
12466004 TTTGCA TTTGCA TTTGCA TTTGCA TTTG
1 TTTGCA TTTGCA TTTGCA TTTGCA TTTG
12466032 TATCTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (6 bp):
TTTGCA
Found at i:12467926 original size:25 final size:25
Alignment explanation
Indices: 12467889--12467938 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
12467879 ATAATAAAGC
* *
12467889 CACACTCTCGTCTTCTCAGACACAA
1 CACACTATCGTCTTCTCAAACACAA
*
12467914 CACACTATTGTCTTCTCAAACACAA
1 CACACTATCGTCTTCTCAAACACAA
12467939 AACTTACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.06, T:0.26
Consensus pattern (25 bp):
CACACTATCGTCTTCTCAAACACAA
Found at i:12470658 original size:36 final size:36
Alignment explanation
Indices: 12470604--12470711 Score: 162
Period size: 36 Copynumber: 3.0 Consensus size: 36
12470594 AGCAAAAATC
* * *
12470604 TTATCTCGCATGAAATAACTTATTTTGAAATTATTT
1 TTATCTCGCATGAGATAACTTCTTTTGAAATTAATT
*
12470640 TTCTCTCGCATGAGATAACTTCTTTTGAAATTAATT
1 TTATCTCGCATGAGATAACTTCTTTTGAAATTAATT
* *
12470676 TTATCTCACATGAGATAAATTCTTTTGAAATTAATT
1 TTATCTCGCATGAGATAACTTCTTTTGAAATTAATT
12470712 GTCTCGCTCG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (36 bp):
TTATCTCGCATGAGATAACTTCTTTTGAAATTAATT
Found at i:12474375 original size:30 final size:30
Alignment explanation
Indices: 12474334--12474398 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
12474324 TTGCTACAGT
* * * *
12474334 GACCACCATAGGTCTTCAGGAGCACATGGC
1 GACCTCCATAGGTATTCAGGAGCACACGAC
12474364 GACCTCCATAGGTATTCAGGAGCACACGAC
1 GACCTCCATAGGTATTCAGGAGCACACGAC
12474394 GACCT
1 GACCT
12474399 ATGGAGCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.17
Consensus pattern (30 bp):
GACCTCCATAGGTATTCAGGAGCACACGAC
Found at i:12474506 original size:19 final size:19
Alignment explanation
Indices: 12474482--12474519 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12474472 TCTTGCAAGG
*
12474482 AGCACTTGACGACCTATGA
1 AGCACTTGACGACCAATGA
*
12474501 AGCACTTGGCGACCAATGA
1 AGCACTTGACGACCAATGA
12474520 GGTCACTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (19 bp):
AGCACTTGACGACCAATGA
Found at i:12481411 original size:23 final size:22
Alignment explanation
Indices: 12481370--12481453 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
12481360 TAGTGCAGAT
*
12481370 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATACCCCCTTGAAGG
*
12481392 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATACCCCC-TTGAAGG
* * * *
12481415 GGATCTGATTCCCCC-TGTAGG
1 GGAACCGATACCCCCTTGAAGG
*
12481436 GGAATCGATACCCCCTTG
1 GGAACCGATACCCCCTTG
12481454 GGGTTCTGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
21 16 0.31
22 15 0.29
23 20 0.39
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (22 bp):
GGAACCGATACCCCCTTGAAGG
Found at i:12483059 original size:18 final size:18
Alignment explanation
Indices: 12483038--12483077 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12483028 GAACAGCACA
* *
12483038 AGGAACAAGCACGAGCAG
1 AGGAACAAGCACAACCAG
12483056 AGGAACAAGCACAACCAG
1 AGGAACAAGCACAACCAG
12483074 AGGA
1 AGGA
12483078 TCAAATGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.23, G:0.30, T:0.00
Consensus pattern (18 bp):
AGGAACAAGCACAACCAG
Found at i:12485056 original size:21 final size:21
Alignment explanation
Indices: 12485010--12485056 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12485000 ATCTATTTTA
*
12485010 AAATTAAATTAAATTTTATTT
1 AAATTAAATTAAATTTGATTT
*
12485031 TAATTAAATTAAATTATGA-TT
1 AAATTAAATTAAATT-TGATTT
12485052 AAATT
1 AAATT
12485057 GATAAGATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATTAAATTAAATTTGATTT
Found at i:12486253 original size:6 final size:6
Alignment explanation
Indices: 12486244--12486277 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
12486234 AAAATAAAAA
12486244 TATAAT TATAAT TATAAT TAT--T TATAAT TATAAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT
12486278 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
6 22 0.85
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TATAAT
Found at i:12496823 original size:21 final size:21
Alignment explanation
Indices: 12496799--12496858 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
12496789 AACTTTGAAA
12496799 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
**
12496820 AAAT-G-TTTC----TTT-TA
1 AAATGGTTTTCAAAGTTTGGT
12496834 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
12496855 AAAT
1 AAAT
12496859 ATTTCTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 14
0.61 0.09 0.30
Matches are distributed among these distances:
14 4 0.14
15 4 0.14
16 4 0.14
19 4 0.14
20 4 0.14
21 8 0.29
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:12496837 original size:35 final size:36
Alignment explanation
Indices: 12496791--12496899 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
12496781 TGGCAACCAA
12496791 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
12496828 CTTT-TAAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
12496863 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
12496900 ATTGAAATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 33 0.51
36 7 0.11
37 25 0.38
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:12499845 original size:19 final size:19
Alignment explanation
Indices: 12499821--12499869 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
12499811 AATGCAATTG
12499821 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
12499840 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
12499859 GTGCATCGATG
1 GTGCATCGATG
12499870 TATCCCCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (19 bp):
GTGCATCGATGCATAAGGA
Found at i:12499969 original size:20 final size:22
Alignment explanation
Indices: 12499924--12499981 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
12499914 GCATGGGTAG
12499924 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
12499948 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
12499968 TGCATCGATGCACT
1 TGCATCGATGCACT
12499982 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:12504001 original size:64 final size:63
Alignment explanation
Indices: 12503885--12504025 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
12503875 TATATTCAAT
* * * *
12503885 GTGCATCGATGCACTCTTTAAAGAAGAAACATTGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * * *
12503948 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
12504012 GTGCATCGATGCAC
1 GTGCATCGATGCAC
12504026 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 18 0.27
64 48 0.73
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:12507792 original size:36 final size:37
Alignment explanation
Indices: 12507677--12507785 Score: 179
Period size: 35 Copynumber: 3.0 Consensus size: 37
12507667 TGGCAACCAA
12507677 CTTTGAAAAAGTGG-TTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTTCAAAGTTTGGTAAATGTTT
12507714 CTTTG-AAAATGGTTTTT-AAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
*
12507749 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
12507786 GTTGAAATAT
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
35 26 0.38
36 20 0.29
37 22 0.32
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (37 bp):
CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:12514176 original size:3 final size:3
Alignment explanation
Indices: 12514159--12514224 Score: 50
Period size: 3 Copynumber: 21.3 Consensus size: 3
12514149 CTTGCAAAAA
12514159 AAT AATT AAT AAAT AAT AAT AAT AAT AAAT AAAT AAAT AAAT AAT -AT
1 AAT AA-T AAT -AAT AAT AAT AAT AAT -AAT -AAT -AAT -AAT AAT AAT
12514206 AAT -AT AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
12514225 TTTTTGTAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.14
3 27 0.48
4 21 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12514180 original size:10 final size:10
Alignment explanation
Indices: 12514158--12514224 Score: 63
Period size: 10 Copynumber: 6.8 Consensus size: 10
12514148 GCTTGCAAAA
12514158 AAATAATTAAT
1 AAATAA-TAAT
12514169 AAATAATAAT
1 AAATAATAAT
12514179 -AATAATAAAT
1 AAATAAT-AAT
12514189 AAAT-A-AAT
1 AAATAATAAT
12514197 AAATAAT-AT
1 AAATAATAAT
12514206 AATATAAT-AT
1 AA-ATAATAAT
12514216 AATATAATA
1 AA-ATAATA
12514225 TTTTTGTAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.14
9 11 0.22
10 23 0.46
11 9 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATAATAAT
Found at i:12514184 original size:20 final size:19
Alignment explanation
Indices: 12514159--12514223 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 19
12514149 CTTGCAAAAA
12514159 AATAATTAATAAATAATAAT
1 AATAATTAATAAAT-ATAAT
*
12514179 AATAATAAATAAATA-AAT
1 AATAATTAATAAATATAAT
12514197 AAATAATATAATATAATATAAT
1 -AATAAT-TAATA-AATATAAT
12514219 -ATAAT
1 AATAAT
12514224 ATTTTTGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 3 0.08
19 7 0.18
20 22 0.56
21 4 0.10
