Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008046.1 Hibiscus syriacus cultivar Beakdansim tig00110534_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: 136486
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:944 original size:23 final size:23
Alignment explanation
Indices: 912--956 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
902 CTGAAACATC
912 ATCAAATCCGTG-TATTGACCAAT
1 ATCAAATCCG-GATATTGACCAAT
*
935 ATCAAGTCCGGATATTGACCAA
1 ATCAAATCCGGATATTGACCAA
957 GACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (23 bp):
ATCAAATCCGGATATTGACCAAT
Found at i:1660 original size:20 final size:20
Alignment explanation
Indices: 1632--1860 Score: 212
Period size: 20 Copynumber: 11.5 Consensus size: 20
1622 AAATTTCAGT
* * *
1632 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1652 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1672 GTTGCGATTTTACAGATTCTC
1 GTTGCGA-TTTACGGATTCGC
**
1693 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1713 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1733 GTTGCGATATACGGA-TAGC
1 GTTGCGATTTACGGATTCGC
* ** *
1752 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1772 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1792 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1812 GTTGCGATTTA-TG-TGTCGC
1 GTTGCGATTTACGGAT-TCGC
* **
1831 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1851 GTTGCGATTT
1 GTTGCGATTT
1861 TGGAAAATCG
Statistics
Matches: 175, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
18 1 0.01
19 27 0.15
20 128 0.73
21 19 0.11
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1736 original size:40 final size:39
Alignment explanation
Indices: 1632--1860 Score: 235
Period size: 39 Copynumber: 5.8 Consensus size: 39
1622 AAATTTCAGT
* * *
1632 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGA-TATC
* *
1672 GTTGCGATTTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGA-TTTACAGATACGCGTTGCGATTTACGGA-TATC
* * *
1713 GTTGCGATTTACGGATACGCGTTGCGATATACGGATAGC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGATATC
* ** *
1752 ATTGCGATTTACCCATACGCGTTGCGATTTACGGATACAC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGATA-TC
* * **
1792 GTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TCGC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACG-GATATC
* * *
1831 GTTGCGATTTTCATATTCGCGTTGCGATTT
1 GTTGCGATTTACAGATACGCGTTGCGATTT
1861 TGGAAAATCG
Statistics
Matches: 165, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 63 0.38
40 61 0.37
41 41 0.25
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (39 bp):
GTTGCGATTTACAGATACGCGTTGCGATTTACGGATATC
Found at i:1795 original size:79 final size:81
Alignment explanation
Indices: 1632--1819 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 81
1622 AAATTTCAGT
* * * * * * * * * *
1632 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTTACAGATTCTCGTTG
1 GTTGCGATTTACGGATACGCGTTGCGATATACGGATTAGCATTGCGATTTTACACATACGCGTTG
*
1697 CGATTTACGGATTATC
66 CGATTTACGGATTAAC
*
1713 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TAGCATTGCGA-TTTACCCATACGCGTTG
1 GTTGCGATTTACGGATACGCGTTGCGATATACGGATTAGCATTGCGATTTTACACATACGCGTTG
1776 CGATTTACGGA-TACAC
66 CGATTTACGGATTA-AC
1792 GTTGCGATTTACGGATACGCGTTGCGAT
1 GTTGCGATTTACGGATACGCGTTGCGAT
1820 TTATGTGTCG
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
78 2 0.02
79 53 0.56
80 9 0.10
81 30 0.32
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (81 bp):
GTTGCGATTTACGGATACGCGTTGCGATATACGGATTAGCATTGCGATTTTACACATACGCGTTG
CGATTTACGGATTAAC
Found at i:1832 original size:59 final size:58
Alignment explanation
Indices: 1651--1840 Score: 195
Period size: 59 Copynumber: 3.2 Consensus size: 58
1641 TACAGATTCT
* * * * **
1651 CGTTGCGATTTACGGATTA-TCGTTGCGATTTTACAGATTCTCGTTGCGATTTACGGATTAT
1 CGTTGCGATTTACGGA-TACACGTTGCGA-TTTACGGATACGCGTTGCGATTTACGG--TCG
* * * **
1712 CGTTGCGATTTACGGATACGCGTTGCGATATACGGATA-GCATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTA-CGGT-CG
*
1771 CGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTCG
1 CGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTACG-GTCG
1830 CGTTGCGATTT
1 CGTTGCGATTT
1841 TCATATTCGC
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
58 1 0.01
59 60 0.56
60 23 0.21
61 24 0.22
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (58 bp):
CGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTACGGTCG
Found at i:1836 original size:79 final size:79
Alignment explanation
Indices: 1632--1860 Score: 237
Period size: 79 Copynumber: 2.9 Consensus size: 79
1622 AAATTTCAGT
* * * * * * * * * *
1632 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTTACAGATTCTCGTTG
1 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TAGCATTGCGA-TTTACACATACGCGTTG
*
1697 CGATTTACGGATTATC
64 CGATTTACGGATTAAC
*
1713 GTTGCGATTTACGGATACGCGTTGCGATATACGGATAGCATTGCGATTTACCCATACGCGTTGCG
1 GTTGCGATTTACGGATACGCGTTGCGATATACGGATAGCATTGCGATTTACACATACGCGTTGCG
1778 ATTTACGGA-TACAC
66 ATTTACGGATTA-AC
* * * * * * *
1792 GTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TCGCGTTGCGATTTTCATATTCGCGTTGC
1 GTTGCGATTTACGGATACGCGTTGCGATATACG-GATAGCATTGCGATTTACACATACGCGTTGC
1856 GATTT
65 GATTT
1861 TGGAAAATCG
Statistics
Matches: 126, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
78 2 0.02
79 84 0.67
80 10 0.08
81 30 0.24
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (79 bp):
GTTGCGATTTACGGATACGCGTTGCGATATACGGATAGCATTGCGATTTACACATACGCGTTGCG
ATTTACGGATTAAC
Found at i:1877 original size:21 final size:21
Alignment explanation
Indices: 1847--1929 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
1837 ATTTTCATAT
*
1847 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1868 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
1889 TCGCATTGCAATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1910 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1930 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2121 original size:24 final size:25
Alignment explanation
Indices: 2068--2123 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 25
2058 TTTTCTCTTT
2068 ATTTTAACCCCTGAACTTCATATAAA
1 ATTTTAACCCCTGAACTTCA-ATAAA
2094 ATTTTAACCCCTGAACTTC-ATAAA
