Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold160
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: 1852349
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 51288 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:1168832 original size:27 final size:26
Alignment explanation
Indices: 1168789--1168851 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
1168779 CTCTCGAATT
*
1168789 CAGTAAACAAAGGGTAGTCCTCCAAGA
1 CAGTAAAC-AAGGGTAGTCCACCAAGA
* *
1168816 CAGTAAACACGGAGTAGTCCACCTAGA
1 CAGTAAACAAGG-GTAGTCCACCAAGA
1168843 CAGTAAACA
1 CAGTAAACA
1168852 TTGGTTCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (26 bp):
CAGTAAACAAGGGTAGTCCACCAAGA
Found at i:1178085 original size:28 final size:29
Alignment explanation
Indices: 1178024--1178085 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
1178014 AATAAAATAA
* *
1178024 ATGTCTGATTTTATTATTAAGTGTTTAAT
1 ATGTCTGATTTTAATATCAAGTGTTTAAT
* * *
1178053 GTGTCTTATTTTAATA-CAAGTTTTTAAT
1 ATGTCTGATTTTAATATCAAGTGTTTAAT
1178081 ATGTC
1 ATGTC
1178086 ATAACCTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.53
Consensus pattern (29 bp):
ATGTCTGATTTTAATATCAAGTGTTTAAT
Found at i:1181244 original size:18 final size:18
Alignment explanation
Indices: 1181221--1181258 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1181211 ATTCGGGTAA
1181221 AACCGAAAAAATTCGGTT
1 AACCGAAAAAATTCGGTT
**
1181239 AACCGACCAAATTCGGTT
1 AACCGAAAAAATTCGGTT
1181257 AA
1 AA
1181259 TCGGTCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (18 bp):
AACCGAAAAAATTCGGTT
Found at i:1181466 original size:38 final size:39
Alignment explanation
Indices: 1181406--1181483 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 39
1181396 ATCCAACCCA
*
1181406 ACCCAATTACCCAACCTAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCTAATAAAAATAAAACTAAAGTCT
1181445 ACCCAATTA-CCAA-CTCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCT-AATAAAAATAAAACTAAAGTCT
1181483 A
1 A
1181484 ACTCTAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 2 0.05
38 26 0.70
39 9 0.24
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.21
Consensus pattern (39 bp):
ACCCAATTACCCAACCTAATAAAAATAAAACTAAAGTCT
Found at i:1181634 original size:17 final size:17
Alignment explanation
Indices: 1181614--1181679 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
1181604 TAATTTCAAG
1181614 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
1181631 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
1181649 AGACTTATGTAATGTTTTT
1 A-A-TTATGTAATGTTTTT
*
1181668 AATTAAGTAATG
1 AATTATGTAATG
1181680 ATTTNNNNNN
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 20 0.54
18 4 0.11
19 4 0.11
20 9 0.24
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:1181657 original size:37 final size:37
Alignment explanation
Indices: 1181611--1181682 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
1181601 TGTTAATTTC
* *
1181611 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATGTTTTTAATTAAGTAATGATTCA
*
1181648 AAGACTTATGTAATGTTTTTAATTAAGTAATGATT
1 AAGAATTATGTAATGTTTTTAATTAAGTAATGATT
1181683 TNNNNNNNNN
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (37 bp):
AAGAATTATGTAATGTTTTTAATTAAGTAATGATTCA
Found at i:1182632 original size:8 final size:8
Alignment explanation
Indices: 1182619--1182650 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
1182609 CCAAATTATT
1182619 TTTTTTTC
1 TTTTTTTC
1182627 TTTTTTTC
1 TTTTTTTC
1182635 TTTTTTTC
1 TTTTTTTC
1182643 TCTTTTTT
1 T-TTTTTT
1182651 TATGCTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.74
9 6 0.26
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1182640 original size:18 final size:18
Alignment explanation
Indices: 1182617--1182651 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1182607 CCCCAAATTA
*
1182617 TTTTTTTTTCTTTTTTTC
1 TTTTTTTCTCTTTTTTTC
1182635 TTTTTTTCTCTTTTTTT
1 TTTTTTTCTCTTTTTTT
1182652 ATGCTTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTCTCTTTTTTTC
Found at i:1185183 original size:18 final size:18
Alignment explanation
Indices: 1185156--1185192 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1185146 AAGAGTTTGC
* *
1185156 TGTTGGAAATCAAGAACA
1 TGTTGAAAATCAAAAACA
1185174 TGTTGAAAATCAAAAACA
1 TGTTGAAAATCAAAAACA
1185192 T
1 T
1185193 TAGCTGCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (18 bp):
TGTTGAAAATCAAAAACA
Found at i:1188383 original size:27 final size:28
Alignment explanation
Indices: 1188315--1188388 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
1188305 TTTTAATATA
* *
1188315 GTTTTTAATATGTCATAACCTAATACAT
1 GTTTTTATTATGTCCTAACCTAATACAT
*
1188343 GTTATTAATT-TGTCCTAGA-CTAA-ACAT
1 GTT-TTTATTATGTCCTA-ACCTAATACAT
1188370 GTTTTTATTATGTCCTAAC
1 GTTTTTATTATGTCCTAAC
1188389 TGTTGCCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 6 0.16
27 14 0.37
28 13 0.34
29 5 0.13
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (28 bp):
GTTTTTATTATGTCCTAACCTAATACAT
Found at i:1204063 original size:48 final size:48
Alignment explanation
Indices: 1204000--1204126 Score: 118
Period size: 48 Copynumber: 2.7 Consensus size: 48
1203990 TATTTTTAAA
* * *
1204000 TTTTTACTAATTTTTTTATAATTTTTCAATTTTT-GATAATGTTTGATAT
1 TTTTTAC-ATTTTTTTTATAATTTTTC-ATTTTTAAATAATGTTTGAAAT
* * * *
1204049 TTTTTACATTTTTTTGTA-AATTTATCATTTTTAAATTATTTTTTAAAT
1 TTTTTACATTTTTTT-TATAATTTTTCATTTTTAAATAATGTTTGAAAT
* *
1204097 TTTTTA-ATATTTTTAATAATTTTT-ATTTTT
1 TTTTTACATTTTTTTTATAATTTTTCATTTTT
1204127 TAGAATTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
46 7 0.11
47 19 0.29
48 30 0.46
49 9 0.14
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (48 bp):
TTTTTACATTTTTTTTATAATTTTTCATTTTTAAATAATGTTTGAAAT
Found at i:1204116 original size:12 final size:10
Alignment explanation
Indices: 1204075--1204121 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
1204065 TAAATTTATC
*
1204075 ATTTTTAAATT
1 ATTTTTTAA-T
1204086 ATTTTTTAA-
1 ATTTTTTAAT
1204095 ATTTTTTAAT
1 ATTTTTTAAT
1204105 A-TTTTTAAT
1 ATTTTTTAAT
*
1204114 AATTTTTA
1 ATTTTTTA
1204122 TTTTTTAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
9 18 0.55
10 7 0.21
11 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTTAAT
Found at i:1204121 original size:10 final size:10
Alignment explanation
Indices: 1204088--1204185 Score: 50
Period size: 9 Copynumber: 10.5 Consensus size: 10
1204078 TTTAAATTAT
*
1204088 TTTTTAA-AT
1 TTTTTAATAA
1204097 TTTTTAAT-A
1 TTTTTAATAA
1204106 TTTTTAATAA
1 TTTTTAATAA
1204116 TTTTT-AT--
1 TTTTTAATAA
*
1204123 TTTTT-AGAA
1 TTTTTAATAA
* *
1204132 TTTATAAAAA
1 TTTTTAATAA
*
1204142 TTTCT-ATAA
1 TTTTTAATAA
* *
1204151 TTTCTAAATAT
1 TTT-TTAATAA
*
1204162 TTTTTTAT-A
1 TTTTTAATAA
*
1204171 TTTTTAATAC
1 TTTTTAATAA
1204181 TTTTT
1 TTTTT
1204186 TGACTAGTCA
Statistics
Matches: 67, Mismatches: 14, Indels: 15
0.70 0.15 0.16
Matches are distributed among these distances:
7 6 0.09
9 34 0.51
10 21 0.31
11 6 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:1204121 original size:19 final size:18
Alignment explanation
Indices: 1204007--1204185 Score: 80
Period size: 19 Copynumber: 9.6 Consensus size: 18
1203997 AAATTTTTAC
*
1204007 TAATTTTTTTATAATTTT
1 TAATATTTTTATAATTTT
* *
1204025 TCAAT-TTTTGATAATGTT
1 T-AATATTTTTATAATTTT
*
1204043 TGATATTTTT-TACATTTTT
1 TAATATTTTTATA-A-TTTT
** ** *
1204062 TTGTAAATTTATCATTTT
1 TAATATTTTTATAATTTT
1204080 TAAATTATTTTT-TAAATTTTT
1 T-AA-TATTTTTAT-AA-TTTT
1204101 TAATATTTTTAATAATTTT
1 TAATATTTTT-ATAATTTT
*
1204120 T-AT-TTTTTAGAATTTAT
1 TAATATTTTTATAATTT-T
* * *
1204137 AAAAATTTCTATAATTTCT
1 TAATATTTTTATAATTT-T
* *
1204156 AAATATTTTTTTATATTTT
1 TAATATTTTTATA-ATTTT
1204175 TAATACTTTTT
1 TAATA-TTTTT
1204186 TGACTAGTCA
Statistics
Matches: 120, Mismatches: 25, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
16 6 0.05
17 10 0.08
18 26 0.22
19 52 0.43
20 20 0.17
21 6 0.05
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
TAATATTTTTATAATTTT
Found at i:1204134 original size:26 final size:26
Alignment explanation
Indices: 1204095--1204144 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1204085 TATTTTTTAA
* *
1204095 ATTTTTTAATATTTTTAATAATTTTT
1 ATTTTTTAATATTTATAAAAATTTTT
1204121 ATTTTTTAGA-ATTTATAAAAATTT
1 ATTTTTTA-ATATTTATAAAAATTT
1204145 CTATAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTTTTAATATTTATAAAAATTTTT
Found at i:1204151 original size:35 final size:35
Alignment explanation
Indices: 1204084--1204153 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
1204074 CATTTTTAAA
* * * *
1204084 TTATTTTTTAAATTTTTTAATATTTTTAATAATTT
1 TTATTTTTTAAATTTATAAAAATTTCTAATAATTT
1204119 TTATTTTTTAGAATTTATAAAAATTTCT-ATAATTT
1 TTATTTTTTA-AATTTATAAAAATTTCTAATAATTT
1204154 CTAAATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (35 bp):
TTATTTTTTAAATTTATAAAAATTTCTAATAATTT
Found at i:1204908 original size:23 final size:23
Alignment explanation
Indices: 1204882--1204933 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1204872 TAGAGATAAA
**
1204882 TTTAACAC-TTAATGTTTATATTT
1 TTTAACACTTTAACATTTAT-TTT
*
1204905 TTTATCACTTTAACATTTATTTT
1 TTTAACACTTTAACATTTATTTT
1204928 TTTAAC
1 TTTAAC
1204934 TAAATTTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTAACACTTTAACATTTATTTT
Found at i:1205334 original size:24 final size:25
Alignment explanation
Indices: 1205274--1205328 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
1205264 CGAATTAGCT
1205274 AAAAAAAAATAAGTATCAAACCGAC
1 AAAAAAAAATAAGTATCAAACCGAC