22 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAATTAATAAATATAAT
Found at i:12514204 original size:35 final size:35
Alignment explanation
Indices: 12514158--12514224 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
12514148 GCTTGCAAAA
*
12514158 AAATAATTAATA-AATAATAATAATAATA-AATAAAT
1 AAATAAATAATATAAT-ATAAT-ATAATATAATAAAT
12514193 AAATAAATAATATAATATAATATAATATAATA
1 AAATAAATAATATAATATAATATAATATAATA
12514225 TTTTTGTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 6 0.21
35 20 0.69
36 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATAAATAATATAATATAATATAATATAATAAAT
Found at i:12514209 original size:5 final size:5
Alignment explanation
Indices: 12514167--12514225 Score: 65
Period size: 5 Copynumber: 12.4 Consensus size: 5
12514157 AAAATAATTA
12514167 ATAA- ATAAT AATAAT AATAA- ATAA- ATAA- ATAA- ATAAT ATAAT ATAAT
1 ATAAT ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
12514214 ATAAT ATAAT AT
1 ATAAT ATAAT AT
12514226 TTTTGTAGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
4 20 0.38
5 22 0.42
6 10 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:12514685 original size:33 final size:34
Alignment explanation
Indices: 12514609--12514694 Score: 122
Period size: 33 Copynumber: 2.5 Consensus size: 34
12514599 CTCGAAGGTC
*
12514609 TTTGTGTTTCAAGAGAAACATTTTTCAAAGGCTTT
1 TTTGTGTTTCAAGAGAAACA-TTTTCAAAGGATTT
*
12514644 TTTATGTTTCAAGAGAAACGA-TTTCAAA-GATTT
1 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGGATTT
12514677 TTTGTGTTTCAAGAGAAA
1 TTTGTGTTTCAAGAGAAA
12514695 TTGTCTTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
33 21 0.45
34 7 0.15
35 18 0.38
36 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACATTTTCAAAGGATTT
Found at i:12514781 original size:67 final size:68
Alignment explanation
Indices: 12514648--12514799 Score: 184
Period size: 67 Copynumber: 2.2 Consensus size: 68
12514638 GGCTTTTTTA
* * * * *
12514648 TGTTTCAAGAGAAACGATTTCAAAGATTTTTTGTGTTTCAAGAGAAATTGTCTTCAAGGAGGCAA
1 TGTTTCAAGAGAAACGATTTCAAAG--TGTTGGTGTTTCAAGAGAAACTGTCTTCAAGAAGACAA
*
12514713 AATTT
64 AACTT
12514718 TGTTTCAAGAGAAAC-ATATTCAAAG-GTTGGTGTTTCAAGAGAAACTGTC-TCAAGAAAGACAA
1 TGTTTCAAGAGAAACGAT-TTCAAAGTGTTGGTGTTTCAAGAGAAACTGTCTTCAAG-AAGACAA
12514780 AACTT
64 AACTT
*
12514785 TGTTTCAAGGGAAAC
1 TGTTTCAAGAGAAAC
12514800 TGTCTCAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
66 5 0.07
67 44 0.60
69 2 0.03
70 22 0.30
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (68 bp):
TGTTTCAAGAGAAACGATTTCAAAGTGTTGGTGTTTCAAGAGAAACTGTCTTCAAGAAGACAAAA
CTT
Found at i:12514835 original size:36 final size:36
Alignment explanation
Indices: 12514748--12515072 Score: 362
Period size: 36 Copynumber: 9.1 Consensus size: 36
12514738 CAAAGGTTGG
*
12514748 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
12514785 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
12514821 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * * *
12514858 AGTTCCAAAAGAAATTGTCTCAAGGGAGGCGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
12514894 TGTTTCAA-AGAAAACATAT-TC-----A-A-ATATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
12514923 TGTTTCAAGAAAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
12514959 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
12514995 TATTTCAAGTGAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
12515031 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
12515068 TGTTT
1 TGTTT
12515073 TGGGCAAATA
Statistics
Matches: 241, Mismatches: 34, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 16 0.07
30 1 0.00
31 1 0.00
34 1 0.00
35 3 0.01
36 147 0.61
37 70 0.29
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:12514841 original size:73 final size:73
Alignment explanation
Indices: 12514748--12515072 Score: 375
Period size: 73 Copynumber: 4.6 Consensus size: 73
12514738 CAAAGGTTGG
* *
12514748 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
12514813 ACAAAATT
66 ACAAAATT
* * * * *
12514821 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
* *
12514886 GCGAAATT
66 ACAAAATT
* * * * *
12514894 TGTTTCAA-AGAAAACATAT-TC-------A-AATATTTTGTTTCAAGAAAAATTGTCTCAAGAG
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAG
12514949 AGACAAAATT
64 AGACAAAATT
* * * *
12514959 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTTATTTCAAGTGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
*
12515023 ATAAAATT
66 ACAAAATT
*
12515031 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTTGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
12515073 TGGGCAAATA
Statistics
Matches: 208, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
64 2 0.01
65 48 0.23
66 2 0.01
72 67 0.32
73 87 0.42
74 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:12514960 original size:138 final size:138
Alignment explanation
Indices: 12514783--12515044 Score: 382
Period size: 138 Copynumber: 1.9 Consensus size: 138
12514773 AAGACAAAAC
**
12514783 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * *
12514848 GACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGGCGAAATTTGTTTCAA-AGAAAACATA
66 GACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACATA
12514912 TTCAAATAT
130 TTCAAATAT
* *
12514921 TTTGTTTCAAGAAAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
** * ** *
12514986 GACAAATTTTATTTCAAGTGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAGAAA
66 GACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
12515045 CTGTCTCAAG
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
137 34 0.31
138 75 0.69
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (138 bp):
TTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACATAT
TCAAATAT
Found at i:12514984 original size:174 final size:176
Alignment explanation
Indices: 12514690--12515072 Score: 533
Period size: 174 Copynumber: 2.2 Consensus size: 176
12514680 GTGTTTCAAG
*
12514690 AGAAATTGTCTTCAA-GGAGGCAAAATTTTGTTTCAAGAGAAACATATTCAAAGGTTGGTGTTTC
1 AGAAATTGTC-TCAAGGGAGGCAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTC
*
12514754 AAGAGAAACTGTCTCAAGAAAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
65 AAGAAAAACTGTCTCAAGAAAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
12514819 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
130 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAA
* * *
12514867 AGAAATTGTCTCAAGGGAGGCGAAA-TTTGTTTCAA-AGAAAACATATTCAAATATT-TTGTTTC
1 AGAAATTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGAG-AAACATATTCAAAGATTGGTGTTTC
* * *
12514929 AAGAAAAATTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAT
65 AAGAAAAACTGTCTCAAGAAAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
12514993 TTTATTTCAAGTGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAG
130 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
* * ** *
12515040 AGAAACTGTCTCAAGAGAGAAAAAACTTTGTTT
1 AGAAATTGTCTCAAGGGAGGCAAAATTTTGTTT
12515073 TGGGCAAATA
Statistics
Matches: 184, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
173 28 0.15
174 75 0.41
175 33 0.18
176 29 0.16
177 19 0.10
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (176 bp):
AGAAATTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCA
AGAAAAACTGTCTCAAGAAAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
TTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
Found at i:12520710 original size:3 final size:3
Alignment explanation
Indices: 12520683--12520743 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
12520673 CCTGTAAAAA
*
12520683 AAT AATT AAT AA- AAT -AT ATT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
12520728 -AT AAT -AT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT A
12520744 TTTTTATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 10 0.20
3 33 0.67
4 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:12520720 original size:32 final size:31
Alignment explanation
Indices: 12520683--12520743 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
12520673 CCTGTAAAAA
*
12520683 AATAATTAATAAAAT-ATATTAATAATAATAAT
1 AATAATAAATAAAATAATA-TAATAA-AATAAT
*
12520715 AATAATAAATAATATAATATAATAAAATA
1 AATAATAAATAAAATAATATAATAAAATA
12520744 TTTTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 4 0.15
32 19 0.73
33 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AATAATAAATAAAATAATATAATAAAATAAT
Found at i:12525456 original size:53 final size:53
Alignment explanation
Indices: 12525373--12525490 Score: 148
Period size: 53 Copynumber: 2.2 Consensus size: 53
12525363 GTACACGCGT
* * *
12525373 TGCACCTAT-GTGCCGAAATGGAAATCCATAAACTCATTATGAATTCCATGAA
1 TGCACATATAGTGCCAAAATGGAAATCCATAAACTCATTATGAATACCATGAA
** * **
12525425 TGCACATATAGTGCCAAAATGGTCATTCATAAACTCATTATGAATACCATGGG
1 TGCACATATAGTGCCAAAATGGAAATCCATAAACTCATTATGAATACCATGAA
*
12525478 TGCACACATAGTG