1 ATTTTAACCCCTGAACTTCAATAAA
2118 ATTTTA
1 ATTTTA
2124 TTTATGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 11 0.37
26 19 0.63
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (25 bp):
ATTTTAACCCCTGAACTTCAATAAA
Found at i:30899 original size:39 final size:39
Alignment explanation
Indices: 30845--30926 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
30835 TTTAGTATTC
30845 TAAACTTTTAGAATTGTGTATTGATTATTGTCAATTGAA
1 TAAACTTTTAGAATTGTGTATTGATTATTGTCAATTGAA
30884 TAAACTTTTAGAATTGTGTATTGATTATTGTCAATTGAA
1 TAAACTTTTAGAATTGTGTATTGATTATTGTCAATTGAA
30923 TAAA
1 TAAA
30927 AATAATATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (39 bp):
TAAACTTTTAGAATTGTGTATTGATTATTGTCAATTGAA
Found at i:31074 original size:68 final size:68
Alignment explanation
Indices: 30994--31127 Score: 268
Period size: 68 Copynumber: 2.0 Consensus size: 68
30984 CCTCAAAGAT
30994 AGATTTAAGATCAAGATAATATCGATTTAAGGTGAAATATGTTCTAAAGATTACATTCAAAACCT
1 AGATTTAAGATCAAGATAATATCGATTTAAGGTGAAATATGTTCTAAAGATTACATTCAAAACCT
31059 GAC
66 GAC
31062 AGATTTAAGATCAAGATAATATCGATTTAAGGTGAAATATGTTCTAAAGATTACATTCAAAACCT
1 AGATTTAAGATCAAGATAATATCGATTTAAGGTGAAATATGTTCTAAAGATTACATTCAAAACCT
31127 G
66 G
31128 CTATGATCAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (68 bp):
AGATTTAAGATCAAGATAATATCGATTTAAGGTGAAATATGTTCTAAAGATTACATTCAAAACCT
GAC
Found at i:31937 original size:23 final size:22
Alignment explanation
Indices: 31902--31946 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
31892 TAGAGATAGT
31902 GAAACCAAAATAAATAAAATAAA
1 GAAACCAAAATAAAT-AAATAAA
31925 GAAA-CAAAGATAAATAAATAAA
1 GAAACCAAA-ATAAATAAATAAA
31947 ATACGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (22 bp):
GAAACCAAAATAAATAAATAAA
Found at i:35567 original size:6 final size:6
Alignment explanation
Indices: 35556--35598 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
35546 ACCCACCTTA
*
35556 TTTTTC TTTTTC TTTTTC TTTTTC TTTTGTTC TTTATC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTT-TTC TTTTTC TTTTT
35599 TTTCTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 24 0.73
7 6 0.18
8 3 0.09
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:35601 original size:18 final size:18
Alignment explanation
Indices: 35556--35601 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
35546 ACCCACCTTA
* *
35556 TTTTTCTTTTTCTTTTTC
1 TTTTTTTTTTTCTTTATC
35574 TTTTTCTTTTGTTCTTTATC
1 TTTTT-TTTT-TTCTTTATC
35594 TTTTTTTT
1 TTTTTTTT
35602 CTATTTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 6 0.25
20 13 0.54
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTTCTTTATC
Found at i:42358 original size:23 final size:23
Alignment explanation
Indices: 42325--42381 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
42315 ATTATATGGT
* *
42325 ACTACGATGCAATTCTACGTGGC
1 ACTACGGTGCAATTCTACGCGGC
42348 ACTACGGTGCAATTCTACGCGGC
1 ACTACGGTGCAATTCTACGCGGC
*
42371 ACTTCGGTGCA
1 ACTACGGTGCA
42382 TGTATACGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
ACTACGGTGCAATTCTACGCGGC
Found at i:42389 original size:23 final size:23
Alignment explanation
Indices: 42325--42389 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
42315 ATTATATGGT
* * *
42325 ACTACGATGCAATTCTACGTGGC
1 ACTACGGTGCAATTATACGCGGC
*
42348 ACTACGGTGCAATTCTACGCGGC
1 ACTACGGTGCAATTATACGCGGC
*
42371 ACTTCGGTGC-ATGTATACG
1 ACTACGGTGCAAT-TATACG
42390 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 2 0.05
23 35 0.95
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (23 bp):
ACTACGGTGCAATTATACGCGGC
Found at i:42496 original size:2 final size:2
Alignment explanation
Indices: 42489--42518 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42479 AACAAATACA
42489 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
42519 GATGGATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42691 original size:15 final size:13
Alignment explanation
Indices: 42656--42693 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
42646 TAATTTGATG
42656 ATAATGAT-ATAA
1 ATAATGATAATAA
42668 ATAATGATAATAA
1 ATAATGATAATAA
42681 TATATATGATAAT
1 -ATA-ATGATAAT
42694 TCTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 3 0.13
15 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (13 bp):
ATAATGATAATAA
Found at i:46202 original size:26 final size:26
Alignment explanation
Indices: 46151--46202 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
46141 ATACGAATGT
*
46151 AAAAACATGGAAAATATAAAATAAAA
1 AAAAACATGGAAAATATAAAACAAAA
*
46177 AAAAACATGGAATATA-AAAAGCAAAA
1 AAAAACATGGAAAATATAAAA-CAAAA
46203 TATGCAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (26 bp):
AAAAACATGGAAAATATAAAACAAAA
Found at i:49100 original size:27 final size:26
Alignment explanation
Indices: 49045--49128 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 26
49035 AGTGAAACCA
*
49045 AAATGAATAAAATAAAGAAACAAAGAT
1 AAAT-AATAAAATAAAGAAACAAAAAT
*
49072 AAATAAATAAAATAAGGAAA-AATAAAT
1 AAAT-AATAAAATAAAGAAACAA-AAAT
*
49099 AATAATAATAATAATAAAATAAACAAAAAT
1 -A-AATAATAA-AAT-AAAGAAACAAAAAT
49129 GAGGGGAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 2 0.04
27 21 0.46
28 6 0.13
29 6 0.13
30 9 0.20
31 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (26 bp):
AAATAATAAAATAAAGAAACAAAAAT
Found at i:49256 original size:22 final size:23
Alignment explanation
Indices: 49226--49268 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
49216 TATAATATAT
* *
49226 AAATGAAAATAGAAACATATAAA
1 AAATGAAAATAAAAAAATATAAA
49249 AAAT-AAAATAAAAAAATATA
1 AAATGAAAATAAAAAAATATA
49269 CGTATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (23 bp):
AAATGAAAATAAAAAAATATAAA
Found at i:49927 original size:103 final size:102
Alignment explanation
Indices: 49793--50000 Score: 380
Period size: 103 Copynumber: 2.0 Consensus size: 102
49783 GCCGCGGGTC
**
49793 ATCGACGGCAAAACATAATTTTTTTTTGCTTTTCCGAAAGCTTTCTTCCCCCTCTTTACGAAAAC
1 ATCGACGGCAAAACATAAAATTTTTTTGCTTTTCCGAAAGCTTTCTTCCCCCTCTTTACGAAAAC
49858 CAAACTAGGTTTTTAGGAAAATAAGCCTCGGGGTGTGG
66 CAAACTAGGTTTTTAGGAAAATAAGCCTC-GGGTGTGG
49896 ATCGACGGCAAAACATAAAATTTTTTTGCTTTTCCGAAAGCTTTCTTCCCCCTCTTTACGAAAAC
1 ATCGACGGCAAAACATAAAATTTTTTTGCTTTTCCGAAAGCTTTCTTCCCCCTCTTTACGAAAAC
*
