Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 44 of 202
Found at i:13185579 original size:46 final size:46
Alignment explanation
Indices: 13185526--13185620 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
13185516 TGTCAGATTG
*
13185526 CATGGAGTACCAGTCTCCATCATTTTGGATAGAGATCCGCGGTTTA
1 CATGGAGTACCAGTCTCCATCATTTCGGATAGAGATCCGCGGTTTA
*
13185572 CATGGAGTACCAGTCTCCATCATTTCGGATAGAGATCCGTGGTTTA
1 CATGGAGTACCAGTCTCCATCATTTCGGATAGAGATCCGCGGTTTA
13185618 CAT
1 CAT
13185621 CACGATTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (46 bp):
CATGGAGTACCAGTCTCCATCATTTCGGATAGAGATCCGCGGTTTA
Found at i:13197395 original size:7 final size:7
Alignment explanation
Indices: 13197385--13197409 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13197375 ATGTTGAAAT
13197385 AAATTTG
1 AAATTTG
13197392 AAATTTG
1 AAATTTG
13197399 AAATTTG
1 AAATTTG
13197406 AAAT
1 AAAT
13197410 CAAATTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (7 bp):
AAATTTG
Found at i:13199888 original size:43 final size:43
Alignment explanation
Indices: 13199821--13199916 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 43
13199811 CAAACCAATT
* * * *
13199821 TGTGGACAAGTCACTAGTAATTGTAGAT-ATA-CTGCCACAAATA
1 TGTGGACAAGCCACCAATAATTGTAG-TCA-AGCTGCCAAAAATA
*
13199864 TGTGGACAAGCCACCAATATTTGTAGTCAAGCTGCCAAAAATA
1 TGTGGACAAGCCACCAATAATTGTAGTCAAGCTGCCAAAAATA
13199907 TGTGGACAAG
1 TGTGGACAAG
13199917 TTACAAGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.04
43 44 0.96
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (43 bp):
TGTGGACAAGCCACCAATAATTGTAGTCAAGCTGCCAAAAATA
Found at i:13199974 original size:40 final size:40
Alignment explanation
Indices: 13199924--13200022 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 40
13199914 AAGTTACAAG
* *
13199924 TATTACAGATAAACTGTCAGTATTATGGACAAGCCATCAA
1 TATTGCAGATAAACTGTCAGTATTACGGACAAGCCATCAA
* * * *
13199964 TATTGTAGATAAACTATCAGTATTGCGGACAAGCCATCAG
1 TATTGCAGATAAACTGTCAGTATTACGGACAAGCCATCAA
*
13200004 TATTGCAAATAAACTGTCA
1 TATTGCAGATAAACTGTCA
13200023 AATCTTCCTC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (40 bp):
TATTGCAGATAAACTGTCAGTATTACGGACAAGCCATCAA
Found at i:13200002 original size:20 final size:20
Alignment explanation
Indices: 13199940--13200009 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
13199930 AGATAAACTG
**
13199940 TCAGTATTATGGACAAGCCA
1 TCAGTATTGCGGACAAGCCA
* ** * * *
13199960 TCAATATTGTAGATAAACTA
1 TCAGTATTGCGGACAAGCCA
13199980 TCAGTATTGCGGACAAGCCA
1 TCAGTATTGCGGACAAGCCA
13200000 TCAGTATTGC
1 TCAGTATTGC
13200010 AAATAAACTG
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (20 bp):
TCAGTATTGCGGACAAGCCA
Found at i:13203247 original size:16 final size:17
Alignment explanation
Indices: 13203228--13203263 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13203218 ATATTAATGT
*
13203228 TATTTAAT-CTTAAAAA
1 TATTTAATACTAAAAAA
13203244 TATTTAATACTAAAAAA
1 TATTTAATACTAAAAAA
13203261 TAT
1 TAT
13203264 ATAAAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTTAATACTAAAAAA
Found at i:13206298 original size:3 final size:3
Alignment explanation
Indices: 13206290--13206335 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
13206280 GTTTTTTAGT
13206290 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
13206336 ACCTATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13209812 original size:85 final size:88
Alignment explanation
Indices: 13209582--13209931 Score: 526
Period size: 88 Copynumber: 4.0 Consensus size: 88
13209572 AGCTGTATCA
* * * *
13209582 AAGACACCAGCCTTGCCTCCTTGGGTTGCAGCAGATCAGGCTAAAAATAGTAGATCTTACCTTCC
1 AAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGATCTTGCCTTCC
*
13209647 TGCACTGACAGCGAAGCAGATCG
66 TGCACCGACAGCGAAGCAGATCG
*
13209670 AAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGATCTTGCCTTCT
1 AAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGATCTTGCCTTCC
*
13209735 TGCACCGACAACGAAGCAGATC-
66 TGCACCGACAGCGAAGCAGATCG
* * *
13209757 AA-AGA-CAGCCTTGCCTCCCTGGGTTCCAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCC
1 AAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGATCTTGCCTTCC
13209820 TGCACCGACAGCGAAGCAGATCG
66 TGCACCGACAGCGAAGCAGATCG
* * * * *
13209843 AAGACACCAGCCTTGCCTCCCTAGGTTACAGCGAAGTAGGCTAAAAATAGTAGATCTTGCCTTGC
1 AAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGATCTTGCCTTCC
* *
13209908 TGCACTGACTGCGAAGCAGATCG
66 TGCACCGACAGCGAAGCAGATCG
13209931 A
1 A
13209932 TGACCCTAGC
Statistics
Matches: 238, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
85 76 0.32
86 4 0.02
87 4 0.02
88 154 0.65
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
AAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGATCTTGCCTTCC
TGCACCGACAGCGAAGCAGATCG
Found at i:13209816 original size:44 final size:44
Alignment explanation
Indices: 13209681--13209821 Score: 103
Period size: 44 Copynumber: 3.3 Consensus size: 44
13209671 AGACACCAGC
* *
13209681 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGAT
1 CTTGCCTCCCTGGGTTCCAGCGGAGCAGGCTAAAAATAGCAGAT
* * *** * * * * * *
13209725 CTTGCCT-TCTTGCACCGACAACGAAGCA-GAT-CAAAGA-CAG-C
1 CTTGCCTCCCTGGGTTC--CAGCGGAGCAGGCTAAAAATAGCAGAT
13209766 CTTGCCTCCCTGGGTTCCAGCGGAGCAGGCTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTCCAGCGGAGCAGGCTAAAAATAGCAGAT
*
13209810 CTTGCCTTCCTG
1 CTTGCCTCCCTG
13209822 CACCGACAGC
Statistics
Matches: 65, Mismatches: 25, Indels: 14
0.62 0.24 0.13
Matches are distributed among these distances:
40 8 0.12
41 9 0.14
42 10 0.15
43 10 0.15
44 20 0.31
45 8 0.12
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTCCAGCGGAGCAGGCTAAAAATAGCAGAT
Found at i:13209886 original size:173 final size:173
Alignment explanation
Indices: 13209589--13209929 Score: 540
Period size: 173 Copynumber: 2.0 Consensus size: 173
13209579 TCAAAGACAC
* * * * *
13209589 CAGCCTTGCCTCCTTGGGTTGCAGCAGATCAGGCTAAAAATAGTAGATCTTACCTTCCTGCACTG
1 CAGCCTTGCCTCCCTGGGTTCCAGCAGAGCAGGCTAAAAATAGCAGATCTTACCTTCCTGCACCG
* * *
13209654 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATA
66 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTACAGCGAAGCAGGCTAAAAATA
13209719 GTAGATCTTGCCTT-CTTGCACCGACAACGAAGCAGATCAAAGA
131 GTAGATCTTGCCTTGC-TGCACCGACAACGAAGCAGATCAAAGA
* *
13209762 CAGCCTTGCCTCCCTGGGTTCCAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCG
1 CAGCCTTGCCTCCCTGGGTTCCAGCAGAGCAGGCTAAAAATAGCAGATCTTACCTTCCTGCACCG
*
13209827 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTACAGCGAAGTAGGCTAAAAATA
66 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTACAGCGAAGCAGGCTAAAAATA
* **
13209892 GTAGATCTTGCCTTGCTGCACTGACTGCGAAGCAGATC
131 GTAGATCTTGCCTTGCTGCACCGACAACGAAGCAGATC
13209930 GATGACCCTA
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
173 152 0.99
174 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (173 bp):
CAGCCTTGCCTCCCTGGGTTCCAGCAGAGCAGGCTAAAAATAGCAGATCTTACCTTCCTGCACCG
ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTACAGCGAAGCAGGCTAAAAATA
GTAGATCTTGCCTTGCTGCACCGACAACGAAGCAGATCAAAGA
Found at i:13210007 original size:44 final size:43
Alignment explanation
Indices: 13209942--13210151 Score: 269
Period size: 44 Copynumber: 4.8 Consensus size: 43
13209932 TGACCCTAGC
* *
13209942 CCTATCTTCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAT
*
13209986 CTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGATAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG-TAAT
* * * *
13210030 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTA-AT
* * *
13210074 CCTATCTCCCTGGTCAGCAGTAGAATAGGTTGAAGATCGTAAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAT
*
13210118 CCTATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAA
13210152 AATAGCAGAT
Statistics
Matches: 145, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
43 2 0.01
44 140 0.97
45 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAT
Found at i:13210892 original size:128 final size:128
Alignment explanation
Indices: 13210718--13210966 Score: 347
Period size: 128 Copynumber: 1.9 Consensus size: 128
13210708 AGATGGCAAA
* * * * *
13210718 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCTTAAAGTTGCT
1 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATAAAAGACGACAATCCTATCTCCCTAAAGTTGCA
* * *
13210783 GTGGAGCGGATTAAAACCACAGATTTTATCTCTCTGAAGTTACAGAGAGTAGATCGCATCCAG
66 GTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTACAGAGAATAGATCGCATCCAG
* * *
13210846 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAAGAC-ACCAATCCTATCTCCCTGAGGTTGC
1 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATAAAAGACGA-CAATCCTATCTCCCTAAAGTTGC
* * * *
13210910 AGTGGAGTGGATTGAAACCGCAGATCTTATCTCTCTAAAGTTGCAGAGAATAGATCG
65 AGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTACAGAGAATAGATCG
13210967 TATCAAATTC
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
127 1 0.01
128 104 0.99
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (128 bp):
TCTTATCTCCCTGAAATTGCAGTGGAGCAGATAAAAGACGACAATCCTATCTCCCTAAAGTTGCA
GTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTACAGAGAATAGATCGCATCCAG
Found at i:13210911 original size:217 final size:216
Alignment explanation
Indices: 13210493--13210913 Score: 614
Period size: 217 Copynumber: 1.9 Consensus size: 216
13210483 CAACATTGCA
* * *
13210493 ATGGCGAATCTTATCTCCCTGAAGTAGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTG
1 ATGGCAAATCTTATCTCCCTGAAATAGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTA
**** *
13210558 AAGTTGCAGTGGAGCGGATTAAAACTTTGGATCTTATCTCTCTGAAGTTGCAGAGAGTAGATCGC
66 AAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGAGTAGATCGC
* * *
13210623 ATCTAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAA
131 ATCCAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAATCCTATCCTCCTGAA
13210688 GTTGCAGTGAGGCAGACTGAAG
195 GTTGCAGTGAGGCAGACTGAAG
* * *
13210710 ATGGCAAATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCTTA
1 ATGGCAAATCTTATCTCCCTGAAATAGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTA
* *
13210775 AAGTTGCTGTGGAGCGGATTAAAACCACAGATTTTATCTCTCTGAAGTTACAGAGAGTAGATCGC
66 AAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGAGTAGATCGC
*
13210840 ATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAA-AAGACACCAATCCTAT-CTCCCT
131 ATCCAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-CA--AATCCTATCCT-CCT
*
13210902 GAGGTTGCAGTG
192 GAAGTTGCAGTG
13210914 GAGTGGATTG
Statistics
Matches: 182, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
214 3 0.02
215 2 0.01
216 5 0.03
217 172 0.95
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (216 bp):
ATGGCAAATCTTATCTCCCTGAAATAGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTA
AAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGAGTAGATCGC
ATCCAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAATCCTATCCTCCTGAAG
TTGCAGTGAGGCAGACTGAAG
Found at i:13210941 original size:44 final size:43
Alignment explanation
Indices: 13210500--13210955 Score: 257
Period size: 44 Copynumber: 10.5 Consensus size: 43
13210490 GCAATGGCGA
* * * *
13210500 ATCTTATCTCCCTGAAGTAGCAGTGGAGCAGATTAAAGCCAATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCCA-G
* * ***
13210544 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTTTGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC-CCAG
* * * *** * *
13210588 ATCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-TCGCATCTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCCAG
* * * *
13210629 -TATTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCCAG
* *** *
13210673 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-AACCCAG
* * * *
13210717 ATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCCGATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCCA-G
* * * * *
13210761 ATCCTATCTCCTTAAAGTTGCTGTGGAGCGGATTAAAACCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-CAG
* * * * * *** *
13210805 ATTTTATCTCTCTGAAGTTACAG-AGAGTAGA-TCGCATCCAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCCAG
*
13210846 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAAGACACCA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-AC-CCAG
* * ** *
13210889 ATCCTATCTCCCTGAGGTTGCAGTGGAGTGGATTGAAACCGCAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-CAG
* *
13210933 ATCTTATCTCTCTAAAGTTGCAG
1 ATCTTATCTCCCTGAAGTTGCAG
13210956 AGAATAGATC
Statistics
Matches: 307, Mismatches: 85, Indels: 40
0.71 0.20 0.09
Matches are distributed among these distances:
40 39 0.13
41 17 0.06
42 7 0.02
43 20 0.07
44 193 0.63
45 28 0.09
46 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCCAG
Found at i:13211755 original size:17 final size:17
Alignment explanation
Indices: 13211733--13211765 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13211723 TTCTTTTTAC
13211733 TGTTTTTATTTTATTTT
1 TGTTTTTATTTTATTTT
*
13211750 TGTTTTTCTTTTATTT
1 TGTTTTTATTTTATTT
13211766 CTTAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (17 bp):
TGTTTTTATTTTATTTT
Found at i:13213913 original size:2 final size:2
Alignment explanation
Indices: 13213906--13213946 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13213896 CACATCATGG
13213906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13213947 ACAAATGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13220423 original size:23 final size:22
Alignment explanation
Indices: 13220380--13220423 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
13220370 TTCTAAGTCG
13220380 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
13220403 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
13220424 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:13220532 original size:45 final size:45
Alignment explanation
Indices: 13220468--13220561 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
13220458 AACAGATACT
* *
13220468 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
13220513 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
13220558 CGGT
1 CGGT
13220562 TCACATAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:13220684 original size:50 final size:51
Alignment explanation
Indices: 13220556--13220694 Score: 174
Period size: 51 Copynumber: 2.7 Consensus size: 51
13220546 ATCAATGATG
* * * *
13220556 TTCGGTTCACATAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTA
1 TTCGGTACACATAGTAGCCTGCACATAGTACTACACACGCGAGCCAAACTA
* * * *
13220607 TTCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCG-GCCTATC-A
1 TTCGGTACACATAGTAGCCTGCACATAGTACTACACACGCGAGCCAAACTA
*
13220656 TTCCGGTACACGTAGTAGCCTGCACATAGTACTACACAC
1 TT-CGGTACACATAGTAGCCTGCACATAGTACTACACAC
13220695 ATGACCATCA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
49 3 0.04
50 36 0.47
51 37 0.49
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (51 bp):
TTCGGTACACATAGTAGCCTGCACATAGTACTACACACGCGAGCCAAACTA
Found at i:13226265 original size:19 final size:18
Alignment explanation
Indices: 13226241--13226303 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
13226231 TACATGAATT
13226241 CATTTCAATATTCATATCC
1 CATTTCAATATTCATAT-C
13226260 CATTTC-ATCATTTCATATTC
1 CATTTCAAT-A-TTCATA-TC
*
13226280 CATTTCCAAT-CTCATATC
1 CATTT-CAATATTCATATC
13226298 CATTTC
1 CATTTC
13226304 TCATCCTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
17 1 0.03
18 9 0.24
19 12 0.32
20 12 0.32
21 2 0.05
22 2 0.05
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (18 bp):
CATTTCAATATTCATATC
Found at i:13226294 original size:27 final size:27
Alignment explanation
Indices: 13226240--13226294 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
13226230 ATACATGAAT
* *
13226240 TCATTTCAATATTCATATCCCATTTCA
1 TCATTTCAATATTCATATCCAATCTCA
*
13226267 TCATTTC-ATATTCCATTTCCAATCTCA
1 TCATTTCAATATT-CATATCCAATCTCA
13226294 T
1 T
13226295 ATCCATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (27 bp):
TCATTTCAATATTCATATCCAATCTCA
Found at i:13227039 original size:36 final size:34
Alignment explanation
Indices: 13226999--13227065 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
13226989 ATTTATTTGT
* * *
13226999 TTTCATTTTAATTCATTATTATATAATATATATGCA
1 TTTCATGTT-ATTCATTATAACAT-ATATATATGCA
*
13227035 TTTCATGTTATTTATTATAACATATATATAT
1 TTTCATGTTATTCATTATAACATATATATAT
13227066 TAAGTTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 8 0.30
35 11 0.41
36 8 0.30
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTCATGTTATTCATTATAACATATATATATGCA
Found at i:13231892 original size:38 final size:38
Alignment explanation
Indices: 13231835--13231927 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 38
13231825 TCAATTTAAT
* ** *
13231835 CAATAACATTAGATATGCTTAACCTGTA-TTAGGTTCAA
1 CAATAACAGTAGGCATGCTTAACATGTATTTA-GTTCAA
*
13231873 -AATTAATAGTAGGCATGCTTAACATGTATTTAGTTCAA
1 CAA-TAACAGTAGGCATGCTTAACATGTATTTAGTTCAA
13231911 CAATAACAGTAGGCATG
1 CAATAACAGTAGGCATG
13231928 TTGAACAAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
37 2 0.04
38 39 0.85
39 5 0.11
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (38 bp):
CAATAACAGTAGGCATGCTTAACATGTATTTAGTTCAA
Found at i:13235595 original size:7 final size:7
Alignment explanation
Indices: 13235583--13235611 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
13235573 ATCTGATCTG
13235583 AGTACCA
1 AGTACCA
13235590 AGTACCA
1 AGTACCA
13235597 AGTACCA
1 AGTACCA
13235604 AGTACCA
1 AGTACCA
13235611 A
1 A
13235612 TTGCATGCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.28, G:0.14, T:0.14
Consensus pattern (7 bp):
AGTACCA
Found at i:13237342 original size:5 final size:5
Alignment explanation
Indices: 13237332--13237362 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
13237322 TAGGGGATGA
13237332 GATTG GATTG GATTG GATTG GATTG GATTG G
1 GATTG GATTG GATTG GATTG GATTG GATTG G
13237363 TGTCTGGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.39
Consensus pattern (5 bp):
GATTG
Found at i:13241437 original size:31 final size:31
Alignment explanation
Indices: 13241402--13241464 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
13241392 TTTCAAAGTA
13241402 TGTCAAATTCTTTATTTCCTTCCTTAGTAAG
1 TGTCAAATTCTTTATTTCCTTCCTTAGTAAG
*
13241433 TGTCAATTTCTTTATTTCCTTCCTTAGTAAG
1 TGTCAAATTCTTTATTTCCTTCCTTAGTAAG
13241464 T
1 T
13241465 CTTTTTGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.51
Consensus pattern (31 bp):
TGTCAAATTCTTTATTTCCTTCCTTAGTAAG
Found at i:13261244 original size:18 final size:18
Alignment explanation
Indices: 13261218--13261252 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13261208 TAGACTAGAT
*
13261218 TTAACTCCCTAATTTCAC
1 TTAAATCCCTAATTTCAC
13261236 TTAAATCCCTAATTTCA
1 TTAAATCCCTAATTTCA
13261253 AATTTTCACA
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:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAATCCCTAATTTCAC
Found at i:13261274 original size:28 final size:27
Alignment explanation
Indices: 13261241--13261295 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
13261231 TTCACTTAAA
*
13261241 TCCCTAATT-TCAAATTTTCACAATTTAG
1 TCCCT-ATTATCAAAATTT-ACAATTTAG
13261269 TCCCTATTACTCAAAATTTACAATTTA
1 TCCCTATTA-TCAAAATTTACAATTTA
13261296 TTCTACAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.12
28 13 0.54
29 8 0.33
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.42
Consensus pattern (27 bp):