1 TGCACATATAGTG
12525491 TCTAAGTACA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
52 8 0.14
53 48 0.86
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (53 bp):
TGCACATATAGTGCCAAAATGGAAATCCATAAACTCATTATGAATACCATGAA
Found at i:12534760 original size:20 final size:20
Alignment explanation
Indices: 12534735--12534827 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
12534725 TTTTCCCAAT
12534735 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
12534755 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
12534775 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
12534796 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
12534817 TCGCAATGCGA
1 TCGCAATGCGA
12534828 TACTGACTAT
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:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:12534777 original size:41 final size:41
Alignment explanation
Indices: 12534732--12534827 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
12534722 CGATTTTCCC
12534732 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
12534773 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
12534814 AAATCGCAATGCGA
1 AATTCGCAATGCGA
12534828 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:12534781 original size:21 final size:20
Alignment explanation
Indices: 12534735--12534827 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
12534725 TTTTCCCAAT
*
12534735 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
12534755 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
12534775 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
12534796 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
12534817 TCGCAATGCGA
1 TCGCAATGCGA
12534828 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:12534840 original size:41 final size:41
Alignment explanation
Indices: 12534754--12534888 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
12534744 GAATAAGTAA
* * *
12534754 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
12534795 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
12534836 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
12534877 TTCGCAACGCGA
1 ATCGCAACGCGA
12534889 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:12534841 original size:20 final size:20
Alignment explanation
Indices: 12534816--12534910 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
12534806 AATTGGGAAA
*
12534816 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
12534836 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
12534857 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
12534877 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
12534897 TTCGCAACGCGATA
1 ATCGCAACGCGATA
12534911 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:12535127 original size:22 final size:22
Alignment explanation
Indices: 12535099--12535141 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12535089 ACTCTCTCAT
12535099 CCATCTCCGACGAAATCCGTCC
1 CCATCTCCGACGAAATCCGTCC
*
12535121 CCATCTCCGGCGAAATCCGTC
1 CCATCTCCGACGAAATCCGTC
12535142 TATCTAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.19
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCC
Found at i:12535430 original size:20 final size:20
Alignment explanation
Indices: 12535405--12535442 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12535395 CGATTCTCTC
12535405 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
12535425 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
12535443 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:12536782 original size:18 final size:18
Alignment explanation
Indices: 12536761--12536805 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
12536751 TCCACTTTGG
* *
12536761 GAGCCATCACCTCGCCCA
1 GAGCAATCACCTCACCCA
* *
12536779 GAGCTATCACCTCACCTA
1 GAGCAATCACCTCACCCA
12536797 GAGCAATCA
1 GAGCAATCA
12536806 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:0.29, C:0.40, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCAATCACCTCACCCA
Found at i:12537337 original size:19 final size:18
Alignment explanation
Indices: 12537315--12537410 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
12537305 GGAAATGGCT
*
12537315 ATCGCAATGCGAAATAAAA
1 ATCGCAA-GCGAAATCAAA
12537334 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATCAAA
*
12537348 ATCGCAACGCGAAAT-GAA
1 ATCGCAA-GCGAAATCAAA
12537366 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATCAAA
*
12537380 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATCAAA
12537399 ATCGCAATGCGA
1 ATCGCAA-GCGA
12537411 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.18
19 21 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATCAAA
Found at i:12537350 original size:14 final size:14
Alignment explanation
Indices: 12537331--12537388 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
12537321 ATGCGAAATA
12537331 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
12537345 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
12537361 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
12537377 AAAATCGCAACG
1 AAAATCGCAACG
12537389 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:12537373 original size:32 final size:32
Alignment explanation
Indices: 12537315--12537405 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
12537305 GGAAATGGCT
* *
12537315 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAACGCGAAAT-GAAATCGCAACGACAAA
12537348 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
12537380 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATG-AAATCGCAA
12537406 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:12537443 original size:14 final size:14
Alignment explanation
Indices: 12537424--12537479 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
12537414 GTGTTTCGCA
12537424 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
12537438 TTGCGATTTCATTTCGCG
1 TTGCGATTT--TGT--CG
12537456 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
12537470 TTGCGATTTT
1 TTGCGATTTT
12537480 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 21 0.58
16 4 0.11
18 11 0.31
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:12537460 original size:32 final size:33
Alignment explanation
Indices: 12537417--12537495 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
12537407 GCGATTTGTG
12537417 TTTCGCATTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
12537449 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
12537482 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
12537496 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:12537494 original size:19 final size:19
Alignment explanation
Indices: 12537436--12537553 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
12537426 GCGATTTTGT
12537436 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
12537454 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
12537468 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
12537487 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
12537507 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
12537526 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
12537546 TGTTGCGA
1 CGTTGCGA
12537554 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:12539645 original size:20 final size:20
Alignment explanation
Indices: 12539620--12539717 Score: 178
Period size: 20 Copynumber: 4.9 Consensus size: 20
12539610 TCGCATTGCG
* *
12539620 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
12539640 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
12539660 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
12539680 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
12539700 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
12539718 TCAAATGAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:12540804 original size:24 final size:24
Alignment explanation
Indices: 12540777--12540830 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12540767 GTATTCGAAA
* *
12540777 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
12540801 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
12540825 TTTGAT
1 TTTGAT
12540831 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:12541022 original size:12 final size:12
Alignment explanation
Indices: 12541005--12541029 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12540995 ATATAATCCT
12541005 GAAGAAGAAAAA
1 GAAGAAGAAAAA
12541017 GAAGAAGAAAAA
1 GAAGAAGAAAAA
12541029 G
1 G
12541030 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:12543426 original size:66 final size:66
Alignment explanation
Indices: 12543320--12543478 Score: 275
Period size: 66 Copynumber: 2.4 Consensus size: 66
12543310 GAAATTACTA
*
12543320 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAA-GAAAATCGCAACGCTAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-AAAATGAAAATCGCAACGCGAA