49961 CAAACTAGTTTTTTAGGAAAATAAGCCTCGGGTGTGG
66 CAAACTAGGTTTTTAGGAAAATAAGCCTCGGGTGTGG
49998 ATC
1 ATC
50001 TAAGATCGAA
Statistics
Matches: 102, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 11 0.11
103 91 0.89
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (102 bp):
ATCGACGGCAAAACATAAAATTTTTTTGCTTTTCCGAAAGCTTTCTTCCCCCTCTTTACGAAAAC
CAAACTAGGTTTTTAGGAAAATAAGCCTCGGGTGTGG
Found at i:65214 original size:3 final size:3
Alignment explanation
Indices: 65206--65234 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
65196 ACGCTCTTTC
65206 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
65235 CTCCACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:69873 original size:23 final size:23
Alignment explanation
Indices: 69847--69894 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
69837 ATAAAGTACA
* *
69847 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCACTTAT
**
69870 ATAATGTAATAGGTAGCACTTAT
1 ATAACATAATAGGTAGCACTTAT
69893 AT
1 AT
69895 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCACTTAT
Found at i:70346 original size:23 final size:23
Alignment explanation
Indices: 70320--70382 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
70310 ATATAACCAC
70320 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
70343 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
70366 TACCTATTACATCATAT
1 TACCTATTACATTATAT
70383 TTTTACATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:70568 original size:30 final size:29
Alignment explanation
Indices: 70528--70594 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
70518 TCATTTGCAC
* * *
70528 AAAAAATTATTT-GATTTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
70558 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
70587 AATAATAT
1 AA-AATAT
70595 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:70767 original size:23 final size:23
Alignment explanation
Indices: 70739--70811 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
70729 GACACTTTAC
70739 ATATAACCACTACCTATTACATT
1 ATATAACCACTACCTATTACATT
*
70762 ATATAAACGA-TACCTATTACATT
1 ATAT-AACCACTACCTATTACATT
* * *
70785 ATATAAGCGCTACCTATTACATC
1 ATATAACCACTACCTATTACATT
70808 ATAT
1 ATAT
70812 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
22 2 0.05
23 37 0.86
24 4 0.09
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:70797 original size:429 final size:430
Alignment explanation
Indices: 69960--71014 Score: 2003
Period size: 430 Copynumber: 2.5 Consensus size: 430
69950 CTATTACATT
69960 ATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAA
1 ATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAA
*
70025 TTTATGTTTCAATTTTTTTTAATAATG-TTCATGTTTTCCACCTACAATATTAATTTAATAATTT
66 TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
*
70089 CATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 CATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
*
70154 AATAATAATATATATCGTAACGTAAAAAATAAATCAATAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACATAAAAAATAAATCAATAGACGCCTATAATTACTAAATTAATAT
70219 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
70284 TTTATAAAAAGAATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
326 TTTATAAAAAGAATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
70349 TTACATTATATAAGCGCTACCTATTACATCATATTTTTAC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTAC
70389 ATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAA
1 ATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAA
70454 TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
66 TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
70519 CATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 CATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
*
70584 AATAATAATATATATCGTAACATAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACATAAAAAATAAATCAATAGACGCCTATAATTACTAAATTAATAT
70649 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
70714 TTTATAAAAAGGATAGACACTTTAC-ATATAACCACTACCTATTACATTATATAAACGATACCTA
326 TTTATAAAAAGAATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
70778 TTACATTATATAAGCGCTACCTATTACATCATATTTTTAC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTAC
*
70818 CTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTC-TTTAAAGTTATGTAA
1 ATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAA
70881 TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
66 TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
* *
70946 CATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTATAA-TTTAAATTT
131 CATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
71010 AATAA
196 AATAA
71015 CATTAACCAA
Statistics
Matches: 617, Mismatches: 8, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
426 13 0.02
427 134 0.22
428 17 0.03
429 200 0.32
430 253 0.41
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (430 bp):
ATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAA
TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
CATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
AATAATAATATATATCGTAACATAAAAAATAAATCAATAGACGCCTATAATTACTAAATTAATAT
CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
TTTATAAAAAGAATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
TTACATTATATAAGCGCTACCTATTACATCATATTTTTAC
Found at i:74062 original size:365 final size:366
Alignment explanation
Indices: 73372--74079 Score: 1233
Period size: 365 Copynumber: 1.9 Consensus size: 366
73362 TTAAAATTAC
* *
73372 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTAAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
* *
73437 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
73502 ATATTATAAATTTATCTATTACATTATAATTATGGGTTCCAATGTGTAAATGTCGACACTTTTTA
131 ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCAATGTGTAAATGTCGACACTTTTTA
* *
73567 ACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTATCGACACAAGATTAAAAAGTGT
196 ACAATGTATCGAAACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAGATTAAAAAGTGT
* *
73632 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGTTATATTACAAATT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGATACATTACAAATT
*
73697 TATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