1205299 AAAAAAAAATAAGTATCAAACCGAC
1 AAAAAAAAATAAGTATCAAACCGAC
1205324 AAAAA
1 AAAAA
1205329 TTATAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.67, C:0.15, G:0.07, T:0.11
Consensus pattern (25 bp):
AAAAAAAAATAAGTATCAAACCGAC
Found at i:1214903 original size:11 final size:13
Alignment explanation
Indices: 1214887--1214918 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1214877 ATTTCACAGA
1214887 AAAATTTCG-T-G
1 AAAATTTCGTTCG
1214898 AAAATTTCGTTCG
1 AAAATTTCGTTCG
1214911 AAAATTTC
1 AAAATTTC
1214919 AACGTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 1 0.05
13 9 0.47
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (13 bp):
AAAATTTCGTTCG
Found at i:1218818 original size:18 final size:19
Alignment explanation
Indices: 1218788--1218824 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1218778 ATTAGTTTTA
*
1218788 AAAAAAATAAAATGTACAT
1 AAAAAAATAAAATATACAT
1218807 AAAAAAAT-AAATATACAT
1 AAAAAAATAAAATATACAT
1218825 GTATATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAAAAATAAAATATACAT
Found at i:1220541 original size:45 final size:45
Alignment explanation
Indices: 1220484--1220650 Score: 169
Period size: 45 Copynumber: 3.7 Consensus size: 45
1220474 TTGTTTATTT
* * *
1220484 AGTCTGCC-CCACTGCAATTTCAGGGGGATAAGACTTGCTTTCTTG
1 AGTCT-CCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTG
*
1220529 AGTCTCCTCCACTGCAACTTCAGGGAAATAAGACTCGCTTTCTTG
1 AGTCTCCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTG
* * * * * *
1220574 GGCCTGCTCCACTGCAACTTCAGGGAGATAAGAC-CTACTTAC-TC
1 AGTCTCCTCCACTGCAACTTCAGGGAGATAAGACTC-GCTTTCTTG
* * * *
1220618 AATCTACTCCTCTGTAACTTCAGGGAGATAAGA
1 AGTCTCCTCCACTGCAACTTCAGGGAGATAAGA
1220651 ATAGATGTGA
Statistics
Matches: 103, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
44 31 0.30
45 72 0.70
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (45 bp):
AGTCTCCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTG
Found at i:1221280 original size:267 final size:267
Alignment explanation
Indices: 1220805--1221329 Score: 755
Period size: 267 Copynumber: 2.0 Consensus size: 267
1220795 TTTAATCGCA
* *
1220805 ATGTTAGGGAAATAAGATTCGCCGTCGTAGCTTCAATCAGTTCCACTACACCACCAGGGAAGTAA
1 ATGTTAGGGAAACAAGATTCACCGTCGTAGCTTCAATCAGTTCCACTACACCACCAGGGAAGTAA
* * * * *
1220870 GATTCGTCGTTGCAGCTTTAATCTGCTCCACTGTAATGCCAATGAGATAGGGTTCGCTACCCACA
66 GATTCGCCGTTGCAGCTTTAATATGCTCCACTGTAATGCCAAAGAGATAGGATTCACTACCCACA
* *
1220935 GCTTCAATCCGCTCTATTTCATCTAATCCAAGCCTTAACGCCAGGGAGATAAGATTCGCCGTCGT
131 GCTTCAATCCGCTCCATTTCAGCTAATCCAAGCCTTAACGCCAGGGAGATAAGATTCGCCGTCGT
* * * * *
1221000 GGCTTCAATCTGCTCCGCTACAATGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTTTTA
196 GACTTCAATCTGCTCCGCTACAACGCCAAGGAAATAAGATTCCCCGTTGTGACTTCAATCTTTTA
1221065 AATTGCC
261 AATTGCC
* ** * *
1221072 ATGTTAGGGAAACGAGATTCACCGTCGTAGCTTCAATTTGTTCCACTACACCGCCAGGGGAGTAA
1 ATGTTAGGGAAACAAGATTCACCGTCGTAGCTTCAATCAGTTCCACTACACCACCAGGGAAGTAA
* ** * * * *
1221137 GATTTGCCGTTGTGGCTTTAATATTCTCCAGTGTAATGTCAAAGAGATAGGATTCACTGCCCACA
66 GATTCGCCGTTGCAGCTTTAATATGCTCCACTGTAATGCCAAAGAGATAGGATTCACTACCCACA
* * *
1221202 GCTTTAATCCGCTCCACTTT-AGCTAATCCAAGCCTTAACGCCAGGGAGATTAGATTCGCTGTCG
131 GCTTCAATCCGCTCCA-TTTCAGCTAATCCAAGCCTTAACGCCAGGGAGATAAGATTCGCCGTCG
* *
1221266 TGACTTCAATCTGCTCTGCTACAACGCCAAGGTAATAAGATTCCCCGTTGTGACTTCAATCTTT
195 TGACTTCAATCTGCTCCGCTACAACGCCAAGGAAATAAGATTCCCCGTTGTGACTTCAATCTTT
1221330 GCAACATCAT
Statistics
Matches: 226, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
267 223 0.99
268 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (267 bp):
ATGTTAGGGAAACAAGATTCACCGTCGTAGCTTCAATCAGTTCCACTACACCACCAGGGAAGTAA
GATTCGCCGTTGCAGCTTTAATATGCTCCACTGTAATGCCAAAGAGATAGGATTCACTACCCACA
GCTTCAATCCGCTCCATTTCAGCTAATCCAAGCCTTAACGCCAGGGAGATAAGATTCGCCGTCGT
GACTTCAATCTGCTCCGCTACAACGCCAAGGAAATAAGATTCCCCGTTGTGACTTCAATCTTTTA
AATTGCC
Found at i:1222254 original size:25 final size:26
Alignment explanation
Indices: 1222226--1222274 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1222216 AGTGTCTTGA
1222226 AAAGAAAAAAGTATT-CAAGAACAGC
1 AAAGAAAAAAGTATTACAAGAACAGC
**
1222251 AAAGAATGAAGTATTACAAGAACA
1 AAAGAAAAAAGTATTACAAGAACA
1222275 AAAAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.14
Consensus pattern (26 bp):
AAAGAAAAAAGTATTACAAGAACAGC
Found at i:1227580 original size:52 final size:49
Alignment explanation
Indices: 1227476--1227592 Score: 139
Period size: 52 Copynumber: 2.3 Consensus size: 49
1227466 AAATATAAAC
* *
1227476 TCATTTTCGAAAT-TTT-ATTTTTCATTTTTATTTTGGAGAAAATCACAT
1 TCATTTTC-AAATGTTTCATTTTTCATTTTTATTTTGGAGAAAACCACAA
**
1227524 TCATTTTCAAATGATTTCATTTCTTCATTTTTCATTTTGGAGAAAACCGTAA
1 TCATTTTCAAATG-TTTCATTT-TTCATTTTT-ATTTTGGAGAAAACCACAA
*
1227576 TCATTCTCAAATGTTTC
1 TCATTTTCAAATGTTTC
1227593 CTATTTCTCG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
47 4 0.07
48 8 0.14
49 3 0.05
50 4 0.07
51 13 0.22
52 27 0.46
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.49
Consensus pattern (49 bp):
TCATTTTCAAATGTTTCATTTTTCATTTTTATTTTGGAGAAAACCACAA
Found at i:1228934 original size:25 final size:27
Alignment explanation
Indices: 1228906--1228960 Score: 96
Period size: 25 Copynumber: 2.1 Consensus size: 27
1228896 AAAACTCTTC
1228906 TAAAAGAAAACTT-AAGAGAATTTT-T
1 TAAAAGAAAACTTAAAGAGAATTTTAT
1228931 TAAAAGAAAACTTAAAGAGAATTTTAT
1 TAAAAGAAAACTTAAAGAGAATTTTAT
1228958 TAA
1 TAA
1228961 CTCAAAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 13 0.46
26 11 0.39
27 4 0.14
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.31
Consensus pattern (27 bp):
TAAAAGAAAACTTAAAGAGAATTTTAT
Found at i:1230801 original size:31 final size:31
Alignment explanation
Indices: 1230757--1230824 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1230747 TTTTGTTTTG
*
1230757 GTCACTGAACTATTCGAAAGTTTTCATTTAA
1 GTCACTGAACTATTCAAAAGTTTTCATTTAA
* * * *
1230788 GTCATTGAGCTATTCAAAATTTTTTATTTAA
1 GTCACTGAACTATTCAAAAGTTTTCATTTAA
1230819 GTCACT
1 GTCACT
1230825 AGTTTGTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGTTTTCATTTAA
Found at i:1235049 original size:5 final size:5
Alignment explanation
Indices: 1235041--1235081 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
1235031 ACTAAATATT
* *
1235041 ATAAA ATAAA CTGAA AT--A ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1235082 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
3 3 0.10
5 28 0.90
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:1235064 original size:18 final size:18
Alignment explanation
Indices: 1235028--1235073 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1235018 CCTAATACTT
1235028 TAAACTAAATATTATAAAA
1 TAAACTAAATA-TATAAAA
1235047 TAAACTGAAATA-ATAAAA
1 TAAACT-AAATATATAAAA
*
1235065 TAAAATAAA
1 TAAACTAAA
1235074 ATAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 11 0.44
19 6 0.24
20 5 0.20
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
TAAACTAAATATATAAAA
Found at i:1235075 original size:18 final size:18
Alignment explanation
Indices: 1235041--1235077 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1235031 ACTAAATATT
* *
1235041 ATAAAATAAACTGAAATA
1 ATAAAATAAAATAAAATA
1235059 ATAAAATAAAATAAAATA
1 ATAAAATAAAATAAAATA
1235077 A
1 A
1235078 AATATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
ATAAAATAAAATAAAATA
Found at i:1238089 original size:282 final size:282
Alignment explanation
Indices: 1237583--1238970 Score: 1814
Period size: 282 Copynumber: 4.9 Consensus size: 282
1237573 CATTGTTTAC
* * ** * *
1237583 ACCTGAAGAATGTGGCAGCTTAGCTGGATCAGATTCCAGG-CCTTGTTGGACAGCATTATGT-AA
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTCC-GGAAGTTGTTGAACAGC-TT-TGTCTA
* * *** *
1237646 T-TCCTTCAGAGATCTTGCCTCCACAACAGGTAATTTTGATTTGTTATCTGTGTCATCCTGTG--
63 TATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCATGAT-CTG-GCA
* * * ** *
1237708 GTTCCACAATCATACTTGGAACAATTACTTCCTCAACATC-AGCTCCTTCATGCAGTTGCTTAAA
126 GTTTCTCAATCATACTCGGAACAATTACTTCCTCAATGTCGA-CTCCTTCATGAAGTTGCTTAAA
1237772 AGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCT
190 AGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCT
*
1237837 TCATATCTTTTGATGGTTCATTCCTTGA
255 TCATATCTTTTGATGATTCATTCCTTGA
* * * *
1237865 AACTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTTGAATAGCTTTGTCTATGT
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTCCGGAAGTTGTTGAACAGCTTTGTCTATAT
* * *
1237930 CCTCCAGAGATCTTGCCTCGACAACACGTAATTTTGATTTGTTATCTCCATGGTCTGGCAGTTTC
66 CCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
* *
1237995 TCAATCATACTCGGAACAATTACTTCCTCAATGTCCACTCCGTCATGAAGTTGCTTAAAAGCCAA
131 TCAATCATACTCGGAACAATTACTTCCTCAATGTCGACTCCTTCATGAAGTTGCTTAAAAGCCAA
* * **
1238060 ATCAATATCTTCGGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCGGTCTTCGCAT
196 ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCATAT
*
1238125 CTTTTGATGATTCATTCTTTGA
261 CTTTTGATGATTCATTCCTTGA
* ** ** * * * * * * *
1238147 GCCTG-AGCCTGAAG-A-AT-ATGCTGGATTAGGTTTCGCAAGTTGTTGAATAGATTTGTCTAAA
1 ACCTGAAGAATGTGGCAGCTCA-GCTGGATTAGATTCCGGAAGTTGTTGAACAGCTTTGTCTATA
*
1238208 TCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCAAGATCTGGCAGTTT
65 TCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTT
** *
1238273 CTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAAGTTGCTTAAAAGCCA
130 CTCAATCATACTCGGAACAATTACTTCCTCAATGTCGACTCCTTCATGAAGTTGCTTAAAAGCCA
* * * *
1238338 AATCAATATCTTCTGCTGACCTTGTTTCAAGAACTGGAAGCACCACATTAGTCTCAGTATTCATA
