Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 17
Found at i:247187 original size:23 final size:23
Alignment explanation
Indices: 247138--247187 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
247128 ATATCATATT
* **
247138 ATTATTATTGTATTTTTTTTATT
1 ATTATTAATGTATTTTTTTTACA
247161 ATTATTAATGCTA-TTTTTTTACA
1 ATTATTAATG-TATTTTTTTTACA
247184 ATTA
1 ATTA
247188 CATTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTATTAATGTATTTTTTTTACA
Found at i:248648 original size:30 final size:30
Alignment explanation
Indices: 248621--248879 Score: 262
Period size: 30 Copynumber: 8.7 Consensus size: 30
248611 GCCCTTTACC
*
248621 TTTCTATTTTTACTATTTTAGTTCTTTAAG
1 TTTCTATTTTTACTATTTTAGTCCTTTAAG
* *
248651 TTTCTATTTTTGCTATTTTAGTCCTTTAAC
1 TTTCTATTTTTACTATTTTAGTCCTTTAAG
* * *
248681 TTTTTGA-TTTTACTA-TTTAGACCCTTAAG
1 TTTCT-ATTTTTACTATTTTAGTCCTTTAAG
**
248710 TTTCTATTTTT--TATTTTAACCCTTTAAG
1 TTTCTATTTTTACTATTTTAGTCCTTTAAG
*
248738 TTTCTATTTTTACTATTTTAGTCCTTTTAAT
1 TTTCTATTTTTACTATTTTAGTCC-TTTAAG
* * * *
248769 TTTATATTTTTGCTA-TTTAGGCCCTTAAG
1 TTTCTATTTTTACTATTTTAGTCCTTTAAG
* * *
248798 TTTTTTATTTTTACTGTTTTAG-CCTTTTAAT
1 -TTTCTATTTTTACTATTTTAGTCC-TTTAAG
*
248829 TTTCTATTTTTACTATTTTAGTCCTTTAAA
1 TTTCTATTTTTACTATTTTAGTCCTTTAAG
*
248859 TTTTTA-TTTTAGCTATTTTAG
1 TTTCTATTTTTA-CTATTTTAG
248880 CTTTTAAAGT
Statistics
Matches: 189, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
27 2 0.01
28 23 0.12
29 28 0.15
30 106 0.56
31 30 0.16
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.61
Consensus pattern (30 bp):
TTTCTATTTTTACTATTTTAGTCCTTTAAG
Found at i:249076 original size:2 final size:2
Alignment explanation
Indices: 249027--249060 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
249017 ATTTGTAAAC
249027 AT 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 AT
249061 TATTGGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250809 original size:4 final size:4
Alignment explanation
Indices: 250802--250831 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
250792 GTACACTAAC
250802 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
250832 TTGTCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:253472 original size:4 final size:4
Alignment explanation
Indices: 253463--254165 Score: 1392
Period size: 4 Copynumber: 176.2 Consensus size: 4
253453 ATATCAAAAA
253463 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253511 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253559 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253607 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253655 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253703 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253751 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253799 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253847 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253895 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253943 ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
253989 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
254037 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
254085 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
254133 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
254166 ATAAAGCTAA
Statistics
Matches: 697, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
4 695 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:255252 original size:43 final size:40
Alignment explanation
Indices: 255152--255263 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 40
255142 GATAGCCTAC
*
255152 CGTCCTCATCGCATAGGAACCGTGTCATCCCCTGACCAGA
1 CGTCCTCATCGCATAGGAACCGTGTTATCCCCTGACCAGA
* * * *
255192 CCTCCTCATCACGTAGGAGCCGTGTTA-CCCCTAGATAACCA-A
1 CGTCCTCATCGCATAGGAACCGTGTTATCCCCT-G---ACCAGA
*
255234 TCGTCCTCATCGCATAGGAACCATGTTATC
1 -CGTCCTCATCGCATAGGAACCGTGTTATC
255264 ATCATCCCTA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
39 5 0.09
40 23 0.41
42 1 0.02
43 26 0.46
44 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (40 bp):
CGTCCTCATCGCATAGGAACCGTGTTATCCCCTGACCAGA
Found at i:255395 original size:133 final size:133
Alignment explanation
Indices: 255157--255397 Score: 374
Period size: 133 Copynumber: 1.8 Consensus size: 133
255147 CCTACCGTCC
* * *
255157 TCATCGCATAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTTACCC
1 TCATCGCATAGGAACCATGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCC
* *
255222 CTAGATAACCAATCGTCCTCATCGCATAGGAACCATGTTATCATCATCCCTAAAGATGGTTTGTA
66 CTAGATAACCAATCATCCTCATCACATAGGAACCATGTTATCATCATCCCTAAAGATGGTTTGTA
255287 TCA
131 TCA
* * * *
255290 TCATCGCGTAGGAACCATGTCATCCCCCGACCAGACCTCTTCATTACGTAGGAGTCGTGTCACCC
1 TCATCGCATAGGAACCATGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCC
* * *
255355 CTAGATAACCAGTCATCCTCATCACGTAGGAACTATGTTATCA
66 CTAGATAACCAATCATCCTCATCACATAGGAACCATGTTATCA
255398 CCCCTAGATA
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
133 96 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (133 bp):
TCATCGCATAGGAACCATGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCC
CTAGATAACCAATCATCCTCATCACATAGGAACCATGTTATCATCATCCCTAAAGATGGTTTGTA
TCA
Found at i:259762 original size:62 final size:62
Alignment explanation
Indices: 259692--259815 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
259682 AATAATCCAA
259692 GAGAATCATTCATTTCTTCCAACCTATAAATTATGAATAAAAATAAAGCATAAGGGTGGAGG
1 GAGAATCATTCATTTCTTCCAACCTATAAATTATGAATAAAAATAAAGCATAAGGGTGGAGG
259754 GAGAATCATTCATTTCTTCCAACCTATAAATTATGAATAAAAATAAAGCATAAGGGTGGAGG
1 GAGAATCATTCATTTCTTCCAACCTATAAATTATGAATAAAAATAAAGCATAAGGGTGGAGG
259816 AAAAACTCCC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (62 bp):
GAGAATCATTCATTTCTTCCAACCTATAAATTATGAATAAAAATAAAGCATAAGGGTGGAGG
Found at i:271113 original size:35 final size:35
Alignment explanation
Indices: 271052--271120 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
271042 GACCTTCAAG
*
271052 GGGTATCGATACCTGAAGAACAGTATCGGTACCAA
1 GGGTATCGATACCTGAAGAACAGTATCGATACCAA
* *
271087 GGGTATCGATACCTTAAGGAA-GGTATCGATACCA
1 GGGTATCGATACCTGAA-GAACAGTATCGATACCA
271121 TCTTTGAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (35 bp):
GGGTATCGATACCTGAAGAACAGTATCGATACCAA
Found at i:271587 original size:18 final size:18
Alignment explanation
Indices: 271557--271598 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
271547 TGGTATGTGT
*
271557 TACATGATATGT-ATAAA
1 TACATGTTATGTAATAAA
271574 TACATGTTAGTGTAATAAA
1 TACATGTTA-TGTAATAAA
271593 T-CATGT
1 TACATGT
271599 GAATAGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 8 0.36
19 6 0.27
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (18 bp):
TACATGTTATGTAATAAA
Found at i:276943 original size:19 final size:18
Alignment explanation
Indices: 276919--276959 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
276909 GATATGGGTA
* *
276919 TATGTGTTATATGTTATGG
1 TATGTGTTACATGATAT-G
276938 TATGTGTTACATGATATG
1 TATGTGTTACATGATATG
276956 TATG
1 TATG
276960 AATACATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (18 bp):
TATGTGTTACATGATATG
Found at i:278165 original size:18 final size:18
Alignment explanation
Indices: 278142--278176 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
278132 GTTCTTAAGG
278142 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
278160 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
278177 AATTCTAAGT
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:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:280449 original size:61 final size:61
Alignment explanation
Indices: 280384--280505 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
280374 TTTATTTCCT
*
280384 TATTTACTTTTAATATTAGTTTTTTTAGAAGAATAGACTTCCAAACATGTGGACAAGGGTA
1 TATTTACTTTTAATATTAGTTTTTTTAGAAGAATAGACTTCCAAACATATGGACAAGGGTA
*
280445 TATTTACTTTTAATATTAGTTTTTTTAGAAGAATATACTTCCAAACATATGGACAAGGGTA
1 TATTTACTTTTAATATTAGTTTTTTTAGAAGAATAGACTTCCAAACATATGGACAAGGGTA
280506 AAGCCCCCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (61 bp):
TATTTACTTTTAATATTAGTTTTTTTAGAAGAATAGACTTCCAAACATATGGACAAGGGTA
Found at i:285914 original size:14 final size:14
Alignment explanation
Indices: 285895--285927 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
285885 CACAAGTTTG
285895 TCTTCTTTCTTACT
1 TCTTCTTTCTTACT
285909 TCTTCTTTCTTACT
1 TCTTCTTTCTTACT
285923 TCTTC
1 TCTTC
285928 ATCTCCCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTTCTTTCTTACT
Found at i:294665 original size:21 final size:21
Alignment explanation
Indices: 294612--294670 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
294602 TTAATTTTTT
*
294612 CTTTTA-TATTTCAT-TATTAA
1 CTTTTACTCTTTCATCT-TTAA
294632 CTTTTACTCTTTCATCTTTAA
1 CTTTTACTCTTTCATCTTTAA
* *
294653 CTTTTGCTTTTTC-TCTTT
1 CTTTTACTCTTTCATCTTT
294671 CATTTCTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.32