TCCCTATTATCAAAATTTACAATTTAG
Found at i:13261640 original size:18 final size:18
Alignment explanation
Indices: 13261617--13261659 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13261607 TTATTTATTT
13261617 TATTATAATACT-ATAATA
1 TATTATAATA-TAATAATA
*
13261635 TATTATTATATAATAATA
1 TATTATAATATAATAATA
*
13261653 TAATATA
1 TATTATA
13261660 TTTACTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATAATATAATAATA
Found at i:13261646 original size:23 final size:23
Alignment explanation
Indices: 13261612--13261662 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
13261602 TTTACTTATT
*
13261612 TATTTTATTATAATACTATAATA
1 TATTTTATTATAATAATATAATA
13261635 TATTATTA-TATAATAATATAATA
1 TATT-TTATTATAATAATATAATA
13261658 TATTT
1 TATTT
13261663 ACTTAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.85
24 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTTTATTATAATAATATAATA
Found at i:13266395 original size:46 final size:46
Alignment explanation
Indices: 13266329--13266570 Score: 351
Period size: 46 Copynumber: 5.3 Consensus size: 46
13266319 TGACAAGTGG
* *
13266329 AAAGTGATAAGTAATGGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
13266375 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
* ** *
13266421 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
* *
13266467 -AAGTGAAAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
* ** * **
13266512 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAAAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
13266558 AAAGTGATAAGTG
1 AAAGTGATAAGTG
13266571 GCTACACTTA
Statistics
Matches: 176, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 39 0.22
46 137 0.78
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
Found at i:13266494 original size:91 final size:92
Alignment explanation
Indices: 13266329--13266570 Score: 387
Period size: 91 Copynumber: 2.6 Consensus size: 92
13266319 TGACAAGTGG
* ** *
13266329 AAAGTGATAAGTAATGGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
1 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
*
13266394 TCGGCTATACTTATCTGATCAAGTGAC
66 TCGGCTATACTTATCTGATCAAGAGAC
** *
13266421 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGTGAAAAGTGATAGCT
1 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
13266485 TCGGCTATACTTATCTGATCAAGAGAC
66 TCGGCTATACTTATCTGATCAAGAGAC
**
13266512 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAAAGACAAAGTGATAAGTG
1 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
13266571 GCTACACTTA
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
91 85 0.62
92 51 0.38
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (92 bp):
AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
TCGGCTATACTTATCTGATCAAGAGAC
Found at i:13266531 original size:137 final size:141
Alignment explanation
Indices: 13266263--13266571 Score: 482
Period size: 137 Copynumber: 2.2 Consensus size: 141
13266253 TTTGAGTACT
*
13266263 TCTGATCAAGGGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* * *
13266328 GAAAGTGATAAGTAATGGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGC
66 AAAAGTG--AAGTAA-GGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTAATAGC
* *
13266393 TTCGGCTATACTTA
128 TTCAGCTACACTTA
*
13266407 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
13266472 AAAAGTG-A-T-A-GCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTAATAGCTTT
66 AAAAGTGAAGTAAGGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTAATAGCTTC
13266533 AGCTACACTTA
131 AGCTACACTTA
*
13266544 TCTGATCAAAAGACAAAGTGATAAGTGG
1 TCTGATCAAGAGACAAAGTGATAAGTGG
13266572 CTACACTTAT
Statistics
Matches: 156, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
137 83 0.53
139 1 0.01
140 1 0.01
141 1 0.01
144 70 0.45
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (141 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGAAGTAAGGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTAATAGCTTC
AGCTACACTTA
Found at i:13266584 original size:37 final size:37
Alignment explanation
Indices: 13266534--13266716 Score: 309
Period size: 37 Copynumber: 5.0 Consensus size: 37
13266524 AATAGCTTTA
13266534 GCTACACTTATCTGATCAA-AAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAA-ACAAAGTGATAAGTG
13266571 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
13266608 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
13266645 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
13266682 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
13266717 ATCATACGTA
Statistics
Matches: 141, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
35 11 0.08
36 4 0.03
37 124 0.88
38 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:13267629 original size:75 final size:75
Alignment explanation
Indices: 13267491--13267683 Score: 233
Period size: 75 Copynumber: 2.6 Consensus size: 75
13267481 TATATTTACA
* * * ** *
13267491 TGTATATGTTCTTGTATTGAGTTTGGGTATGATTTTTATGTAAGTTTATATGAAATTTGGAAATG
1 TGTATATGTTCTTGTATTGAGTTTAGGTATGACTTTTATATAAGTTTATATGAAATTCAGAAATA
13267556 CAAATATAAT
66 CAAATATAAT
* * **
13267566 TGTATATGTTATTGTTTTGAGTTTAGGTATGACTTTTATATAAGTTTATATGAGGTTCAGAAATA
1 TGTATATGTTCTTGTATTGAGTTTAGGTATGACTTTTATATAAGTTTATATGAAATTCAGAAATA
* *
13267631 TAAATATATT
66 CAAATATAAT
* ** * *
13267641 TGAATATGTTCTTGCGTTAAATTTAGGTATGACTTTTATATAA
1 TGTATATGTTCTTGTATTGAGTTTAGGTATGACTTTTATATAA
13267684 ATGTGTATGA
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 100 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (75 bp):
TGTATATGTTCTTGTATTGAGTTTAGGTATGACTTTTATATAAGTTTATATGAAATTCAGAAATA
CAAATATAAT
Found at i:13268163 original size:41 final size:41
Alignment explanation
Indices: 13268090--13268181 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
13268080 GGCTCAGTGC
* * * * *
13268090 CTAGCAGGCTTGATGCCAATGATATGTTTCAGACTTTATGT
1 CTAGCAGGCTTGATGCCAATGAAATATCTCAGACTATACGT
**
13268131 CTAGCAGGCTTGATGCCGGTGAAATATCTCAGACTATACGT
1 CTAGCAGGCTTGATGCCAATGAAATATCTCAGACTATACGT
*
13268172 CTAGTAGGCT
1 CTAGCAGGCT
13268182 AATTGCCGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (41 bp):
CTAGCAGGCTTGATGCCAATGAAATATCTCAGACTATACGT
Found at i:13275165 original size:20 final size:20
Alignment explanation
Indices: 13275142--13275179 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13275132 CTAAAGAAAG
13275142 TAAATAT-AATGGAAAGTAAT
1 TAAATATAAAT-GAAAGTAAT
*
13275162 TAAATGTAAATGAAAGTA
1 TAAATATAAATGAAAGTA
13275180 GGAAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (20 bp):
TAAATATAAATGAAAGTAAT
Found at i:13278070 original size:24 final size:24
Alignment explanation
Indices: 13278043--13278151 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 24
13278033 AAGCTTGCAA
* *
13278043 GAGCGTCTCGTTATTAGCTCTCAT
1 GAGCATCTCGATATTAGCTCTCAT
* *
13278067 GAGCATCTCGATATTGGCTCTCTT
1 GAGCATCTCGATATTAGCTCTCAT
* *
13278091 GAGCTTC-CTGATATATGGCTCTCAT
1 GAGCATCTC-GATAT-TAGCTCTCAT
** * * * * *
13278116 GAGTTTCCCGTTAATAACTCTTAT
1 GAGCATCTCGATATTAGCTCTCAT
13278140 GAGCATCTCGAT
1 GAGCATCTCGAT
13278152 TGATTGTGAT
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
23 1 0.02
24 46 0.70
25 18 0.27
26 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (24 bp):
GAGCATCTCGATATTAGCTCTCAT
Found at i:13278118 original size:25 final size:25
Alignment explanation
Indices: 13278049--13278123 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 25
13278039 GCAAGAGCGT
* * *
13278049 CTCGTTATTAGCTCTCATGAGCAT-
1 CTCGATATTGGCTCTCATGAGCTTC
*
13278073 CTCGATATTGGCTCTCTTGAGCTTC
1 CTCGATATTGGCTCTCATGAGCTTC
*
13278098 CT-GATATATGGCTCTCATGAGTTTC
1 CTCGATAT-TGGCTCTCATGAGCTTC
13278123 C
1 C
13278124 CGTTAATAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
24 25 0.58
25 18 0.42
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (25 bp):
CTCGATATTGGCTCTCATGAGCTTC
Found at i:13278274 original size:25 final size:25
Alignment explanation
Indices: 13278246--13278331 Score: 111
Period size: 25 Copynumber: 3.4 Consensus size: 25
13278236 GGCTTGCAAG
*
13278246 AGCTTCCCGTTATATGGCTCACATA
1 AGCTTCCCGTTACATGGCTCACATA
* *
13278271 AGCTTCCTGTTACATAGCTCACATA
1 AGCTTCCCGTTACATGGCTCACATA
* *
13278296 AGCTTCCCGTTACATGGCTTAGA-A
1 AGCTTCCCGTTACATGGCTCACATA
13278320 GAGCTTCCCGTT
1 -AGCTTCCCGTT
13278332 TATATGCTCG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
24 1 0.02
25 52 0.98
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.31
Consensus pattern (25 bp):
AGCTTCCCGTTACATGGCTCACATA
Found at i:13285057 original size:27 final size:27
Alignment explanation
Indices: 13285027--13285097 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
13285017 ACGAATACTC
13285027 CACAGCTCGTGTGAGCAAGCCCATTTT
1 CACAGCTCGTGTGAGCAAGCCCATTTT
*
13285054 CACAGCTCGTGTGAGCAAGCCTATTTT
1 CACAGCTCGTGTGAGCAAGCCCATTTT
13285081 CACAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
13285098 TATATGTACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (27 bp):
CACAGCTCGTGTGAGCAAGCCCATTTT
Found at i:13288662 original size:39 final size:40
Alignment explanation
Indices: 13288608--13288689 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 40
13288598 TTCATAAACC
13288608 TAAGCATATTTATAACTCATAAACCTCAT-AAAAAATTAA
1 TAAGCATATTTATAACTCATAAACCTCATAAAAAAATTAA
13288647 TAAGCATATTTATAACTCATAAACCTCATAAAAAAATTAA
1 TAAGCATATTTATAACTCATAAACCTCATAAAAAAATTAA
13288687 TAA
1 TAA
13288690 CCAGCAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 29 0.69
40 13 0.31
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.30
Consensus pattern (40 bp):
TAAGCATATTTATAACTCATAAACCTCATAAAAAAATTAA
Found at i:13290790 original size:18 final size:18