195 AATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCATA
*
1238403 TCTGTTGATGATTCATTCCTT-A
260 TCTTTTGATGATTCATTCCTTGA
* * * *
1238425 AGCCTGAAGAATGTGGCGGCTCAGCTGGATTAGATTCCGGAAGTTGTCGAACAGCTTTATGTATA
1 A-CCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTCCGGAAGTTGTTGAACAGCTTTGTCTATA
* * *
1238490 TCCTCCAGAGACCTTGCCTCAACAATAGGTAATTTTGATTTGTTATCTCCATGATCTGTCAGTTT
65 TCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTT
* *
1238555 CTCGATCATACTTGGAACAATTACTTCCTCAATGTCGACTCCTTCATGAAGTTGCTTAAAAGCCA
130 CTCAATCATACTCGGAACAATTACTTCCTCAATGTCGACTCCTTCATGAAGTTGCTTAAAAGCCA
* * * *
1238620 AATCAATATCTTCGGCTGATCTTGCTTCAAGAA-TAGGCAGCACCAGATTAGTCTCAGTTTTCGT
195 AATCAATATCTTCTGCTGATCTTGCTTCAAGAACT-GGCAGCACCACATTAGTCTCAGTCTTCAT
*
1238684 ATCTTTTGATGATTCATTCTTTGA
259 ATCTTTTGATGATTCATTCCTTGA
* * * * *
1238708 GCCTGAAGAATGTGGCGGCTCAGCTGGATTAGATTCCGGAAGTTGTCGAACAGCTTTATGTATAT
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTCCGGAAGTTGTTGAACAGCTTTGTCTATAT
* * *
1238773 CCTCCAGAGACCTTGCCTCGAA-AACAGGTAATTTTGATTTGTTACCTCCATGATCTGGCGGTTT
66 CCTCCAGAGATCTTGCCTC-AACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTT
* * * * *
1238837 CTCGATCATACTCAGAACAGTTGCTTCCTCAATGTCGACTCCTTCATGAAGTTGCTTAAAAGACA
130 CTCAATCATACTCGGAACAATTACTTCCTCAATGTCGACTCCTTCATGAAGTTGCTTAAAAGCCA
* ** *
1238902 AATAAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACTGCATTAGTCTTC-GCCTTCAT
195 AATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTC-TCAGTCTTCAT
1238966 ATCTT
259 ATCTT
1238971 CCTGTAACAA
Statistics
Matches: 976, Mismatches: 113, Indels: 34
0.87 0.10 0.03
Matches are distributed among these distances:
278 2 0.00
279 239 0.24
280 10 0.01
281 15 0.02
282 702 0.72
283 8 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (282 bp):
ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTCCGGAAGTTGTTGAACAGCTTTGTCTATAT
CCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
TCAATCATACTCGGAACAATTACTTCCTCAATGTCGACTCCTTCATGAAGTTGCTTAAAAGCCAA
ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCATAT
CTTTTGATGATTCATTCCTTGA
Found at i:1238672 original size:561 final size:562
Alignment explanation
Indices: 1237638--1238955 Score: 1860
Period size: 561 Copynumber: 2.3 Consensus size: 562
1237628 TTGGACAGCA
* * * * *** *
1237638 TTATGTAATTCCTTCAGAGATCTTGCCTCCACAACAGGTAATTTTGATTTGTTATCTGTGTCATC
1 TTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCATGAT-
* * * * *
1237703 CTGTG-GTTCCACAATCATACTTGGAACAATTACTTCCTCAACA-TCAGCTCCTTCATGCAGTTG
65 CTG-GCGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGA-CTCCTTCATGAAGTTG
1237766 CTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCT
128 CTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCT
* * *
1237831 CAGTCTTCATATCTTTTGATGGTTCATTCCTTGAAACTGAAGAATGTGGCAGCTCAGCTGGATTA
193 CAGTATTCATATCTGTTGATGATTCATTCCTTGAAACTGAAGAATGTGGCAGCTCAGCTGGATTA
* * * * * * *
1237896 GATTTCGGAAGTTGTTGAATAGCTTTGTCTATGTCCTCCAGAGATCTTGCCTCGACAACACGTAA
258 GATTCCGGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGACCTTGCCTCAACAACACGTAA
*
1237961 TTTTGATTTGTTATCTCCATGGTCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAA
323 TTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAA
1238026 TGTCCACTCCGTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCGGCTGATCTTGCTTCAAGA
388 TGTCCACTCCGTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCGGCTGATCTTGCTTCAAGA
*
1238091 ACTGGCAGCACCACATTAGTCTCGGTCTTCGCATCTTTTGATGATTCATTCTTTGAGCCTG-AG-
453 ACTGGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCATTCTTTGAGCCTGAAGA
* * * *
1238154 CCTGAAGAAT-ATGCTGGATTAGGTTTCGCAAGTTGTTGAATAGAT
518 CCTGAAGAATCA-GCTGGATTAGATTCCGCAAGTTGTCGAACAGAT
* *
1238199 TTGTCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCAAGATC
1 TTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCATGATC
1238264 TGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAAGTTGCT
66 TGGC-GTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAAGTTGCT
* * *
1238329 TAAAAGCCAAATCAATATCTTCTGCTGACCTTGTTTCAAGAACTGGAAGCACCACATTAGTCTCA
130 TAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCA
* *
1238394 GTATTCATATCTGTTGATGATTCATTCCTT-AAGCCTGAAGAATGTGGCGGCTCAGCTGGATTAG
195 GTATTCATATCTGTTGATGATTCATTCCTTGAA-ACTGAAGAATGTGGCAGCTCAGCTGGATTAG
* * *
1238458 ATTCCGGAAGTTGTCGAACAGCTTTATGTATATCCTCCAGAGACCTTGCCTCAACAATAGGTAAT
259 ATTCCGGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGACCTTGCCTCAACAACACGTAAT
* * *
1238523 TTTGATTTGTTATCTCCATGATCTGTCAGTTTCTCGATCATACTTGGAACAATTACTTCCTCAAT
324 TTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAAT
* *
1238588 GTCGACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCGGCTGATCTTGCTTCAAGAA
389 GTCCACTCCGTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCGGCTGATCTTGCTTCAAGAA
* * *
1238653 -TAGGCAGCACCAGATTAGTCTCAGTTTTCGTATCTTTTGATGATTCATTCTTTGAGCCTGAAGA
454 CT-GGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCATTCTTTGAGCCTGAAG-
** ** ** * *
1238717 ATGTGGCGGCTCAGCTGGATTAGATTCCGGAAGTTGTCGAACAGCT
517 ACCTGAAGAATCAGCTGGATTAGATTCCGCAAGTTGTCGAACAGAT
* * * *
1238763 TTATGTATATCCTCCAGAGACCTTGCCTCGAA-AACAGGTAATTTTGATTTGTTACCTCCATGAT
1 TTATCTAAATCCTCCAGAGATCTTGCCTC-AACAACAGGTAATTTTGATTTGTTATCTCCATGAT
* * * * ** *
1238827 CTGGCGGTTTCTCGATCATACTCAGAACAGTTGCTTCCTCAATGTCGACTCCTTCATGAAGTTGC
65 CTGGC-GTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAAGTTGC
* * **
1238892 TTAAAAGACAAATAAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACTGCATTAGTCT
129 TTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCT
1238956 TCGCCTTCAT
Statistics
Matches: 671, Mismatches: 76, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
559 1 0.00
560 6 0.01
561 457 0.68
562 4 0.01
564 200 0.30
565 3 0.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (562 bp):
TTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCATGATC
TGGCGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAAGTTGCTT
AAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAG
TATTCATATCTGTTGATGATTCATTCCTTGAAACTGAAGAATGTGGCAGCTCAGCTGGATTAGAT
TCCGGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGACCTTGCCTCAACAACACGTAATTT
TGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAATGT
CCACTCCGTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCGGCTGATCTTGCTTCAAGAACT
GGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCATTCTTTGAGCCTGAAGACCT
GAAGAATCAGCTGGATTAGATTCCGCAAGTTGTCGAACAGAT
Found at i:1245578 original size:31 final size:31
Alignment explanation
Indices: 1245543--1245605 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1245533 ATATTCAATC
1245543 AACTTATTAATTTTCATAAGCAAAACATCAT
1 AACTTATTAATTTTCATAAGCAAAACATCAT
1245574 AACTTATTAATTTTCATAAGCAAAACATCAT
1 AACTTATTAATTTTCATAAGCAAAACATCAT
1245605 A
1 A
1245606 TTATGTGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (31 bp):
AACTTATTAATTTTCATAAGCAAAACATCAT
Found at i:1248493 original size:59 final size:56
Alignment explanation
Indices: 1248410--1248569 Score: 205
Period size: 56 Copynumber: 2.8 Consensus size: 56
1248400 AAGAATTTTC
* *
1248410 AGGAGAATTCTCATCTTTTGAGAGCTAGGTTGACTTAGGAAAATTTGAAG-TAAAGAAAT
1 AGGAGAATTCTCATCTTTTAAGAGCTAGGCTGACTTAGGAAAATTT-AAGCT---GAAAT
* *** * *
1248469 AGGAGAATTCTCATCTTTTAAGAGCTAGGCTAACTTAGGCTGACTTAAGCTGACAT
1 AGGAGAATTCTCATCTTTTAAGAGCTAGGCTGACTTAGGAAAATTTAAGCTGAAAT
1248525 AGGAGAATTCTCATCTTTTAAGAGCTAGGCTGACTTAGGAAAATT
1 AGGAGAATTCTCATCTTTTAAGAGCTAGGCTGACTTAGGAAAATT
1248570 CTCACCAGGC
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
56 44 0.51
58 3 0.03
59 40 0.46
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.31
Consensus pattern (56 bp):
AGGAGAATTCTCATCTTTTAAGAGCTAGGCTGACTTAGGAAAATTTAAGCTGAAAT
Found at i:1250303 original size:45 final size:44
Alignment explanation
Indices: 1250252--1250339 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 44
1250242 GCAGGTCAAA
*
1250252 TAATATTAAAATAACTTACACTAATTAGAGTTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATTAGAG-TTTAAGTGGGAAAC
1250297 TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAA
1 TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAA
1250340 TTAAAAACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 13 0.31
45 29 0.69
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAAC
Found at i:1251505 original size:15 final size:15
Alignment explanation
Indices: 1251485--1251514 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1251475 TCAATATTTT
*
1251485 TTAAATCATTCAAAA
1 TTAAATAATTCAAAA
1251500 TTAAATAATTCAAAA
1 TTAAATAATTCAAAA
1251515 GAGTAATAAA
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:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAATAATTCAAAA
Found at i:1276079 original size:33 final size:33
Alignment explanation
Indices: 1276041--1276117 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
1276031 TCCCAAAATA
1276041 GGTAAAATGACCATGACCAAAATACCCCTAAAG
1 GGTAAAATGACCATGACCAAAATACCCCTAAAG
1276074 GGTAAAATGACCATGACCAAAATACCCCTAAAG
1 GGTAAAATGACCATGACCAAAATACCCCTAAAG
1276107 GGTAAAATGAC
1 GGTAAAATGAC
1276118 TATTTTACCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (33 bp):
GGTAAAATGACCATGACCAAAATACCCCTAAAG
Found at i:1276522 original size:33 final size:33
Alignment explanation
Indices: 1276460--1276523 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1276450 GCATTATTGC
*
1276460 ACTGTACTGATACTGTATTTGGCTAAGGCCCAT
1 ACTGTACTGATACTGTATTGGGCTAAGGCCCAT
* *
1276493 ACTGTACTGTTACTG-ATTAGGGCTCAGGCCC