21 22 0.65
22 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.02, T:0.63
Consensus pattern (21 bp):
CTTTTACTCTTTCATCTTTAA
Found at i:312823 original size:15 final size:15
Alignment explanation
Indices: 312805--312840 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
312795 CTGTGGTTTC
* *
312805 TTTTTTCTTTTCTTT
1 TTTTTTCCTTTATTT
312820 TTTTTTCCTTTATTT
1 TTTTTTCCTTTATTT
312835 TTTTTT
1 TTTTTT
312841 TTACTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTCCTTTATTT
Found at i:312824 original size:16 final size:16
Alignment explanation
Indices: 312805--312842 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
312795 CTGTGGTTTC
312805 TTTTTTCTTT-TCTTTT
1 TTTTTTCTTTAT-TTTT
*
312821 TTTTTCCTTTATTTTT
1 TTTTTTCTTTATTTTT
312837 TTTTTT
1 TTTTTT
312843 ACTATTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTCTTTATTTTT
Found at i:313825 original size:23 final size:23
Alignment explanation
Indices: 313796--313851 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
313786 CTCTGCATAA
313796 AAATTATATTAAATATAGAATTT
1 AAATTATATTAAATATAGAATTT
*
313819 ATATTATATTAAATATAGAATTT
1 AAATTATATTAAATATAGAATTT
313842 AAATTATATT
1 AAATTATATT
313852 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
AAATTATATTAAATATAGAATTT
Found at i:313932 original size:27 final size:28
Alignment explanation
Indices: 313857--313933 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 28
313847 ATATTTATTT
* * *
313857 TTAAATAATTAAAATAAATTATTAAGTA
1 TTAAATTATTAAAATAAAATGTTAAGTA
* ***
313885 ATAAATTATT-TTTTAAGAATGTTAA-TA
1 TTAAATTATTAAAATAA-AATGTTAAGTA
313912 TTAAATTATTAAAATAAAATGT
1 TTAAATTATTAAAATAAAATGT
313934 AACTACATAA
Statistics
Matches: 36, Mismatches: 11, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
27 19 0.53
28 17 0.47
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (28 bp):
TTAAATTATTAAAATAAAATGTTAAGTA
Found at i:326865 original size:20 final size:21
Alignment explanation
Indices: 326840--326891 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
326830 TTTTTCCAAT
*
326840 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
326860 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
326881 TCGCAATGCGA
1 TCGCAATGCGA
326892 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:326904 original size:41 final size:41
Alignment explanation
Indices: 326877--326954 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
326867 GCGAATTGGG
* * *
326877 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
326918 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
326955 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:326905 original size:20 final size:20
Alignment explanation
Indices: 326880--326974 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
326870 AATTGGGAAA
*
326880 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
326900 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
326921 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
326941 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
326961 TTCGCAACGCGATA
1 ATCGCAACGCGATA
326975 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:327190 original size:22 final size:22
Alignment explanation
Indices: 327162--327205 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
327152 CACTCTCTCA
327162 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
327184 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
327206 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:328846 original size:18 final size:18
Alignment explanation
Indices: 328825--328869 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
328815 TCCACTTCGG
* *
328825 GAGCCATCTCCTCGCCCA
1 GAGCCATCACCTCACCCA
*
328843 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
328861 GAGCCATCA
1 GAGCCATCA
328870 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.44, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:329376 original size:20 final size:20
Alignment explanation
Indices: 329351--329396 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
329341 TAGTTTACTT
329351 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
329371 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
329391 TCGCAA
1 TCGCAA
329397 TGCGAAACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:329425 original size:14 final size:14
Alignment explanation
Indices: 329406--329463 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
329396 ATGCGAAACG
329406 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
329420 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
329436 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
329452 AAAATCGCAACG
1 AAAATCGCAACG
329464 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:329448 original size:32 final size:33
Alignment explanation
Indices: 329390--329480 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
329380 GGAAATGGCT
*
329390 ATCGCAATGCGAAACGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
329423 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
329455 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
329481 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:329516 original size:14 final size:14
Alignment explanation
Indices: 329497--329554 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
329487 TTGTGTTTCG
329497 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
329511 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
329527 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
329543 CGTTGCGATTTT
1 CGTTGCGATTTT
329555 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:329531 original size:32 final size:33
Alignment explanation
Indices: 329492--329570 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
329482 GCGATTTGTG
329492 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
329524 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
329557 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
329571 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:329569 original size:19 final size:19
Alignment explanation
Indices: 329513--329612 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
329503 GATTTTGTCG
*
329513 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
329531 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
329545 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
***
329564 TTGCGATAGCCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
** *
329584 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
329603 TTGCGATTTT
1 TTGCGATTTT
329613 AAGTTTCGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 4 0.06
17 4 0.06
18 9 0.13
19 23 0.34
20 18 0.27
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:329585 original size:20 final size:19
Alignment explanation
Indices: 329555--329609 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
329545 TTGCGATTTT
329555 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
329574 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
329594 CATTTCGCGTTGCGAT
1 CATTTCGCATTGCGAT
329610 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:331499 original size:14 final size:14
Alignment explanation
Indices: 331480--331515 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
331470 ATTGTTTAAT
331480 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
331494 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
331508 TGATTTGT
1 TGATTTGT
331516 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:331641 original size:14 final size:14
Alignment explanation
Indices: 331622--331675 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
331612 CGAAATGGTT
331622 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
331636 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
331655 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
331669 ATCGCAA
1 ATCGCAA
331676 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:331693 original size:33 final size:33
Alignment explanation
Indices: 331603--331680 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
331593 AAAACAGGCT
* ***
331603 ATCGCAACGCGAAATGGTTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
331636 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
331669 ATCGCAATGCGA
1 ATCGCAATGCGA
331681 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:331756 original size:20 final size:20
Alignment explanation
Indices: 331699--331756 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
331689 TCGCATTGCG
* *
331699 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
331719 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
331739 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
331757 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:332093 original size:29 final size:29
Alignment explanation
Indices: 332017--332086 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