326 TACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
73738 CGACACTTTTTAACAAT-GTATCGACACATTTTT-TTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
73801 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
*
73866 TATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTT
130 TATATTACAAATTTATCTATTACATTATAATTATGGGTTCCAATGTGTAAATGTCGACACTTTTT
73931 AACAATGTATCGAAACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAGATTAAAAAGTG
195 AACAATGTATCGAAACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAGATTAAAAAGTG
* * *
73996 TCGATATATGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACC-GATAGCATTGCAAA
260 TCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGATA-CATTACAAA
**
74060 TTTACCTATTTTATTATAAT
324 TTTACCTATTACATTATAAT
74080 ATGTTGAAAG
Statistics
Matches: 324, Mismatches: 16, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
364 3 0.01
365 290 0.90
366 28 0.09
367 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (366 bp):
CGACACTTTTTAAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCAATGTGTAAATGTCGACACTTTTTA
ACAATGTATCGAAACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAGATTAAAAAGTGT
CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGATACATTACAAATT
TACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:74079 original size:183 final size:183
Alignment explanation
Indices: 73372--74046 Score: 1228
Period size: 183 Copynumber: 3.7 Consensus size: 183
73362 TTAAAATTAC
* *
73372 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAACAAT-GTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAA
* * *
73436 TATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
* *
73501 TATATTATAAATTTATCTATTACATTATAATTATGGGTTCCAATGTGTAAATGT
130 TATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
73555 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTATCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
*
73620 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
73685 ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
73738 CGACACTTTTTAACAATGTATCGACACA-TTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
73802 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
73867 ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
73920 CGACACTTTTTAACAATGTATCGAAACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
*
73985 ATTAAAAAGTGTCGATATATGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
74047 ATAGCATTGC
Statistics
Matches: 477, Mismatches: 13, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
182 179 0.38
183 295 0.62
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAATTTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:75556 original size:3 final size:3
Alignment explanation
Indices: 75548--75628 Score: 63
Period size: 3 Copynumber: 27.0 Consensus size: 3
75538 ACTTGTTTGG
* * * * * *
75548 ATC ATC ATC TTC ATC ATC ATC ATC GTC GTC GTC ATC ATC TTC ATC GTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
75596 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
75629 GTCAGCTTCA
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:75565 original size:12 final size:12
Alignment explanation
Indices: 75561--75640 Score: 79
Period size: 12 Copynumber: 6.4 Consensus size: 12
75551 ATCATCTTCA
* *
75561 TCATCATCATCG
1 TCATCGTCATCT
*
75573 TCGTCGTCATCAT
1 TCATCGTCATC-T
*
75586 CTTCATCGTCAGCT
1 -T-CATCGTCATCT
*
75600 TCATCGTCATCA
1 TCATCGTCATCT
75612 TCATCGTCATCT
1 TCATCGTCATCT
*
75624 TCATCGTCAGCT
1 TCATCGTCATCT
75636 TCATC
1 TCATC
75641 TTCTGCGACC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
12 45 0.80
13 1 0.02
14 2 0.04
15 8 0.14
ACGTcount: A:0.19, C:0.34, G:0.11, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:75571 original size:18 final size:18
Alignment explanation
Indices: 75552--75643 Score: 85
Period size: 18 Copynumber: 5.1 Consensus size: 18
75542 GTTTGGATCA
* *
75552 TCATCTTCATCATCATCA
1 TCATCGTCATCATCATCT
* *
75570 TCGTCGTCGTCATCATCT
1 TCATCGTCATCATCATCT
* * *
75588 TCATCGTCAGCTTCATCG
1 TCATCGTCATCATCATCT
* *
75606 TCATCATCATCGTCATCT
1 TCATCGTCATCATCATCT
* *
75624 TCATCGTCAGCTTCATCT
1 TCATCGTCATCATCATCT
75642 TC
1 TC
75644 TGCGACCGCT
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.18, C:0.34, G:0.10, T:0.38
Consensus pattern (18 bp):
TCATCGTCATCATCATCT
Found at i:75609 original size:24 final size:24
Alignment explanation
Indices: 75582--75640 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
75572 GTCGTCGTCA
75582 TCATCTTCATCGTCAGCTTCATCG
1 TCATCTTCATCGTCAGCTTCATCG
* *
75606 TCATCATCATCGTCATCTTCATCG
1 TCATCTTCATCGTCAGCTTCATCG
*
75630 TCAGCTTCATC
1 TCATCTTCATC
75641 TTCTGCGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.34, G:0.10, T:0.37
Consensus pattern (24 bp):
TCATCTTCATCGTCAGCTTCATCG
Found at i:75643 original size:6 final size:6
Alignment explanation
Indices: 75552--75643 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
75542 GTTTGGATCA
* * * * * * * *
75552 TCATCT TCATCA TCATCA TCGTCG TCGTCA TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
75600 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
75644 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.18, C:0.34, G:0.10, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:78064 original size:200 final size:200
Alignment explanation
Indices: 77624--78250 Score: 1204
Period size: 200 Copynumber: 3.1 Consensus size: 200
77614 GATGATTTTG
77624 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAAC
*
77689 TAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTAAACTTG--CCGGTTA
66 TAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTA
77752 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
77817 TATAT
196 TATAT
77822 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAAC
77887 TAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTA
66 TAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTA
77952 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
78017 TATAT
196 TATAT
78022 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAAC
*
78087 TAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGACTTGTACCGGTTA
66 TAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTA
*