1 ACTGTACTGATACTGTATT-GGGCTAAGGCCC
1276524 GGACTATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (33 bp):
ACTGTACTGATACTGTATTGGGCTAAGGCCCAT
Found at i:1278625 original size:42 final size:42
Alignment explanation
Indices: 1278566--1278657 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
1278556 GCCCTGTGGC
*
1278566 CAGGCCGTGTGACTCACATGGCTGAGACAAATGCTCGTGTCT
1 CAGGCCGTGTGACTCACATGGCTGAGACAAATGCCCGTGTCT
1278608 CAGGCCGTGTGACTCACATGGCTGAGACAAATGCCCGTGTCT
1 CAGGCCGTGTGACTCACATGGCTGAGACAAATGCCCGTGTCT
1278650 CAGGCCGT
1 CAGGCCGT
1278658 TTGGGCATTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (42 bp):
CAGGCCGTGTGACTCACATGGCTGAGACAAATGCCCGTGTCT
Found at i:1284171 original size:13 final size:13
Alignment explanation
Indices: 1284153--1284177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1284143 CAATATAATG
1284153 GATTCAACTCAAT
1 GATTCAACTCAAT
1284166 GATTCAACTCAA
1 GATTCAACTCAA
1284178 CACTTAAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (13 bp):
GATTCAACTCAAT
Found at i:1293884 original size:12 final size:13
Alignment explanation
Indices: 1293855--1293894 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
1293845 GCAGTTACAT
1293855 AGCCTAGCACAC-
1 AGCCTAGCACACG
1293867 AGCCTAGCACACG
1 AGCCTAGCACACG
*
1293880 A-CCTAGCGCACG
1 AGCCTAGCACACG
1293892 AGC
1 AGC
1293895 ATATGAGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 23 0.92
13 2 0.08
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (13 bp):
AGCCTAGCACACG
Found at i:1302785 original size:22 final size:22
Alignment explanation
Indices: 1302759--1302814 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 22
1302749 CTGTGGTGTA
1302759 GTGGCAAGGTGGCGACACAGGT
1 GTGGCAAGGTGGCGACACAGGT
*
1302781 GTGGCAAGGAGGTGGCGTCACAGGT
1 GTGGC-A--AGGTGGCGACACAGGT
*
1302806 GTGGTAAGG
1 GTGGCAAGG
1302815 AGGTTAGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 8 0.28
23 1 0.03
24 1 0.03
25 19 0.66
ACGTcount: A:0.21, C:0.14, G:0.48, T:0.16
Consensus pattern (22 bp):
GTGGCAAGGTGGCGACACAGGT
Found at i:1302793 original size:25 final size:25
Alignment explanation
Indices: 1302765--1302818 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
1302755 TGTAGTGGCA
1302765 AGGTGGCGACACAGGTGTGGCAAGG
1 AGGTGGCGACACAGGTGTGGCAAGG
* *
1302790 AGGTGGCGTCACAGGTGTGGTAAGG
1 AGGTGGCGACACAGGTGTGGCAAGG
1302815 AGGT
1 AGGT
1302819 TAGAGCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.13, G:0.48, T:0.17
Consensus pattern (25 bp):
AGGTGGCGACACAGGTGTGGCAAGG
Found at i:1303289 original size:10 final size:10
Alignment explanation
Indices: 1303274--1303305 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1303264 AATACTTCTT
1303274 TCCTCTCCTA
1 TCCTCTCCTA
1303284 TCCTCTCCTA
1 TCCTCTCCTA
*
1303294 TCCTCTTCTA
1 TCCTCTCCTA
1303304 TC
1 TC
1303306 GAAATCTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.09, C:0.47, G:0.00, T:0.44
Consensus pattern (10 bp):
TCCTCTCCTA
Found at i:1304015 original size:27 final size:27
Alignment explanation
Indices: 1303984--1304631 Score: 683
Period size: 27 Copynumber: 23.7 Consensus size: 27
1303974 TAATGGGCCT
* * *
1303984 AAATTATCGAAATACACTCAATGGATA
1 AAATTATCGAAATACCCTCGATGGGTA
* * *
1304011 AAATTACCGAAATACCTTCGATGTGTA
1 AAATTATCGAAATACCCTCGATGGGTA
1304038 AAATTATCGAAATACCCTCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
1304065 AAATTATCGAAATACCCTCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
*
1304092 AAATTATCGAAATACACTCAATGGATCGATGGTA
1 AAATTATCGAAATAC-C-C--TCGAT-G--GGTA
*
1304126 AAACTATCGAAATACCCTCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
*
1304153 AAACTATCGAAATACCCTCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* * *
1304180 AAACTACCAAAATACCCTCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* *
1304207 AAATTACCAAAATACCCTCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* * *
1304234 AAATTACCAAAATAACCTCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
*
1304261 AAATTATTGAAATACCCTCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* *
1304288 AAATTAACGAAATACCCCCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
*
1304315 AAATTATTGAAATA-CCTCCGATGGGTA
1 AAATTATCGAAATACCCT-CGATGGGTA
* * *
1304342 AAATTATTGACATACCCCCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* * **
1304369 AAATTATTGAAATACCCCCCGAAAGGTA
1 AAATTATCGAAATA-CCCTCGATGGGTA
*
1304397 AAATT-TCCAAAATACCCAT-GATGGGTA
1 AAATTAT-CGAAATACCC-TCGATGGGTA
* *
1304424 AAATTACCGAAATACCCCCGATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* * ** *
1304451 AAATTACCAAAATACCCTTAAAGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* *
1304478 AAATTATCGAAATACTCTCAATGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* * * *
1304505 AAACTACCGAAATACCCCCGAAGGGT-
1 AAATTATCGAAATACCCTCGATGGGTA
* * *
1304531 AAATTTTCCAAAATACCCTTGATGGGTA
1 AAATTAT-CGAAATACCCTCGATGGGTA
* *
1304559 AAATTATCGAAATACCCTCAAAGGGTA
1 AAATTATCGAAATACCCTCGATGGGTA
* ** * *
1304586 AAATTTTTAAAATACCCTTGATGGTTA
1 AAATTATCGAAATACCCTCGATGGGTA
*
1304613 AAATTACCGAAATACCCTC
1 AAATTATCGAAATACCCTC
1304632 ATACGGTAAA
Statistics
Matches: 526, Mismatches: 79, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
26 6 0.01
27 459 0.87
28 30 0.06
29 2 0.00
30 4 0.01
31 4 0.01
32 2 0.00
33 1 0.00
34 18 0.03
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (27 bp):
AAATTATCGAAATACCCTCGATGGGTA
Found at i:1304128 original size:34 final size:35
Alignment explanation
Indices: 1304082--1304149 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
1304072 CGAAATACCC
*
1304082 TCGATGGGTAAAATTATCGAAATACACTCAATGGA
1 TCGATGGGTAAAACTATCGAAATACACTCAATGGA
* *
1304117 TCGAT-GGTAAAACTATCGAAATACCCTCGATGG
1 TCGATGGGTAAAACTATCGAAATACACTCAATGG
1304150 GTAAAACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 25 0.83
35 5 0.17
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (35 bp):
TCGATGGGTAAAACTATCGAAATACACTCAATGGA
Found at i:1307767 original size:25 final size:25
Alignment explanation
Indices: 1307739--1307792 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
1307729 TGTATTGGCA
*
1307739 AGGTGGCGACACAGGTGTGGCAATG
1 AGGTGGCGACACAGGTGTGGCAAGG
* *
1307764 AGGTGGCGTCACAGGTGTGGTAAGG
1 AGGTGGCGACACAGGTGTGGCAAGG
1307789 AGGT
1 AGGT
1307793 CAGAGGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.13, G:0.46, T:0.19
Consensus pattern (25 bp):
AGGTGGCGACACAGGTGTGGCAAGG
Found at i:1307926 original size:13 final size:14
Alignment explanation
Indices: 1307903--1307945 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
1307893 ATTGGTCAAA
1307903 AGAGTGATTTAAGG
1 AGAGTGATTTAAGG
1307917 AGAG-GATTTAA-G
1 AGAGTGATTTAAGG
*
1307929 A-AGTGATTTTAGG
1 AGAGTGATTTAAGG
1307942 AGAG
1 AGAG
1307946 AATTTGGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 2 0.08
12 8 0.32
13 9 0.36
14 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.35, T:0.28
Consensus pattern (14 bp):
AGAGTGATTTAAGG
Found at i:1308977 original size:27 final size:27
Alignment explanation
Indices: 1308946--1309367 Score: 499
Period size: 27 Copynumber: 15.6 Consensus size: 27
1308936 TAATGGGCCT
* *
1308946 AAATTATCAAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
**
1308973 AAATTACCGAAATACCCTCGATAAGTA
1 AAATTACCGAAATACCCTCGATGGGTA
*
1309000 AAATTATCGAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* *
1309027 AAACTACCGAAATACTCTCGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* *
1309054 AAATTACCAAAATACCCTAGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
1309081 AAATTATCAAAATA-CCTCGACGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
*
1309107 AAATTACCAAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
1309134 AAATTATCGAAATATCCTCAATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
1309161 TAATTACCGAAATACCTTCGATGGATA
1 AAATTACCGAAATACCCTCGATGGGTA
* *
1309188 AAACTACCGAAATACCCTCGATGGGTT
1 AAATTACCGAAATACCCTCGATGGGTA
* *
1309215 AAATTACCGAAATACCCTTGACGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
*
1309242 AAATTATCGAAATACCC-CTGATGGGTA
1 AAATTACCGAAATACCCTC-GATGGGTA
* * *
1309269 AATTTACTGAAATACCCTTGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
1309296 AAATTACC-AAGATACCCACAAAGGGTA
1 AAATTACCGAA-ATACCCTCGATGGGTA
*
1309323 AAATTACCGAAATACTCCCCGATGGGTA
1 AAATTACCGAAATAC-CCTCGATGGGTA
**
1309351 AAATTACTAAAATACCC
1 AAATTACCGAAATACCC
1309368 CCATAGGGTA
Statistics
Matches: 333, Mismatches: 56, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
26 25 0.08
27 284 0.85
28 24 0.07
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATGGGTA
Found at i:1310008 original size:10 final size:10
Alignment explanation
Indices: 1309993--1310018 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1309983 GCGTTAGACG
1309993 GTTTTATTCT
1 GTTTTATTCT
1310003 GTTTTATTCT
1 GTTTTATTCT
1310013 GTTTTA
1 GTTTTA
1310019 CTCATTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.12, T:0.69
Consensus pattern (10 bp):
GTTTTATTCT
Found at i:1312797 original size:12 final size:12
Alignment explanation
Indices: 1312780--1312843 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
1312770 GAATTAATTC
1312780 TGAATTCGTTTG
1 TGAATTCGTTTG
**
1312792 TGAATTAATTT-
1 TGAATTCGTTTG
*
1312803 TGAATTCGTTTA
1 TGAATTCGTTTG
** *
1312815 TGAATT-AATTC
1 TGAATTCGTTTG
1312826 TGAATTCGTTTG
1 TGAATTCGTTTG
1312838 TGAATT
1 TGAATT
1312844 AATTCACTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
11 17 0.43
12 23 0.57
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (12 bp):