12543384 TT
65 TT
* *
12543386 TCGCAATGCAAAATGAAAATCGCAACGAGGGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
12543451 T
66 T
12543452 TCGCAATGCGAAATGAAAATCGCAACG
1 TCGCAATGCGAAATGAAAATCGCAACG
12543479 CGAATTTAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
65 4 0.05
66 84 0.95
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.15
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
T
Found at i:12543500 original size:19 final size:20
Alignment explanation
Indices: 12543478--12543520 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
12543468 AAATCGCAAC
12543478 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
12543497 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
12543517 GCGA
1 GCGA
12543521 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:12543500 original size:38 final size:33
Alignment explanation
Indices: 12543320--12543485 Score: 221
Period size: 33 Copynumber: 5.0 Consensus size: 33
12543310 GAAATTACTA
* *
12543320 TCGCAATGCGAAATGAAAATCGCAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
* *
12543353 TCGCAATGCGAAAAGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
* *
12543386 TCGCAATGCAAAATGAAAATCGCAACGAGGGAA--
1 TCGCAATGCGAAATGAAAATCGCAAC--GCGAATT
*
12543419 TCGCAATGCAAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
12543452 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
12543485 T
1 T
12543486 AATTTCGCGT
Statistics
Matches: 118, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
31 4 0.03
32 1 0.01
33 110 0.93
35 3 0.03
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:12543505 original size:14 final size:14
Alignment explanation
Indices: 12543506--12543539 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12543496 TGCGATTTTC
12543506 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
12543520 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
12543534 ATTTTC
1 ATTTTC
12543540 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:12543680 original size:14 final size:14
Alignment explanation
Indices: 12543661--12543697 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12543651 CATCAATTAA
12543661 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12543675 ACAAATCACCTTTT
1 ACAAATCAACTTTT
12543689 ACAAATCAA
1 ACAAATCAA
12543698 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:12545140 original size:42 final size:42
Alignment explanation
Indices: 12545094--12545177 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
12545084 CGATGACAGT
* * * *
12545094 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGG
* * *
12545136 GGCCTCTTCAACGATAGGAGTGGAATCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGG
12545178 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGG
Found at i:12547211 original size:20 final size:19
Alignment explanation
Indices: 12547180--12547323 Score: 83
Period size: 20 Copynumber: 7.9 Consensus size: 19
12547170 TCTTTTGGTT
12547180 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
12547199 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
12547220 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
12547239 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
12547253 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
12547269 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
12547286 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
12547306 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
12547324 CGATTTTGGT
Statistics
Matches: 96, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 19 0.20
20 48 0.50
21 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:12547262 original size:33 final size:33
Alignment explanation
Indices: 12547205--12547303 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
12547195 ACGAGATAAT
*
12547205 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
12547239 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
12547272 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
12547304 GCGAAATGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:12547345 original size:19 final size:19
Alignment explanation
Indices: 12547323--12547366 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12547313 AAATCGCAAC
*
12547323 GCGATTTTGGTTTCGCGTT
1 GCGATTTTGATTTCGCGTT
*
12547342 GCGATTTTTATTTCGCGTT
1 GCGATTTTGATTTCGCGTT
*
12547361 ACGATT
1 GCGATT
12547367 ATCTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
GCGATTTTGATTTCGCGTT
Found at i:12548006 original size:20 final size:20
Alignment explanation
Indices: 12547921--12548014 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
12547911 CGCTATCTAA
*
12547921 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
12547941 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* * ** * *
12547961 ATCTCGTTGAGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
12547982 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
12548002 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
12548015 TTTCTCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:12548033 original size:41 final size:41
Alignment explanation
Indices: 12547942--12548076 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
12547932 AAAGTCAGTA
* * * * * *
12547942 TCGCGTTGCGAAAGTAAGTATCTCGTTGAGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* *
12547982 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* ** * *
12548024 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
12548065 TCGCGTTGCGAT
1 TCGCGTTGCGAT
12548077 TTACTTATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 71 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:12548047 original size:20 final size:20
Alignment explanation
Indices: 12548003--12548095 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
12547993 ATAGTCAGTA
*
12548003 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
12548024 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
12548044 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
12548065 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
12548085 TCGCATTGCGA
1 TCGCATTGCGA
12548096 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:12548077 original size:41 final size:41
Alignment explanation
Indices: 12548003--12548098 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
12547993 ATAGTCAGTA
* *
12548003 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
12548044 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
12548085 TCGCATTGCGAATT
1 TCGCATTGCGAATT
12548099 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:12555507 original size:2 final size:2
Alignment explanation
Indices: 12555500--12555525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12555490 TATTTGTATC
12555500 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12555526 TCAAATATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12557165 original size:36 final size:36
Alignment explanation
Indices: 12557121--12557246 Score: 175
Period size: 36 Copynumber: 3.4 Consensus size: 36
12557111 ATTAATATTA
12557121 TATATGTTTTCAAAAACTGTTTTAAAAACTATATAT
1 TATATGTTTTCAAAAACTGTTTTAAAAACTATATAT
12557157 TATATGTTTTCAAAAA-TACGTTTTCAAAAACTATAT-T
1 TATATGTTTTCAAAAACT--GTTTT-AAAAACTATATAT
* *
12557194 ATATACGTTTTCAAAAACCGTTTTAAAAACTATATAT
1 -TATATGTTTTCAAAAACTGTTTTAAAAACTATATAT
*
12557231 CATATGTTTTCAAAAA
1 TATATGTTTTCAAAAA
12557247 ATATATTATA
Statistics
Matches: 80, Mismatches: 4, Indels: 12
0.83 0.04 0.12
Matches are distributed among these distances:
35 1 0.01
36 41 0.51
37 12 0.15
38 26 0.32
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (36 bp):
TATATGTTTTCAAAAACTGTTTTAAAAACTATATAT
Found at i:12557251 original size:24 final size:24
Alignment explanation
Indices: 12557213--12557294 Score: 132
Period size: 24 Copynumber: 3.5 Consensus size: 24
12557203 TTCAAAAACC
12557213 GTTTT-AAAAACTATA-TATCATAT
1 GTTTTCAAAAACTATATTAT-ATAT
*
12557236 GTTTTCAAAAAATATATTATATAT
1 GTTTTCAAAAACTATATTATATAT
12557260 GTTTTCAAAAACTATATTATATAT
1 GTTTTCAAAAACTATATTATATAT
12557284 GTTTTCAAAAA
1 GTTTTCAAAAA
12557295 TCGTTTTTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
23 5 0.09
24 47 0.85
25 3 0.05
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (24 bp):
GTTTTCAAAAACTATATTATATAT
Found at i:12557271 original size:84 final size:83
Alignment explanation
Indices: 12557176--12557336 Score: 261
Period size: 84 Copynumber: 1.9 Consensus size: 83
12557166 TCAAAAATAC
12557176 GTTTTCAAAAACTATATTATATACGTTTTCAAAAACCG-TTTTAAAAACTATATATCATATGTTT
1 GTTTTCAAAAACTATATTATATACGTTTTCAAAAACCGTTTTTAAAAACTATATAT--TATGTTT
12557240 TCAAAAAATATATTATATAT
64 TCAAAAAATATATTATATAT
* * *
12557260 GTTTTCAAAAACTATATTATATATGTTTTCAAAAATCGTTTTTCAAAACTATATATTATGTTTTC