Alignment explanation
Indices: 13290761--13290805 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
13290751 GAACAACACC
13290761 GTGTTA-ATTTGTGT-TCT
1 GTGTTATATTTGTGTCT-T
13290778 GTGTTATATTTGTGTCTT
1 GTGTTATATTTGTGTCTT
13290796 GTGTTATATT
1 GTGTTATATT
13290806 GTTAACAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.23
18 19 0.73
19 1 0.04
ACGTcount: A:0.13, C:0.04, G:0.22, T:0.60
Consensus pattern (18 bp):
GTGTTATATTTGTGTCTT
Found at i:13292723 original size:17 final size:17
Alignment explanation
Indices: 13292701--13292791 Score: 57
Period size: 17 Copynumber: 5.4 Consensus size: 17
13292691 ATTTTAATAT
13292701 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
*
13292718 TTTAATATT-TATCTTAA
1 TTTAATATTAAAT-TTAA
**
13292735 --TAATATTTTA-TTAA
1 TTTAATATTAAATTTAA
* *
13292749 TCTAATAATAAACTGATT-A
1 TTTAATATTAAA-T--TTAA
13292768 TCTTAATATTAAATTTAA
1 T-TTAATATTAAATTTAA
13292786 TTTAAT
1 TTTAAT
13292792 GTTTATCTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 4 0.07
15 7 0.12
16 11 0.19
17 20 0.34
18 2 0.03
19 3 0.05
20 11 0.19
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:13292866 original size:19 final size:18
Alignment explanation
Indices: 13292833--13292878 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
13292823 TAATAAGATT
13292833 TAATA-TTATATTTAATC
1 TAATATTTATATTTAATC
13292850 TAATATTTATAATTTAATC
1 TAATATTTAT-ATTTAATC
13292869 TAATATTTAT
1 TAATATTTAT
13292879 CTTGATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 18 0.67
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATATTTATATTTAATC
Found at i:13298827 original size:29 final size:30
Alignment explanation
Indices: 13298778--13298846 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
13298768 TATAAAAAAA
* * * *
13298778 CATATCATTTCAGTAATTAAT-TTTTTATC
1 CATATTATTTCAATAAATAATAATTTTATC
*
13298807 CATATTATTTCAATAAATAATAATTTTATT
1 CATATTATTTCAATAAATAATAATTTTATC
*
13298837 TATATTATTT
1 CATATTATTT
13298847 GAGTAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (30 bp):
CATATTATTTCAATAAATAATAATTTTATC
Found at i:13299279 original size:16 final size:16
Alignment explanation
Indices: 13299255--13299285 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13299245 CAACTCTGCC
*
13299255 TTTCTTTTTTCTTTTT
1 TTTCCTTTTTCTTTTT
13299271 TTTCCTTTTTCTTTT
1 TTTCCTTTTTCTTTT
13299286 GTGTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTCCTTTTTCTTTTT
Found at i:13302491 original size:3 final size:3
Alignment explanation
Indices: 13302483--13302512 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13302473 GTTCTGGTGA
13302483 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
13302513 AAAATTGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:13308349 original size:59 final size:59
Alignment explanation
Indices: 13308257--13308376 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
13308247 CCAGCCTTTC
13308257 ATTGTAGCTACAGCAAGAACTGTACGTATGGTGACAGCCCTTACTACTGGACTGAATGT
1 ATTGTAGCTACAGCAAGAACTGTACGTATGGTGACAGCCCTTACTACTGGACTGAATGT
*
13308316 ATTGTAGCTACAGCCAGAACTGTACGTATGGTGACAGCCCTTACTACTGGACTGAATGT
1 ATTGTAGCTACAGCAAGAACTGTACGTATGGTGACAGCCCTTACTACTGGACTGAATGT
13308375 AT
1 AT
13308377 CTCGAAAGTC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (59 bp):
ATTGTAGCTACAGCAAGAACTGTACGTATGGTGACAGCCCTTACTACTGGACTGAATGT
Found at i:13308773 original size:15 final size:15
Alignment explanation
Indices: 13308753--13308784 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
13308743 ACGAGTGGGG
13308753 TATCGAGACACTAGA
1 TATCGAGACACTAGA
13308768 TATCGAGACACTAGA
1 TATCGAGACACTAGA
13308783 TA
1 TA
13308785 GTCTAGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (15 bp):
TATCGAGACACTAGA
Found at i:13311925 original size:73 final size:73
Alignment explanation
Indices: 13311806--13311980 Score: 280
Period size: 73 Copynumber: 2.4 Consensus size: 73
13311796 ATGATTAGGA
* * * *
13311806 ATTTAGCGGCGTTTTTGAGAAAGCGCCGTAAAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGC
1 ATTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACTATTTTCTGAGC
13311871 TTTCGGGG
66 TTTCGGGG
* *
13311879 ATTTAGCGGCGTTTTTGAAAAAGCACCGCAAAAAAACCTAAGCCCAACGGCACTATTTTCTGAGC
1 ATTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACTATTTTCTGAGC
13311944 TTTCGGGG
66 TTTCGGGG
13311952 ATTTAGCGGCGTTTTT-AAGAAAGCGCCGC
1 ATTTAGCGGCGTTTTTGAA-AAAGCGCCGC
13311981 TAATGCTCAG
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 2 0.02
73 92 0.98
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (73 bp):
ATTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACTATTTTCTGAGC
TTTCGGGG
Found at i:13312206 original size:114 final size:114
Alignment explanation
Indices: 13311876--13312229 Score: 476
Period size: 114 Copynumber: 3.1 Consensus size: 114
13311866 TGAGCTTTCG
* * * * * * *
13311876 GGGATTTAGCGGCGTTTTTGAAAAAGCACCGCAAAAAAACCTAAGCCCAACGGCACTATTTTCTG
1 GGGATTTAGAGGCGTTTTTGAGAAAGCGCCGAAAAAAAAACTAAGCCCAACGGCGCCATTTTCTG
*
13311941 AGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
66 AGCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCA
* ** * **
13311990 GGGATTTAGTGGCGTTTTTGAGAAAGCGCCGCAAAAAAAAAAACCTAAGCGTAATGATGCCATTT
1 GGGATTTAGAGGCGTTTTTGAGAAAGCGCCG---AAAAAAAAA-CTAAGCCCAACGGCGCCATTT
13312055 TCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCA
62 TCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCA
* * *
13312108 GGGCTTTAGAGGCGTTTTTTG-GAAAGCGCCGTAAAAAAAACTAAGCCCAACGGCGCCGTTTTCT
1 GGGATTTAGAGGCG-TTTTTGAGAAAGCGCCGAAAAAAAAACTAAGCCCAACGGCGCCATTTTCT
* *
13312172 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGTGTCGCTAATGCTCA
65 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCA
*
13312222 AGGATTTA
1 GGGATTTA
13312230 AAATAATTTG
Statistics
Matches: 209, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
114 100 0.48
115 8 0.04
117 7 0.03
118 88 0.42
119 6 0.03
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (114 bp):
GGGATTTAGAGGCGTTTTTGAGAAAGCGCCGAAAAAAAAACTAAGCCCAACGGCGCCATTTTCTG
AGCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCA
Found at i:13312475 original size:7 final size:7
Alignment explanation
Indices: 13312465--13312538 Score: 67
Period size: 7 Copynumber: 9.9 Consensus size: 7
13312455 GATTTAAGGT
13312465 TTAGGGG
1 TTAGGGG
13312472 TTAGGGGG
1 TTA-GGGG
13312480 ATTTAGGGG
1 --TTAGGGG
13312489 TTAGGGG
1 TTAGGGG
* **
13312496 TTATGCT
1 TTAGGGG
13312503 TTAGGGG
1 TTAGGGG
13312510 TTAGGGG
1 TTAGGGG
13312517 ATTTAGGGG
1 --TTAGGGG
*
13312526 TTAGGGT
1 TTAGGGG
13312533 TTAGGG
1 TTAGGG
13312539 TTTCAACGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
7 37 0.67
8 4 0.07
9 11 0.20
10 3 0.05
ACGTcount: A:0.16, C:0.01, G:0.49, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:13312490 original size:38 final size:37
Alignment explanation
Indices: 13312441--13312541 Score: 132
Period size: 37 Copynumber: 2.7 Consensus size: 37
13312431 GTCGGGGTAT
* *
13312441 GGATTTA-GGGTTTGGATTTAAGGTTTAGGGGTTAGGG
1 GGATTTAGGGGTTAGGGTTTAAGGTTTAGGGGTTA-GG
* * *
13312478 GGATTTAGGGGTTAGGGGTTATGCTTTAGGGGTTAGG
1 GGATTTAGGGGTTAGGGTTTAAGGTTTAGGGGTTAGG
*
13312515 GGATTTAGGGGTTAGGGTTTAGGGTTT
1 GGATTTAGGGGTTAGGGTTTAAGGTTT
13312542 CAACGGTTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 33 0.60
38 22 0.40
ACGTcount: A:0.17, C:0.01, G:0.45, T:0.38
Consensus pattern (37 bp):
GGATTTAGGGGTTAGGGTTTAAGGTTTAGGGGTTAGG
Found at i:13312525 original size:30 final size:28
Alignment explanation
Indices: 13312482--13312538 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
13312472 TTAGGGGGAT
*
13312482 TTAGGGGTTAGGGGTTATGCTTTAGGGG
1 TTAGGGGTTAGGGGTTAGGCTTTAGGGG
*
13312510 TTAGGGGATTTAGGGGTTAGGGTTTAGGG
1 TTAGGGG--TTAGGGGTTAGGCTTTAGGG
13312539 TTTCAACGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
30 18 0.72
ACGTcount: A:0.16, C:0.02, G:0.47, T:0.35
Consensus pattern (28 bp):
TTAGGGGTTAGGGGTTAGGCTTTAGGGG
Found at i:13312539 original size:7 final size:7
Alignment explanation
Indices: 13312444--13312541 Score: 63
Period size: 7 Copynumber: 13.4 Consensus size: 7
13312434 GGGGTATGGA
13312444 TTTAGGG
1 TTTAGGG
*
13312451 TTT-GGA
1 TTTAGGG
*
13312457 TTTAAGG
1 TTTAGGG
13312464 TTTAGGG
1 TTTAGGG
*
13312471 GTTAGGGGG
1 TTTA--GGG
13312480 ATTTAGGG
1 -TTTAGGG
*
13312488 GTTAGGG
1 TTTAGGG
* * *
13312495 GTTATGC
1 TTTAGGG
13312502 TTTAGGG
1 TTTAGGG
*
13312509 GTTAGGGG
1 TTTA-GGG
13312517 ATTTAGGG
1 -TTTAGGG
*
13312525 GTTAGGG
1 TTTAGGG
13312532 TTTAGGG
1 TTTAGGG
13312539 TTT
1 TTT
13312542 CAACGGTTAG
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
6 5 0.07
7 46 0.67
8 9 0.13
9 6 0.09
10 3 0.04
ACGTcount: A:0.16, C:0.01, G:0.44, T:0.39
Consensus pattern (7 bp):
TTTAGGG
Found at i:13317576 original size:46 final size:46
Alignment explanation
Indices: 13317509--13317693 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
13317499 ACATTGCTAT
* *
13317509 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * *
13317555 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAG
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
13317601 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAG
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
13317647 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
13317693 A
1 A
13317694 CTTTGTCATG
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:13320330 original size:44 final size:43
Alignment explanation
Indices: 13320259--13320353 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 43
13320249 AAAGTCATGA
* * **
13320259 TTTAGCGGCGTTTGTAATAGAATCGCCGCTAAAGGTTATGATC