TGAATTCGTTTG
Found at i:1312799 original size:23 final size:23
Alignment explanation
Indices: 1312769--1312848 Score: 142
Period size: 23 Copynumber: 3.5 Consensus size: 23
1312759 GGACCCAAGA
1312769 TGAATTAATTCTGAATTCGTTTG
1 TGAATTAATTCTGAATTCGTTTG
* *
1312792 TGAATTAATTTTGAATTCGTTTA
1 TGAATTAATTCTGAATTCGTTTG
1312815 TGAATTAATTCTGAATTCGTTTG
1 TGAATTAATTCTGAATTCGTTTG
1312838 TGAATTAATTC
1 TGAATTAATTC
1312849 ACTTGTGATG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (23 bp):
TGAATTAATTCTGAATTCGTTTG
Found at i:1315089 original size:26 final size:27
Alignment explanation
Indices: 1315025--1315089 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1315015 TTTTGCTTCA
**
1315025 ATAAAATTTTGATGATTTTACCCCCTG
1 ATAAAATTTTGACAATTTTACCCCCTG
*
1315052 ATAAAATTTTGACAATTTTACTCCC-G
1 ATAAAATTTTGACAATTTTACCCCCTG
*
1315078 GTAAAATTTTGA
1 ATAAAATTTTGA
1315090 GAAATTTCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (27 bp):
ATAAAATTTTGACAATTTTACCCCCTG
Found at i:1315246 original size:6 final size:6
Alignment explanation
Indices: 1315230--1315275 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
1315220 GGATTGTAAG
*
1315230 TTTCAAT TTTCAT TTTCAT TTTCAT TTAT-AT TTTCAT TTCCAT TTT
1 TTTC-AT TTTCAT TTTCAT TTTCAT TT-TCAT TTTCAT TTTCAT TTT
1315276 TGGAAACCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 1 0.03
6 29 0.83
7 5 0.14
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTCAT
Found at i:1317965 original size:15 final size:15
Alignment explanation
Indices: 1317945--1317974 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1317935 ACAGGGGCTG
1317945 GCACATGGTGGGTTC
1 GCACATGGTGGGTTC
*
1317960 GCACATGGTGTGTTC
1 GCACATGGTGGGTTC
1317975 ACATCCTTAC
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:0.13, C:0.20, G:0.37, T:0.30
Consensus pattern (15 bp):
GCACATGGTGGGTTC
Found at i:1323579 original size:21 final size:21
Alignment explanation
Indices: 1323555--1323598 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1323545 TTGAACTAGT
*
1323555 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
1323576 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
1323597 TA
1 TA
1323599 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:1328585 original size:51 final size:51
Alignment explanation
Indices: 1328530--1328722 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 51
1328520 GATCAATGCT
*
1328530 ATCCGGTACACATAGTAGCCTACACTTAGTACCACACATGTGACCAATACC
1 ATCCGGTACACATAGTAGCCTACACATAGTACCACACATGTGACCAATACC
* * * * *
1328581 ATCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAA-AGCT
1 ATCCGGTACACATAGTAGCCTACACATAGTACCACACATGTGACCAATA-CC
* * * * *
1328632 ATCCGGTACACATAGTAACCTGCACTTAGTACTACACATGTGTCC-ATAACC
1 ATCCGGTACACATAGTAGCCTACACATAGTACCACACATGTGACCAAT-ACC
*** * * *
1328683 ATCTTATACTCATAGTATCCTACACACAGTACCACACATG
1 ATCCGGTACACATAGTAGCCTACACATAGTACCACACATG
1328723 AGTTCTCATG
Statistics
Matches: 118, Mismatches: 21, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
50 2 0.02
51 115 0.97
52 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (51 bp):
ATCCGGTACACATAGTAGCCTACACATAGTACCACACATGTGACCAATACC
Found at i:1328699 original size:102 final size:102
Alignment explanation
Indices: 1328527--1328720 Score: 255
Period size: 102 Copynumber: 1.9 Consensus size: 102
1328517 TATGATCAAT
* *
1328527 GCTATCCGGTACACATAGTAGCCTACACTTAGTACCACACATGTGACCAATACCATCCGGTACAC
1 GCTATCCGGTACACATAGTAACCTACACTTAGTACCACACATGTGACCAATACCATCCGATACAC
* * * *
1328592 GTAGTAGCCTGCACATAGTACTACACACGTGACCAAA
66 ATAGTAGCCTACACACAGTACCACACACGTGACCAAA
* * * ** *
1328629 GCTATCCGGTACACATAGTAACCTGCACTTAGTACTACACATGTGTCC-ATAACCATCTTATACT
1 GCTATCCGGTACACATAGTAACCTACACTTAGTACCACACATGTGACCAAT-ACCATCCGATACA
*
1328693 CATAGTATCCTACACACAGTACCACACA
65 CATAGTAGCCTACACACAGTACCACACA
1328721 TGAGTTCTCA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 2 0.03
102 76 0.97
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.23
Consensus pattern (102 bp):
GCTATCCGGTACACATAGTAACCTACACTTAGTACCACACATGTGACCAATACCATCCGATACAC
ATAGTAGCCTACACACAGTACCACACACGTGACCAAA
Found at i:1331593 original size:26 final size:25
Alignment explanation
Indices: 1331529--1331602 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
1331519 TGATTATCTT
*
1331529 AATATTAAATTAATTTTAATGTAAGATA
1 AATATTATATT-ATTTTAA--TAAGATA
* *
1331557 AACATTTTATTATTTTAATAAGATTA
1 AATATTATATTATTTTAATAAGA-TA
*
1331583 AATATTATATTAATTTAATA
1 AATATTATATTATTTTAATA
1331603 TTAAAGTGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 5 0.13
26 19 0.49
27 7 0.18
28 8 0.21
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTATATTATTTTAATAAGATA
Found at i:1331601 original size:90 final size:90
Alignment explanation
Indices: 1331493--1331701 Score: 409
Period size: 90 Copynumber: 2.3 Consensus size: 90
1331483 TTATCTTAAT
*
1331493 AATATTGTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAATTTTAATGTAAGATAA
1 AATATTATATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAATTTTAATGTAAGATAA
1331558 ACATTTTATTATTTTAATAAGATTA
66 ACATTTTATTATTTTAATAAGATTA
1331583 AATATTATATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAATTTTAATGTAAGATAA
1 AATATTATATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAATTTTAATGTAAGATAA
1331648 ACATTTTATTATTTTAATAAGATTA
66 ACATTTTATTATTTTAATAAGATTA
1331673 AATATTATATTAATTTAATATTAAAGTGA
1 AATATTATATTAATTTAATATTAAAGTGA
1331702 CTAAGTTTAA
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 118 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.47
Consensus pattern (90 bp):
AATATTATATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAATTTTAATGTAAGATAA
ACATTTTATTATTTTAATAAGATTA
Found at i:1331683 original size:26 final size:25
Alignment explanation
Indices: 1331619--1331692 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
1331609 TGATTATCTT
*
1331619 AATATTAAATTAATTTTAATGTAAGATA
1 AATATTATATT-ATTTTAA--TAAGATA
* *
1331647 AACATTTTATTATTTTAATAAGATTA
1 AATATTATATTATTTTAATAAGA-TA
*
1331673 AATATTATATTAATTTAATA
1 AATATTATATTATTTTAATA
1331693 TTAAAGTGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 5 0.13
26 19 0.49
27 7 0.18
28 8 0.21
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTATATTATTTTAATAAGATA
Found at i:1336073 original size:6 final size:6
Alignment explanation
Indices: 1336059--1336092 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1336049 ATCATTTCAT
*
1336059 ATTTTC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1336093 TTTGGGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTTCC
Found at i:1337961 original size:45 final size:45
Alignment explanation
Indices: 1337902--1337987 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1337892 ATTTCTTTAG
* * *
1337902 TTAATTAATTTACATAGTATTTGTTATTAATTATTTATACTAAAT
1 TTAACTAATTTACATAGTATTTATCATTAATTATTTATACTAAAT
*
1337947 TTAACTAATTTACATATTATTTATCATTAATTATTTATACT
1 TTAACTAATTTACATAGTATTTATCATTAATTATTTATACT
1337988 TGGTCAATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (45 bp):
TTAACTAATTTACATAGTATTTATCATTAATTATTTATACTAAAT
Found at i:1349017 original size:2 final size:2
Alignment explanation
Indices: 1349012--1349043 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1349002 TATATTTTGA
1349012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1349044 CTCAAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1349144 original size:15 final size:15
Alignment explanation
Indices: 1349126--1349158 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1349116 ACAATACGTG
1349126 TTTA-AAAATTTTGGT
1 TTTATAAAA-TTTGGT
1349141 TTTATAAAATTTGGT
1 TTTATAAAATTTGGT
1349156 TTT
1 TTT
1349159 GAATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTATAAAATTTGGT
Found at i:1351135 original size:9 final size:9
Alignment explanation
Indices: 1351123--1351159 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1351113 GCGTCACTAG
1351123 CATCAATAT
1 CATCAATAT
*
1351132 CATCACTAT
1 CATCAATAT
*
1351141 CATCACTAT
1 CATCAATAT
1351150 CATCAATAT
1 CATCAATAT
1351159 C
1 C
1351160 GATATCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.38, C:0.30, G:0.00, T:0.32
Consensus pattern (9 bp):
CATCAATAT
Found at i:1351150 original size:18 final size:18
Alignment explanation
Indices: 1351106--1351159 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
1351096 CAAAGTCACG
* * *
1351106 ATCAATAGCGTCACTAGC
1 ATCAATATCATCACTATC
1351124 ATCAATATCATCACTATC
1 ATCAATATCATCACTATC
* *
1351142 ATCACTATCATCAATATC
1 ATCAATATCATCACTATC
1351160 GATATCATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.30
Consensus pattern (18 bp):
ATCAATATCATCACTATC
Found at i:1352297 original size:13 final size:13
Alignment explanation
Indices: 1352279--1352308 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1352269 AATATAGGGG
*
1352279 AAAATGTACCATT
1 AAAATGGACCATT
1352292 AAAATGGACCATT
1 AAAATGGACCATT
1352305 AAAA
1 AAAA
1352309 GTATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.23
Consensus pattern (13 bp):
AAAATGGACCATT
Found at i:1352915 original size:23 final size:23
Alignment explanation
Indices: 1352889--1352933 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1352879 TTCGCTTGAA
*
1352889 AATCATT-TTTTTCGTACTGAATT
1 AATCATTCTTTTTCAT-CTGAATT
*
1352912 AATCTTTCTTTTTCATCTGAAT
1 AATCATTCTTTTTCATCTGAAT
1352934 CCCATTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (23 bp):
AATCATTCTTTTTCATCTGAATT
Found at i:1370274 original size:17 final size:17