332007 TCGTTGCGAT
*
332017 TTGCATTTCGCATTGCGATGGTCAAATGA
1 TTGCCTTTCGCATTGCGATGGTCAAATGA
332046 TTGCCTTTCGCATTGCGATGGTCAAATGA
1 TTGCCTTTCGCATTGCGATGGTCAAATGA
332075 TTGCCTTTCGCA
1 TTGCCTTTCGCA
332087 ACGCGATTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (29 bp):
TTGCCTTTCGCATTGCGATGGTCAAATGA
Found at i:332881 original size:24 final size:24
Alignment explanation
Indices: 332847--332900 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
332837 GTATTCGAAA
* *
332847 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
332871 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
332895 TTTGAT
1 TTTGAT
332901 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:333092 original size:12 final size:12
Alignment explanation
Indices: 333075--333099 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
333065 ATATAATCCT
333075 GAAGAAGAAAAA
1 GAAGAAGAAAAA
333087 GAAGAAGAAAAA
1 GAAGAAGAAAAA
333099 G
1 G
333100 TCCCTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:335414 original size:19 final size:19
Alignment explanation
Indices: 335392--335522 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
335382 GGAAATTACT
335392 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
335411 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
335425 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
335444 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
335458 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
335477 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
335491 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
335510 ATCGCAACGCGAA
1 ATCGCAATGCGAA
335523 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:335434 original size:33 final size:33
Alignment explanation
Indices: 335392--335518 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
335382 GGAAATTACT
335392 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
335425 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
335457 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
335491 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
335519 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:335499 original size:66 final size:66
Alignment explanation
Indices: 335393--335525 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
335383 GAAATTACTA
*
335393 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
335458 T
66 T
*
335459 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
335524 T
66 T
335525 T
1 T
335526 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:335721 original size:14 final size:14
Alignment explanation
Indices: 335702--335738 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
335692 CATCAATTAA
335702 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
335716 ACAAATTACCTTTT
1 ACAAATCAACTTTT
335730 ACAAATCAA
1 ACAAATCAA
335739 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:337162 original size:21 final size:21
Alignment explanation
Indices: 337096--337162 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
337086 GTGAATCGGG
337096 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
337116 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
337138 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
337159 CTCT
1 CTCT
337163 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:337181 original size:42 final size:41
Alignment explanation
Indices: 337096--337218 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
337086 GTGAATCGGG
* * * *
337096 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
337138 CTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * * *
337180 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGATAGG
337219 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:339336 original size:19 final size:19
Alignment explanation
Indices: 339219--339383 Score: 152
Period size: 19 Copynumber: 9.1 Consensus size: 19
339209 TCTTTTGGTT
*
339219 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
339238 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
339258 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
339276 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
339292 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
339310 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
339325 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
339344 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
339363 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
339382 GA
1 GA
339384 TTTTGGTTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.16
15 3 0.02
16 2 0.02
17 1 0.01
18 4 0.03
19 63 0.52
20 27 0.22
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:339356 original size:38 final size:36
Alignment explanation
Indices: 339219--339383 Score: 153
Period size: 33 Copynumber: 4.6 Consensus size: 36
339209 TCTTTTGGTT
*
339219 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCG--AA-GAGAATCGCAACGC
**
339258 GGAAATGACTATCGCAA--CG-AGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
** * *
339292 GAAATGACTATCGCGAC-C--AGACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
*
339325 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCG-AA-GAGAATCGCAACGC
*
339363 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
339384 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 10, Indels: 15
0.81 0.07 0.11
Matches are distributed among these distances:
33 43 0.39
34 16 0.15
35 1 0.01
37 2 0.02
38 33 0.30
40 14 0.13
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (36 bp):
GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
Found at i:339412 original size:19 final size:19
Alignment explanation
Indices: 339379--339459 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
339369 AAAATCGCAA
**
339379 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
339398 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
339417 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
339431 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
339451 TGCGATTTT
1 TGCGATTTT
339460 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:340001 original size:20 final size:20
Alignment explanation
Indices: 339976--340028 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
339966 GCGCTATGTA
339976 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
339996 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
340016 TATCTCGTTGCGA
1 AATCGCGTTGCGA
340029 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:340062 original size:20 final size:20
Alignment explanation
Indices: 340037--340090 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
340027 GATTTTGTAT
340037 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
340057 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
340077 TATCGCATTGCGAT
1 TATCGCATTGCGAT
340091 TTTCTCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:340109 original size:61 final size:61
Alignment explanation
Indices: 339977--340111 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
339967 CGCTATGTAA
* * * * * * *
339977 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCTAAT
* * *
340038 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCT-AAT
340100 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
340112 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCTAAT
Found at i:340123 original size:20 final size:21
Alignment explanation
Indices: 340079--340130 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
340069 ATAGTCAGTA
*
340079 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACTCAAT
* *
340100 TCGCGTTGCGATTTACT-TAT
1 TCGCATTGCGATTTACTCAAT
340120 TCGCATTGCGA
1 TCGCATTGCGA
340131 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTACTCAAT
Found at i:347007 original size:23 final size:22
Alignment explanation
Indices: 346952--347034 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
346942 TTAGTGCAGA
*
346952 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATTCCCCCTTGAAG
*
346974 GGGTA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATTCCCCC-TTGAAG
* *
346997 GGGAATCGATT-CCCCTTGTAT
1 GGGAATCGATTCCCCCTTGAAG
* *
347018 GAGAATCGATACCCCCT
1 GGGAATCGATTCCCCCT
347035 GGGGTTCTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 14 0.28
22 21 0.42
23 14 0.28
24 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (22 bp):
GGGAATCGATTCCCCCTTGAAG
Found at i:347011 original size:22 final size:22
Alignment explanation
Indices: 346952--347013 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
346942 TTAGTGCAGA
* *
346952 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATTCCCCTTTGAAG
*
346974 GGGTA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATT-CCCCTTTGAAG
346997 GGGAATCGATTCCCCTT
1 GGGAATCGATTCCCCTT
347014 GTATGAGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.03