1 GTTTTCAAAAACTATATTATATACGTTTTCAAAAACCGTTTTTAAAAACTATATATTATGTTTTC
*
12557325 AAAAACTATATT
66 AAAAAATATATT
12557337 GTATCTTCAA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
83 20 0.28
84 36 0.50
85 16 0.22
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (83 bp):
GTTTTCAAAAACTATATTATATACGTTTTCAAAAACCGTTTTTAAAAACTATATATTATGTTTTC
AAAAAATATATTATATAT
Found at i:12557356 original size:22 final size:21
Alignment explanation
Indices: 12557301--12557357 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
12557291 AAAATCGTTT
* *
12557301 TTCAAAACTATATATTATGTT
1 TTCAAAACTATATATTATATC
*
12557322 TTCAAAA--ACTATATTGTATC
1 TTCAAAACTA-TATATTATATC
12557342 TTCAACAACTATATAT
1 TTCAA-AACTATATAT
12557358 ATTATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.45
21 9 0.31
22 5 0.17
23 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (21 bp):
TTCAAAACTATATATTATATC
Found at i:12557365 original size:83 final size:83
Alignment explanation
Indices: 12557181--12557370 Score: 226
Period size: 83 Copynumber: 2.3 Consensus size: 83
12557171 AATACGTTTT
*
12557181 CAAAAACTATATTATATACGTTTTCAAAAACCGTTTTAAAAACTATATATCATATGTTTTCAAAA
1 CAAAAACTATATTATATATGTTTTCAAAAACCGTTTTAAAAACTATATAT-ATATGTTTTCAAAA
***
12557246 AATATATTATATATGTTTT
65 AATATATTATATATGTCAA
* *
12557265 CAAAAACTATATTATATATGTTTTCAAAAATCGTTTTTCAAAACTATATAT-TATGTTTTCAAAA
1 CAAAAACTATATTATATATGTTTTCAAAAACCG-TTTTAAAAACTATATATATATGTTTTCAAAA
* * *
12557329 ACTATATTGTATCT-TCAA
65 AATATATTATATATGTCAA
*
12557347 CAACTATA-TATATTATATAT-TTTT
1 CAA--AAACTATATTATATATGTTTT
12557371 GAAACTATTA
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
82 8 0.09
83 36 0.39
84 33 0.35
85 16 0.17
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (83 bp):
CAAAAACTATATTATATATGTTTTCAAAAACCGTTTTAAAAACTATATATATATGTTTTCAAAAA
ATATATTATATATGTCAA
Found at i:12557927 original size:15 final size:15
Alignment explanation
Indices: 12557907--12557936 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12557897 CAGTTTACTT
12557907 TATTTTATATTTTAA
1 TATTTTATATTTTAA
*
12557922 TATTTTATTTTTTAA
1 TATTTTATATTTTAA
12557937 AAAATAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTATATTTTAA
Found at i:12565090 original size:16 final size:16
Alignment explanation
Indices: 12565069--12565129 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
12565059 TAATAAATAA
12565069 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
12565085 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
** *
12565101 ACGAACATAAATAAAA
1 ACGAACATAAACGAAC
12565117 ACGAACATAAACG
1 ACGAACATAAACG
12565130 TTGGAGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:12569485 original size:20 final size:20
Alignment explanation
Indices: 12569462--12569538 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 20
12569452 AGAACCCCAG
*
12569462 GGGGGTATCGATTCCCCT-A
1 GGGGGAATCGATTCCCCTCA
*
12569481 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCC-TC-A
*
12569503 GGGGGAATCGGTT-CCCTCA
1 GGGGGAATCGATTCCCCTCA
* *
12569522 TGAGGGTATCGATTCCC
1 -GGGGGAATCGATTCCC
12569539 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.33
20 13 0.27
21 5 0.10
22 14 0.29
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTCA
Found at i:12575824 original size:14 final size:14
Alignment explanation
Indices: 12575807--12575849 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
12575797 ATAAATAAAT
12575807 GAACATAACCGAAC
1 GAACATAACCGAAC
*
12575821 GAACATAACTGAAC
1 GAACATAACCGAAC
*
12575835 TAACATAACCGAAC
1 GAACATAACCGAAC
12575849 G
1 G
12575850 TTCACGAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.26, G:0.14, T:0.12
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:12579605 original size:43 final size:43
Alignment explanation
Indices: 12579557--12579748 Score: 180
Period size: 42 Copynumber: 4.6 Consensus size: 43
12579547 TTACAAACAT
* * *
12579557 CACTAAAAACAACAGAATTAGCGGCATTTGTAGCAAAAAATGC
1 CACTAAAGACAAGAGAATTAGCGGCATTTGTGGCAAAAAATGC
** * * *
12579600 CACTAAAGACTTGATAATTAGCGACGTTTGTGGC-AAAAA--C
1 CACTAAAGACAAGAGAATTAGCGGCATTTGTGGCAAAAAATGC
*
12579640 CACTAAAGACAAGAG-A-TAGTGGCATTTGTGGCAAAAAAATGC
1 CACTAAAGACAAGAGAATTAGCGGCATTTGTGGC-AAAAAATGC
* * * * * **
12579682 CACTAAAGATAGGAGAATTAGCGACGTTTGCGG-AAAAAACAC
1 CACTAAAGACAAGAGAATTAGCGGCATTTGTGGCAAAAAATGC
*
12579724 CACTAAAGATAAGAGAATTAGCGGC
1 CACTAAAGACAAGAGAATTAGCGGC
12579749 GTGGTGTTTG
Statistics
Matches: 119, Mismatches: 24, Indels: 13
0.76 0.15 0.08
Matches are distributed among these distances:
38 13 0.11
39 1 0.01
40 18 0.15
42 49 0.41
43 27 0.23
44 11 0.09
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (43 bp):
CACTAAAGACAAGAGAATTAGCGGCATTTGTGGCAAAAAATGC
Found at i:12579674 original size:81 final size:84
Alignment explanation
Indices: 12579551--12579739 Score: 233
Period size: 82 Copynumber: 2.3 Consensus size: 84
12579541 TTTGTATTAC
* * * * *
12579551 AAACATCACTAAAAACAACAGAATTAGCGGCATTTGTAGC-AAAAAATGCCACTAAAGACT-TGA
1 AAACACCACTAAAGACAAGAG-A-TAGTGGCATTTGTAGCAAAAAAATGCCACTAAAGA-TAGGA
* * *
12579614 TAATTAGCGACGTTTGTGG-CA
63 GAATTAGCGACGTTTGCGGAAA
*
12579635 AAA-ACCACTAAAGACAAGAGATAGTGGCATTTGTGGCAAAAAAATGCCACTAAAGATAGGAGAA
1 AAACACCACTAAAGACAAGAGATAGTGGCATTTGTAGCAAAAAAATGCCACTAAAGATAGGAGAA
12579699 TTAGCGACGTTTGCGGAAA
66 TTAGCGACGTTTGCGGAAA
*
12579718 AAACACCACTAAAGATAAGAGA
1 AAACACCACTAAAGACAAGAGA
12579740 ATTAGCGGCG
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
81 15 0.16
82 38 0.42
83 18 0.20
84 20 0.22
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.19
Consensus pattern (84 bp):
AAACACCACTAAAGACAAGAGATAGTGGCATTTGTAGCAAAAAAATGCCACTAAAGATAGGAGAA
TTAGCGACGTTTGCGGAAA
Found at i:12580692 original size:565 final size:564
Alignment explanation
Indices: 12579485--12581178 Score: 2130
Period size: 565 Copynumber: 3.0 Consensus size: 564
12579475 AACCTTTTGC
* *
12579485 AAATAGCGGCGTTTGTGGTAAAAAAACCCACTACAAATCATAATATATAGCAGCGTTTTGTATTA
1 AAATAGCGGCGTTTGTGGT-AAAAAAGCCACTACAAATCATAATATATAGCAGTGTTTTGTATTA
*
12579550 CAAACATCACTAAAAACAACAGAATTAGCGGCATTTGTAGC--AAAAAATGCCACTAAAGACTTG
65 CAAAC-GCACTAAAAACAACAGAATTAGCGGCATTTGTA-CAAAAAAAATGCCACTAAAGACTTG
*
12579613 ATAATTAGCGACGTTTGTGGC-AAAAACCACTAAAGACAAGAGATAGTGGCATTTGTGGCAAAAA
128 ATAATTAGCGACATTTGTGGCAAAAAACCACTAAAGACAAGAGATAGTGGCATTTGTGGC-AAAA
*
12579677 AATGCCACTAAAGATAGGAGAATTAGCGACGTTTGCGGAAAAAACACCACTAAAGATAAGAGAAT
192 AACGCCACTAAAGATAGGAGAATTAGCGACGTTTGCGGAAAAAACACCACTAAAGATAAGAGAAT
* *
12579742 TAGCGGCGTGGTGTTTGAAAGAACAAACGCCACTATATAGCTCGACCTTTTGCAGTGTTTTAGGT
257 TAGCGGCGCGGTGTTTGAAAGAACAAACGCCACTATATAGCTCGACCTTTTGCAGCGTTTTAGGT
12579807 TCAAAAACGTTGCTACCTTTTGCAGCGTTCGTTTTAGTGGCGCTTCTTGCGACGCTCTTACTAGC
322 TC-AAAACG-TGCTACCTTTTGCAGCGTTCGTTTTA-----G---C--G-G-CGCTCTTACTAGC
* * *
12579872 GCCAATAGTGTTTTTAGTTACGCTTAAAAATGCCACTATAGGACTAAAAAATACCACTAAAAACC
373 GCCAATAGTGTTTTTAGTGACGCTTAAAAACGCCACTATAGGACTAAAAAATGCCACTAAAAACC
* * * *
12579937 TATTTTGCTATAGTCGACAACGCAAGACAACATTGCCTTTGATTATTATAGAAAACGAGAAACCA
438 TGTTTTGCTGTAGTCCACAACGCAAGACAACATTGCCTTTGATTATTATAGAAAACGAGAAAACA
12580002 AATGTATAGTGACACATAAAGGATGAATGAAATATAAAATATAATAACAAATAAATAAAATA
503 AATGTATAGTGACACATAAAGGATGAATGAAATATAAAATATAATAACAAATAAATAAAATA
* * *
12580064 AAATAGCGTCGTTTGTGGTAAAAAAGCCACTATAAATCATAATATATAGCA-TCATTTTGTATTA
1 AAATAGCGGCGTTTGTGGTAAAAAAGCCACTACAAATCATAATATATAGCAGT-GTTTTGTATTA
*
12580128 CAAACGCAAATAAAAACAACAGAATTAGCGGCATTTGTACAAAAAAAATGCCACTAAAGACTTGA
65 CAAACGC-ACTAAAAACAACAGAATTAGCGGCATTTGTACAAAAAAAATGCCACTAAAGACTTGA
* *
12580193 TAATTAGCGACATTTGTGGCAAAAAACCACTAAAGACAAAAGATAGTGGCATTTATGGCAAAAAA
129 TAATTAGCGACATTTGTGGCAAAAAACCACTAAAGACAAGAGATAGTGGCATTTGTGGCAAAAAA
12580258 -GCCACTAAAGATAGGAGAATTAGCGACGTTTGCGGAAAAAACACCACTAAAGATAAGAGAATTA
194 CGCCACTAAAGATAGGAGAATTAGCGACGTTTGCGGAAAAAACACCACTAAAGATAAGAGAATTA
12580322 GCGGCGCGGTGTTTGAAAGAACAAACGCCACTATATAGCTCGACCTTTTGCAGCGTTTTAGGTTC
259 GCGGCGCGGTGTTTGAAAGAACAAACGCCACTATATAGCTCGACCTTTTGCAGCGTTTTAGGTTC
*
12580387 ACAAACGCTGCTACCTTTTGCAGCGTTCGTTTTAGCGGCGCTCTTACTAGCGCCAATAGT-ATTT
324 A-AAACG-TGCTACCTTTTGCAGCGTTCGTTTTAGCGGCGCTCTTACTAGCGCCAATAGTGTTTT
12580451 TAGTGACGCTTAAAAACGCCACTATAGGACTAAAAAATGCCACTAAAAACCTGTTTTGCTGTAGT
387 TAGTGACGCTTAAAAACGCCACTATAGGACTAAAAAATGCCACTAAAAACCTGTTTTGCTGTAGT
*
12580516 CCACAACGCAAGACAACATTGCCTTTGATTATTATAAAAAACGAGAAAACAAATGTATAGTGACA
452 CCACAACGCAAGACAACATTGCCTTTGATTATTATAGAAAACGAGAAAACAAATGTATAGTGACA
12580581 CATAAAGGATGAATGAAATATAAAATATAATAACAAATAAATAAAATA
517 CATAAAGGATGAATGAAATATAAAATATAATAACAAATAAATAAAATA
* *
12580629 AAATAGAGGCATTTGTGGTAAAAAAGCCACTACAAATCATAATATATAGCAGTGTTTTGTATTAC
1 AAATAGCGGCGTTTGTGGTAAAAAAGCCACTACAAATCATAATATATAGCAGTGTTTTGTATTAC
* * *
12580694 AAACGCCACTAAAAACAATAGAATTAGTGGCATTTGTA-ACAAAAAAATGCCACTAAAGACTAAA
66 AAACG-CACTAAAAACAACAGAATTAGCGGCATTTGTACA-AAAAAAATGCCACTAAAGACT--T