Alignment explanation
Indices: 1370252--1370284 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1370242 ACCTTCAGTA
1370252 AAACTA-AAATTAAATAT
1 AAACTATAAA-TAAATAT
1370269 AAACTATAAATAAATA
1 AAACTATAAATAAATA
1370285 ACTAATTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
AAACTATAAATAAATAT
Found at i:1370368 original size:176 final size:176
Alignment explanation
Indices: 1370074--1370426 Score: 697
Period size: 176 Copynumber: 2.0 Consensus size: 176
1370064 ATATATATAT
*
1370074 TAAAACTAAAATTAAATATAAACTATGAATAAATAACTAATTACTTAATTTGAAAAGTAAAAAAA
1 TAAAACTAAAATTAAATATAAACTATAAATAAATAACTAATTACTTAATTTGAAAAGTAAAAAAA
1370139 TTACCTTAACGGGTGAAAAATAAAAATAGGGGAAGGGTATAGGCATAGTAAAAACAATTGTTATG
66 TTACCTTAACGGGTGAAAAATAAAAATAGGGGAAGGGTATAGGCATAGTAAAAACAATTGTTATG
1370204 GATGTCGACTATAATTAATTGTCATAATTGCAAAAAATACCTTCAG
131 GATGTCGACTATAATTAATTGTCATAATTGCAAAAAATACCTTCAG
1370250 TAAAACTAAAATTAAATATAAACTATAAATAAATAACTAATTACTTAATTTGAAAAGTAAAAAAA
1 TAAAACTAAAATTAAATATAAACTATAAATAAATAACTAATTACTTAATTTGAAAAGTAAAAAAA
1370315 TTACCTTAACGGGTGAAAAATAAAAATAGGGGAAGGGTATAGGCATAGTAAAAACAATTGTTATG
66 TTACCTTAACGGGTGAAAAATAAAAATAGGGGAAGGGTATAGGCATAGTAAAAACAATTGTTATG
1370380 GATGTCGACTATAATTAATTGTCATAATTGCAAAAAATACCTTCAG
131 GATGTCGACTATAATTAATTGTCATAATTGCAAAAAATACCTTCAG
1370426 T
1 T
1370427 GTTTAGGGGT
Statistics
Matches: 176, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 176 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (176 bp):
TAAAACTAAAATTAAATATAAACTATAAATAAATAACTAATTACTTAATTTGAAAAGTAAAAAAA
TTACCTTAACGGGTGAAAAATAAAAATAGGGGAAGGGTATAGGCATAGTAAAAACAATTGTTATG
GATGTCGACTATAATTAATTGTCATAATTGCAAAAAATACCTTCAG
Found at i:1395164 original size:15 final size:15
Alignment explanation
Indices: 1395140--1395183 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1395130 TGGATCCTAC
1395140 CCTCCACAAGGATAT
1 CCTCCACAAGGATAT
*
1395155 CCTCCTCAAGGATAT
1 CCTCCACAAGGATAT
*
1395170 CCCCCACAAGGATA
1 CCTCCACAAGGATA
1395184 CCCACCGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.32, C:0.36, G:0.14, T:0.18
Consensus pattern (15 bp):
CCTCCACAAGGATAT
Found at i:1395233 original size:18 final size:18
Alignment explanation
Indices: 1395212--1395272 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
1395202 TCCACCAGCG
1395212 GGATATCCTCCTCATGGC
1 GGATATCCTCCTCATGGC
1395230 GGATA-CC-CAC-C-T-GC
1 GGATATCCTC-CTCATGGC
*
1395244 AGGATATCCTCCTCATGGA
1 -GGATATCCTCCTCATGGC
*
1395263 GGATACCCTC
1 GGATATCCTC
1395273 ATCCACCTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
14 2 0.06
15 6 0.18
16 5 0.15
17 5 0.15
18 15 0.44
19 1 0.03
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.23
Consensus pattern (18 bp):
GGATATCCTCCTCATGGC
Found at i:1395240 original size:33 final size:33
Alignment explanation
Indices: 1395203--1395270 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1395193 TGGATATCCT
* *
1395203 CCACCAGCGGGATATCCTCCTCATGGCGGATAC
1 CCACCAGCAGGATATCCTCCTCATGGAGGATAC
*
1395236 CCACCTGCAGGATATCCTCCTCATGGAGGATAC
1 CCACCAGCAGGATATCCTCCTCATGGAGGATAC
1395269 CC
1 CC
1395271 TCATCCACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.19
Consensus pattern (33 bp):
CCACCAGCAGGATATCCTCCTCATGGAGGATAC
Found at i:1395516 original size:21 final size:21
Alignment explanation
Indices: 1395479--1395519 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1395469 TGTTTACGGG
1395479 GCTCACCATTTGTCACATGGA
1 GCTCACCATTTGTCACATGGA
*
1395500 GCTCATCATGTTG-CACATGG
1 GCTCACCAT-TTGTCACATGG
1395520 GGGATACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
GCTCACCATTTGTCACATGGA
Found at i:1397363 original size:28 final size:28
Alignment explanation
Indices: 1397328--1397405 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
1397318 TTAATTAATC
*
1397328 TTTAGATAATAATGTTTAAATTGT-ATAA
1 TTTAGATAATAA-ATTTAAATTGTAATAA
* * *
1397356 TTTAGATAATAAATTTCAATTTTAATAT
1 TTTAGATAATAAATTTAAATTGTAATAA
1397384 TTTAGATAATAAATTATAAATT
1 TTTAGATAATAAATT-TAAATT
1397406 AATTTAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.19
28 30 0.70
29 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (28 bp):
TTTAGATAATAAATTTAAATTGTAATAA
Found at i:1409444 original size:16 final size:16
Alignment explanation
Indices: 1409423--1409455 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1409413 TAAATATGAT
1409423 TTAAAAT-TTATAAAAA
1 TTAAAATCTT-TAAAAA
1409439 TTAAAATCTTTAAAAA
1 TTAAAATCTTTAAAAA
1409455 T
1 T
1409456 ATATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATCTTTAAAAA
Found at i:1409625 original size:16 final size:16
Alignment explanation
Indices: 1409604--1409636 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1409594 TAAATATGAT
1409604 TTAAAAT-TTATAAAAA
1 TTAAAATCTT-TAAAAA
1409620 TTAAAATCTTTAAAAA
1 TTAAAATCTTTAAAAA
1409636 T
1 T
1409637 ATATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATCTTTAAAAA
Found at i:1409677 original size:181 final size:182
Alignment explanation
Indices: 1409364--1409726 Score: 719
Period size: 181 Copynumber: 2.0 Consensus size: 182
1409354 TCAAATAATA
1409364 CATCAACCAAATAAAATTAAAACTCCATGAGATAAATATAAAAATAATATAAATATGATTTAAAA
1 CATCAACCAAATAAAATTAAAACTCCATGAGATAAATATAAAAATAATATAAATATGATTTAAAA
1409429 TTTATAAAAATTAAAATCTTTAAAAATATATATATATATATAAAATACACGTAAAAGTATACAAA
66 TTTATAAAAATTAAAATCTTTAAAAATATATATATATATATAAAATACACGTAAAAGTATACAAA
1409494 TATATCAACATCAAAGTTAACAAAAATATTTGTTGTAACATGCATGCATGTT
131 TATATCAACATCAAAGTTAACAAAAATATTTGTTGTAACATGCATGCATGTT
1409546 CATCAACC-AATAAAATTAAAACTCCATGAGATAAATATAAAAATAATATAAATATGATTTAAAA
1 CATCAACCAAATAAAATTAAAACTCCATGAGATAAATATAAAAATAATATAAATATGATTTAAAA
1409610 TTTATAAAAATTAAAATCTTTAAAAATATATATATATATATAAAATACACGTAAAAGTATACAAA
66 TTTATAAAAATTAAAATCTTTAAAAATATATATATATATATAAAATACACGTAAAAGTATACAAA
1409675 TATATCAACATCAAAGTTAACAAAAATATTTGTTGTAACATGCATGCATGTT
131 TATATCAACATCAAAGTTAACAAAAATATTTGTTGTAACATGCATGCATGTT
1409727 GGTTGACAAC
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 173 0.96
182 8 0.04
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (182 bp):
CATCAACCAAATAAAATTAAAACTCCATGAGATAAATATAAAAATAATATAAATATGATTTAAAA
TTTATAAAAATTAAAATCTTTAAAAATATATATATATATATAAAATACACGTAAAAGTATACAAA
TATATCAACATCAAAGTTAACAAAAATATTTGTTGTAACATGCATGCATGTT
Found at i:1409953 original size:14 final size:14
Alignment explanation
Indices: 1409936--1409988 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1409926 CATCTAAGCT
1409936 TTTACATTTTGTTA
1 TTTACATTTTGTTA
* *
1409950 TTTACGTCTTGTTA
1 TTTACATTTTGTTA
* * *
1409964 TTTCACTTTTTTTTT
1 TTT-ACATTTTGTTA
1409979 TTTACATTTT
1 TTTACATTTT
1409989 ATAAATTATA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.15, C:0.11, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTACATTTTGTTA
Found at i:1411431 original size:18 final size:19
Alignment explanation
Indices: 1411395--1411445 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
1411385 TCTAACTTTT
* *
1411395 TTTTTTTAGATTTTCTAAA
1 TTTTTTTAAATATTCTAAA
1411414 TTTTTTTAAATATT-TAAA
1 TTTTTTTAAATATTCTAAA
** *
1411432 AGTTTTAAAATATT
1 TTTTTTTAAATATT
1411446 ANNNNNNNNN
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTTTTAAATATTCTAAA
Found at i:1413857 original size:21 final size:21
Alignment explanation
Indices: 1413833--1413900 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
1413823 TTTCACACCA
1413833 ATTTGATTTTTCTTAGTTAGT
1 ATTTGATTTTTCTTAGTTAGT
* * *
1413854 ATTTGATTTTTCTTACTGACT
1 ATTTGATTTTTCTTAGTTAGT
* *
1413875 A-TAGATTTTTCGTAGTTAGT
1 ATTTGATTTTTCTTAGTTAGT
1413895 ATTTGA
1 ATTTGA
1413901 ACTATTGATT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (21 bp):
ATTTGATTTTTCTTAGTTAGT
Found at i:1417194 original size:28 final size:28
Alignment explanation
Indices: 1417154--1417209 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1417144 AGATGTAAAG
1417154 AATCCTACCCCCATCTTCTACACACTAT
1 AATCCTACCCCCATCTTCTACACACTAT
1417182 AATCCTACCCCCATCTTCTACACACTAT
1 AATCCTACCCCCATCTTCTACACACTAT
1417210 CTCCGACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (28 bp):
AATCCTACCCCCATCTTCTACACACTAT
Found at i:1422716 original size:29 final size:31
Alignment explanation
Indices: 1422671--1422735 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 31
1422661 GAGGACTCAA
*
1422671 CTTCCCTTTTTTGACCAAATCTTAAAATTTT
1 CTTCCCTTTTTTGACCAAATCTCAAAATTTT
1422702 -TTCCC-TTTTTGACCAAATCTCAAAATTTT
1 CTTCCCTTTTTTGACCAAATCTCAAAATTTT
1422731 CTTCC
1 CTTCC
1422736 AAGGCTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.25, C:0.26, G:0.03, T:0.46
Consensus pattern (31 bp):
CTTCCCTTTTTTGACCAAATCTCAAAATTTT
Found at i:1441939 original size:68 final size:68
Alignment explanation
Indices: 1441853--1441990 Score: 154
Period size: 67 Copynumber: 2.0 Consensus size: 68
1441843 TTGCACCCAC
* ** ** * *
1441853 AATAACATGAAAAGAGTTGAAGTTTTGCAAAAACAAAACTAACAAACAACATAATAGTTGTACC-
1 AATAAAATGAAAAGAGTTGAAACTTCACAAAAA-AAAACCAACAAACAACACAATAGTTGTACCT
1441917 AAAA
65 AAAA
* * *
1441921 AATAAAATG-AAAGAAGTTGAAACTTCACAAAAATAAACCAACAAATATCACAATAGTTGTACCT
1 AATAAAATGAAAAG-AGTTGAAACTTCACAAAAAAAAACCAACAAACAACACAATAGTTGTACCT
1441985 AAAA
65 AAAA
1441989 AA
1 AA
1441991 CCACATAAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
67 29 0.50
68 29 0.50
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (68 bp):
AATAAAATGAAAAGAGTTGAAACTTCACAAAAAAAAACCAACAAACAACACAATAGTTGTACCTA
AAA
Found at i:1447668 original size:30 final size:30
Alignment explanation