1 TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGGCCATGATC
* *
13320302 TTTAGCGGCATTTTGTGATAAAAGCGCCGCTAAAGGCCATGATC
1 TTTAGCGGC-GTTTGTAATAAAAGCGCCGCTAAAGGCCATGATC
13320346 TTTAGCGG
1 TTTAGCGG
13320354 TGCTTTTGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 9 0.20
44 36 0.80
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGGCCATGATC
Found at i:13322145 original size:12 final size:12
Alignment explanation
Indices: 13322128--13322187 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
13322118 TTTGAACCTT
13322128 TGCTTCTCTCGC
1 TGCTTCTCTCGC
*
13322140 TGCTTCTCTAGC
1 TGCTTCTCTCGC
**
13322152 TGCAGCT-T--C
1 TGCTTCTCTCGC
*
13322161 TGCTTCTCTCAC
1 TGCTTCTCTCGC
*
13322173 TGTTTCTCTCGC
1 TGCTTCTCTCGC
13322185 TGC
1 TGC
13322188 AGCCTCTGCT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 6 0.16
10 1 0.03
11 1 0.03
12 29 0.78
ACGTcount: A:0.05, C:0.37, G:0.17, T:0.42
Consensus pattern (12 bp):
TGCTTCTCTCGC
Found at i:13322165 original size:33 final size:33
Alignment explanation
Indices: 13322128--13322208 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
13322118 TTTGAACCTT
* *
13322128 TGCTTCTCTCGCTGCTTCTCTAGCTGCAGCTTC
1 TGCTTCTCTCACTGCTTCTCTAGCTGCAGCCTC
* *
13322161 TGCTTCTCTCACTGTTTCTCTCGCTGCAGCCTC
1 TGCTTCTCTCACTGCTTCTCTAGCTGCAGCCTC
13322194 TGCTTC-CTTCACTGC
1 TGCTTCTC-TCACTGC
13322209 AGCCTCTACT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 1 0.02
33 41 0.98
ACGTcount: A:0.06, C:0.38, G:0.16, T:0.40
Consensus pattern (33 bp):
TGCTTCTCTCACTGCTTCTCTAGCTGCAGCCTC
Found at i:13326018 original size:31 final size:32
Alignment explanation
Indices: 13325960--13326028 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
13325950 GGGCTTCATA
*
13325960 ATAACA-AAAAGATAAAATCCTTCAACAGTTC
1 ATAACATAAAAGATAAAATCCTTCAACAGTAC
*
13325991 ATAACATAAAA-ATAATA-CCTTCGAACAGTAC
1 ATAACATAAAAGATAAAATCCTTC-AACAGTAC
13326022 ATAACAT
1 ATAACAT
13326029 TTAAAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 5 0.15
31 25 0.74
32 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (32 bp):
ATAACATAAAAGATAAAATCCTTCAACAGTAC
Found at i:13326073 original size:7 final size:7
Alignment explanation
Indices: 13326061--13326088 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
13326051 CTTTGGACAG
13326061 CATAAAA
1 CATAAAA
13326068 CATAAAA
1 CATAAAA
13326075 CATAAAA
1 CATAAAA
13326082 CATAAAA
1 CATAAAA
13326089 TAAGATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (7 bp):
CATAAAA
Found at i:13327369 original size:7 final size:7
Alignment explanation
Indices: 13327354--13327428 Score: 77
Period size: 7 Copynumber: 11.0 Consensus size: 7
13327344 AACTATAAAC
*
13327354 CCCTAAA
1 CCCTTAA
13327361 CCCTTAA
1 CCCTTAA
*
13327368 CCC-CAA
1 CCCTTAA
13327374 CCCTTAA
1 CCCTTAA
13327381 CCCTTAA
1 CCCTTAA
13327388 ---TTAAA
1 CCCTT-AA
13327393 CCCTTAA
1 CCCTTAA
13327400 CCCTTAAA
1 CCCTT-AA
13327408 CCCTTAA
1 CCCTTAA
13327415 CCCTTAA
1 CCCTTAA
*
13327422 ACCTTAA
1 CCCTTAA
13327429 ACACCAACCC
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 5 0.09
7 40 0.69
8 9 0.16
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (7 bp):
CCCTTAA
Found at i:13327371 original size:15 final size:15
Alignment explanation
Indices: 13327349--13327428 Score: 84
Period size: 15 Copynumber: 5.7 Consensus size: 15
13327339 ACATTAACTA
*
13327349 TAAACCCCTAAACCCT
1 TAAA-CCCTTAACCCT
*
13327365 T-AACCC-CAACCCT
1 TAAACCCTTAACCCT
13327378 T-AACCCTTAA---T
1 TAAACCCTTAACCCT
13327389 TAAACCCTTAACCCT
1 TAAACCCTTAACCCT
13327404 TAAACCCTTAACCCT
1 TAAACCCTTAACCCT
13327419 TAAA-CCTTAA
1 TAAACCCTTAA
13327429 ACACCAACCC
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
11 2 0.04
12 9 0.16
13 12 0.21
14 11 0.19
15 22 0.39
16 1 0.02
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAACCCTTAACCCT
Found at i:13327377 original size:13 final size:13
Alignment explanation
Indices: 13327359--13327383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13327349 TAAACCCCTA
13327359 AACCCTTAACCCC
1 AACCCTTAACCCC
13327372 AACCCTTAACCC
1 AACCCTTAACCC
13327384 TTAATTAAAC
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:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCTTAACCCC
Found at i:13327415 original size:34 final size:32
Alignment explanation
Indices: 13327357--13327421 Score: 103
Period size: 34 Copynumber: 2.0 Consensus size: 32
13327347 TATAAACCCC
*
13327357 TAAACCCTTAACCCCAACCCTTAACCCTTAAT
1 TAAACCCTTAACCCAAACCCTTAACCCTTAAT
13327389 TAAACCCTTAACCCTTAAACCCTTAACCCTTAA
1 TAAACCCTTAACCC--AAACCCTTAACCCTTAA
13327422 ACCTTAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.47
34 16 0.53
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (32 bp):
TAAACCCTTAACCCAAACCCTTAACCCTTAAT
Found at i:13327429 original size:22 final size:21
Alignment explanation
Indices: 13327351--13327445 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
13327341 ATTAACTATA
* *
13327351 AACCCCTAAACCCTT-AACCCC
1 AACCCTTAAA-CCTTAAACACC
* **
13327372 AACCCTTAACCCTTAATTA--
1 AACCCTTAAACCTTAAACACC
*
13327391 AACCCTTAACCCTTAAAC-CC
1 AACCCTTAAACCTTAAACACC
13327411 TTAACCCTTAAACCTTAAACACC
1 --AACCCTTAAACCTTAAACACC
13327434 AACCCTTAAACC
1 AACCCTTAAACC
13327446 ATAATCCATA
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
19 16 0.27
20 4 0.07
21 21 0.35
22 17 0.28
23 2 0.03
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTTAAACCTTAAACACC
Found at i:13327644 original size:20 final size:20
Alignment explanation
Indices: 13327606--13327647 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13327596 ATTAACTATA
**
13327606 AACCCCTAACCCCTGCCCTT
1 AACCCCTAACCCCAACCCTT
*
13327626 AACCCTTAACCCCAACCCTT
1 AACCCCTAACCCCAACCCTT
13327646 AA
1 AA
13327648 ACCATAATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.50, G:0.02, T:0.19
Consensus pattern (20 bp):
AACCCCTAACCCCAACCCTT
Found at i:13327723 original size:39 final size:39
Alignment explanation
Indices: 13327679--13327755 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
13327669 ACCCATATCC
13327679 CTTAAACCCTAAATCATAAAACATATATAAACTATAAAT
1 CTTAAACCCTAAATCATAAAACATATATAAACTATAAAT
* * ** *
13327718 CTTAAACCCTGATTCATAGCATATATATAAACTATAAA
1 CTTAAACCCTAAATCATAAAACATATATAAACTATAAA
13327756 GTGTAAACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (39 bp):
CTTAAACCCTAAATCATAAAACATATATAAACTATAAAT
Found at i:13328371 original size:114 final size:114
Alignment explanation
Indices: 13328221--13328482 Score: 271
Period size: 114 Copynumber: 2.3 Consensus size: 114
13328211 AACGACTACA
* * * *
13328221 TTTTCTTAACAGTTTTACGGCGCTT-TG-TCAAAAGCGCCGCCAAATCTTGGCTATTGTGGCATT
1 TTTTCTTAACAGTTTTGCGGCGCTTATGAT--AAAGCGCCGCCAAATCTTGACCATTGCGGCATT
* * * * *
13328284 TTTC-GATAATCGCCACTATC-GTCTTGAAAAGATAAACGTAAAACGGCAACG
64 TTCCAG-TAATCGCCACTAACTGTCCT-AAAACATAAACCTAAAACGGCAACG
* * * * *
13328335 TTTTCTTAACAGTTTTGTGGCGCTTATGATAGAGCGCCGCTAATTCTTGACCGTTGCGGCATTTT
1 TTTTCTTAACAGTTTTGCGGCGCTTATGATAAAGCGCCGCCAAATCTTGACCATTGCGGCATTTT
* * **
13328400 CCAGTAATCGCCACTAACTTTCCTAAAACCTAAACCTAAAACGGCTCCG
66 CCAGTAATCGCCACTAACTGTCCTAAAACATAAACCTAAAACGGCAACG
* *
13328449 TTTTCTTAGCAGTTTTTGCGGCGTTTATGATAAA
1 TTTTCTTAACAG-TTTTGCGGCGCTTATGATAAA
13328483 ATGTCGGTAA
Statistics
Matches: 121, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
114 96 0.79
115 24 0.20
116 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (114 bp):
TTTTCTTAACAGTTTTGCGGCGCTTATGATAAAGCGCCGCCAAATCTTGACCATTGCGGCATTTT
CCAGTAATCGCCACTAACTGTCCTAAAACATAAACCTAAAACGGCAACG
Found at i:13331637 original size:7 final size:7
Alignment explanation
Indices: 13331625--13331659 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
13331615 CGGAGGAAGG
13331625 AATGTGC
1 AATGTGC
13331632 AATGTGC
1 AATGTGC
13331639 AATGTGC
1 AATGTGC
13331646 AATGTGC
1 AATGTGC
13331653 AATGTGC
1 AATGTGC
13331660 TTTTGTCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
AATGTGC
Found at i:13342840 original size:21 final size:21
Alignment explanation
Indices: 13342801--13342840 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13342791 TACTATAGAG
* *
13342801 TTTTATTTATTAGTATATTAA
1 TTTTATTTATAAATATATTAA
*
13342822 TTTTATTTATAAATTTATT
1 TTTTATTTATAAATATATT
13342841 CCAACATCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTATTTATAAATATATTAA
Found at i:13348408 original size:14 final size:13
Alignment explanation
Indices: 13348389--13348430 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
13348379 ATAACTTAGA
13348389 ATTTAATTTAATTT
1 ATTTAATTT-ATTT
13348403 ATTTAATTTATTT
1 ATTTAATTTATTT
13348416 ATATT-ATATTATTT
1 AT-TTAAT-TTATTT
13348430 A
1 A
13348431 ATTGAATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTAATTTATTT
Found at i:13350295 original size:67 final size:67
Alignment explanation
Indices: 13350224--13350349 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 67
13350214 AAGGTCTAAA
*
13350224 ACCATAGCTCGAATATGACAACCAATG-G-AGTCCACCAAGACATTAAACATGGGGTTACATGTG
1 ACCATAGCTCGAATATGACAA-C-ATGAGTAGTCCACCAAGACATAAAACATGGGGTTACATGTG
13350287 TATG
64 TATG
* * * *
13350291 ACCATAGCTCGACTATGACCACATGAGTAGTCCACCAGGACGTAAAACATGGGGTTACA
1 ACCATAGCTCGAATATGACAACATGAGTAGTCCACCAAGACATAAAACATGGGGTTACA
13350350 CATGTGAAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
65 3 0.06
66 2 0.04
67 47 0.90
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (67 bp):
ACCATAGCTCGAATATGACAACATGAGTAGTCCACCAAGACATAAAACATGGGGTTACATGTGTA
TG
Found at i:13359188 original size:12 final size:12
Alignment explanation
Indices: 13359171--13359201 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13359161 CCTCACATGC
13359171 CCGTGTGTCAGG