22 13 0.39
23 18 0.55
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.26
Consensus pattern (22 bp):
GGGAATCGATTCCCCTTTGAAG
Found at i:349278 original size:21 final size:21
Alignment explanation
Indices: 349247--349298 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
349237 CAGAGGGAAC
349247 CGATT-CCCCCAAGGGGATAT
1 CGATTCCCCCCAAGGGGATAT
*
349267 CGATTCCCCCCAAGGGGGTAT
1 CGATTCCCCCCAAGGGGATAT
349288 CGATTCCCCCC
1 CGATTCCCCCC
349299 CCTGAATGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.19, C:0.38, G:0.23, T:0.19
Consensus pattern (21 bp):
CGATTCCCCCCAAGGGGATAT
Found at i:351823 original size:21 final size:22
Alignment explanation
Indices: 351805--351879 Score: 107
Period size: 23 Copynumber: 3.4 Consensus size: 22
351795 CACTGAAGTG
*
351805 CCACATA-TTTGTCCCGAAGGA
1 CCACATAGTTTATCCCGAAGGA
351826 CCACATAGGTTTATCCCGAAGGA
1 CCACATA-GTTTATCCCGAAGGA
*
351849 CCATATAGTTTTATCCCGAAGGA
1 CCACATAG-TTTATCCCGAAGGA
351872 CCACATAG
1 CCACATAG
351880 AACCTTCGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
21 7 0.15
22 1 0.02
23 40 0.83
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (22 bp):
CCACATAGTTTATCCCGAAGGA
Found at i:351845 original size:23 final size:23
Alignment explanation
Indices: 351816--351879 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
351806 CACATATTTG
351816 TCCCGAAGGACCACATAGGTTTA
1 TCCCGAAGGACCACATAGGTTTA
* *
351839 TCCCGAAGGACCATATAGTTTTA
1 TCCCGAAGGACCACATAGGTTTA
351862 TCCCGAAGGACCACATAG
1 TCCCGAAGGACCACATAG
351880 AACCTTCGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGGTTTA
Found at i:352739 original size:20 final size:20
Alignment explanation
Indices: 352694--352745 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
352684 TCTTTACTTA
*
352694 CAGTATCGATACCTTATCCT
1 CAGTATCGATACCTTATCAT
**
352714 TGGTATCGATACCTTCA-CAT
1 CAGTATCGATACCTT-ATCAT
352734 CAGTATCGATAC
1 CAGTATCGATAC
352746 TTCTTAAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGTATCGATACCTTATCAT
Found at i:355738 original size:7 final size:7
Alignment explanation
Indices: 355726--355751 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
355716 CATGTATCAA
355726 AACATAT
1 AACATAT
355733 AACATAT
1 AACATAT
355740 AACATAT
1 AACATAT
355747 AACAT
1 AACAT
355752 TTATGTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AACATAT
Found at i:356223 original size:20 final size:21
Alignment explanation
Indices: 356198--356250 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
356188 TATTTCAAAA
356198 ATGGTATCGATACTGACCTT-
1 ATGGTATCGATACTGACCTTC
*
356218 ATGGTATCGATACTGCCCTTC
1 ATGGTATCGATACTGACCTTC
*
356239 A-GGTATCCATAC
1 ATGGTATCGATAC
356251 CTCATGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (21 bp):
ATGGTATCGATACTGACCTTC
Found at i:356528 original size:20 final size:20
Alignment explanation
Indices: 356503--356542 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
356493 TCCATATAAA
356503 TCATCAT-TATCTTCAAAATC
1 TCATCATATATCTT-AAAATC
*
356523 TCATCATATGTCTTAAAATC
1 TCATCATATATCTTAAAATC
356543 AAGAATCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (20 bp):
TCATCATATATCTTAAAATC
Found at i:361031 original size:15 final size:15
Alignment explanation
Indices: 361011--361068 Score: 98
Period size: 15 Copynumber: 3.9 Consensus size: 15
361001 AGGAGAAATG
*
361011 AATGAATGAAAATAA
1 AATGAAGGAAAATAA
361026 AATGAAGGAAAATAA
1 AATGAAGGAAAATAA
361041 AATGAAGGAAAATAA
1 AATGAAGGAAAATAA
*
361056 AAAGAAGGAAAAT
1 AATGAAGGAAAAT
361069 GAGAGATCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (15 bp):
AATGAAGGAAAATAA
Found at i:364927 original size:3 final size:3
Alignment explanation
Indices: 364919--364943 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
364909 ATTTATTTAA
364919 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
364944 GATCGGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:365445 original size:16 final size:17
Alignment explanation
Indices: 365409--365448 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
365399 AATTACATTT
* *
365409 TAAAAAATAATTCATGC
1 TAAAAAATAAATCATGA
365426 TAAAAAATAAAT-ATGA
1 TAAAAAATAAATCATGA
365442 TAAAAAA
1 TAAAAAA
365449 ATTAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (17 bp):
TAAAAAATAAATCATGA
Found at i:367394 original size:73 final size:72
Alignment explanation
Indices: 367271--367471 Score: 185
Period size: 73 Copynumber: 2.8 Consensus size: 72
367261 CCAAAAAAAT
** * *
367271 ATAAAAA-ATAAAAATTT-AAATATTAATACTTATGAGATAATGA-CAAATACTTTTAAAAATTA
1 ATAAAAAGATAAAAATTTAAAATATCGATACTTATGA-ATGATGATC-GATACTTTTAAAAATTA
367333 AAAAAGTTG
64 AAAAAGTTG
* *
367342 ATAAAAAGATCAAAATTTAAAATATCGATACTTATGCAATGATGATCGATACTTTTAGAAATTAA
1 ATAAAAAGATAAAAATTTAAAATATCGATACTTATG-AATGATGATCGATACTTTTAAAAATTAA
*
367407 ACAAGTTG
65 AAAAGTTG
* * ** * * * *
367415 ATGAATATGATTGATAGTTAAAATATCGATA-TATATGTTATGATGTTCGATACTTTT
1 AT-AAAAAGATAAAAATTTAAAATATCGATACT-TATG-AATGATGATCGATACTTTT
367472 TATTTATATT
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
71 7 0.06
72 9 0.08
73 47 0.44
74 45 0.42
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.35
Consensus pattern (72 bp):
ATAAAAAGATAAAAATTTAAAATATCGATACTTATGAATGATGATCGATACTTTTAAAAATTAAA
AAAGTTG
Found at i:367465 original size:74 final size:73
Alignment explanation
Indices: 367317--367471 Score: 186
Period size: 74 Copynumber: 2.1 Consensus size: 73
367307 ATAATGACAA
*
367317 ATACTTTTAAAAATTAAAAAAGTTGATAAAAAGATCAAAATTTAAAATATCGATACTTATGCAAT
1 ATACTTTTAAAAATTAAAAAAGTTGATAAAAAGATCAAAAGTTAAAATATCGATACTTATGCAAT
367382 GATGATCG
66 GATGATCG
* * * * ** * **
367390 ATACTTTTAGAAATTAAACAAGTTGATGAATATGATTGATAGTTAAAATATCGATA-TATATGTT
1 ATACTTTTAAAAATTAAAAAAGTTGAT-AAAAAGATCAAAAGTTAAAATATCGATACT-TATGCA
*
367454 ATGATGTTCG
64 ATGATGATCG
367464 ATACTTTT
1 ATACTTTT
367472 TATTTATATT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
73 26 0.38
74 43 0.62
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (73 bp):
ATACTTTTAAAAATTAAAAAAGTTGATAAAAAGATCAAAAGTTAAAATATCGATACTTATGCAAT
GATGATCG
Found at i:367822 original size:100 final size:100
Alignment explanation
Indices: 367718--368139 Score: 396
Period size: 100 Copynumber: 4.3 Consensus size: 100
367708 ATAAAAAACT
* * * *
367718 TGTTTTGTCTTACTTTTACATAATATAAATAATTTCATATTTATAACATACACGGTTAACATTAA
1 TGTTTTGTCTTACTTTTACATAATATAAATGATTTCATATTTATAACTTAAACGGTTGACATTAA
* * *
367783 AAAAGACGCTACCTATTACATTATCATGAGCATCA
66 AAAAGACGCTACCTACTACGTTATCATGAGCAACA
* * *
367818 TGTTTTGTCTTACTTTTGCATAATATAAATGATTTCATACTTT-TAATTTAAACTGTTGACATTA
1 TGTTTTGTCTTACTTTTACATAATATAAATGATTTCATA-TTTATAACTTAAACGGTTGACATTA
* * *
367882 AAAAA-ATGCTACTTAGTACGTTATCATGAGCAACA
65 AAAAAGACGCTACCTACTACGTTATCATGAGCAACA
* * * * * * * * *
367917 TGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCTTACTTAAAACTTAAACGATTGATATAAA
1 TGTTTTGTCTTACTTTTACATAATATAAATGATTTCATATTTATAACTTAAACGGTTGACATTAA
* * *
367982 AAAATG-CGATATCTACTACGTTATCATGAGAAACA
66 AAAA-GACGCTACCTACTACGTTATCATGAGCAACA
* * * * * * * *
368017 TGTTTTGTCTTATTTTTACATCATATAAACG-----GT-TGTAT-ACTTATACGATTGACATAAA
1 TGTTTTGTCTTACTTTTACATAATATAAATGATTTCATATTTATAACTTAAACGGTTGACAT-TA
* ** *
368075 AAAAAGGCGCTACCTACTACAATATCATGAGAAACA
65 AAAAAGACGCTACCTACTACGTTATCATGAGCAACA
* *
368111 TGTTTTGTCTTATTTTTACATCATATAAA
1 TGTTTTGTCTTACTTTTACATAATATAAA
368140 CGGTTGTATA
Statistics
Matches: 275, Mismatches: 41, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
93 16 0.06
94 63 0.23
95 1 0.00
98 2 0.01
99 81 0.29
100 109 0.40
101 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (100 bp):
TGTTTTGTCTTACTTTTACATAATATAAATGATTTCATATTTATAACTTAAACGGTTGACATTAA
AAAAGACGCTACCTACTACGTTATCATGAGCAACA
Found at i:368116 original size:94 final size:93
Alignment explanation
Indices: 367903--368199 Score: 396
Period size: 94 Copynumber: 3.1 Consensus size: 93
367893 CTTAGTACGT
* * * * * *
367903 TATCATGAGCAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCTTACTTAAAACTTAA
1 TATCATGAGAAACATGTTTTGTCTTATTTTTACATCATATAAACGG-TT-GTA--T---ACTTAT
* * * **
367968 ACGATTGATATAAAAAAATGCGATATCTACTACGT
59 ACGATTGACATAAAAAAAGGCGATACCTACTACAA
368003 TATCATGAGAAACATGTTTTGTCTTATTTTTACATCATATAAACGGTTGTATACTTATACGATTG
1 TATCATGAGAAACATGTTTTGTCTTATTTTTACATCATATAAACGGTTGTATACTTATACGATTG
*
368068 ACATAAAAAAAAGGCGCTACCTACTACAA
66 ACAT-AAAAAAAGGCGATACCTACTACAA
368097 TATCATGAGAAACATGTTTTGTCTTATTTTTACATCATATAAACGGTTGTATACTTATACGATTG
1 TATCATGAGAAACATGTTTTGTCTTATTTTTACATCATATAAACGGTTGTATACTTATACGATTG
*
368162 ACATTAAAAAAAGGCGTTACCTACTACAA
66 ACA-TAAAAAAAGGCGATACCTACTACAA
368191 TATCATGAG
1 TATCATGAG
368200 CATAACAAAA
Statistics
Matches: 182, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
93 15 0.08
94 119 0.65
95 1 0.01
96 1 0.01
98 2 0.01
99 2 0.01
100 42 0.23
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (93 bp):