Indices: 1447629--1447685 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1447619 CACAGGTTGG
*
1447629 GTGATTCCACACA-GGCTAGGCACATGGCTGT
1 GTGATTCCACA-AGGGCTA-CCACATGGCTGT
1447660 GTGA-TCCACAAGGGCTACCACATGGC
1 GTGATTCCACAAGGGCTACCACATGGC
1447686 CATTTGCCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 9 0.38
30 11 0.46
31 4 0.17
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (30 bp):
GTGATTCCACAAGGGCTACCACATGGCTGT
Found at i:1458024 original size:5 final size:5
Alignment explanation
Indices: 1458014--1458040 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1458004 CTCTCTCCAA
1458014 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
1458041 TTCAGTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:1459182 original size:42 final size:42
Alignment explanation
Indices: 1459120--1459199 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1459110 TGAAAAGTTT
* * * *
1459120 GTTAGGAAAACTGATGATAGATGGTTGGCATCTTTTCTGTTA
1 GTTAGGAAAACTGATCATAGATGGCTGACAGCTTTTCTGTTA
1459162 GTTAGGAAAATCT-ATCATAGATGGCTGACAGCTTTTCT
1 GTTAGGAAAA-CTGATCATAGATGGCTGACAGCTTTTCT
1459200 TGACTGTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (42 bp):
GTTAGGAAAACTGATCATAGATGGCTGACAGCTTTTCTGTTA
Found at i:1472929 original size:18 final size:18
Alignment explanation
Indices: 1472906--1472942 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1472896 AGATTTGAAC
1472906 AAAGAAAATTCCAGTAAA
1 AAAGAAAATTCCAGTAAA
1472924 AAAGAAAATTCCAGTAAA
1 AAAGAAAATTCCAGTAAA
1472942 A
1 A
1472943 GTTTTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAGAAAATTCCAGTAAA
Found at i:1472996 original size:24 final size:26
Alignment explanation
Indices: 1472949--1472996 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
1472939 AAAAGTTTTC
*
1472949 TTCTCTTCTCTTCTGTTCTCTTCTTT
1 TTCTCTTCTCTTCTGCTCTCTTCTTT
*
1472975 TTCT-TTC-CTTCTGCTCTTTTCT
1 TTCTCTTCTCTTCTGCTCTCTTCT
1472997 GCTATTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 3 0.15
26 4 0.20
ACGTcount: A:0.00, C:0.31, G:0.04, T:0.65
Consensus pattern (26 bp):
TTCTCTTCTCTTCTGCTCTCTTCTTT
Found at i:1473762 original size:31 final size:31
Alignment explanation
Indices: 1473724--1473785 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1473714 TTGAAGTTAT
*
1473724 GAAATATGCAATATGCTAGCACAATTCAATC
1 GAAATATGCAACATGCTAGCACAATTCAATC
*
1473755 GAAATATGCAACATGCTAGCACGATTCAATC
1 GAAATATGCAACATGCTAGCACAATTCAATC
1473786 TTATTCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (31 bp):
GAAATATGCAACATGCTAGCACAATTCAATC
Found at i:1490943 original size:22 final size:22
Alignment explanation
Indices: 1490915--1490960 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1490905 AACGTGAGAA
1490915 AAAAGAAAAAAAAATTCTTTAC
1 AAAAGAAAAAAAAATTCTTTAC
*
1490937 AAAAGAAAAAAAATTTCTTTAC
1 AAAAGAAAAAAAAATTCTTTAC
1490959 AA
1 AA
1490961 CTTGGTCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (22 bp):
AAAAGAAAAAAAAATTCTTTAC
Found at i:1492371 original size:22 final size:22
Alignment explanation
Indices: 1492344--1492390 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1492334 TGTGCTTATC
1492344 GTTTTGCACTTCAATGCCTACT
1 GTTTTGCACTTCAATGCCTACT
**
1492366 GTTTTGCACTTTGATGCCTACT
1 GTTTTGCACTTCAATGCCTACT
1492388 GTT
1 GTT
1492391 ATATTAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (22 bp):
GTTTTGCACTTCAATGCCTACT
Found at i:1494355 original size:26 final size:26
Alignment explanation
Indices: 1494318--1494371 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1494308 ATCTGGCATC
*
1494318 CTTACCCTCTTTCGAGTTCTCAAATAT
1 CTTACCCTCTTTCGAGTCCTCAAA-AT
1494345 CTTA-CCTCTTTCGAGTCCTCAAAAT
1 CTTACCCTCTTTCGAGTCCTCAAAAT
1494370 CT
1 CT
1494372 GAATCTCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.22, C:0.31, G:0.07, T:0.39
Consensus pattern (26 bp):
CTTACCCTCTTTCGAGTCCTCAAAAT
Found at i:1499156 original size:1 final size:1
Alignment explanation
Indices: 1499150--1499175 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1499140 TTTATTGTTG
1499150 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1499176 AATTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1499225 original size:1 final size:1
Alignment explanation
Indices: 1499221--1499247 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1499211 ATTTTTTACA
1499221 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1499248 GTAAATATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1513613 original size:40 final size:40
Alignment explanation
Indices: 1513528--1513661 Score: 110
Period size: 40 Copynumber: 3.4 Consensus size: 40
1513518 GCGTTTGGAC
* * * **
1513528 AAAAAACGCCACTAACAATCGAGCATTAGCGGCATTTTAC-
1 AAAAAACGCCGC-AAAAATCGAGCATTAGCGGCGTTACACA
* * *
1513568 GAAAAATGCCGCAAAATATCGAGCATTAGCGGCGTTACATA
1 AAAAAACGCCGCAAAA-ATCGAGCATTAGCGGCGTTACACA
* * * **
1513609 AAAAAACGCCGCTAAAACCAAGCATTAGCGGCGTTTTAC-
1 AAAAAACGCCGCAAAAATCGAGCATTAGCGGCGTTACACA
*
1513648 AAAAAGCGCCGCAA
1 AAAAAACGCCGCAA
1513662 TAGAGTAACA
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
39 15 0.20
40 46 0.62
41 13 0.18
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (40 bp):
AAAAAACGCCGCAAAAATCGAGCATTAGCGGCGTTACACA
Found at i:1513908 original size:54 final size:54
Alignment explanation
Indices: 1513840--1513947 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
1513830 TAGCGGCGTT
* *
1513840 TTTTTTAAACCGCCGCTGATTCTCCGCTCTAAAGCAGCGTTTATGGAGAATCGC
1 TTTTATAAACCGCCGCTGATGCTCCGCTCTAAAGCAGCGTTTATGGAGAATCGC
*
1513894 TTTTATAAACCGCCGCTGATGCTCCGCTCTAAAGCGGCGTTTATGGAGAATCGC
1 TTTTATAAACCGCCGCTGATGCTCCGCTCTAAAGCAGCGTTTATGGAGAATCGC
1513948 CGCTAATGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (54 bp):
TTTTATAAACCGCCGCTGATGCTCCGCTCTAAAGCAGCGTTTATGGAGAATCGC
Found at i:1513990 original size:41 final size:41
Alignment explanation
Indices: 1513904--1514036 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 41
1513894 TTTTATAAAC
* * * * * * * *
1513904 CGCCGCTGATGCTCCGCTCTAAAGCGGCGTTTATGGAGAAT
1 CGCCGCTAATGTTCCGGTCTATAGCGGCGTTTGTGTAAAAA
* *
1513945 CGCCGCTAATGTTCCGGTCTATAGCGGCATTTGTGTAAAAG
1 CGCCGCTAATGTTCCGGTCTATAGCGGCGTTTGTGTAAAAA
* * *
1513986 CGCCGGTAAT-TCTTCGGTCTATAGCGACGTTTGTGTAAAAA
1 CGCCGCTAATGT-TCCGGTCTATAGCGGCGTTTGTGTAAAAA
1514027 CGCCGCTAAT
1 CGCCGCTAAT
1514037 TAGAAAATCT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 1 0.01
41 75 0.99
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (41 bp):
CGCCGCTAATGTTCCGGTCTATAGCGGCGTTTGTGTAAAAA
Found at i:1514070 original size:17 final size:18
Alignment explanation
Indices: 1514036--1514071 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1514026 ACGCCGCTAA
1514036 TTAGAAAATCTAAAATAT
1 TTAGAAAATCTAAAATAT
1514054 TTAGAAAATCT-AAATAT
1 TTAGAAAATCTAAAATAT
1514071 T
1 T
1514072 ATTTCATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (18 bp):
TTAGAAAATCTAAAATAT
Found at i:1525143 original size:65 final size:64
Alignment explanation
Indices: 1525038--1525202 Score: 190
Period size: 65 Copynumber: 2.5 Consensus size: 64
1525028 GAGCAAATTA
* * ** *
1525038 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAGATATGAAG-AACTCCA
1 CACAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGGTTCAACAAAG-TATG-AGCAACTCCA
1525101 G
64 G
*
1525102 CTACAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAGCAACTGCA
1 C-ACAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGGTTCAAC-AAAGTATGAGCAACTCCA
1525167 G
64 G
* * *
1525168 CAGTAGCTTAAAGAAGATGCGGCAGCGAGAGAAGC
1 CA-CAACTTAAAGCAGATGCGGCAGCGAGAGAAGC
1525203 AGCGGTTGCA
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
64 1 0.01
65 41 0.47
66 41 0.47
67 4 0.05
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (64 bp):
CACAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGGTTCAACAAAGTATGAGCAACTCCAG
Found at i:1525189 original size:66 final size:65
Alignment explanation
Indices: 1525062--1525202 Score: 189
Period size: 66 Copynumber: 2.2 Consensus size: 65
1525052 GAGGCAACAT
*
1525062 CGAGAGAAGCTGAGGTTCAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCAG
1 CGAGAGAAGCTGAGGTTCAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGAAGATGCGGCAG
* * *
1525127 CGAGAGAAGCTGAGGTTCAACGAAAG-TATG-AGCAACTGCAGC-AGTAGCTTAAAGAAGATGCG
1 CGAGAGAAGCTGAGGTTCAA--AAAGATATGAAG-AACTCCAGCTA-CAACTTAAAGAAGATGCG
1525189 GCAG
62 GCAG
1525193 CGAGAGAAGC
1 CGAGAGAAGC
1525203 AGCGGTTGCA
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
65 23 0.34
66 41 0.60
67 4 0.06
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.14
Consensus pattern (65 bp):
CGAGAGAAGCTGAGGTTCAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGAAGATGCGGCAG
Found at i:1526105 original size:43 final size:43
Alignment explanation
Indices: 1525575--1526104 Score: 724
Period size: 43 Copynumber: 12.4 Consensus size: 43
1525565 AAAGCGCCAA
* * *
1525575 GGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCGAAAGATCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
* * * *
1525618 AGTC---AGCGGCATTTTATGGGTAAGCGCCGCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
*
1525658 GGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
*
1525701 GGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
* * **
1525744 GGTCTATAGCGGCGTTTGATGCAAAAGCGCTTCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
* * * *
1525787 GGTCCATAGCGGCGTTTGATGCAAAAGTGCCGCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
*
1525830 GGTCTATAGCGGCGTTTTATGGATAAGCGCCGCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