* * * * * * * * * * *
12580758 GACAAGAGATAGTGGCATTTGTGGAAAAAAATGCCACTAAAGATAGGAGAATTAGCGACGTTTGC
127 GA-TA-A-TTAGCGACATTTGTGGCAAAAAA--CCACTAAAGACAAGAG-A-TAGTGGCATTTGT
* * ** * *
12580823 GG-AAAAAACACCACTAAAGATAAGAGAATTAGTGGCG-CGGTGTTTGAAAGAACAAACGCCACT
185 GGCAAAAAACGCCACTAAAGATAGGAGAATTA---GCGAC---GTTTG-CGGAAAAAACACCACT
* * * *** * * * ** *
12580886 ----AT-ATAG-CTTGACCTTTTGCAGTGTTT-TAGGTTC--A---CA--A-AT-GCTACTACCT
243 AAAGATAAGAGAATT-AGC-GGCGCGGTGTTTGAAAGAACAAACGCCACTATATAGCT-CGACCT
* * *
12580935 TTTGCAGCG--TT-CGTT-------T--TAGC---GGC-GC-TTC---TT-GCGGCGCTCTTACT
305 TTTGCAGCGTTTTAGGTTCAAAACGTGCTACCTTTTGCAGCGTTCGTTTTAGCGGCGCTCTTACT
*
12580979 AGCGCCAATAGTGTTTTTAGTGACGCTTAAAAACGCCACTATAGAACTAAAAAATGCCACTAAAA
370 AGCGCCAATAGTGTTTTTAGTGACGCTTAAAAACGCCACTATAGGACTAAAAAATGCCACTAAAA
12581044 ACCTGTTTTGCTGTAGTCCACAACGCAAGACAACATTGCCTTTGATTATTATAGAAAACGAGAAA
435 ACCTGTTTTGCTGTAGTCCACAACGCAAGACAACATTGCCTTTGATTATTATAGAAAACGAGAAA
*
12581109 ATAAATGTATAGTGACACATAAAGGATGAATGAAATATAAAATATAATAACAAATAAATAAAATA
500 ACAAATGTATAGTGACACATAAAGGATGAATGAAATATAAAATATAATAACAAATAAATAAAATA
12581174 AAATA
1 AAATA
12581179 ATGAAATACT
Statistics
Matches: 1016, Mismatches: 69, Indels: 94
0.86 0.06 0.08
Matches are distributed among these distances:
544 26 0.03
545 185 0.18
548 3 0.00
549 2 0.00
550 2 0.00
553 3 0.00
555 1 0.00
564 4 0.00
565 287 0.28
566 27 0.03
567 19 0.02
568 3 0.00
569 1 0.00
570 22 0.02
572 13 0.01
573 9 0.01
574 32 0.03
575 8 0.01
576 11 0.01
577 6 0.01
578 233 0.23
579 71 0.07
580 48 0.05
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (564 bp):
AAATAGCGGCGTTTGTGGTAAAAAAGCCACTACAAATCATAATATATAGCAGTGTTTTGTATTAC
AAACGCACTAAAAACAACAGAATTAGCGGCATTTGTACAAAAAAAATGCCACTAAAGACTTGATA
ATTAGCGACATTTGTGGCAAAAAACCACTAAAGACAAGAGATAGTGGCATTTGTGGCAAAAAACG
CCACTAAAGATAGGAGAATTAGCGACGTTTGCGGAAAAAACACCACTAAAGATAAGAGAATTAGC
GGCGCGGTGTTTGAAAGAACAAACGCCACTATATAGCTCGACCTTTTGCAGCGTTTTAGGTTCAA
AACGTGCTACCTTTTGCAGCGTTCGTTTTAGCGGCGCTCTTACTAGCGCCAATAGTGTTTTTAGT
GACGCTTAAAAACGCCACTATAGGACTAAAAAATGCCACTAAAAACCTGTTTTGCTGTAGTCCAC
AACGCAAGACAACATTGCCTTTGATTATTATAGAAAACGAGAAAACAAATGTATAGTGACACATA
AAGGATGAATGAAATATAAAATATAATAACAAATAAATAAAATA
Found at i:12580757 original size:51 final size:48
Alignment explanation
Indices: 12580701--12580800 Score: 137
Period size: 48 Copynumber: 2.0 Consensus size: 48
12580691 TACAAACGCC
*
12580701 ACTAAAAACAATAGAATTAGTGGCATTTGTAACAAAAAAATGCCACTAAAG
1 ACTAAAAACAAGAG-A-TAGTGGCATTTGT-ACAAAAAAATGCCACTAAAG
* **
12580752 ACTAAAGACAAGAGATAGTGGCATTTGTGGAAAAAAATGCCACTAAAG
1 ACTAAAAACAAGAGATAGTGGCATTTGTACAAAAAAATGCCACTAAAG
12580800 A
1 A
12580801 TAGGAGAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
48 19 0.42
49 13 0.29
50 1 0.02
51 12 0.27
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (48 bp):
ACTAAAAACAAGAGATAGTGGCATTTGTACAAAAAAATGCCACTAAAG
Found at i:12581191 original size:21 final size:20
Alignment explanation
Indices: 12581137--12581196 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
12581127 ATAAAGGATG
*
12581137 AATGAAATATAAAATATAAT
1 AATGAAATATAAAATAAAAT
*
12581157 AA-CAAATAAATAAAATAAAAT
1 AATGAAAT--ATAAAATAAAAT
12581178 AATGAAATACTAAAATAAA
1 AATGAAATA-TAAAATAAA
12581197 TAAATAGCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 22 0.67
22 4 0.12
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
AATGAAATATAAAATAAAAT
Found at i:12584565 original size:43 final size:43
Alignment explanation
Indices: 12584512--12584937 Score: 450
Period size: 43 Copynumber: 9.9 Consensus size: 43
12584502 TGAGAACCAA
* * *
12584512 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCGTTTTTGGAAC
* * * *
12584555 AAACGCCGCAAAAGGTTTATATCTATAGCGGCGTTTTCGGAAC
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCGTTTTTGGAAC
* * * *
12584598 AAACGCCGCAAAAGGTTGATATCTATAGAGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCGTTTTTGGAAC
* * * *
12584641 TAACGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTTGGAAC
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCG-TTTTTGGAAC
*
12584685 AAACGCCGCAATAGG-TCAGATATATAGCGGCGTTTTTTTGGAAC
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCG--TTTTTGGAAC
* * * * *
12584729 ATACACCGTAATAGG-TCAGATAGATAGCGGCGTTTTTTGGAAC
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCG-TTTTTGGAAC
* * *
12584772 AAACGCCGCAAAAGG-TCAGATCTATAGTGGCGTTTTT-TATAC
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCGTTTTTGGA-AC
* * *
12584814 AAACGCCGCAAAAGATTGATATATATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCGTTTTTGGAAC
* * ** *
12584857 AAACGCCGCAATAGGTT-AGATAGATAGCAACGTTTTTTTAGAAC
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCG--TTTTTGGAAC
*
12584901 AAACGCCGCAAAAGG-TCAGATATATAGCGACGTTTTT
1 AAACGCCGCAAAAGGTTCAGATATATAGCGGCGTTTTT
12584938 TATACAAACT
Statistics
Matches: 333, Mismatches: 42, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.00
42 37 0.11
43 196 0.59
44 99 0.30
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTTCAGATATATAGCGGCGTTTTTGGAAC
Found at i:12584867 original size:216 final size:216
Alignment explanation
Indices: 12584536--12584938 Score: 589
Period size: 216 Copynumber: 1.9 Consensus size: 216
12584526 GTTGAGATCT
* * *
12584536 ATAGCGGCGTTTTTGGAATAAACGCCGCAAAAGGTTTATATCTATAGCGGCGTTTTCGGAACAAA
1 ATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTCGGAACAAA
* * * *
12584601 CGCCGCAAAAGGTTGATATCTATAGAGGCGTTTTTGGAACTAACGCCGCAAAAGGTT-GATATCT
66 CGCCGCAAAAGATTGATATATATAGAGGCGTTTTTGGAACAAACGCCGCAAAAGGTTAGATA--G
** * * *
12584665 ATAGCGGCG-TTTTTTGGAACAAACGCCGCAATAGGTCAGATATATAGCGGCGTTTTTTTGGAAC
129 ATAGCAACGTTTTTTTAGAACAAACGCCGCAAAAGGTCAGATATATAGCGACGTTTTTTTGGAAC
12584729 ATACACCGTAATAGGTCAGATAG
194 ATACACCGTAATAGGTCAGATAG
* **
12584752 ATAGCGGCGTTTTTTGGAACAAACGCCGCAAAAGG-TCAGATCTATAGTGGCGTTTT-TTATACA
1 ATAGCGGCG-TTTTTGGAACAAACGCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTCGGA-ACA
* *
12584815 AACGCCGCAAAAGATTGATATATATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTTAGATAG
64 AACGCCGCAAAAGATTGATATATATAGAGGCGTTTTTGGAACAAACGCCGCAAAAGGTTAGATAG
12584880 ATAGCAACGTTTTTTTAGAACAAACGCCGCAAAAGGTCAGATATATAGCGACGTTTTTT
129 ATAGCAACGTTTTTTTAGAACAAACGCCGCAAAAGGTCAGATATATAGCGACGTTTTTT
12584939 ATACAAACTC
Statistics
Matches: 166, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
215 8 0.05
216 130 0.78
217 28 0.17
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (216 bp):
ATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTCGGAACAAA
CGCCGCAAAAGATTGATATATATAGAGGCGTTTTTGGAACAAACGCCGCAAAAGGTTAGATAGAT
AGCAACGTTTTTTTAGAACAAACGCCGCAAAAGGTCAGATATATAGCGACGTTTTTTTGGAACAT
ACACCGTAATAGGTCAGATAG
Found at i:12589000 original size:82 final size:83
Alignment explanation
Indices: 12588833--12589005 Score: 180
Period size: 82 Copynumber: 2.1 Consensus size: 83
12588823 GTTTGTTACC
* * * *
12588833 AAAACGCCGCTAAAGTTATAATTTGTTGCGGCGTTTATTAAAAAACGCTACTATAGGTGAACCCT
1 AAAATGCCGCTAAAGTTATAATCTGTTGCGGCGTTTATTAAAAAACGCCACTATAGATGAACCCT
*
12588898 ATTACAACGTTTGTAT-A
66 ATTACAACGTTTATATAA
12588915 AAAATGCCGCTAAAG-TACTAATCTGTTGCGGC-TTTAATTGAAAAAACGCCA-TAATAGAT-AG
1 AAAATGCCGCTAAAGTTA-TAATCTGTTGCGGCGTTT-ATT-AAAAAACGCCACT-ATAGATGA-
**
12588976 A-CCTATTACTGCGTTTAT-TGAA
61 ACCCTATTACAACGTTTATAT-AA
12588998 AAAATGCC
1 AAAATGCC
12589006 ACTATAGATA
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
81 6 0.08
82 46 0.60
83 25 0.32
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (83 bp):
AAAATGCCGCTAAAGTTATAATCTGTTGCGGCGTTTATTAAAAAACGCCACTATAGATGAACCCT
ATTACAACGTTTATATAA
Found at i:12592360 original size:23 final size:21
Alignment explanation
Indices: 12592316--12592360 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
12592306 CATATTTTAC
*
12592316 ATGTTAAAAGCGGAACACAAA
1 ATGTTAAAAGCGGAACAAAAA
12592337 ATGTTATAAAGCGGAATCAAAAA
1 ATGTTA-AAAGCGGAA-CAAAAA
12592360 A
1 A
12592361 AAAAATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 9 0.43
23 6 0.29
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (21 bp):
ATGTTAAAAGCGGAACAAAAA
Found at i:12592633 original size:77 final size:77
Alignment explanation
Indices: 12592533--12592700 Score: 230
Period size: 77 Copynumber: 2.2 Consensus size: 77
12592523 TAAGAAATAC
* * * *
12592533 GGTTGCGCCTAAAAATGTCATGGTTCACTAAGAAATATGTTGCGATCTGGAATGTTAATATTTTT
1 GGTTGCACCTAAAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATAGAATGTTAATATTTTT
*
12592598 ATTGATAAAATG
66 ATTGATAAAACG
* * * * *
12592610 GGTTGCACCTAAGAATGTCATGGTTCACTAATAAATAGGTTGTGATATAGAATGTTACTGTTTTT
1 GGTTGCACCTAAAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATAGAATGTTAATATTTTT
12592675 ATTGATAAAACG
66 ATTGATAAAACG
12592687 GGTTGCGA-CTAAAA
1 GGTTGC-ACCTAAAA
12592701 TGTTATCAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 78 0.99