78152 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACACTTTTTA
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
78217 TATAT
196 TATAT
*
78222 GGATCGACACTTTATGGTTGCACCCTGTT
1 GGATCGACACTTTATGGGTGCACCCTGTT
78251 GGCCATATTG
Statistics
Matches: 423, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
198 120 0.28
200 303 0.72
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (200 bp):
GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAAC
TAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
TATAT
Found at i:78415 original size:19 final size:19
Alignment explanation
Indices: 78369--78417 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
78359 TTATATTCAC
*
78369 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
78388 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
78407 ATACAAAATTA
1 ATACAAAATTA
78418 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:80244 original size:33 final size:33
Alignment explanation
Indices: 80207--80272 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
80197 CATCTTAATA
*
80207 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
80240 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
80273 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:80331 original size:21 final size:21
Alignment explanation
Indices: 80306--80370 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
80296 CCCCTTATGC
* *
80306 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
80327 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
80348 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
80369 CT
1 CT
80371 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:82797 original size:20 final size:20
Alignment explanation
Indices: 82770--82816 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
82760 TCCGGTAACG
82770 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
82789 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
82810 TTTTACC
1 TTTTACC
82817 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:83030 original size:181 final size:181
Alignment explanation
Indices: 82556--83028 Score: 669
Period size: 181 Copynumber: 2.6 Consensus size: 181
82546 CGTACTTACG
* * *
82556 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
* * *
82621 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* * * *
82686 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAATGTTGATCCTTGTAT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATAT
* * * *
82737 AAAATATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
* *
82802 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
82867 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATA-T
* * * * *
82919 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACTGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACTGGTT
* * *
82983 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
83029 AATTTGGATC
Statistics
Matches: 258, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
181 161 0.62
182 96 0.37
183 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATAT
Found at i:83496 original size:229 final size:228
Alignment explanation
Indices: 83095--83581 Score: 893
Period size: 229 Copynumber: 2.1 Consensus size: 228
83085 ACCTACTTTT
*
83095 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
83160 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
83225 ATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* *
83290 CAAATATAATAATAAATATGTTTTCAACAGTGAA
196 CAAAGATAATAATAAATATATTTTC-ACAGTGAA
*
83324 ATAAGTATGAACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
*
83389 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
83454 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
*
83519 TAAAGATAATAATAAATATATTTTCACAGTGAA
196 CAAAGATAATAATAAATATATTTTCACAGTGAA
*
83552 ATAAGTATGGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
83582 GATAATTTAC
Statistics
Matches: 249, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
228 36 0.14
229 213 0.86
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:91609 original size:43 final size:41
Alignment explanation
Indices: 91485--91614 Score: 134
Period size: 42 Copynumber: 3.0 Consensus size: 41
91475 CATAAACGTT
* * *
91485 GCAAAAGGTCAGATTTATAGCGACGGTTTTGGATACAAACGTC
1 GCAAAAGGTCAGATCTATAGCG--GGTTTTAGATACAAACGCC
* ****
91528 GCAAAAGGTCAGATCTATAGCGGCATTTTTCCCACAAACGCC
1 GCAAAAGGTCAGATCTATAGCGG-GTTTTAGATACAAACGCC
*
91570 GCAAAAAGTCAGATCTATAGCGGTGTGTTTAGATACAAACGCC
1 GCAAAAGGTCAGATCTATAGCGG-GT-TTTAGATACAAACGCC
91613 GC
1 GC
91615 TAATTACCAT
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 35 0.49
43 35 0.49
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (41 bp):
GCAAAAGGTCAGATCTATAGCGGGTTTTAGATACAAACGCC
Found at i:91970 original size:15 final size:15
Alignment explanation
Indices: 91950--91979 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
91940 CCCATTTTTC
91950 TTTGTCTGCAATCAT
1 TTTGTCTGCAATCAT
*
91965 TTTGTCTGGAATCAT
1 TTTGTCTGCAATCAT
91980 CCAACAAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.47
Consensus pattern (15 bp):
TTTGTCTGCAATCAT
Found at i:93879 original size:14 final size:14
Alignment explanation
Indices: 93860--93912 Score: 97
Period size: 14 Copynumber: 3.8 Consensus size: 14
93850 AATAATAAGA
93860 AGAAGAGGAAGTGG
1 AGAAGAGGAAGTGG
93874 AGAAGAGGAAGTGG
1 AGAAGAGGAAGTGG
93888 AGAAGAGGAAGTGG
1 AGAAGAGGAAGTGG
*
93902 AGAAGAAGAAG
1 AGAAGAGGAAG
93913 AAGAAGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.06
Consensus pattern (14 bp):
AGAAGAGGAAGTGG
Found at i:94437 original size:41 final size:41
Alignment explanation
Indices: 94374--94753 Score: 261
Period size: 41 Copynumber: 9.2 Consensus size: 41
94364 TGGCGTGTGT
* * ** *
94374 GCCACTAAAGTACGAGTC-TATAGTGGCGTAAGCATATAAAC
1 GCCACTAAAGTACAAG-CGTATAGCGGCGTTTGTATATAAAC
*
94415 GCCACTAAAGTACAAGCGTATAGCGGCGTTTGTATAAAAAC
1 GCCACTAAAGTACAAGCGTATAGCGGCGTTTGTATATAAAC
* *
94456 GCTACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAAC
1 GCCACTAAAGTACAAGCGTATAGCGGCGTTTGTATATAAAC
* * * * * * *
94497 GCCACTAAAGTACGAGTC-TTTAGCGACGTTTCTAAACACAAAA
1 GCCACTAAAGTACAAG-CGTATAGCGGCGTTTGT--ATATAAAC
* * *
94540 GCCACTAAAGTACGAGTC-TATAGCGGCGTTTGTATAAAAAT