* *
1525873 GGTCTATAGCGGCGTTTGATGGGTAAGCGCCACTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
* * *
1525916 GGGCTATAGCGGCGTTTGATGGGTAAGTGCCGCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
* * * **
1525959 GATCTATAGCGGCGTTTGATGCAAAAGCGCTTCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
* * * *
1526002 GGTCTTTAGCGGTGTTTGATGCAAAAGCGCCGCTAAAGACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
* * *
1526045 GGTCTATAACGGCGTTTAATGGATAAGCGCCGCTAAATACCAT
1 GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
1526088 GGTCTATAGCGGCGTTT
1 GGTCTATAGCGGCGTTT
1526105 ATTATAAAAA
Statistics
Matches: 435, Mismatches: 49, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
40 35 0.08
43 400 0.92
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (43 bp):
GGTCTATAGCGGCGTTTGATGGATAAGCGCCGCTAAAGACCAT
Found at i:1532387 original size:26 final size:26
Alignment explanation
Indices: 1532348--1532400 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1532338 AGTTCTTCAT
1532348 TGCTTTTGAAAAGTGCTGTGGAAAAA
1 TGCTTTTGAAAAGTGCTGTGGAAAAA
* * *
1532374 TGCTTTTGAGAAGTGCTTTTGAAAAA
1 TGCTTTTGAAAAGTGCTGTGGAAAAA
1532400 T
1 T
1532401 TTGAGTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTGTGGAAAAA
Found at i:1532390 original size:13 final size:13
Alignment explanation
Indices: 1532348--1532398 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
1532338 AGTTCTTCAT
1532348 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
1532361 TGCTGTGGAAAAA
1 TGCTTTTGAAAAG
*
1532374 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
1532387 TGCTTTTGAAAA
1 TGCTTTTGAAAA
1532399 ATTTGAGTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1535134 original size:19 final size:19
Alignment explanation
Indices: 1535110--1535149 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1535100 ATGCTGAAGC
1535110 AAAATGAAAAAACAAATTG
1 AAAATGAAAAAACAAATTG
1535129 AAAATGAAAAAACAAATTG
1 AAAATGAAAAAACAAATTG
1535148 AA
1 AA
1535150 GAGCCATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.70, C:0.05, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAATGAAAAAACAAATTG
Found at i:1536605 original size:21 final size:20
Alignment explanation
Indices: 1536539--1536622 Score: 64
Period size: 21 Copynumber: 4.2 Consensus size: 20
1536529 TGTTTAATTG
* *
1536539 AATTTA-TTTCATAAATCTT
1 AATTTATTTTAATTAATCTT
* *
1536558 ATTTATATTTTAATTAATCAT
1 AATT-TATTTTAATTAATCTT
**
1536579 GTTTTAGTTTTAATTAATCTT
1 AATTTA-TTTTAATTAATCTT
* *
1536600 AATTTA-CTTAATTAAGCTT
1 AATTTATTTTAATTAATCTT
1536619 AATT
1 AATT
1536623 GTTAATTTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
19 18 0.35
20 4 0.08
21 30 0.58
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.55
Consensus pattern (20 bp):
AATTTATTTTAATTAATCTT
Found at i:1537499 original size:14 final size:14
Alignment explanation
Indices: 1537480--1537506 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1537470 GTACAATAAT
1537480 AAAAATATTTTATG
1 AAAAATATTTTATG
1537494 AAAAATATTTTAT
1 AAAAATATTTTAT
1537507 ATGCAAACGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
AAAAATATTTTATG
Found at i:1545815 original size:24 final size:25
Alignment explanation
Indices: 1545776--1545829 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1545766 TTGTATAAAT
*
1545776 TATATTTTAATTATAA-TATATTTAA
1 TATA-TTTAATAATAATTATATTTAA
*
1545801 TATATTTAATAATAATTATGTTTAA
1 TATATTTAATAATAATTATATTTAA
1545826 -ATAT
1 TATAT
1545830 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATATTTAATAATAATTATATTTAA
Found at i:1545996 original size:39 final size:40
Alignment explanation
Indices: 1545953--1546057 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
1545943 TTCCATTATG
1545953 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
1545992 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
1546037 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
1546058 ACACCTCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:1546051 original size:45 final size:44
Alignment explanation
Indices: 1545951--1546060 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
1545941 TTTTCCATTA
1545951 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
1545990 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
1546035 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
1546061 CCTCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:1546060 original size:16 final size:16
Alignment explanation
Indices: 1546039--1546092 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
1546029 TTGATTTGCT
1546039 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
1546055 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
1546071 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
1546087 AATACA
1 ATTACA
1546093 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:1546477 original size:17 final size:17
Alignment explanation
Indices: 1546455--1546490 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1546445 TACTTGTTTT
1546455 TAAAATTATT-TGATAAA
1 TAAAATT-TTATGATAAA
1546472 TAAAATTTTATGATAAA
1 TAAAATTTTATGATAAA
1546489 TA
1 TA
1546491 TTATAATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
TAAAATTTTATGATAAA
Found at i:1547459 original size:30 final size:30
Alignment explanation
Indices: 1547425--1547506 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
1547415 CTGAGCATTT
* * *
1547425 CCACATGGGCTGGATACATGCCTGTGTGAG
1 CCACATGGGCTGGACACACGCCTGTGTAAG
1547455 CCACATGGGCTGGACACACGCCTGTGTAAG
1 CCACATGGGCTGGACACACGCCTGTGTAAG
1547485 CCACATGGGCTGGACACACGCC
1 CCACATGGGCTGGACACACGCC
1547507 CATGTGCCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.22, C:0.30, G:0.30, T:0.17
Consensus pattern (30 bp):
CCACATGGGCTGGACACACGCCTGTGTAAG
Found at i:1552368 original size:23 final size:23
Alignment explanation
Indices: 1552342--1552402 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 23
1552332 AGGCACTTTA
1552342 TGTGTTGTATTTCAGGCACCTCG
1 TGTGTTGTATTTCAGGCACCTCG
*
1552365 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTTGTATTTCAGGCACCTCG
*
1552386 TGTG-T-CATTTCAGGCAC
1 TGTGTTGTATTTCAGGCAC
1552403 TTATGTGTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.03
21 24 0.73
23 8 0.24
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (23 bp):
TGTGTTGTATTTCAGGCACCTCG
Found at i:1552377 original size:21 final size:21
Alignment explanation
Indices: 1552353--1552415 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
1552343 GTGTTGTATT
1552353 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
* *
1552374 TCAGGCACCTCGTGTGTCATT
1 TCAGGCACCTCGTGTGTCGTA
**
1552395 TCAGGCA-CTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
1552415 T
1 T
1552416 ACTGATCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 10 0.28
21 26 0.72
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCGTA
Found at i:1555154 original size:27 final size:31
Alignment explanation
Indices: 1555093--1555155 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
1555083 TATTTATTTG
* *
1555093 TTTATTATTCTTCTTTTTTTATTCTCTGTTA
1 TTTATTATTCTTCTTTTTCTAGTCTCTGTTA
1555124 -TTATTATT-TTCTTTTTCTAGT-T-T-TTA
1 TTTATTATTCTTCTTTTTCTAGTCTCTGTTA
1555150 TTTATT
1 TTTATT
1555156 TATTATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 3 0.10
27 6 0.21
28 1 0.03
29 11 0.38
30 8 0.28
ACGTcount: A:0.14, C:0.10, G:0.03, T:0.73
Consensus pattern (31 bp):
TTTATTATTCTTCTTTTTCTAGTCTCTGTTA
Found at i:1555705 original size:12 final size:12
Alignment explanation
Indices: 1555690--1555734 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
1555680 ACTAATTCTT
1555690 TCTCAAATTTCC
1 TCTCAAATTTCC
*
1555702 TCTC-AATTTGC
1 TCTCAAATTTCC
1555713 TCTCAAA-TTCC
1 TCTCAAATTTCC
1555724 T-TCCAAATTTC
1 TCT-CAAATTTC
1555735 TCTTAAATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 18 0.64
12 9 0.32
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (12 bp):
TCTCAAATTTCC
Found at i:1555732 original size:23 final size:21
Alignment explanation
Indices: 1555690--1555742 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1555680 ACTAATTCTT
1555690 TCTCAAATTTCCTCTCAATTTGC
1 TCTCAAA-TTCCTCTCAATTT-C
1555713 TCTCAAATTCCT-TCCAAATTTC
1 TCTCAAATTCCTCT-C-AATTTC
*
1555735 TCTTAAAT
1 TCTCAAAT
1555743 CCATATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 12 0.44
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.43
Consensus pattern (21 bp):
TCTCAAATTCCTCTCAATTTC
Found at i:1555783 original size:51 final size:51
Alignment explanation
Indices: 1555702--1555801 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
1555692 TCAAATTTCC
1555702 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTTAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTTAAATCCATATTTAA
* * *
1555753 TCTCAATTTGCTCTCAATTTCC-TCTTAAATTTCTCTTAAATCCTTATTT
1 TCTCAATTTGCTCTCAAATTCCTTC-CAAATTTCTCTTAAATCCATATTT
1555802 TTAAATAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.04
51 43 0.96
ACGTcount: A:0.26, C:0.25, G:0.02, T:0.47
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTTAAATCCATATTTAA
Found at i:1555827 original size:15 final size:15
Alignment explanation
Indices: 1555804--1555844 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1555794 CCTTATTTTT
*
1555804 AAATAATTTTAAAAA
1 AAATTATTTTAAAAA
*
1555819 AAATTATTTT-TAAA
1 AAATTATTTTAAAAA
1555833 AAATT-TTTTAAA
1 AAATTATTTTAAA
1555845 TCGTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTATTTTAAAAA
Done.