TATCATGAGAAACATGTTTTGTCTTATTTTTACATCATATAAACGGTTGTATACTTATACGATTG
ACATAAAAAAAGGCGATACCTACTACAA
Found at i:368559 original size:77 final size:76
Alignment explanation
Indices: 368469--368647 Score: 234
Period size: 77 Copynumber: 2.3 Consensus size: 76
368459 ACAACTTGCT
* *
368469 TTTTTAGTAAACCATAATATTCTTGTACGCAACTCATTTTATGAATAAAAA-TATTAACGTTCCA
1 TTTTTAGTGAACCATGATATTCTTG-ACGCAACTCATTTTATGAATAAAAAGTATTAACGTTCCA
* *
368533 TTTCGTAATATA
65 TATCGTAACATA
* * * * *
368545 TTTCTTAGTGAACCATGATAGTCTTAGGCGTAACTCATTTTATTAATAAAAAGTATTAACTTTCC
1 TTT-TTAGTGAACCATGATATTCTT-GACGCAACTCATTTTATGAATAAAAAGTATTAACGTTCC
368610 ATATCGTAACATA
64 ATATCGTAACATA
*
368623 TTTTTAGTGAACAATGATATTCTTG
1 TTTTTAGTGAACCATGATATTCTTG
368648 GGTGCACTCG
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
76 4 0.04
77 59 0.66
78 26 0.29
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (76 bp):
TTTTTAGTGAACCATGATATTCTTGACGCAACTCATTTTATGAATAAAAAGTATTAACGTTCCAT
ATCGTAACATA
Found at i:374884 original size:13 final size:13
Alignment explanation
Indices: 374866--374891 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
374856 TAAATAAATT
374866 TATTTTAAATTTA
1 TATTTTAAATTTA
374879 TATTTTAAATTTA
1 TATTTTAAATTTA
374892 AATATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTAAATTTA
Found at i:379352 original size:26 final size:26
Alignment explanation
Indices: 379323--379373 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
379313 TAGATAATTA
* *
379323 TTTATTTA-ATTATGTTCATTTTAAAT
1 TTTATTTATATT-TATTCAATTTAAAT
379349 TTTATTTATATTTATTCAATTTAAA
1 TTTATTTATATTTATTCAATTTAAA
379374 AATTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTATTTATATTTATTCAATTTAAAT
Found at i:388327 original size:150 final size:146
Alignment explanation
Indices: 387982--388344 Score: 389
Period size: 146 Copynumber: 2.5 Consensus size: 146
387972 ATGGAGTCTA
* * * * * *
387982 ATATGTCACTGAATTGAGGTGATATATCATTGAAAAGCTTACAAATGATGTGATT-GAGCACTGA
1 ATATATCACTAAATTGAAGTGATATATCACTGAAAAGTTTAAAAATGATGTGATTGGA-CACTGA
** * * * *
388046 AAAATTTTCTTCATTGTTCATTGAATGGTCGAGAAATGATATTTTTAATTAAAAATGGTCAAAAA
65 AAAATCGTCTTCATTGTTCACTCAATGATCAAGAAATGATATTTTTAATTAAAAATGGTCAAAAA
*
388111 CATCATTCAATGGTTTG
130 CACCATTCAATGGTTTG
* *
388128 ATATATCACTAAATTGAAGTGATATATCACTAAAAAGTTCAAAAATGATGTGATTGGACACTGAA
1 ATATATCACTAAATTGAAGTGATATATCACTGAAAAGTTTAAAAATGATGTGATTGGACACTGAA
* *
388193 AAA-CGTCTATCATTGTTCACTCCATGATCACTAAGAAA-GATCATTTTT-ATTTAAAATGGTCA
66 AAATCGTCT-TCATTGTTCACTCAATGAT--C-AAGAAATGAT-ATTTTTAATTAAAAATGGTCA
388255 AAAACACCATTCAATGGTCTT-
126 AAAACACCATTCAATGGT-TTG
* * * *
388276 ATA-ATTCA-TAGACAATTGAAGTGACATATCACTGAAAAGTTTAGAAATGATGTGATTGGGCAA
1 ATATA-TCACT--A-AATTGAAGTGATATATCACTGAAAAGTTTAAAAATGATGTGATTGGACAC
388339 TGAAAA
62 TGAAAA
388345 GTTTATTTCA
Statistics
Matches: 183, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
145 3 0.02
146 72 0.39
147 4 0.02
148 40 0.22
149 14 0.08
150 50 0.27
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (146 bp):
ATATATCACTAAATTGAAGTGATATATCACTGAAAAGTTTAAAAATGATGTGATTGGACACTGAA
AAATCGTCTTCATTGTTCACTCAATGATCAAGAAATGATATTTTTAATTAAAAATGGTCAAAAAC
ACCATTCAATGGTTTG
Found at i:388356 original size:150 final size:149
Alignment explanation
Indices: 387982--388383 Score: 439
Period size: 150 Copynumber: 2.7 Consensus size: 149
387972 ATGGAGTCTA
* * * * * * *
387982 ATATGTCACTGAATTGAGGTGATATATCATTGAAAAGCTTACAAATGATGTGATTGAGCACTGAA
1 ATATATCACTAAATTGAAGTGATATATCACTGAAAAGTTTAAAAATGATGTGATTGGGCACTGAA
* *
388047 AAATTT-TCTTCATTGTTCATTGAATGGT--C-GAGAAATGATATTTTTAATTAAAAATGGTCAA
66 AAGTTTAT-TTCATTGTTCATTCAATGGTCACTGAGAAATGATATTTTTAATTAAAAATGGTCAA
*
388108 AAACATCATTCAATGGTTTG
130 AAACACCATTCAATGGTTTG
* * *
388128 ATATATCACTAAATTGAAGTGATATATCACTAAAAAGTTCAAAAATGATGTGATTGGACACTGAA
1 ATATATCACTAAATTGAAGTGATATATCACTGAAAAGTTTAAAAATGATGTGATTGGGCACTG-A
* * * * * *
388193 AAACGTCTA--TCATTGTTCACTCCATGATCACTAAGAAA-GATCATTTTT-ATTTAAAATGGTC
65 AAA-GTTTATTTCATTGTTCATTCAATGGTCACTGAGAAATGAT-ATTTTTAATTAAAAATGGTC
388254 AAAAACACCATTCAATGGTCTT-
128 AAAAACACCATTCAATGGT-TTG
* * *
388276 ATA-ATTCA-TAGACAATTGAAGTGACATATCACTGAAAAGTTTAGAAATGATGTGATTGGGCAA
1 ATATA-TCACT--A-AATTGAAGTGATATATCACTGAAAAGTTTAAAAATGATGTGATTGGGCAC
*
388339 TGAAAAGTTTATTTCATTATTCATTCAATGGTCACTGAGAAATGA
62 TGAAAAGTTTATTTCATTGTTCATTCAATGGTCACTGAGAAATGA
388384 CGTTTTTCTT
Statistics
Matches: 210, Mismatches: 31, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
146 68 0.32
147 6 0.03
148 46 0.22
149 18 0.09
150 70 0.33
151 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (149 bp):
ATATATCACTAAATTGAAGTGATATATCACTGAAAAGTTTAAAAATGATGTGATTGGGCACTGAA
AAGTTTATTTCATTGTTCATTCAATGGTCACTGAGAAATGATATTTTTAATTAAAAATGGTCAAA
AACACCATTCAATGGTTTG
Found at i:400657 original size:55 final size:54
Alignment explanation
Indices: 400598--400808 Score: 271
Period size: 55 Copynumber: 3.8 Consensus size: 54
400588 TAGAATTAAC
*
400598 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAG-CAAAAAT
* **
400653 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGT---G-TAGCAAAAAT
* ** * * *
400711 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCAAAAAT
400765 GATTGAGCACCTCTGTGCTTCAATCGATGA-CTGACACCTCTGTG
1 GATTGAGCACCTCTGTGCTTCAATCGA-GAGCTGACACCTCTGTG
400809 CTTCAATCTA
Statistics
Matches: 134, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
54 43 0.32
55 45 0.34
58 44 0.33
59 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCAAAAAT
Found at i:400696 original size:27 final size:27
Alignment explanation
Indices: 400605--400816 Score: 107
Period size: 27 Copynumber: 7.7 Consensus size: 27
400595 AACGATTGAG
*
400605 CACCTCTGTGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTTCAATCGAGAACTGA
* ** * *
400632 CACCTCTGTG-TAGCCAAAAGTG-ATTGA
1 CACCTCTGTGCT--TCAATCGAGAACTGA
400659 GCACCTCTGTGCTTCAATCGAGAACTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
*** *
400687 CACCTCTGTGCAGTT-AAAAAAAATGACTGA
1 CACCTCTGTGC--TTCAATCGAGA--ACTGA
** * *
400717 GCACCTCTGTGCTTCAGCCGGGAGCTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
* *
400745 CACCTCTGTG-TAGCTAA--GATG-ATTGA
1 CACCTCTGTGCT-TC-AATCGA-GAACTGA
400771 GCACCTCTGTGCTTCAATCGATG-ACTGA
1 -CACCTCTGTGCTTCAATCGA-GAACTGA
400799 CACCTCTGTGCTTCAATC
1 CACCTCTGTGCTTCAATC
400817 TAAATTCTGG
Statistics
Matches: 138, Mismatches: 29, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
26 8 0.06
27 70 0.51
28 37 0.27
29 5 0.04
30 7 0.05
31 11 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (27 bp):
CACCTCTGTGCTTCAATCGAGAACTGA
Found at i:400805 original size:112 final size:113
Alignment explanation
Indices: 400601--400809 Score: 350
Period size: 113 Copynumber: 1.9 Consensus size: 113
400591 AATTAACGAT
*
400601 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
400666 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAATGAC
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAATGAC
* * * *
400714 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGA-TGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
400778 TGTGCTTCAATCGATG-ACTGACACCTCTGTGC
66 TGTGCTTCAATCGA-GAACTGACACCTCTGTGC
400810 TTCAATCTAA
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 44 0.49
113 46 0.51
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (113 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAATGAC
Found at i:408732 original size:29 final size:26
Alignment explanation
Indices: 408689--408756 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 26
408679 TAAAAATAAC
* *
408689 AAAAACTTAAAGGACTAAAATAGCAGA
1 AAAAAATTGAAGGACTAAAATAGCA-A
*
408716 AAATAAATATGAAGGACTAAAATAGTAA
1 AAA-AAAT-TGAAGGACTAAAATAGCAA
408744 AAAAAATTGAAGG
1 AAAAAATTGAAGG
408757 GCTGAACAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.17
27 7 0.19
28 7 0.19
29 16 0.44
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.18
Consensus pattern (26 bp):
AAAAAATTGAAGGACTAAAATAGCAA
Found at i:410195 original size:3 final size:3
Alignment explanation
Indices: 410181--410227 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
410171 GTGTAAACAA
* * *
410181 AAT AATT AAT AAT AAT AAT AAT AAC GAT AAT ATT AAT -AT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
410226 AA
1 AA
410228 AAAATTTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:410609 original size:40 final size:40
Alignment explanation
Indices: 410555--410750 Score: 124
Period size: 40 Copynumber: 4.6 Consensus size: 40
410545 TATCTAGGGT
**
410555 TGACACAACTCCTACGTGATGAGGAGGTCTGGTTAGTGGA
1 TGACACAGTTCCTACGTGATGAGGAGGTCTGGTTAGTGGA
* * * **
410595 TGACACGGTTCCTACGCGATGAGGATGATATACCATCTTTAG-GGA
1 TGACACAGTTCCTACGTGATGAGGA-G--GT--C-TGGTTAGTGGA
* * * * * *
410640 TGATAACACAGTTCTTACCTGATGAGGACGACTGGTTATCTAGGGG
1 TG---ACACAGTTCCTACGTGATGAGGAGGTCTGGTTA-GT--GGA
* * **
410686 TGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGA
1 TGACACAGTTCCTACGTGATGAGGAGGTCTGGTTAGTGGA