1 GCCACTAAAGTACAAG-CGTATAGCGGCGTTTGTATATAAAC
* * * * * * *
94581 GCCACTAAAGTACGAGTC-TTTAGCGACGTTTCTAAACACAAAT
1 GCCACTAAAGTACAAG-CGTATAGCGGCGTTTGT--ATATAAAC
** *
94624 GCCACTAAAGTATGAGTC-TATAGCGGCGTTTGTATAAAAAC
1 GCCACTAAAGTACAAG-CGTATAGCGGCGTTTGTATATAAAC
* ** * * * *
94665 GCCACTAAAATATGAGTC-TTTAGCGGTGTTTGTATAAAAAT
1 GCCACTAAAGTACAAG-CGTATAGCGGCGTTTGTATATAAAC
* * *
94706 GCCACTAAAGTACAAGTC-TTTAGCGGCGTTTGTTTAAAAAC
1 GCCACTAAAGTACAAG-CGTATAGCGGCGTTTGTATATAAAC
*
94747 ACCACTA
1 GCCACTA
94754 TGGCTGAACC
Statistics
Matches: 286, Mismatches: 47, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
40 1 0.00
41 215 0.75
43 70 0.24
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (41 bp):
GCCACTAAAGTACAAGCGTATAGCGGCGTTTGTATATAAAC
Found at i:94589 original size:84 final size:82
Alignment explanation
Indices: 94373--94753 Score: 458
Period size: 84 Copynumber: 4.6 Consensus size: 82
94363 GTGGCGTGTG
* ** * * * *
94373 TGCCACTAAAGTACGAGTCTATAGTGGCGTAAGCATATAAACGCCACTAAAGTACAAG-CGTATA
1 TGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTC-TTTA
* * *
94437 GCGGCGTTTGTATAAAAA
65 GCGACGTTTCTAAAAAAA
* * * * *
94455 CGCTACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAG
1 TGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAG
94520 CGACGTTTCTAAACACAAA
66 CGACGTTTCTAAA-A-AAA
* *
94539 AGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAG
1 TGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAG
94604 CGACGTTTCTAAACACAAA
66 CGACGTTTCTAAA-A-AAA
* * *
94623 TGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAATATGAGTCTTTAG
1 TGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAG
** * *
94688 CGGTGTTTGTATAAAAA
66 CGACGTTTCTAAAAAAA
* * * *
94705 TGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTTTAAAAACACCACTA
1 TGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTA
94754 TGGCTGAACC
Statistics
Matches: 263, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
82 110 0.42
83 3 0.01
84 150 0.57
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (82 bp):
TGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAG
CGACGTTTCTAAAAAAA
Found at i:94605 original size:125 final size:123
Alignment explanation
Indices: 94374--94753 Score: 422
Period size: 125 Copynumber: 3.1 Consensus size: 123
94364 TGGCGTGTGT
* * ** * * * *
94374 GCCACTAAAGTACGAGTCTATAGTGGCGTAAGC-ATATAAACGCCACTAAAGTACAAG-CGTATA
1 GCCACTAAAGTACGAGTCTATAGCGACGT-TTCTAAAAAAAAGCCACTAAAGTACGAGTC-TATA
* * * * *
94437 GCGGCGTTTGTATAAAAACGCTACTAAAGTACAAGTGTATAGCGGCGTTTGTATATAAAC
64 GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAAAAAC
*
94497 GCCACTAAAGTACGAGTCTTTAGCGACGTTTCTAAACACAAAAGCCACTAAAGTACGAGTCTATA
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTCTAAA-A-AAAAGCCACTAAAGTACGAGTCTATA
* * * * *
94562 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGACGTTTCTAAACACAAAT
64 GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATA-A-AAAC
* * * * * * * *
94624 GCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAATATGAGTCTTTAGC
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTCTAAAAAAAAGCCACTAAAGTACGAGTCTATAGC
* *
94689 GGTGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTTTAAAAAC
66 GGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAAAAAC
*
94747 ACCACTA
1 GCCACTA
94754 TGGCTGAACC
Statistics
Matches: 215, Mismatches: 36, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
122 1 0.00
123 37 0.17
124 1 0.00
125 140 0.65
126 2 0.01
127 34 0.16
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (123 bp):
GCCACTAAAGTACGAGTCTATAGCGACGTTTCTAAAAAAAAGCCACTAAAGTACGAGTCTATAGC
GGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAAAAAC
Found at i:101506 original size:14 final size:15
Alignment explanation
Indices: 101482--101515 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
101472 AATGAATTAC
101482 ATTTTTCTGAAAAAT
1 ATTTTTCTGAAAAAT
101497 ATTTTT-TGAAAAAT
1 ATTTTTCTGAAAAAT
*
101511 GTTTT
1 ATTTT
101516 ACGATGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (15 bp):
ATTTTTCTGAAAAAT
Found at i:101621 original size:22 final size:22
Alignment explanation
Indices: 101596--101685 Score: 55
Period size: 25 Copynumber: 4.0 Consensus size: 22
101586 AAATATTAAA
101596 TATAATAAATAATATTATTTAT
1 TATAATAAATAATATTATTTAT
*
101618 TATAAAATTTAATAATATTATTT-T
1 TAT--AA-TAAATAATATTATTTAT
*
101642 TAAAATATTAA-AATAATTTATTTAT
1 TATAATA--AATAAT-A-TTATTTAT
*
101667 TAT--TAAATATTATT-TTTAT
1 TATAATAAATAATATTATTTAT
101686 AATTTTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 21
0.68 0.06 0.26
Matches are distributed among these distances:
19 5 0.09
20 2 0.04
21 4 0.07
22 10 0.19
23 5 0.09
24 11 0.20
25 17 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAATAAATAATATTATTTAT
Found at i:101637 original size:25 final size:26
Alignment explanation
Indices: 101602--101674 Score: 91
Period size: 25 Copynumber: 2.9 Consensus size: 26
101592 TAAATATAAT
101602 AAATAATATTATTTATTATAAAATT-
1 AAATAATATTATTTATTATAAAATTA
*
101627 TAATAATATTATTT-TTA-AAATATTA
1 AAATAATATTATTTATTATAAA-ATTA
*
101652 AAATAAT-TTATTTATTATTAAAT
1 AAATAATATTATTTATTATAAAAT
101675 ATTATTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 3 0.07
24 12 0.29
25 24 0.59
26 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATAATATTATTTATTATAAAATTA
Found at i:101831 original size:23 final size:23
Alignment explanation
Indices: 101782--101832 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
101772 TTATTATATT
**
101782 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
101805 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
101828 ATATT
1 ATATT
101833 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:101974 original size:23 final size:23
Alignment explanation
Indices: 101945--102013 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
101935 TAAAATAAAA
101945 AATATAACAT-ATTATATTATTAT
1 AATATAA-ATAATTATATTATTAT
* *
101968 AATATAATTAATTATTTTATTAT
1 AATATAAATAATTATATTATTAT
*
101991 AATATTAAA-AA-TATAATATTAT
1 AATA-TAAATAATTATATTATTAT
102013 A
1 A
102014 TTATTATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 11 0.28
23 25 0.64
24 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATAAATAATTATATTATTAT
Found at i:101982 original size:55 final size:53
Alignment explanation
Indices: 101898--102047 Score: 161
Period size: 53 Copynumber: 2.9 Consensus size: 53
101888 AAATTAATAA
* * *
101898 ATAATA-TAAATT-TTATTAATAATTTATTATATATTATTAAA-ATAAAAAAT
1 ATAATATTATATTATTATAAATAATTAATTATATATTATTAAATATAAAAAAT
*
101948 ATAACATATTATATTATTATAATATAATTAATTAT-T-TTATTATAATATTAAAAAT
1 AT-A-ATATTATATTATTATAA-ATAATTAATTATATATTATTA-AATATAAAAAAT
*
102003 ATAATATTATATTATTATAAAT-ATTAATAAATATATT-TTAAATAT
1 ATAATATTATATTATTATAAATAATTAAT-TATATATTATTAAATAT
102048 TTTAATAATT
Statistics
Matches: 85, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
50 2 0.02
51 7 0.08
52 12 0.14
53 32 0.38
54 11 0.13
55 21 0.25
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (53 bp):
ATAATATTATATTATTATAAATAATTAATTATATATTATTAAATATAAAAAAT
Found at i:101997 original size:31 final size:32
Alignment explanation
Indices: 101954--102051 Score: 103
Period size: 31 Copynumber: 3.1 Consensus size: 32
101944 AAATATAACA
*
101954 TATTATATTATT-ATAATATAATTAATTATTT
1 TATTATAATATTAATAATATAATTAATTATTT
* *
101985 TATTATAATATTAAAAATATAA-T-ATTATAT
1 TATTATAATATTAATAATATAATTAATTATTT
* *
102015 TATTATAAATATTAATAAATATATTTTAAATATTT
1 TATTAT-AATATTAAT-AATATA-ATTAATTATTT
102050 TA
1 TA
102052 ATAATTAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
30 12 0.22
31 20 0.37
32 14 0.26
34 1 0.02
35 7 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTATAATATTAATAATATAATTAATTATTT
Found at i:102013 original size:22 final size:23
Alignment explanation
Indices: 101985--102031 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
101975 TTAATTATTT
101985 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
102007 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
102030 TA
1 TA
102032 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:102036 original size:22 final size:22
Alignment explanation
Indices: 101958--102048 Score: 64
Period size: 22 Copynumber: 4.2 Consensus size: 22
101948 ATAACATATT
* *
101958 ATATTATTATAATATAAT-TAA
1 ATATTAATATAATATATTATAA
* * * *
101979 TTATT-TTATTATAATATTAAAA
1 ATATTAATATAAT-ATATTATAA
*
102001 ATA-TAATATTATATTATTATAA
1 ATATTAATATAATA-TATTATAA
*
102023 ATATTAATA-AATATATTTTAA
1 ATATTAATATAATATATTATAA
102044 ATATT
1 ATATT
102049 TTAATAATTA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
20 6 0.11
21 22 0.39
22 23 0.41
23 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTAATATAATATATTATAA
Found at i:102061 original size:53 final size:53
Alignment explanation
Indices: 101942--102063 Score: 142
Period size: 53 Copynumber: 2.3 Consensus size: 53
101932 TATTAAAATA
* *
101942 AAAAATATAACATATTATATTATTATAATATAATTAATTATTTTATTATAATATT
1 AAAAATAT-A-ATATTATATTATTATAATATAATAAATTATTTTATAATAATATT
*
101997 AAAAATATAATATTATATTATTATAAATATTAATAAATATATTTTA-AAT-ATTTT
1 AAAAATATAATATTATATTATTAT-AATA-TAATAAAT-TATTTTATAATAATATT
*
102051 AATAAT-TAATATT
1 AAAAATATAATATT
102064 TTGATTTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
53 22 0.37
54 14 0.23
55 17 0.28
56 7 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (53 bp):
AAAAATATAATATTATATTATTATAATATAATAAATTATTTTATAATAATATT
Found at i:104578 original size:17 final size:17
Alignment explanation
Indices: 104556--104589 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
104546 ACCTAAGTAG
104556 GTCGCCATGCAATCCAT
1 GTCGCCATGCAATCCAT
*
104573 GTCGCCATGCAGTCCAT
1 GTCGCCATGCAATCCAT
104590 ACTTAGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (17 bp):
GTCGCCATGCAATCCAT
Found at i:107639 original size:4 final size:4
Alignment explanation
Indices: 107630--107660 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
107620 ATAGCTGTAG
*
107630 TTTC TTTC TTTC TTTC TTTC TTTC TTAC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
107661 ATTTGAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:110950 original size:16 final size:16
Alignment explanation
Indices: 110929--110961 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
110919 TAATAAATAG
110929 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
110945 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
110961 A
1 A
110962 AAATTTTTTT
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:111042 original size:10 final size:10
Alignment explanation
Indices: 111027--111101 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
111017 CATTTAATAA
111027 ATAAACGAAC
1 ATAAACGAAC
111037 ATAAACGAAC
1 ATAAACGAAC
111047 ----ACGAAC
1 ATAAACGAAC
111053 ATAAACGAAC
1 ATAAACGAAC
** *
111063 ACGAAC-ATAA
1 ATAAACGA-AC
111073 ATGAACACGAAC
1 AT-AA-ACGAAC
111085 ATAAACGAAC
1 ATAAACGAAC
111095 ATAAACG
1 ATAAACG
111102 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:111052 original size:16 final size:16
Alignment explanation
Indices: 111031--111095 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
111021 TAATAAATAA
111031 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
111047 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
111063 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
111079 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
111095 A
1 A
111096 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:111864 original size:14 final size:14
Alignment explanation
Indices: 111847--111902 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
111837 AATGAACATA
111847 AACGAACATAATCG
1 AACGAACATAATCG
111861 AACGAACAT-A---
1 AACGAACATAATCG
* *
111871 AACAAACATAACCG
1 AACGAACATAATCG
111885 AACGAACATAATCG
1 AACGAACATAATCG
111899 AACG
1 AACG
111903 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:111867 original size:24 final size:24
Alignment explanation
Indices: 111827--111901 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
111817 GATTGAGTTA
*
111827 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
111851 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
111875 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
111899 AAC
1 AAC
111902 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:113698 original size:76 final size:76
Alignment explanation
Indices: 113572--113723 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
113562 AACATCATTT