78 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (77 bp):
GGTTGCACCTAAAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATAGAATGTTAATATTTTT
ATTGATAAAACG
Found at i:12593028 original size:78 final size:77
Alignment explanation
Indices: 12592807--12593026 Score: 271
Period size: 77 Copynumber: 2.9 Consensus size: 77
12592797 GTTGAGCCCA
* * *
12592807 CAAGAATGTAATGATTCACTAAGAAATATGTTGCAATATGGAATGCTAATATTTTTATTAATAAA
1 CAAGAATGTAATGATTCACTAAGAAATAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAA
* ***
12592872 ATGGATTTTTCC
66 ATAGATTGCGCC
* * * * * *
12592884 CAAAAATATCATGGTTCACTAAAAAATAGGTTGCGATATGGAATGTTAATATTTTTATTAATAAA
1 CAAGAATGTAATGATTCACTAAGAAATAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAA
12592949 ATAGATTGCGCC
66 ATAGATTGCGCC
* * * *
12592961 CGAGAATGTTATGATTCACTAAGAAAGTAAGTTCCGATCTGGAATGTTAATATTTTTATT-ATAA
1 CAAGAATGTAATGATTCACTAAGAAA-TAAGTTGCGATATGGAATGTTAATATTTTTATTAATAA
12593025 AA
65 AA
12593027 ATTCAAAAGT
Statistics
Matches: 121, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
77 91 0.75
78 30 0.25
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (77 bp):
CAAGAATGTAATGATTCACTAAGAAATAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAA
ATAGATTGCGCC
Found at i:12593127 original size:20 final size:20
Alignment explanation
Indices: 12593102--12593139 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12593092 AAAAGGCTGT
12593102 AAAGTATCGATATTTTTATA
1 AAAGTATCGATATTTTTATA
*
12593122 AAAGTATTGATATTTTTA
1 AAAGTATCGATATTTTTA
12593140 GATTCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (20 bp):
AAAGTATCGATATTTTTATA
Found at i:12593215 original size:20 final size:20
Alignment explanation
Indices: 12593190--12593257 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
12593180 CGAAATTATA
*
12593190 GATACTTTTTCACAA-GTATT
1 GATACTTTTCCA-AACGTATT
*
12593210 GATACTTTTCCAAATGTATT
1 GATACTTTTCCAAACGTATT
*
12593230 GATACTTTTCCAAACATATT
1 GATACTTTTCCAAACGTATT
12593250 GATACTTT
1 GATACTTT
12593258 CGAATTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 2 0.05
20 42 0.95
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (20 bp):
GATACTTTTCCAAACGTATT
Found at i:12593571 original size:100 final size:100
Alignment explanation
Indices: 12593392--12593714 Score: 298
Period size: 100 Copynumber: 3.2 Consensus size: 100
12593382 TGCTCGTGAA
**** * *
12593392 AACGTAGTAGGTAACA--TTTTTTTAATGTCAGTTGTTTAAGTTACAAGTATTAAACCATTTATA
1 AACGTAGTAGGTAACACCTTTTTTTAATGTCAACCATTTAAGTTATAAGTATAAAACCATTTATA
* * * *
12593455 TGATACAACAGAAAGACAAAACAGGTTTCTCATGAT
66 TTATGCAAAAGTAAGACAAAACAGGTTT-TCATGAT
* *
12593491 AACGTAGTACGTAACACCTTTTTTT-ATGTCAACCATTTAAGTTATAAGTATAAAACTATTTATA
1 AACGTAGTAGGTAACACCTTTTTTTAATGTCAACCATTTAAGTTATAAGTATAAAACCATTTATA
*
12593555 TTATGCAAAAGTAAGACAAAACA--TGTTCATGAT
66 TTATGCAAAAGTAAGACAAAACAGGTTTTCATGAT
* * * * * ** * * * *
12593588 AACGTACTAGG-CACTGCATTTTTTTTAATGTTAACTGTTTTAAATTATAAGTATGAAGCCGTTT
1 AACGTAGTAGGTAAC-AC-CTTTTTTTAATGTCAAC-CATTTAAGTTATAAGTATAAAACCATTT
* *
12593652 ATATTATGCAAAAGTAAGATAAAATAGGTTTTTCATGAT
63 ATATTATGCAAAAGTAAGACAAAACAGG-TTTTCATGAT
* **
12593691 AACATAGTAGGTAATGCCTTTTTT
1 AACGTAGTAGGTAACACCTTTTTT
12593715 ATGCAAAAGT
Statistics
Matches: 180, Mismatches: 34, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
96 2 0.01
97 17 0.09
98 9 0.05
99 22 0.12
100 96 0.53
101 7 0.04
102 6 0.03
103 20 0.11
104 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (100 bp):
AACGTAGTAGGTAACACCTTTTTTTAATGTCAACCATTTAAGTTATAAGTATAAAACCATTTATA
TTATGCAAAAGTAAGACAAAACAGGTTTTCATGAT
Found at i:12594345 original size:94 final size:97
Alignment explanation
Indices: 12594173--12594408 Score: 248
Period size: 94 Copynumber: 2.4 Consensus size: 97
12594163 TTTACGATAC
* * * * * *
12594173 AAGTATGAAACCGTTTATATAATACAACAGTGAGACAAAACATGTTTATCATGATAACGTAGTAG
1 AAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTTCATCATGATAACGTACTAG
* *
12594238 GTAGCGCCCTTTTTT-CTGTCAAC-CA-TTAT
66 GTAGCGCCCTTTTTTAATGTCAACTAATTTAT
12594267 AAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTTGCA-CATGATAACGTACTA
1 AAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTT-CATCATGATAACGTACTA
* * * *
12594331 TGTA-CTGTCTTTTTTTAATGTTAACTATTTTAATTTAT
65 GGTAGC-GCCCTTTTTTAATGTCAAC-----TAATTTAT
* *
12594369 AAGTATGAAGCCGTTTATATTATGCCAAAGTAAGACAAAA
1 AAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAA
12594409 TAGATTTTTC
Statistics
Matches: 118, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
93 1 0.01
94 67 0.57
95 7 0.06
101 1 0.01
102 42 0.36
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (97 bp):
AAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTTCATCATGATAACGTACTAG
GTAGCGCCCTTTTTTAATGTCAACTAATTTAT
Found at i:12594446 original size:102 final size:102
Alignment explanation
Indices: 12594263--12594447 Score: 259
Period size: 102 Copynumber: 1.8 Consensus size: 102
12594253 CTGTCAACCA
*
12594263 TTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTTGCACATGATAACGTA
1 TTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTTGCACATGATAACATA
* *
12594328 CTATGTACTGTCTTTTTTTAATGTTAACTATTTTAAT
66 CTAGGTAATGTCTTTTTTTAATGTTAACTATTTTAAT
* * * ***
12594365 TTATAAGTATGAAGCCGTTTATATTATGCCAAAGTAAGACAAAATA-GATTTTTCATGATAACAT
1 TTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATG-TTGCACATGATAACAT
12594429 A-TAGGTAATGT-TTTTTTTA
65 ACTAGGTAATGTCTTTTTTTA
12594448 TACAAAAGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
100 8 0.11
101 9 0.12
102 56 0.77
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (102 bp):
TTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTTGCACATGATAACATA
CTAGGTAATGTCTTTTTTTAATGTTAACTATTTTAAT
Found at i:12594742 original size:734 final size:731
Alignment explanation
Indices: 12593433--12594899 Score: 2237
Period size: 734 Copynumber: 2.0 Consensus size: 731
12593423 TTGTTTAAGT
* * *
12593433 TACAAGTATTAAACCATTTATATGATACAACAGAAAGACAAAACAGGTTTCTCATGATAACGTAG
1 TACAAGTATGAAACCATTTATATAATACAACAGAAAGACAAAACAGGTTTATCATGATAACGTAG
* *
12593498 TACGTAACACCTTTTTTTATGTCAACCATTTAAGTTATAAGTATAAAACTATTTATATTATGCAA
66 TACGTAACACCCTTTTTTATGTCAACC---T-AGTTATAAGTATAAAACCATTTATATTATGCAA
*
12593563 AAGTAAGACAAAACATGTTCATGATAACGTACTAGGCACTGCATTTTTTTTAATGTTAACTGTTT
127 AAGTAAGACAAAACATGTTCATGATAACGTACTAGGCACTGCA-TTTTTTTAATGTTAACTATTT
* *
12593628 TAAATTATAAGTATGAAGCCGTTTATATTATGCAAAAGTAAGATAAAATAGGTTTTTCATGATAA
191 TAAATTATAAGTATGAAGCCGTTTATATTATGCAAAAGTAAGACAAAATAGATTTTTCATGATAA
* * *
12593693 CATAGTAGGTAATGCCTTTTTTATGCAAAAGTATCGATCAATATAGATTAAGTATCGATATTTTA
256 CATAGTAGGTAATGCCTTTTTTATACAAAAGTATCGATCAATATAGATTAAATATCAATATTTTA
* * * *
12593758 TATTTCAAGTTGTTTTCTTAAATAATTTGTCTTGATTCACTCATAATTAATATCGATACTTCTCC
321 TATTTCAAATTGTTTTCTTAAATAATTTATCTTGATTCACTCATAATAAATACCGATACTTCTCC
*
12593823 ATAAAAATCGATACATTTCGAATTAAAAATATTAACATAAAATATCACAACATATTTCTTAGTAA
386 ACAAAAATCGATACATTTCGAATTAAAAATATTAACATAAAATATCACAACATATTTCTTAGTAA
* *
12593888 ACTATGACATTCTTAGGCGCAACTTTATTAAAAAAATATTAATATTACATTACAAATCATAACCT
451 ACTATGACATTCTTAGGCGCAACTTTATTAAAAAAATATTAACATTACATTACAAATCACAACCT
*
12593953 ACTTTCTCAGTGAAACATAACATTTTTTGGTGCAACCTATTTTATTACTAAAAATATTAAAATTA
516 ACTTTCTCAGTGAAACATAACATTTTTTGGCGCAACCTATTTTATTACTAAAAATATTAAAATTA
* * * * * *
12594018 CAAATCGCGA-CATGTTTATTAGTGAACCATGACATTATTGGAAGCAACCGTATTTTTTTATATA
581 CAAATCGCAATC-TGTTTATTAGTGAACCATGACATTATTAGAAGAAACCATA-TTTCTTACATA
12594082 TATTCATAACATTTTCAGCTTTTAACTTATTTTCTTATAGTGGGAAAATCAATGCCACATTAGCT
644 TATTCATAACATTTTCAGCTTTTAACTTATTTTCTTATAGTGGGAAAATCAATGCCACATTAGCT
*
12594147 TAAACTCTGATAACATTTTACGA
709 TAAACTCTAATAACATTTTACGA
* ** *
12594170 TACAAGTATGAAACCGTTTATATAATACAACAGTGAGACAAAACATGTTTATCATGATAACGTAG
1 TACAAGTATGAAACCATTTATATAATACAACAGAAAGACAAAACAGGTTTATCATGATAACGTAG
* * * * * *
12594235 TAGGTAGCGCCCTTTTTTCTGTCAACC-A-TTATAAGTATGAAACCGTTTATATTATGCAAAAGT
66 TACGTAACACCCTTTTTTATGTCAACCTAGTTATAAGTATAAAACCATTTATATTATGCAAAAGT
* *
12594298 AAGACAAAACATGTTGCACATGATAACGTACTATGTACTGTC-TTTTTTTAATGTTAACTATTTT
131 AAGACAAAACATGTT---CATGATAACGTACTAGGCACTG-CATTTTTTTAATGTTAACTATTTT
* *
12594362 AATTTATAAGTATGAAGCCGTTTATATTATGCCAAAGTAAGACAAAATAGATTTTTCATGATAAC
192 AAATTATAAGTATGAAGCCGTTTATATTATGCAAAAGTAAGACAAAATAGATTTTTCATGATAAC
**
12594427 ATA-TAGGTAATGTTTTTTTTATACAAAAGTATCGATCAATATAGATTAAATATCAATATTTTAT
257 ATAGTAGGTAATGCCTTTTTTATACAAAAGTATCGATCAATATAGATTAAATATCAATATTTTAT
*
12594491 CTTTCAAATT-TCTTTCTTAAATAATTTATCTTGATTCACTCATAATAAAAATACCGATACTTCT
322 ATTTCAAATTGT-TTTCTTAAATAATTTATCTTGATTCACTCATAAT--AAATACCGATACTTCT
* * *
12594555 CCACAAAAATCTATAC-TTTCGAATTAAAAAATATTAACATAAAATATCACAGCCTATTTCTTAG
384 CCACAAAAATCGATACATTTCGAATT-AAAAATATTAACATAAAATATCACAACATATTTCTTAG
* * * *
12594619 TAAATTATGACATTCTTAGGTGCAACTTTATTAAAAAAATATTAACATTACATTACAGATCGCAA