410726 TGACACAGTTCCTACGTGATGAGGA
1 TGACACAGTTCCTACGTGATGAGGA
410751 CGACATGCCA
Statistics
Matches: 113, Mismatches: 30, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
40 46 0.41
41 1 0.01
42 5 0.04
43 27 0.24
45 6 0.05
46 9 0.08
48 19 0.17
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (40 bp):
TGACACAGTTCCTACGTGATGAGGAGGTCTGGTTAGTGGA
Found at i:410707 original size:131 final size:131
Alignment explanation
Indices: 410412--410771 Score: 429
Period size: 131 Copynumber: 2.7 Consensus size: 131
410402 GTTATGGTCG
* * * * *
410412 TCTAAGGGTGACACAGCTCCTACGTGATGAGGAGATCTAGTCGGTAGATGACACTGTTCCTACGT
1 TCTAGGGGTGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGT
* ** * **
410477 GATGAGGACG-TCTTGGCCATCTTTAGGGAGGGTGATAACATGGTTGCTACGCAATGCGGATTAC
66 GATGAGGACGAT-AT-GCCATCTTTAGGGA---TGATAACACAGTTGCTACGCAATGAGGACGAC
410541 TGGTTA
126 TGGTTA
* * ** * *
410547 TCTAGGGTTGACACAACTCCTACGTGATGAGGAGGTCTGGTTAGTGGATGACACGGTTCCTACGC
1 TCTAGGGGTGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGT
* * *
410612 GATGAGGATGATATACCATCTTTAGGGATGATAACACAGTT-CTTAC-CTGATGAGGACGACTGG
66 GATGAGGACGATATGCCATCTTTAGGGATGATAACACAGTTGC-TACGC-AATGAGGACGACTGG
410675 TTA
129 TTA
*
410678 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGT
1 TCTAGGGGTGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGT
* *
410743 GATGAGGACGACATGCCATCTTTATGGAT
66 GATGAGGACGATATGCCATCTTTAGGGAT
410772 AATGTCTCAA
Statistics
Matches: 192, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
130 2 0.01
131 111 0.58
134 13 0.07
135 65 0.34
136 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (131 bp):
TCTAGGGGTGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGT
GATGAGGACGATATGCCATCTTTAGGGATGATAACACAGTTGCTACGCAATGAGGACGACTGGTT
A
Found at i:410794 original size:15 final size:15
Alignment explanation
Indices: 410774--410802 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
410764 TTATGGATAA
410774 TGTCTCAAGAGAGAC
1 TGTCTCAAGAGAGAC
410789 TGTCTCAAGAGAGA
1 TGTCTCAAGAGAGA
410803 AAAAAATCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (15 bp):
TGTCTCAAGAGAGAC
Found at i:410892 original size:36 final size:35
Alignment explanation
Indices: 410842--411023 Score: 111
Period size: 36 Copynumber: 5.4 Consensus size: 35
410832 AAGATGATGG
410842 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAACT
* * * *
410878 TGTTTCAAGGGAAACAGACTCAA--AGAC----TT
1 TGTTTCAAGAGAAACTGTCTCAAGGAGACAAAACT
* * *
410907 TTTTTCAAGACAAATTGTCTCAATGGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAACT
* * *
410943 TGTTTCAAGAGAAACAGACTCAA--AG-----ATT
1 TGTTTCAAGAGAAACTGTCTCAAGGAGACAAAACT
* *
410971 TTTCTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGT-TTCAAGAGAAACTGTCTCAAG-GAGACAAAAC-T
*
411009 TATTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
411024 AATTTCAAAG
Statistics
Matches: 105, Mismatches: 24, Indels: 33
0.65 0.15 0.20
Matches are distributed among these distances:
28 4 0.04
29 35 0.33
32 6 0.06
33 6 0.06
36 39 0.37
37 12 0.11
38 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGGAGACAAAACT
Found at i:410935 original size:65 final size:63
Alignment explanation
Indices: 410778--411068 Score: 279
Period size: 65 Copynumber: 4.4 Consensus size: 63
410768 GGATAATGTC
* * * *
410778 TCAAGAGAGACTGTCTCAAGAGAGAAAAAAATCGTTTCAA-AGGAAAC-GATCTCAAAGATGATG
1 TCAAGAGAAACTGTCTCAAG-GAGACAAAACTTGTTTCAAGA-GAAACAGA-CTCAAAGAT--T-
*
410841 GTGTT
60 -TTTT
*
410846 TCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAGACTCAAAGACTTTTTT
1 TCAAGAGAAACTGTCTCAA-GGAGACAAAACTTGTTTCAAGAGAAACAGACTCAAAGA-TTTTTT
* *
410911 TCAAGACAAATTGTCTCAATGGAGACAAAACTTGTTTCAAGAGAAACAGACTCAAAGATTTTTCT
1 TCAAGAGAAACTGTCTCAA-GGAGACAAAACTTGTTTCAAGAGAAACAGACTCAAAGATTTTT-T
* * *
410976 TCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTATTTCAAGAGAAACA-ATTTCAAAG-TTTGT
1 TCAAGAGAAACTGTCTCAAG-GAGACAAAAC-TTGTTTCAAGAGAAACAGA-CTCAAAGATTT-T
*
411039 CT
62 TT
411041 T-AAGA-AAGACTGTCTCAAGTGAGACAAA
1 TCAAGAGAA-ACTGTCTCAAG-GAGACAAA
411069 GTTTGTTTTG
Statistics
Matches: 195, Mismatches: 18, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
63 2 0.01
64 28 0.14
65 90 0.46
66 23 0.12
67 1 0.01
68 47 0.24
69 4 0.02
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (63 bp):
TCAAGAGAAACTGTCTCAAGGAGACAAAACTTGTTTCAAGAGAAACAGACTCAAAGATTTTTT
Found at i:411083 original size:36 final size:36
Alignment explanation
Indices: 411029--411100 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
411019 GAAACAATTT
* **
411029 CAAAGTTTGTCTTAAGAAAGACTGTCTCAAGTGAGA
1 CAAAGTTTGTCTTAAGAAAAACAATCTCAAGTGAGA
* *
411065 CAAAGTTTGTTTTGAGAAAAACAATCTCAAGTGAGA
1 CAAAGTTTGTCTTAAGAAAAACAATCTCAAGTGAGA
411101 TCAACTTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (36 bp):
CAAAGTTTGTCTTAAGAAAAACAATCTCAAGTGAGA
Found at i:411198 original size:36 final size:36
Alignment explanation
Indices: 411155--411269 Score: 124
Period size: 36 Copynumber: 3.2 Consensus size: 36
411145 AGGAAAAATG
411155 TCTCAAGCGAGACAAAATTTGTTTTGAGAGAAATTA
1 TCTCAAGCGAGACAAAATTTGTTTTGAGAGAAATTA
* * * *
411191 TCTCAAGCGAGACAAAGTTCGTTTTTA-AGAAAATTG
1 TCTCAAGCGAGACAAAATTTGTTTTGAGAG-AAATTA
* * * **
411227 TCTCTAGCGAGACGACATTTTGTTTTGAGAGAAACAA
1 TCTCAAGCGAGAC-AAAATTTGTTTTGAGAGAAATTA
411264 TCTCAA
1 TCTCAA
411270 AGGCGAAAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
35 2 0.03
36 41 0.65
37 18 0.29
38 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (36 bp):
TCTCAAGCGAGACAAAATTTGTTTTGAGAGAAATTA
Found at i:412445 original size:13 final size:14
Alignment explanation
Indices: 412427--412460 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
412417 TTCTTCGATC
*
412427 TTTCTTTGT-TTTT
1 TTTCTTTGTCTCTT
412440 TTTCTTTGTCTCTT
1 TTTCTTTGTCTCTT
412454 TTTCTTT
1 TTTCTTT
412461 TCTTTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTCTTTGTCTCTT
Found at i:412469 original size:18 final size:18
Alignment explanation
Indices: 412435--412470 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
412425 TCTTTCTTTG
412435 TTTTTTTTCTTTGTCTCT
1 TTTTTTTTCTTTGTCTCT
412453 TTTTCTTTTCTTT-TCTCT
1 TTTT-TTTTCTTTGTCTCT
412471 CTACTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTTTTCTTTGTCTCT
Found at i:413858 original size:16 final size:17
Alignment explanation
Indices: 413826--413858 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
413816 GATAAAAGCC
413826 TCCACATTACAAGACAT
1 TCCACATTACAAGACAT
*
413843 TCCACTTTAC-AGACAT
1 TCCACATTACAAGACAT
413859 GCTTTCGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.27
Consensus pattern (17 bp):
TCCACATTACAAGACAT
Found at i:415974 original size:16 final size:15
Alignment explanation
Indices: 415947--415978 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
415937 TTAAATAAAG
415947 AAATACAATGGAAAT
1 AAATACAATGGAAAT
415962 AAATACGAATGGAAAT
1 AAATAC-AATGGAAAT
415978 A
1 A
415979 TGCGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.59, C:0.06, G:0.16, T:0.19
Consensus pattern (15 bp):
AAATACAATGGAAAT
Found at i:416185 original size:30 final size:30
Alignment explanation
Indices: 416128--416212 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
416118 TTATGGGACC
* * * *
416128 AAAATAA-AAATAACATAAACTTAAAGGACT
1 AAAATAACAAA-AACAAAAATTTGAAGGAAT
* *
416158 AAAATAACAAAAATAGAAATTTGAAGGAAT
1 AAAATAACAAAAACAAAAATTTGAAGGAAT
**
416188 AAAATAGTAAAAACAAAAATTTGAA
1 AAAATAACAAAAACAAAAATTTGAA
416213 AGGTTTAACA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 42 0.93
31 3 0.07
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.20
Consensus pattern (30 bp):
AAAATAACAAAAACAAAAATTTGAAGGAAT
Found at i:416845 original size:37 final size:37
Alignment explanation
Indices: 416787--416861 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
416777 TCTCTCATTG
*
416787 GAGAAGGTATCAATCGCCGCCGTCGGTGGCGCTCACA
1 GAGAAGGTATCAACCGCCGCCGTCGGTGGCGCTCACA
*
416824 GAGAAGGTATCAACCGTCGCCGTCGGTGGCGCTCACA
1 GAGAAGGTATCAACCGCCGCCGTCGGTGGCGCTCACA
416861 G
1 G
416862 CGGCTGACGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.16
Consensus pattern (37 bp):
GAGAAGGTATCAACCGCCGCCGTCGGTGGCGCTCACA
Found at i:418267 original size:8 final size:8
Alignment explanation
Indices: 418219--418280 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
418209 CTTAAGGATC
418219 GAGAGAAG
1 GAGAGAAG
*
418227 GTGAGAAG
1 GAGAGAAG
**
418235 GACAGAGATC
1 G--AGAGAAG
418245 GAGAGAAG
1 GAGAGAAG
418253 GA-A-AAG
1 GAGAGAAG
418259 GAGAGAAG
1 GAGAGAAG
418267 GA-A-AAG
1 GAGAGAAG
418273 GAGAGAAG
1 GAGAGAAG
418281 TAAGCAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
6 10 0.24
7 4 0.10
8 23 0.55
10 5 0.12
ACGTcount: A:0.50, C:0.03, G:0.44, T:0.03
Consensus pattern (8 bp):
GAGAGAAG
Found at i:418276 original size:12 final size:14
Alignment explanation
Indices: 418245--418280 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
418235 GACAGAGATC