1 CCGTGTGTCAGG
*
13359183 CCGTGTGTTAGG
1 CCGTGTGTCAGG
13359195 CCGTGTG
1 CCGTGTG
13359202 AAAACTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.42, T:0.29
Consensus pattern (12 bp):
CCGTGTGTCAGG
Found at i:13362707 original size:41 final size:41
Alignment explanation
Indices: 13362562--13362705 Score: 218
Period size: 41 Copynumber: 3.5 Consensus size: 41
13362552 CAGTTTAGGT
* *
13362562 CTTAGCCCATCTCAGTAT-AGTATCAAATATGCAGTAGGGC
1 CTTAGCCCATCACAGAATCAGTATCAAATATGCAGTAGGGC
* *
13362602 CTTAGCCCATCACAGTATCAATATCAAATATGCAGTAGGGC
1 CTTAGCCCATCACAGAATCAGTATCAAATATGCAGTAGGGC
* * *
13362643 TTTAGCCCATCACAGAATCAGTTTCAAATATGCAGTAAGGC
1 CTTAGCCCATCACAGAATCAGTATCAAATATGCAGTAGGGC
13362684 CTTAGCCCATCACAGAATCAGT
1 CTTAGCCCATCACAGAATCAGT
13362706 TTGGGCCTTA
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 17 0.18
41 78 0.82
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (41 bp):
CTTAGCCCATCACAGAATCAGTATCAAATATGCAGTAGGGC
Found at i:13365460 original size:3 final size:3
Alignment explanation
Indices: 13365452--13365485 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
13365442 AGTATACCAA
13365452 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
13365486 CGTGCTATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13368852 original size:22 final size:22
Alignment explanation
Indices: 13368827--13368903 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
13368817 CCAAAATATT
13368827 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
* * * *
13368849 ATCTCCT-AA-TTAAACCAAAATATT
1 ATCTCCTAAACTT-TAGC---ATCTA
13368873 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
13368895 ATCTCCTAA
1 ATCTCCTAA
13368904 TTAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 19 0.46
24 10 0.24
25 4 0.10
26 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:13368866 original size:46 final size:46
Alignment explanation
Indices: 13368814--13368908 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
13368804 ACAAAGATAG
13368814 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
13368860 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
13368906 AAA
1 AAA
13368909 AGAAAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:13374098 original size:50 final size:50
Alignment explanation
Indices: 13373983--13374231 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
13373973 GATAATAACA
* * ** * *
13373983 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
13374034 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
13374084 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
13374134 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
13374189 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
13374232 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
50 92 0.54
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:13374169 original size:100 final size:104
Alignment explanation
Indices: 13373982--13374231 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
13373972 TGATAATAAC
** * *
13373982 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
13374047 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* *
13374084 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
13374148 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* *
13374189 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
13374232 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:13374347 original size:13 final size:13
Alignment explanation
Indices: 13374326--13374357 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13374316 GCTTGGATCA
*
13374326 TCATCAAATAAAT
1 TCATAAAATAAAT
13374339 TCATAAAATAAAT
1 TCATAAAATAAAT
13374352 TCATAA
1 TCATAA
13374358 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:13374604 original size:30 final size:30
Alignment explanation
Indices: 13374569--13374626 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
13374559 CCTCGACTCT
*
13374569 AACTTTTTCAAAATTACGA-TTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTTTGCCCCTA
*
13374599 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACATTTTTGCCCC
13374627 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACATTTTTGCCCCTA
Found at i:13378841 original size:22 final size:24
Alignment explanation
Indices: 13378816--13378871 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
13378806 CTTGTTTAAA
13378816 TTTGATTAATA-A-GTATTTATTT
1 TTTGATTAATATACGTATTTATTT
13378838 TTTG-TATAATATTATCGTATTTATTT
1 TTTGAT-TAATA-TA-CGTATTTATTT
13378864 TTT-ATTAA
1 TTTGATTAA
13378872 ACTTATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
21 1 0.04
22 9 0.32
24 1 0.04
25 3 0.11
26 14 0.50
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (24 bp):
TTTGATTAATATACGTATTTATTT
Found at i:13383841 original size:43 final size:43
Alignment explanation
Indices: 13383793--13383936 Score: 270
Period size: 43 Copynumber: 3.3 Consensus size: 43
13383783 AGATGGAGAA
*
13383793 ATGTGGAAATATGAAATTGATATTGGCGAAAGATACATATGAG
1 ATGTGGAAATATGAAATTGATATTGGCAAAAGATACATATGAG
13383836 ATGTGGAAATATGAAATTGATATTGGCAAAAGATACATATGAG
1 ATGTGGAAATATGAAATTGATATTGGCAAAAGATACATATGAG
13383879 ATGTGGAAATATGAAATTGATATTGGCAAAAGATACATATGAG
1 ATGTGGAAATATGAAATTGATATTGGCAAAAGATACATATGAG
13383922 ATGTGGAAAATATGA
1 ATGTGG-AAATATGA
13383937 TATGAATATG
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
43 91 0.92
44 8 0.08
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.28
Consensus pattern (43 bp):
ATGTGGAAATATGAAATTGATATTGGCAAAAGATACATATGAG
Found at i:13383844 original size:21 final size:21
Alignment explanation
Indices: 13383820--13383930 Score: 86
Period size: 21 Copynumber: 5.2 Consensus size: 21
13383810 TGATATTGGC
13383820 GAAAGATACATATGAGATGTG
1 GAAAGATACATATGAGATGTG
* * *
13383841 GAAATATGAAAT-TGATAT-TG
1 GAAAGAT-ACATATGAGATGTG
13383861 GCAAAAGATACATATGAGATGTG
1 G--AAAGATACATATGAGATGTG
* * *
13383884 GAAATATGAAAT-TGATAT-TG
1 GAAAGAT-ACATATGAGATGTG
13383904 GCAAAAGATACATATGAGATGTG
1 G--AAAGATACATATGAGATGTG
13383927 GAAA
1 GAAA
13383931 ATATGATATG
Statistics
Matches: 68, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
20 6 0.09
21 30 0.44
22 26 0.38
23 6 0.09
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (21 bp):
GAAAGATACATATGAGATGTG
Found at i:13383939 original size:21 final size:21
Alignment explanation
Indices: 13383829--13383941 Score: 72
Period size: 22 Copynumber: 5.3 Consensus size: 21
13383819 CGAAAGATAC
13383829 ATATGAGATGTGG-AAATATG
1 ATATGAGATGTGGAAAATATG
* * * *
13383849 AAATTGATAT-TGGCAAAAGATAC
1 ATA-TGAGATGTGG-AAAATAT-G
13383872 ATATGAGATGTGG-AAATATG
1 ATATGAGATGTGGAAAATATG
* * * *
13383892 AAATTGATAT-TGGCAAAAGATAC
1 ATA-TGAGATGTGG-AAAATAT-G
13383915 ATATGAGATGTGGAAAATATG
1 ATATGAGATGTGGAAAATATG
13383936 ATATGA
1 ATATGA
13383942 ATATGAGCAA
Statistics
Matches: 67, Mismatches: 16, Indels: 19
0.66 0.16 0.19
Matches are distributed among these distances:
20 10 0.15
21 21 0.31
22 26 0.39
23 10 0.15
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.28
Consensus pattern (21 bp):
ATATGAGATGTGGAAAATATG
Found at i:13398068 original size:2 final size:2
Alignment explanation
Indices: 13398056--13398091 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13398046 AGTTTTGGGT
*
13398056 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13398092 ACACATAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13398434 original size:9 final size:9
Alignment explanation
Indices: 13398404--13398454 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
13398394 CGTTTTTTAA
13398404 AAAAATAAT
1 AAAAATAAT
13398413 AACAAAATAAT
1 -A-AAAATAAT
*
13398424 AAAAATCAT
1 AAAAATAAT
13398433 AAAAATAAT
1 AAAAATAAT
*
13398442 AATAATAAT
1 AAAAATAAT
13398451 AAAA
1 AAAA
13398455 TGAAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
9 26 0.72
10 2 0.06
11 8 0.22
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATAAT
Found at i:13399905 original size:46 final size:44
Alignment explanation
Indices: 13399720--13400010 Score: 160
Period size: 44 Copynumber: 6.7 Consensus size: 44
13399710 CTTCAATCTA
* * * * *
13399720 CTCCTCTGCAACTTCAGGGAGATAAGACTAG-AT-GTGA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCATACTTAGTCTG
* * * * * *
13399761 CT-CTCTGCAACTTCAGAGAGATAAGA-TT-CAAGATTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGC-ATA-CTTAGTCTG
* * * * *
13399804 CTCCACTACACCTTCAGGGAGATAGGATTATCGGC-T--TTAATCTT
1 CTCCACTGCAACTTCAGGGAGATAAGATT-T--GCATACTTAGTCTG
*
13399848 CTCCACTGCAACTTTAGGGAGATAAGATTTGCCAT-CTTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-CATAC-TT-AGTCTG
* *
13399894 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGATTTGCATACTTAGTCTG
* * * *
13399938 CTCCACTGCAACTTCAGGGAGATAGGATTAT-CGGT-TTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-TGC-ATACTTAGTCTG
*
13399982 CTCCACTGCAACTTCGGGGAGATAAGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
13400011 CGTACGTTTG
Statistics
Matches: 197, Mismatches: 30, Indels: 43
0.73 0.11 0.16
Matches are distributed among these distances:
39 1 0.01
40 24 0.12
41 3 0.02
42 3 0.02
43 7 0.04
44 112 0.57
45 17 0.09
46 29 0.15
49 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGCATACTTAGTCTG
Found at i:13400393 original size:44 final size:43
Alignment explanation
Indices: 13400319--13400430 Score: 152
Period size: 44 Copynumber: 2.6 Consensus size: 43
13400309 AACCTGCTCT
* *
13400319 CTGCAACTTTAGAGAGATAAGATCTATGGTTTTAATCCGCTCCA
1 CTGCAACTTTAGGGAGATAAGAT-TATGGTTTTAATCCACTCCA
* * * *
13400363 TTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATCTACTCCA
1 CTGCAACTTTAGGGAGATAAGATTA-TGGTTTTAATCCACTCCA