448 TAAACTATGACATTCTTAGGCGCAACTTTATTAAAAAAATATTAACATTACATTACAAATCACAA
* * *
12594684 CTTACTTTCTCAGTGAACCATAACATTTTTTGGCGCAACCTATTTTATTACTAAAAATATTAACA
513 CCTACTTTCTCAGTGAAACATAACATTTTTTGGCGCAACCTATTTTATTACTAAAAATATTAAAA
* *
12594749 TTACAAATCGCAATCTGTTTCTTAGTGAACCATGACATTATTAGACGAAACCATATTTCTTACAT
578 TTACAAATCGCAATCTGTTTATTAGTGAACCATGACATTATTAGAAGAAACCATATTTCTTACAT
* *
12594814 ATATTCATAACATTTTCAGTTTTTAACTTATTTTCTTATAGTGGGAAAATCAATTCCACATTAGC
643 ATATTCATAACATTTTCAGCTTTTAACTTATTTTCTTATAGTGGGAAAATCAATGCCACATTAGC
12594879 TTAAACTCTAATAACATTTTA
708 TTAAACTCTAATAACATTTTA
12594900 TGCGCAACTA
Statistics
Matches: 664, Mismatches: 57, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
731 48 0.07
732 98 0.15
733 185 0.28
734 251 0.38
735 2 0.00
737 80 0.12
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (731 bp):
TACAAGTATGAAACCATTTATATAATACAACAGAAAGACAAAACAGGTTTATCATGATAACGTAG
TACGTAACACCCTTTTTTATGTCAACCTAGTTATAAGTATAAAACCATTTATATTATGCAAAAGT
AAGACAAAACATGTTCATGATAACGTACTAGGCACTGCATTTTTTTAATGTTAACTATTTTAAAT
TATAAGTATGAAGCCGTTTATATTATGCAAAAGTAAGACAAAATAGATTTTTCATGATAACATAG
TAGGTAATGCCTTTTTTATACAAAAGTATCGATCAATATAGATTAAATATCAATATTTTATATTT
CAAATTGTTTTCTTAAATAATTTATCTTGATTCACTCATAATAAATACCGATACTTCTCCACAAA
AATCGATACATTTCGAATTAAAAATATTAACATAAAATATCACAACATATTTCTTAGTAAACTAT
GACATTCTTAGGCGCAACTTTATTAAAAAAATATTAACATTACATTACAAATCACAACCTACTTT
CTCAGTGAAACATAACATTTTTTGGCGCAACCTATTTTATTACTAAAAATATTAAAATTACAAAT
CGCAATCTGTTTATTAGTGAACCATGACATTATTAGAAGAAACCATATTTCTTACATATATTCAT
AACATTTTCAGCTTTTAACTTATTTTCTTATAGTGGGAAAATCAATGCCACATTAGCTTAAACTC
TAATAACATTTTACGA
Found at i:12598607 original size:46 final size:46
Alignment explanation
Indices: 12598535--12598626 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
12598525 CAAATATAGC
12598535 CTTAGAGATATGTACTCACTAAATAATTGAAGATAAAATTTATACA
1 CTTAGAGATATGTACTCACTAAATAATTGAAGATAAAATTTATACA
* *
12598581 CTTATAGATATGTACTTACTAAATAATTGAAGATAAAATTTATACA
1 CTTAGAGATATGTACTCACTAAATAATTGAAGATAAAATTTATACA
12598627 TGTGTATTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (46 bp):
CTTAGAGATATGTACTCACTAAATAATTGAAGATAAAATTTATACA
Found at i:12600526 original size:42 final size:41
Alignment explanation
Indices: 12600310--12600527 Score: 104
Period size: 42 Copynumber: 5.2 Consensus size: 41
12600300 AAGAACATGG
*
12600310 CACAAAGAACTTGCCTGAGCCTGACGAGACTGACCAAAAGGT
1 CACAAAGAACTTGCCTGAGCCTGAGGAGACTGACC-AAAGGT
** * *
12600352 CACAAAGAGGTTGTCTGAGTCT-ATGGAGACTGACCAAAGTGT
1 CACAAAGAACTTGCCTGAGCCTGA-GGAGACTGACCAAAG-GT
** * * * * * ***
12600394 CGGAAA-CAGTGTGGCTAAGCC-GATGAGGACTGACCGATTTGT
1 CACAAAGAACT-TGCCTGAGCCTGAGGA-GACTGACC-AAAGGT
* * * ** * * *
12600436 CTCAAAAAACGTGGTTAAGCCAATG-GG-GACCGACCAATGTGT
1 CACAAAGAACTTGCCTGAGCC--TGAGGAGACTGACCAAAG-GT
12600478 CACAAAGAACTTGCCTGAGCCTGAGGAGACTGACCAAAAGGT
1 CACAAAGAACTTGCCTGAGCCTGAGGAGACTGACC-AAAGGT
12600520 CACAAAGA
1 CACAAAGA
12600528 GGTTGTCTGT
Statistics
Matches: 128, Mismatches: 34, Indels: 28
0.67 0.18 0.15
Matches are distributed among these distances:
40 2 0.02
41 13 0.10
42 106 0.83
43 5 0.04
44 1 0.01
45 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (41 bp):
CACAAAGAACTTGCCTGAGCCTGAGGAGACTGACCAAAGGT
Found at i:12608206 original size:60 final size:63
Alignment explanation
Indices: 12608085--12608207 Score: 171
Period size: 60 Copynumber: 2.0 Consensus size: 63
12608075 TAAGAAGGTC
* * * * *
12608085 ACACATTTGCAAAAGGGAAAAGCTATATTCTCTTCTTTTTTTCTTCACCCAAGCTTGTCTTCT
1 ACACAGTTGCAAAAGGAAAAAACTATATTCTCTTCTTTTTTTCTTCACCCAAACTTATCTTCT
*
12608148 ACACAGTTG-AAAAGGAAAAAACTATCTTCTC-T-TTTTTTTCTTCACCCAAACTTATCTTCT
1 ACACAGTTGCAAAAGGAAAAAACTATATTCTCTTCTTTTTTTCTTCACCCAAACTTATCTTCT
12608208 CCTATTCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
60 26 0.48
61 1 0.02
62 19 0.35
63 8 0.15
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (63 bp):
ACACAGTTGCAAAAGGAAAAAACTATATTCTCTTCTTTTTTTCTTCACCCAAACTTATCTTCT
Found at i:12610576 original size:20 final size:19
Alignment explanation
Indices: 12610548--12610609 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
12610538 GAATCCTTGA
12610548 TTTTTTTTGTTGTTT-TTCT
1 TTTTTTTTGTT-TTTCTTCT
*
12610567 TTTCTTTTTGTTTTTCCTCT
1 TTT-TTTTTGTTTTTCTTCT
12610587 TTTTCTTTTGTTTTTCTTCT
1 TTTT-TTTTGTTTTTCTTCT
12610607 TTT
1 TTT
12610610 GGCACTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (19 bp):
TTTTTTTTGTTTTTCTTCT
Found at i:12611489 original size:16 final size:17
Alignment explanation
Indices: 12611449--12611499 Score: 68
Period size: 16 Copynumber: 3.0 Consensus size: 17
12611439 ACATAGAAAT
*
12611449 TTGTCCCGAATGACCAC
1 TTGTCCCGAAGGACCAC
*
12611466 TATGTCCCGAAGGATCA-
1 T-TGTCCCGAAGGACCAC
12611483 TTGTCCCGAAGGACCAC
1 TTGTCCCGAAGGACCAC
12611500 ATAAAACACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 14 0.48
17 2 0.07
18 13 0.45
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (17 bp):
TTGTCCCGAAGGACCAC
Found at i:12614433 original size:19 final size:19
Alignment explanation
Indices: 12614409--12614450 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12614399 ATATCTTTTC
* *
12614409 TTTCATACTCCCTTACTCT
1 TTTCATACTACCTTACACT
*
12614428 TTTCATATTACCTTACACT
1 TTTCATACTACCTTACACT
12614447 TTTC
1 TTTC
12614451 TATCAATCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTCATACTACCTTACACT
Found at i:12616098 original size:28 final size:28
Alignment explanation
Indices: 12616055--12616127 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
12616045 AATGACCACT
*
12616055 ATGTCCCGAAGGACCACATAGAACTCAC
1 ATGTCCCGAAGGACCACATAGAACACAC
* *
12616083 ATGTCCCGAAGAACCACATAGAACACAT
1 ATGTCCCGAAGGACCACATAGAACACAC
12616111 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
12616128 GTAAAACCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.37, C:0.32, G:0.18, T:0.14
Consensus pattern (28 bp):
ATGTCCCGAAGGACCACATAGAACACAC
Found at i:12619256 original size:22 final size:22
Alignment explanation
Indices: 12619228--12619271 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12619218 GGTAGTAAAC
**
12619228 TTATTACTCTTTGTATATATAT
1 TTATTACTCTTTACATATATAT
12619250 TTATTACTCTTTACATATATAT
1 TTATTACTCTTTACATATATAT
12619272 CGCTATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATTACTCTTTACATATATAT
Found at i:12620357 original size:46 final size:46
Alignment explanation
Indices: 12620302--12620762 Score: 787
Period size: 46 Copynumber: 10.0 Consensus size: 46
12620292 TTTAGTTGTG
*
12620302 GCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * *
12620348 GCATTCTTTCATGCATTTTAGTCATGGCATCCTTTCAAGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
12620394 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
*
12620440 GCATCCTTTCATGCATTTTAGTTATGGCATCCCTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
12620486 GTATCATTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
12620532 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
12620578 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
12620624 GCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATTCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * *
12620670 GCATCTTTTCATGCATTTTAGTTATGTCATCCATTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * *
12620716 GCATCATTTCATGCATTTTAGTTATGGAATCCTTTAATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
12620762 G
1 G
12620763 ATACCATATT
Statistics
Matches: 391, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 391 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
Found at i:12623891 original size:20 final size:20
Alignment explanation
Indices: 12623866--12623907 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12623856 AGGTTAGTTG
12623866 TTTTATTTT-AAATTAATTAT
1 TTTTATTTTGAAA-TAATTAT
*
12623886 TTTTATTTTGTAATAATTAT
1 TTTTATTTTGAAATAATTAT
12623906 TT
1 TT
12623908 ACATAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTATTTTGAAATAATTAT
Found at i:12625390 original size:33 final size:33
Alignment explanation
Indices: 12625353--12625434 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
12625343 AATAGCATTC
*
12625353 TTTGGTGAAA-AGACATGACTTGAAATTACACCT
1 TTTGGT-AAAGAGACATGACTTGAAAATACACCT
***
12625386 TTTGGTAAAGAGGTGTGACTTGAAAATACACCT
1 TTTGGTAAAGAGACATGACTTGAAAATACACCT
* *
12625419 CTTGATAAAGAGACAT
1 TTTGGTAAAGAGACAT
12625435 CTATTAGTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 3 0.08
33 36 0.92
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (33 bp):
TTTGGTAAAGAGACATGACTTGAAAATACACCT
Found at i:12627405 original size:3 final size:3
Alignment explanation
Indices: 12627397--12627440 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
12627387 ATATTAACGA
* * * *
12627397 AAT AAT AAT AAT ACT AAT ACT ACT AAT AAT AAT ATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12627441 AGAAGCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Done.