418245 GAGAGAAGGAAAAG
1 GAGAGAAGGAAAAG
418259 GAGAGAAGGAAAAG
1 GAGAGAAGGAAAAG
418273 GAGAGAAG
1 GAGAGAAG
418281 TAAGCAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (14 bp):
GAGAGAAGGAAAAG
Found at i:420999 original size:13 final size:13
Alignment explanation
Indices: 420978--421032 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
420968 AAGTTCGATA
*
420978 AATTCAAATACTT
1 AATTGAAATACTT
420991 AATTGAAATACTT
1 AATTGAAATACTT
* *
421004 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
421018 AATTGAAATACTT
1 AATTGAAATACTT
421031 AA
1 AA
421033 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:421114 original size:32 final size:33
Alignment explanation
Indices: 421018--421116 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
421008 AACTCAACAT
* * *
421018 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
421051 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
421084 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
421116 A
1 A
421117 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:421135 original size:21 final size:21
Alignment explanation
Indices: 421111--421150 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
421101 ACTTCAAGTT
421111 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
421132 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
421151 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:423613 original size:27 final size:28
Alignment explanation
Indices: 423581--423638 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
423571 AAAAAATCAG
423581 TTTTTCCCAAAACCGG-T-TTCGGATATT
1 TTTTTCCCAAAACCGGATATTCGGAT-TT
* *
423608 TTTTTCGCAAAATCGGATATTCGGATTT
1 TTTTTCCCAAAACCGGATATTCGGATTT
423636 TTT
1 TTT
423639 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (28 bp):
TTTTTCCCAAAACCGGATATTCGGATTT
Found at i:424056 original size:32 final size:32
Alignment explanation
Indices: 424015--424082 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
424005 GTAATTCAAA
* * *
424015 AACCCTACCACCATCGGATCTCATCATTCGAT
1 AACCCTACCACCACCAGATCTCATCATTCGAC
*
424047 AACCCTACCACCACCATATCTCATCATTCGAC
1 AACCCTACCACCACCAGATCTCATCATTCGAC
424079 AACC
1 AACC
424083 GAAAGAAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.41, G:0.06, T:0.22
Consensus pattern (32 bp):
AACCCTACCACCACCAGATCTCATCATTCGAC
Found at i:426317 original size:3 final size:3
Alignment explanation
Indices: 426302--426353 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
426292 ATTTATTTAT
* * * *
426302 TAA TAA TAT TAA TAA TAA TAT TAA TAA TAA TAC TAA -AA T-A TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
426348 TAA TAA
1 TAA TAA
426354 AAAGATGAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:426317 original size:12 final size:12
Alignment explanation
Indices: 426302--426353 Score: 77
Period size: 12 Copynumber: 4.2 Consensus size: 12
426292 ATTTATTTAT
426302 TAATAATATTAA
1 TAATAATATTAA
426314 TAATAATATTAA
1 TAATAATATTAA
*
426326 TAATAATACTAA
1 TAATAATATTAA
*
426338 AATATAATATTAA
1 TA-ATAATATTAA
426351 TAA
1 TAA
426354 AAAGATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 25 0.71
13 10 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:428495 original size:3 final size:3
Alignment explanation
Indices: 428487--428532 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
428477 ATTTATTTAT
* * *
428487 TAA TAA TAA TAA TAT TAA TAA TAA TAC T-A TAA T-A TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
428533 AAAGATGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 3 0.09
3 32 0.91
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:428502 original size:15 final size:15
Alignment explanation
Indices: 428484--428525 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
428474 GTAATTTATT
428484 TATTAATAATAATAA
1 TATTAATAATAATAA
*
428499 TATTAATAATAATAC
1 TATTAATAATAATAA
428514 TA-TAAT-ATAATA
1 TATTAATAATAATA
428526 TTAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 6 0.23
14 4 0.15
15 16 0.62
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TATTAATAATAATAA
Found at i:428776 original size:73 final size:73
Alignment explanation
Indices: 428655--429056 Score: 660
Period size: 73 Copynumber: 5.5 Consensus size: 73
428645 GATTGAAATG
428655 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
*
428720 AAGGATTT
66 AAGGCTTT
* * *
428728 TTGAAAACATCATGCACTGTAGGTCTTACAGATGATCCTGAGGCTTTAAAATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
428793 AAGGCTTT
66 AAGGCTTT
* *
428801 TTGAAAACATCATGTACTGTAGGTCTTACAGATGACCCTGAGGATTTAAAAACTTCAAAAAGCTC
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTT-AAGA--TCAAAAAGCTC
428866 CCGAAGGCTTT
63 CCGAAGGCTTT
* * * *
428877 TTGAAAACATCCTACACTGCAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCTCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
*
428942 GAGGCTTT
66 AAGGCTTT
*
428950 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
429015 AAGGCTTT
66 AAGGCTTT
*
429023 TTGAAAACATCATGCACTGTAGGGCTTACAGATG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATG
429057 TTGGAAATAG
Statistics
Matches: 305, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
73 233 0.76
74 4 0.01
75 3 0.01
76 65 0.21
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (73 bp):
TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
AAGGCTTT
Found at i:428925 original size:149 final size:146
Alignment explanation
Indices: 428655--429056 Score: 660
Period size: 149 Copynumber: 2.7 Consensus size: 146
428645 GATTGAAATG
428655 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
* * *
428720 AAGGATTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGATCCTGAGGCTTTAAAATCAAAA
66 AAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAAATCAAAA
428785 AGCTCCCGAAGGCTTT
131 AGCTCCCGAAGGCTTT
* *
428801 TTGAAAACATCATGTACTGTAGGTCTTACAGATGACCCTGAGGATTTAAAAACTTCAAAAAGCTC
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTT-AAGA--TCAAAAAGCTC
* * * *
428866 CCGAAGGCTTTTTGAAAACATCCTACACTGCAGGTCTTACAGATGACCCTGAGGATTTAAGATCA
63 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAAATCA
* *
428931 AAAAGCTCTCGGAGGCTTT
128 AAAAGCTCCCGAAGGCTTT
*
428950 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
*
429015 AAGGCTTTTTGAAAACATCATGCACTGTAGGGCTTACAGATG
66 AAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
429057 TTGGAAATAG
Statistics
Matches: 235, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
146 98 0.42
147 3 0.01
148 3 0.01
149 131 0.56
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (146 bp):
TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
AAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAAATCAAAA
AGCTCCCGAAGGCTTT
Found at i:429044 original size:222 final size:222
Alignment explanation
Indices: 428655--429056 Score: 714
Period size: 222 Copynumber: 1.8 Consensus size: 222
428645 GATTGAAATG
* *
428655 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
1 TTGAAAACATCATACACTGCAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
*
428720 AAGGATTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGATCCTGAGGCTTTAAAATCAAAA
66 AAGGATTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAA
* *
428785 AGCTCCCGAAGGCTTTTTGAAAACATCATGTACTGTAGGTCTTACAGATGACCCTGAGGATTTAA
131 AGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGGCTTACAGATGACCCTGAGGATTTAA
428850 AAACTTCAAAAAGCTCCCGAAGGCTTT
196 AAACTTCAAAAAGCTCCCGAAGGCTTT
* *
428877 TTGAAAACATCCTACACTGCAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCTCG
1 TTGAAAACATCATACACTGCAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
* * *
428942 GAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAA
66 AAGGATTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAA
429007 AGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGGCTTACAGATG
131 AGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGGCTTACAGATG
429057 TTGGAAATAG
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
222 170 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (222 bp):
TTGAAAACATCATACACTGCAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCCG
AAGGATTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAA
AGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGGCTTACAGATGACCCTGAGGATTTAA
AAACTTCAAAAAGCTCCCGAAGGCTTT
Found at i:430215 original size:54 final size:54
Alignment explanation
Indices: 430121--430223 Score: 125
Period size: 54 Copynumber: 1.9 Consensus size: 54
430111 TGAATAACTG
* * *
430121 GTTTGTAAAATATTTGACAACACATTCATCCTCTCATGTGGTTTCTGCCCAGAT
1 GTTTATAAAACATTTGACAACACATTCATCCTCTCATGTGGCTTCTGCCCAGAT
* * * * * *
430175 GTTTATAAAACATTTGATAACGCATTTATCTTTTCCTGTGGCTTCTGCC
1 GTTTATAAAACATTTGACAACACATTCATCCTCTCATGTGGCTTCTGCC
430224 ACATTTTCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 40 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (54 bp):