113572 ATGTCTGAACTGCAATTAAAACTAAACTATCTTTAAGTACCCCGATTATTCAGAGATCCAATAAG
1 ATGTCTGAACTGCAATTAAAACTAAACTATCTTTAAGTACCCCGATTATTCAGAGATCCAATAAG
113637 AATTCCTTTTG
66 AATTCCTTTTG
113648 ATGTCTGAACTGCAATTAAAACTAAACTATCTTTAAGTACCCCGATTATTCAGAGATCCAATAAG
1 ATGTCTGAACTGCAATTAAAACTAAACTATCTTTAAGTACCCCGATTATTCAGAGATCCAATAAG
113713 AATTCCTTTTG
66 AATTCCTTTTG
113724 GTAAGGTCAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (76 bp):
ATGTCTGAACTGCAATTAAAACTAAACTATCTTTAAGTACCCCGATTATTCAGAGATCCAATAAG
AATTCCTTTTG
Found at i:114124 original size:91 final size:91
Alignment explanation
Indices: 114023--114197 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 91
114013 ATTTGCGGTG
* * * *
114023 GGTTTTAACCTAAACTATTATCTTGTCTACTCTAAAAAGTTACACAATTGATAATAATTTCAGTT
1 GGTTTTAACCTAAAATATTACCATATCTACTCTAAAAAGTTACACAATTGATAATAATTTCAGTT
114088 ACAACCGAGAATGTTACATTGCGGCC
66 ACAACCGAGAATGTTACATTGCGGCC
* * * *
114114 GGTTTTAACCTAAAATGTTACCATATCTACTCTAAAAAGTTACATAATTGGTAATAATTTCGGTT
1 GGTTTTAACCTAAAATATTACCATATCTACTCTAAAAAGTTACACAATTGATAATAATTTCAGTT
*
114179 ACAACTGAGAATGTTACAT
66 ACAACCGAGAATGTTACAT
114198 GAGTTTCTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (91 bp):
GGTTTTAACCTAAAATATTACCATATCTACTCTAAAAAGTTACACAATTGATAATAATTTCAGTT
ACAACCGAGAATGTTACATTGCGGCC
Found at i:116527 original size:3 final size:3
Alignment explanation
Indices: 116516--116570 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
116506 TTTTTTTCCG
** *
116516 TTA TT- TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
116561 TTTA TTA TTA
1 -TTA TTA TTA
116571 CAATTTTTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 5 0.12
3 34 0.81
4 3 0.07
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:116540 original size:23 final size:22
Alignment explanation
Indices: 116514--116558 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
116504 GGTTTTTTTC
*
116514 CGTTATTTTATTATTATTATTAT
1 CGTTATCTTATTATT-TTATTAT
116537 CGTTATCTTATTATTTTATTAT
1 CGTTATCTTATTATTTTATTAT
116559 TATTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64
Consensus pattern (22 bp):
CGTTATCTTATTATTTTATTAT
Found at i:116694 original size:25 final size:25
Alignment explanation
Indices: 116665--116789 Score: 214
Period size: 25 Copynumber: 5.0 Consensus size: 25
116655 CCAACAACCC
*
116665 ATCAGATTAGGGTTTTAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
116690 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
116715 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
116740 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
116765 ATCAGACTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
116790 TCCCCTAACT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 96 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:130379 original size:9 final size:8
Alignment explanation
Indices: 130354--130379 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
130344 AAAAAAAAGG
130354 AAATGAAA
1 AAATGAAA
130362 AAATGAAA
1 AAATGAAA
130370 AAATGAAA
1 AAATGAAA
130378 AA
1 AA
130380 GAAGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:130389 original size:16 final size:16
Alignment explanation
Indices: 130354--130388 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
130344 AAAAAAAAGG
*
130354 AAATGAAAAAATGAAA
1 AAATGAAAAAAAGAAA
130370 AAATGAAAAAGAAGAAA
1 AAATGAAAAA-AAGAAA
130387 AA
1 AA
130389 TAAATAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (16 bp):
AAATGAAAAAAAGAAA
Found at i:131601 original size:89 final size:89
Alignment explanation
Indices: 131340--131634 Score: 353
Period size: 89 Copynumber: 3.2 Consensus size: 89
131330 CCAGACTTCC
* *
131340 TCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTTATCACGTAGGAACCGAGTT
1 TCATCACGTAGGAGCCGTGTCAAC-CTA-GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTT
*
131405 ATCACCCTTCCTAAAGGTGGCCAGAGT-TCT
64 ATCA----TCCTAAAGATGGCCAGA-TCTCT
* * * *
131435 TCATCATGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAATCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACC-TAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTA
**
131500 TCA-CCTTTAGATGGCCAGATCTCT
65 TCATCCTAAAGATGGCCAGATCTCT
* * *
131524 TCATCACGTAAGAGCCGTGTCAACCT-GATAACCAGTCGTCCTCATTACGTAGGAACCGAGTTAT
1 TCATCACGTAGGAGCCGTGTCAACCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTAT
* *
131588 CATCCCTAAAGATGACCAGATCTCC
66 CAT-CCTAAAGATGGCCAGATCTCT
*
131613 TCATCACGTAGGAGCCATGTCA
1 TCATCACGTAGGAGCCGTGTCA
131635 CCCTTAGACG
Statistics
Matches: 175, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
87 36 0.21
88 2 0.01
89 76 0.43
94 37 0.21
95 24 0.14
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (89 bp):
TCATCACGTAGGAGCCGTGTCAACCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTAT
CATCCTAAAGATGGCCAGATCTCT
Found at i:131875 original size:23 final size:23
Alignment explanation
Indices: 131830--131872 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
131820 TTTTTTTTTC
*
131830 CGTTATTTTATTATTATTATTAT
1 CGTTATCTTATTATTATTATTAT
*
131853 CGTTATCTTATT-TTTTTATT
1 CGTTATCTTATTATTATTATT
131873 TATTATTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (23 bp):
CGTTATCTTATTATTATTATTAT
Found at i:132100 original size:24 final size:25
Alignment explanation
Indices: 131975--132098 Score: 205
Period size: 25 Copynumber: 5.0 Consensus size: 25
131965 CCAACAACCC
*
131975 ATCAGATTAGGGTTTTAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
132000 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
132025 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
132050 ATCAGTTTAGGGTTTCAAA-CCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
132074 ATCAGACTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
132099 TCCCCTAACT
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
24 22 0.23
25 72 0.77
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:134220 original size:12 final size:11
Alignment explanation
Indices: 134202--134228 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
134192 CGAGAAAAGG
134202 ATTTTTTTTTT
1 ATTTTTTTTTT
134213 ATTTTTTTTTT
1 ATTTTTTTTTT
134224 ATTTT
1 ATTTT
134229 AACTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (11 bp):
ATTTTTTTTTT
Done.