13400407 CTGCAACTTTAGGGAGATAAGATT
1 CTGCAACTTTAGGGAGATAAGATT
13400431 CTCAATCTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 2 0.03
44 56 0.97
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (43 bp):
CTGCAACTTTAGGGAGATAAGATTATGGTTTTAATCCACTCCA
Found at i:13400793 original size:44 final size:44
Alignment explanation
Indices: 13400743--13401029 Score: 279
Period size: 44 Copynumber: 6.7 Consensus size: 44
13400733 ATCTGCTATT
* * * *
13400743 TTCAACCTACTCCACTGCTG-CTCAAGGAGATAGGGTTCACGATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
* *
13400787 TTCAACCTATTCCACTACTGACCAGGGAGATAGGA-CCTACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATC
* * * * * *
13400831 TTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAGTT
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
13400875 TTCAACCTATTCCACTGCTGACCAGGGAGGTAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
13400919 TTTAACCTATTCCACTGCT-ATCCAAGGAGAT-GAGATT--C--T-
1 TTCAACCTATTCCACTGCTGA-CCAGGGAGATAG-GATTCACAATC
* * * *
13400958 TT-AATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
**
13401001 TTCAGTCTATTCCACTGCTGACCAGGGAG
1 TTCAACCTATTCCACTGCTGACCAGGGAG
13401030 GCAAGGCTGG
Statistics
Matches: 200, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
38 27 0.14
39 3 0.01
40 2 0.01
42 2 0.01
43 5 0.03
44 159 0.80
45 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:13401060 original size:43 final size:42
Alignment explanation
Indices: 13401011--13401144 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 42
13401001 TTCAGTCTAT
13401011 TCCACTGCTGACCAGGGAGGCAAGGCTGGTATCTTCGATCTGC
1 TCCACTGC-GACCAGGGAGGCAAGGCTGGTATCTTCGATCTGC
* * * * * *
13401054 TTCACTGTCGGTA-CAGGAAGGCAAGATCTGCTATCTTCAACCTGC
1 TCCACTG-C-G-ACCAGGGAGGCAAG-GCTGGTATCTTCGATCTGC
* * *
13401099 TCCACTACGACCCAGAGAGGCAAGGCTGGTATCTTCGGTCTGC
1 TCCACTGCGA-CCAGGGAGGCAAGGCTGGTATCTTCGATCTGC
13401142 TCC
1 TCC
13401145 GCTACTGCTT
Statistics
Matches: 70, Mismatches: 16, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
42 1 0.01
43 24 0.34
44 24 0.34
45 21 0.30
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (42 bp):
TCCACTGCGACCAGGGAGGCAAGGCTGGTATCTTCGATCTGC
Found at i:13401532 original size:86 final size:87
Alignment explanation
Indices: 13401297--13401532 Score: 285
Period size: 86 Copynumber: 2.7 Consensus size: 87
13401287 AAGGGAGGCG
* * * * * *
13401297 AGGCTAGTGTCTTCGATCTACTCCACTACTGCTTAAGGAGATAAGATTTGCAATTATTTTTAACC
1 AGGCTAGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGC-A--ATTTTCAACC
* * *
13401362 TACTCCGCTGCTACTCAGGGAGATA
63 TACTCCACTGCTACTCAAGGAAATA
* * * * *
13401387 AGGCTGGGGACTTCGATCTGTTCTACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTAT
1 AGGCTAGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTAC
*
13401452 TCCACTGCTGCTCAAGGAAAT-
66 TCCACTGCTACTCAAGGAAATA
* *
13401473 AGGCTAGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAA
1 AGGCTAGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAA
13401533 TCTGCTTCGC
Statistics
Matches: 125, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
86 54 0.43
87 28 0.22
89 1 0.01
90 42 0.34
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (87 bp):
AGGCTAGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTAC
TCCACTGCTACTCAAGGAAATA
Found at i:13403934 original size:330 final size:330
Alignment explanation
Indices: 13403333--13403991 Score: 1264
Period size: 330 Copynumber: 2.0 Consensus size: 330
13403323 GGTTCCATAC
13403333 TGACATAGGATTCTTCAAGAATTTGCTGACTGTCGACTTTATGACATTGGCATACGAGGCAGCTT
1 TGACATAGGATTCTTCAAGAATTTGCTGACTGTCGACTTTATGACATTGGCATACGAGGCAGCTT
*
13403398 CCACCTATTTAGTAAAGTAATTGACGACCACAAAGACGAATCGATGACCGTAAGACTTTTTTGGC
66 CCACCCATTTAGTAAAGTAATTGACGACCACAAAGACGAATCGATGACCGTAAGACTTTTTTGGC
*
13403463 GAGATTGACCAAATGACCTTCATGCCCCACATAAGGAGAAGTCATGTATCCCAATGATTTTTTTG
131 GAGATCGACCAAATGACCTTCATGCCCCACATAAGGAGAAGTCATGTATCCCAATGATTTTTTTG
* *
13403528 TGTAGGGTAAGATCCGTTTCTCGACTTGTTCTACTATCCTTAACAAGTTCAGAAATAGGCTACAA
196 TGTAGGGTAAGATCCGTTTCTCGACTTGTTCTACTATACTTAACAAGTTCAGAAATAGGATACAA
*
13403593 TCTATGTCATCTTCAAAGTTATGAGATCCTTCTAAACACATATCTCGCTCAAAAGGAGATTCTAA
261 TCTATGTCATCTTCAAAGTTATAAGATCCTTCTAAACACATATCTCGCTCAAAAGGAGATTCTAA
13403658 GTTTA
326 GTTTA
13403663 TGACATAGGATTCTTCAAGAATTTGCTGACTGTCGACTTTATGACATTGGCATACGAGGCAGCTT
1 TGACATAGGATTCTTCAAGAATTTGCTGACTGTCGACTTTATGACATTGGCATACGAGGCAGCTT
*
13403728 CCACCCATTTAGTAAAGTAATTGACGACCACAAAGACGAATCGATGACCGTCAGACTTTTTTGGC
66 CCACCCATTTAGTAAAGTAATTGACGACCACAAAGACGAATCGATGACCGTAAGACTTTTTTGGC
13403793 GAGATCGACCAAATGACCTTCATGCCCCACATAAGGAGAAGTCATGTATCCCAATGATTTTTTTG
131 GAGATCGACCAAATGACCTTCATGCCCCACATAAGGAGAAGTCATGTATCCCAATGATTTTTTTG
13403858 TGTAGGGTAAGATCCGTTTCTCGACTTGTTCTACTATACTTAACAAGTTCAGAAATAGGATACAA
196 TGTAGGGTAAGATCCGTTTCTCGACTTGTTCTACTATACTTAACAAGTTCAGAAATAGGATACAA
13403923 TCTATGTCATCTTCAAAGTTATAAGATCCTTCTAAACACATATCTCGCTCAAAAGGAGATTCTAA
261 TCTATGTCATCTTCAAAGTTATAAGATCCTTCTAAACACATATCTCGCTCAAAAGGAGATTCTAA
13403988 GTTT
326 GTTT
13403992 GTACCAGCGT
Statistics
Matches: 323, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
330 323 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (330 bp):
TGACATAGGATTCTTCAAGAATTTGCTGACTGTCGACTTTATGACATTGGCATACGAGGCAGCTT
CCACCCATTTAGTAAAGTAATTGACGACCACAAAGACGAATCGATGACCGTAAGACTTTTTTGGC
GAGATCGACCAAATGACCTTCATGCCCCACATAAGGAGAAGTCATGTATCCCAATGATTTTTTTG
TGTAGGGTAAGATCCGTTTCTCGACTTGTTCTACTATACTTAACAAGTTCAGAAATAGGATACAA
TCTATGTCATCTTCAAAGTTATAAGATCCTTCTAAACACATATCTCGCTCAAAAGGAGATTCTAA
GTTTA
Found at i:13407731 original size:16 final size:16
Alignment explanation
Indices: 13407710--13407742 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13407700 AATATATATA
13407710 TTAAGTTTTTTATGTT
1 TTAAGTTTTTTATGTT
13407726 TTAAGTTTTTTATGTT
1 TTAAGTTTTTTATGTT
13407742 T
1 T
13407743 AAAATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (16 bp):
TTAAGTTTTTTATGTT
Found at i:13407840 original size:20 final size:20
Alignment explanation
Indices: 13407817--13407857 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13407807 CCCCTGACAG
*
13407817 TTTAAGTTTTCAATTTTATT
1 TTTAAGTTTTCAATTTCATT
*
13407837 TTTATGTTTTCAATTTCATT
1 TTTAAGTTTTCAATTTCATT
13407857 T
1 T
13407858 CCCCGACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTAAGTTTTCAATTTCATT
Found at i:13407953 original size:19 final size:19
Alignment explanation
Indices: 13407899--13407965 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 19
13407889 ATATATTTAT
*
13407899 TTTTATGTTTAAGTTTTCAA
1 TTTTAT-TTTTAGTTTTCAA
13407919 TTTTATTTTTATGTTTTCAA
1 TTTTATTTTTA-GTTTTCAA
13407939 TTTTATTTTTAGTTTTCAA
1 TTTTATTTTTAGTTTTCAA
*
13407958 TTTCATTT
1 TTTTATTT
13407966 CCCCGACAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 19 0.43
20 25 0.57
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTATTTTTAGTTTTCAA
Found at i:13408223 original size:16 final size:16
Alignment explanation
Indices: 13408202--13408240 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
13408192 ATTTTGTTAC
*
13408202 AACAATTAATATAATT
1 AACAATTAATACAATT
13408218 AACAATTAATACAATT
1 AACAATTAATACAATT
*
13408234 AATAATT
1 AACAATT
13408241 TGATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:13408331 original size:16 final size:16
Alignment explanation
Indices: 13408310--13408351 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
13408300 AATAATTTGA
*
13408310 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
13408326 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
13408342 TAGTTTTAAT
1 TAATTTTAAT
13408352 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:13409952 original size:18 final size:17
Alignment explanation
Indices: 13409931--13409984 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 17
13409921 ATAGTTGTTT
13409931 TAAAAAAAAACAAAATAA
1 TAAAAAAAAA-AAAATAA
13409949 TAAAAATAAAAAAAATAA
1 TAAAAA-AAAAAAAATAA
*
13409967 AAAAAAATAAAAAAATAA
1 TAAAAAA-AAAAAAATAA
13409985 AGCTTAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.85
19 4 0.12
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (17 bp):
TAAAAAAAAAAAAATAA
Found at i:13409954 original size:9 final size:9
Alignment explanation
Indices: 13409942--13409985 Score: 58
Period size: 8 Copynumber: 5.2 Consensus size: 9
13409932 AAAAAAAAAC
13409942 AAAATAATA
1 AAAATAATA
*
13409951 AAAATAAAA
1 AAAATAATA
13409960 AAAATAA-A
1 AAAATAATA
13409968 AAAA-AATA
1 AAAATAATA
13409976 AAAA-AATA
1 AAAATAATA
13409984 AA
1 AA
13409986 GCTTAAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
7 2 0.06
8 16 0.48
9 15 0.45
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAATAATA
Found at i:13409960 original size:25 final size:25
Alignment explanation
Indices: 13409931--13409979 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13409921 ATAGTTGTTT
* *
13409931 TAAAAAAAA-ACAAAATAATAAAAA
1 TAAAAAAAATAAAAAAAAATAAAAA
13409955 TAAAAAAAATAAAAAAAAATAAAAA
1 TAAAAAAAATAAAAAAAAATAAAAA
13409980 AATAAAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.86, C:0.02, G:0.00, T:0.12
Consensus pattern (25 bp):
TAAAAAAAATAAAAAAAAATAAAAA
Found at i:13414984 original size:69 final size:69
Alignment explanation
Indices: 13414908--13415036 Score: 204
Period size: 69 Copynumber: 1.9 Consensus size: 69
13414898 GTTCTGGAAA
*
13414908 TTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTGAGTAGAAGATGAAACTGTTCTA
1 TTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATGAAACTGTTCTA
13414973 GCAG
66 GCAG
* * * * *
13414977 TTGTTTTGATTGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAATATGAAACTG
1 TTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATGAAACTG
13415037 GAACTTGATT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (69 bp):
TTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATGAAACTGTTCTA
GCAG
Found at i:13417251 original size:22 final size:22
Alignment explanation
Indices: 13417226--13417300 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
13417216 GTGATATAGA
13417226 AGTACGTTAGCCATGAGAGCTT
1 AGTACGTTAGCCATGAGAGCTT
* *
13417248 AGTACGTTAGCCATGAGGGTTT
1 AGTACGTTAGCCATGAGAGCTT
* **
13417270 AGTTCGTTAAACATGAGAGCTT
1 AGTACGTTAGCCATGAGAGCTT
13417292 AGTACGTTA
1 AGTACGTTA
13417301 AACATGTGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (22 bp):
AGTACGTTAGCCATGAGAGCTT
Found at i:13419680 original size:47 final size:45
Alignment explanation
Indices: 13419629--13419796 Score: 132
Period size: 47 Copynumber: 3.6 Consensus size: 45
13419619 TATTTAATAT
*
13419629 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTAT-AA
* * **
13419676 TAATT-TTATGAAA-TTATATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAATT-TAT-T-ATAA
* * *
13419720 TAATTATTTTAAATTATACAAATTCATATAAGATAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTA-TAA
13419767 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
13419797 TTTTAATTAA
Statistics
Matches: 95, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 14 0.15
45 12 0.13
46 10 0.11
47 36 0.38
48 9 0.09
49 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAATTTATTATAA
Found at i:13419702 original size:91 final size:91
Alignment explanation
Indices: 13419555--13419762 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 91
13419545 TTGATTTTAG
* *
13419555 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
13419620 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* * *
13419647 TAAATTCATATAAGAAAAATTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
13419712 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
13419738 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
13419763 GTTATAATTA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 89 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:13419723 original size:44 final size:43
Alignment explanation
Indices: 13419576--13419737 Score: 116
Period size: 44 Copynumber: 3.6 Consensus size: 43
13419566 AAGAACATTT
* * *
13419576 TATTATTAAGAATT-TTATGAAATTATATATCATTATTAAATTA
1 TATTAATAATAATTATT-TGAAATTATATATAATTATTAAATTA
* * * *
13419619 TATTTAATATTAATTATTTTAAATTGTATA-AATTCATATAAGA-AA
1 TA-TTAATAATAATTATTTGAAATTATATATAATT-AT-TAA-ATTA
* *
13419664 AATTATTATCAATAATT-TTATGAAATTATATATTATTATTAAATTA
1 TATTA--AT-AATAATTATT-TGAAATTATATATAATTATTAAATTA
*
13419710 TATGTAATAATAATTATTTTAAATTATA
1 TAT-TAATAATAATTATTTGAAATTATA
13419738 CAAATTCATA
Statistics
Matches: 91, Mismatches: 15, Indels: 25
0.69 0.11 0.19
Matches are distributed among these distances:
43 5 0.05
44 40 0.44
45 12 0.13
46 11 0.12
47 20 0.22
48 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (43 bp):
TATTAATAATAATTATTTGAAATTATATATAATTATTAAATTA
Found at i:13419737 original size:26 final size:28
Alignment explanation
Indices: 13419575--13419651 Score: 52
Period size: 28 Copynumber: 2.8 Consensus size: 28
13419565 TAAGAACATT
* *
13419575 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
* ** *
13419605 TCATTATTAAATTATATTTAATATTA-A
1 TTATTATTAAATTATATGAAATAATATA
*
13419632 TTATT-TTAAATTGTAT-AAAT
1 TTATTATTAAATTATATGAAAT
13419652 TCATATAAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.08
26 10 0.26
27 5 0.13
28 12 0.32
29 1 0.03
30 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:13419902 original size:120 final size:120
Alignment explanation
Indices: 13419778--13420075 Score: 490
Period size: 120 Copynumber: 2.5 Consensus size: 120
13419768 AATTATTTTA
* * * **
13419778 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATCAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATCATGTT-AAATTAAATTT
13419842 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
13419898 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTAAATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATCATGTTAAATTAAATTTT
*
13419963 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
13420018 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATCATG-TTAAAT
13420076 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 160 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATCATGTTAAATTAAATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:13419915 original size:59 final size:59
Alignment explanation
Indices: 13419852--13420035 Score: 182
Period size: 59 Copynumber: 3.1 Consensus size: 59
13419842 TATAGTATCA
13419852 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* * * * * * *
13419911 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTA-AATTTTA-TAGTAT
1 TATATTATGATTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
13419970 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
13420031 TATAT
1 TATAT
13420036 ATTTTAATTA
Statistics
Matches: 96, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
56 6 0.06
57 11 0.11
58 10 0.10
59 20 0.21
60 8 0.08
61 15 0.16
62 9 0.09
63 11 0.11
64 6 0.06
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:13419916 original size:61 final size:61
Alignment explanation
Indices: 13419851--13420038 Score: 201
Period size: 61 Copynumber: 3.1 Consensus size: 61
13419841 TTATAGTATC
13419851 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
13419912 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-AATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
13419970 C
61 T
*
13419971 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
13420032 ATATATT
1 ATATATT
13420039 TTAATTATAA
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 19 0.19
60 16 0.16
61 26 0.27
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:13419938 original size:15 final size:15
Alignment explanation
Indices: 13419903--13419954 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
13419893 TTAAGAATTT
*
13419903 TATTAAATTAT-ATA
1 TATTTAATTATAATA
13419917 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
13419931 TATTTAATAATAAT-
1 TATTTAATTATAATA
13419945 TATGTTAATT
1 TAT-TTAATT
13419955 TAAATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:13420053 original size:16 final size:16
Alignment explanation
Indices: 13420032--13420073 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
13420022 TTATTAAATT
*
13420032 ATATATTTTAATTATA
1 ATATATTTTAATAATA
13420048 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
13420063 AT-TATGTTTAA
1 ATATAT-TTTAA
13420074 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:13420058 original size:15 final size:15
Alignment explanation
Indices: 13420023--13420064 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13420013 TTAAGAATTT
*
13420023 TATTAAATTAT-ATA
1 TATTTAATTATAATA
13420037 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
13420051 TATTTAATAATAAT
1 TATTTAATTATAAT
13420065 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:13420250 original size:39 final size:40
Alignment explanation
Indices: 13420207--13420311 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
13420197 TTCCATTATG
13420207 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
13420246 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTC
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
13420291 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
13420312 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:0.04, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:13420305 original size:45 final size:44
Alignment explanation
Indices: 13420224--13420314 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
13420214 ACCTCTATTC
*
13420224 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
13420268 CATTCAACCAAACAGTTGATTTCCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
13420313 CA
1 CA
13420315 CCTCTATTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:13420314 original size:16 final size:16
Alignment explanation
Indices: 13420288--13420346 Score: 82
Period size: 16 Copynumber: 3.6 Consensus size: 16
13420278 AACAGTTGAT
13420288 TTCCTATTACACCTCTA
1 TTCC-ATTACACCTCTA
13420305 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
*
13420321 TTCCATTACGCCTCTA
1 TTCCATTACACCTCTA
* *
13420337 ATCCAATACA
1 TTCCATTACA
13420347 GCGAACCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
16 34 0.89
17 4 0.11
ACGTcount: A:0.27, C:0.36, G:0.02, T:0.36
Consensus pattern (16 bp):
TTCCATTACACCTCTA
Found at i:13420783 original size:34 final size:34
Alignment explanation
Indices: 13420743--13420833 Score: 139
Period size: 34 Copynumber: 2.7 Consensus size: 34
13420733 ACTTTTTTTA
**
13420743 AAATTAATTAAATTA-GGTTTTTGGAGTTTTAAAT
1 AAATTAATTAAATTAGGGTTTAGGGA-TTTTAAAT
13420777 AAATTAATTAAATTAGGGTTTAGGGATTTTAAAT
1 AAATTAATTAAATTAGGGTTTAGGGATTTTAAAT
*
13420811 TAATTAATTAAATTAGGGTTTAG
1 AAATTAATTAAATTAGGGTTTAG
13420834 TTTTTTAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
34 45 0.85
35 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (34 bp):
AAATTAATTAAATTAGGGTTTAGGGATTTTAAAT
Found at i:13430082 original size:18 final size:18
Alignment explanation
Indices: 13430059--13430094 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13430049 ATGTCGGTTT
13430059 TGAGAGCGGCGAGGATGA
1 TGAGAGCGGCGAGGATGA
13430077 TGAGAGCGGCGAGGATGA
1 TGAGAGCGGCGAGGATGA
13430095 AGGGGTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.50, T:0.11
Consensus pattern (18 bp):
TGAGAGCGGCGAGGATGA
Done.