GTTTATAAAACATTTGACAACACATTCATCCTCTCATGTGGCTTCTGCCCAGAT
Found at i:437590 original size:17 final size:17
Alignment explanation
Indices: 437570--437611 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
437560 CTATGCCTGA
*
437570 CACGGAGAATAAATTCT
1 CACGAAGAATAAATTCT
437587 CACGAAGAATAAATTCT
1 CACGAAGAATAAATTCT
437604 CACGAAGA
1 CACGAAGA
437612 CATAGAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (17 bp):
CACGAAGAATAAATTCT
Found at i:438460 original size:2 final size:2
Alignment explanation
Indices: 438453--438491 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
438443 TATTAATAAA
* *
438453 AT AT AT AT AT AT AT AT AT AT AT -T TT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
438492 TTTAAAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:438485 original size:17 final size:17
Alignment explanation
Indices: 438463--438497 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
438453 ATATATATAT
438463 ATATATATATATTTTAA
1 ATATATATATATTTTAA
438480 ATATATATATATTTTAA
1 ATATATATATATTTTAA
438497 A
1 A
438498 GAATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATATATATTTTAA
Found at i:440132 original size:3 final size:3
Alignment explanation
Indices: 440124--440172 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
440114 ATTTATTTAT
* * *
440124 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAC TAA -AA T-A TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
440170 TAA
1 TAA
440173 AAAGATGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:440173 original size:16 final size:16
Alignment explanation
Indices: 440126--440174 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
440116 TTATTTATTA
*
440126 ATAATAATAATAATATT
1 ATAATAATAATAA-AAT
*
440143 AATAATAATACTAAAAT
1 -ATAATAATAATAAAAT
*
440160 ATAATATTAATAAAA
1 ATAATAATAATAAAA
440175 AGATGAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.48
17 2 0.07
18 12 0.44
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATAATAAAAT
Found at i:454261 original size:24 final size:24
Alignment explanation
Indices: 454229--454279 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
454219 TAAAATGATT
454229 TTCTAAGTATATTCGATATAATTA
1 TTCTAAGTATATTCGATATAATTA
454253 TTCTAAGTATATTCGATATAATTA
1 TTCTAAGTATATTCGATATAATTA
454277 TTC
1 TTC
454280 GAATATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (24 bp):
TTCTAAGTATATTCGATATAATTA
Found at i:456490 original size:32 final size:32
Alignment explanation
Indices: 456421--456500 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
456411 ATGAGGGAAA
* *
456421 CTTTGAAGATTCAACATCAAATGTTGAGGCAT
1 CTTTGGAGATTCAACATCAAATATTGAGGCAT
* * *
456453 CTTTGGAGATTCAACATCGAATATTGGGGTAT
1 CTTTGGAGATTCAACATCAAATATTGAGGCAT
* *
456485 CTTTGGGGATTTAACA
1 CTTTGGAGATTCAACA
456501 CCCTGATGCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (32 bp):
CTTTGGAGATTCAACATCAAATATTGAGGCAT
Found at i:456980 original size:124 final size:124
Alignment explanation
Indices: 456832--457139 Score: 456
Period size: 124 Copynumber: 2.5 Consensus size: 124
456822 CGTAGGAACC
* *
456832 GTGTTATCACCCTTAGATGGCCAAGATTCATCATAGTATGAGCAGTGTCATTCCCGACCAGATTT
1 GTGTTATCACCCTTAGATGGCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCCGACCAGATTT
* ** * * ** *
456897 CCTCATTACGTAGGAACTGTGTTAACCTTGGATAACCAAGATTCATCATAGTATGATCA
66 CCTCATCACGTAGGAACCATATCAACAGTGGATAACCAAGATTCATCATAGTATGAGCA
*
456956 GTGTTATCACCCTTAGATGTCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCCGACCAGATTT
1 GTGTTATCACCCTTAGATGGCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCCGACCAGATTT
*
457021 CCTCATCACGTAGGAGCCATATCAACAGTGGATAACCAAGATTCATCATAGTATGAGCA
66 CCTCATCACGTAGGAACCATATCAACAGTGGATAACCAAGATTCATCATAGTATGAGCA
* * **
457080 GTGTTCTCACCTTTAGATGGCCAAGATTCATCGCA-TATGAGCAGTGTCATCCCCTGACCA
1 GTGTTATCACCCTTAGATGGCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCC-GACCA
457140 AACCTCTTCG
Statistics
Matches: 166, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
123 19 0.11
124 147 0.89
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (124 bp):
GTGTTATCACCCTTAGATGGCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCCGACCAGATTT
CCTCATCACGTAGGAACCATATCAACAGTGGATAACCAAGATTCATCATAGTATGAGCA
Found at i:457157 original size:124 final size:124
Alignment explanation
Indices: 456832--457282 Score: 444
Period size: 124 Copynumber: 3.6 Consensus size: 124
456822 CGTAGGAACC
* *
456832 GTGTTATCACCCTTAGATGGCCAAGATTCATCATAGTATGAGCAGTGTCATTCCCGACCAGATTT
1 GTGTTATCACCCTTAGATGGCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCCGACCAGATTT
* ** * * ** *
456897 CCTCAT-TACGTAGGAACTGTGTTAACCTTGGATAACCAAGATTCATCATAGTATGATCA
66 CCTCATCT-CGTAGGAGCCATATCAACAGTGGATAACCAAGATTCATCATAGTATGAGCA
*
456956 GTGTTATCACCCTTAGATGTCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCCGACCAGATTT
1 GTGTTATCACCCTTAGATGGCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCCGACCAGATTT
*
457021 CCTCATCACGTAGGAGCCATATCAACAGTGGATAACCAAGATTCATCATAGTATGAGCA
66 CCTCATCTCGTAGGAGCCATATCAACAGTGGATAACCAAGATTCATCATAGTATGAGCA
* * ** * **
457080 GTGTTCTCACCTTTAGATGGCCAAGATTCATCGCA-TATGAGCAGTGTCATCCCCTGACCAAACC
1 GTGTTATCACCCTTAGATGGCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCC-GACCAGATT
* * * * * **** ** * * * *
457144 TCTTCGTCTCGTAGGAGCCGTGTAAACCCCAGATAACC-AGCCGTCCTCATCACGTAGGAACC
65 TCCTCATCTCGTAGGAGCCATATCAACAGTGGATAACCAAG-ATTCATCAT-A-GTATGAGCA
* * **
457206 GTGTTATCACCCTTAGATGAG-CAAAACTCATCCTA-TATGAGCAGTGTCATCCCCTGACCAGAT
1 GTGTTATCACCCTTAGATG-GCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCC-GACCAGAT
* *
457269 CTCCTCATCACGTA
64 TTCCTCATCTCGTA
457283 AGAGTCGTCT
Statistics
Matches: 274, Mismatches: 47, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
123 21 0.08
124 181 0.66
125 1 0.00
126 70 0.26
127 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (124 bp):
GTGTTATCACCCTTAGATGGCCAAGATTCATCAAAGTATGAGCAGTGTCATCCCCGACCAGATTT
CCTCATCTCGTAGGAGCCATATCAACAGTGGATAACCAAGATTCATCATAGTATGAGCA
Found at i:458031 original size:32 final size:32
Alignment explanation
Indices: 457986--458047 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
457976 TAATTCAAGA
457986 AACCCTACAACCACCATATCTCATCATTCGAT
1 AACCCTACAACCACCATATCTCATCATTCGAT
*
458018 AACCCTACTACCACCATATCTCATCATTCG
1 AACCCTACAACCACCATATCTCATCATTCG
458048 GCAATCGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26
Consensus pattern (32 bp):
AACCCTACAACCACCATATCTCATCATTCGAT
Found at i:464355 original size:22 final size:22
Alignment explanation
Indices: 464330--464410 Score: 144
Period size: 22 Copynumber: 3.7 Consensus size: 22
464320 TCAGCTGTCA
464330 TAACTCCTGAAATTATATCATG
1 TAACTCCTGAAATTATATCATG
464352 TAACTCCTGAAATTATATCATG
1 TAACTCCTGAAATTATATCATG
*
464374 TAACTCCTGAAATTAAATCATG
1 TAACTCCTGAAATTATATCATG
*
464396 TAACTCCTGATATTA
1 TAACTCCTGAAATTA
464411 ACAGCTTGTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (22 bp):
TAACTCCTGAAATTATATCATG
Found at i:464671 original size:6 final size:6
Alignment explanation
Indices: 464660--464708 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
464650 GACACGTATT
* * * *
464660 ACCACG ACCACG ACCACG ACCACG ACCATG TCCTCG ACCATG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
464708 A
1 A
464709 GTCGAGCCGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.31, C:0.45, G:0.16, T:0.08
Consensus pattern (6 bp):
ACCACG
Found at i:466024 original size:10 final size:10
Alignment explanation
Indices: 465992--466052 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
465982 AAAGAAACTA
465992 AAAATAA-AT
1 AAAATAATAT
466001 GAAAATAA-AT
1 -AAAATAATAT
*
466011 -AAATAGTAT
1 AAAATAATAT
*
466020 AAAATAATAA
1 AAAATAATAT
466030 AAAAT-ATAT
1 AAAATAATAT
466039 ATAAA-AATAT
1 A-AAATAATAT
466049 AAAA
1 AAAA
466053 ATGTATGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 5 0.12
9 9 0.21
10 29 0.67
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
AAAATAATAT
Found at i:466063 original size:22 final size:22
Alignment explanation
Indices: 466004--466074 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
465994 AATAAATGAA
466004 AATAAATAAATA-GTAT-AAAAT
1 AATAAA-AAATATGTATAAAAAT
*
466025 AATAAAAAATATATATAAAAAT
1 AATAAAAAATATGTATAAAAAT
* *
466047 -ATAAAAATGTATGTAT-AATAT
1 AATAAAAA-ATATGTATAAAAAT
466068 AATAAAA
1 AATAAAA
466075 TACTAAATAG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 5 0.12
21 20 0.48
22 17 0.40
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AATAAAAAATATGTATAAAAAT
Found at i:466263 original size:23 final size:24
Alignment explanation
Indices: 466237--466287 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
466227 GTAAACATAG
* *
466237 ATAAAAATAATAATATAATAT-AT
1 ATAAAAATAAGAAAATAATATAAT
* *
466260 ATAATAATAGGAAAATAATATAAT
1 ATAAAAATAAGAAAATAATATAAT
466284 ATAA
1 ATAA
466288 CGTAAAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAAAAATAAGAAAATAATATAAT
Done.