Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002142.1 Hibiscus syriacus cultivar Beakdansim tig00004378_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: 103386
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:828 original size:23 final size:23
Alignment explanation
Indices: 802--849 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
792 ATAAAGTACA
*
802 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
825 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
848 AT
1 AT
850 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1259 original size:23 final size:23
Alignment explanation
Indices: 1233--1294 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
1223 ATATAACCAC
1233 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1256 TACCTATTA-ATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1278 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1295 GTTTACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1281 original size:22 final size:23
Alignment explanation
Indices: 1223--1294 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
1213 ACACTTTACA
* *
1223 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1246 ATATAAACGATACCTATTA-ATT
1 ATATAAACGCTACCTATTACATT
** *
1268 ATATAAGGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1291 ATAT
1 ATAT
1295 GTTTACTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 19 0.46
23 22 0.54
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1746 original size:39 final size:39
Alignment explanation
Indices: 1692--1778 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1682 TCAAGTTGTA
*
1692 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
1731 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1770 GATTTTGAT
1 GATTTTGAT
1779 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:2055 original size:18 final size:18
Alignment explanation
Indices: 2032--2068 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2022 CGAAATATAT
2032 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2050 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2068 A
1 A
2069 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2343 original size:25 final size:25
Alignment explanation
Indices: 2315--2365 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2305 TTAATCCAAA
*
2315 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
2340 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
2365 T
1 T
2366 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:2667 original size:23 final size:23
Alignment explanation
Indices: 2641--2703 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2631 ATATAACCAC
2641 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
2664 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
2687 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2704 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:3083 original size:21 final size:20
Alignment explanation
Indices: 3066--3122 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 20
3056 CAATATAACC
3066 ACTACCTATTACATTATATAA
1 ACTACCTATTACATTATA-AA
*
3087 ACGATA-CTATTACATTATAAGG
1 AC--TACCTATTACATTATAA-A
*
3109 GCTACCTATTACAT
1 ACTACCTATTACAT
3123 CATATGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.07
21 12 0.40
22 14 0.47
23 2 0.07
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (20 bp):
ACTACCTATTACATTATAAA
Found at i:3154 original size:424 final size:425
Alignment explanation
Indices: 2397--3223 Score: 1506
Period size: 428 Copynumber: 1.9 Consensus size: 425
2387 TTTGAATTAT
2397 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
* *
2462 TTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTATACGCCTATA
66 TTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
2527 ATTACTAAATTAATATCTTAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
131 ATTACTAAATTAATATCTTAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
2592 AAAAGTATGGACACTTTATAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
196 AAAAGTATGGACACTTTATAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
2657 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
*
2722 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTTA
326 AAGTGTCCATAC--TTTATAAAAAGGATCGATACTTTTTTT-AAACTTATGTAATTTATGTTTCA
2787 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
388 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
* *
2825 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
2890 TTAGAATTTTTAATTTAATAATAA-ATATACCGTAACGT-AAAAA-AAATCATTAGACGCCTATA
66 TTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
2952 ATTAC-AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
131 ATTACTAAATTAATATCTTAAAACTCACTC-AAAGATAACCTTAAATTAATGTTTTCCACAGTGA
3016 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
195 AAAAAGTATGGACAC-TTTAT-AAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
3081 ATATAAACGATA-CTATTACA-T-TATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
258 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
3143 TGAAAGTGTCCATACTTTATAAAAAGGATCGATACTTTTTTTAAACTTATGTAATTTATGTTTCA
323 TGAAAGTGTCCATACTTTATAAAAAGGATCGATACTTTTTTTAAACTTATGTAATTTATGTTTCA
3208 ATTTTTTTAACAGTGT
388 ATTTTTTTAACAGTGT
3224 ACTGCGAATT
Statistics
Matches: 391, Mismatches: 5, Indels: 13
0.96 0.01 0.03
Matches are distributed among these distances:
421 38 0.10
422 27 0.07
424 80 0.20
425 73 0.19
426 18 0.05
427 68 0.17
428 87 0.22
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (425 bp):
TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
TTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
ATTACTAAATTAATATCTTAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
AAAAGTATGGACACTTTATAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
AAGTGTCCATACTTTATAAAAAGGATCGATACTTTTTTTAAACTTATGTAATTTATGTTTCAATT
TTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
Found at i:6109 original size:198 final size:199
Alignment explanation
Indices: 5728--6695 Score: 1842
Period size: 198 Copynumber: 4.9 Consensus size: 199
5718 TATTTAAATT
5728 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
5793 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
5858 ATCGACACTTTGTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGG
131 ATCGACACTTT-TTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG
5922 AAAAA
195 AAAAA
5927 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
5992 TAA-TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
6056 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
6121 AAAA
196 AAAA
*
6125 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTTTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
6190 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
6255 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
6319 AAAA
196 AAAA
*
6323 CGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
6388 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
6453 ATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
6517 AAAA
196 AAAA
6521 AGTATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
6584 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
6649 ATTGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
6696 GGCCATATTG
Statistics
Matches: 759, Mismatches: 6, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
196 153 0.20
197 76 0.10
198 355 0.47
199 175 0.23
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (199 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
AAAA
Found at i:6461 original size:397 final size:395
Alignment explanation
Indices: 5728--6695 Score: 1852
Period size: 397 Copynumber: 2.5 Consensus size: 395
5718 TATTTAAATT
5728 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
5793 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
5858 ATCGACACTTTGTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGA
131 ATCGACACTTT-TTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGA
5923 AAAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC
195 AAAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC
5988 GGTATAATGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GGTATAATGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
6053 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTG
325 GGGATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTG
6118 GGAAAAA
389 GGAAAAA
*
6125 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTTTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
6190 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
6255 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
*
6320 AAACGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
196 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
6385 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
261 GTATAA-TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
6450 GGGATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGG
325 GGGATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGG
6515 GAAAAA
390 GAAAAA
6521 AGTATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
6584 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
6649 ATTGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
6696 GGCCATATTG
Statistics
Matches: 565, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
393 33 0.06
394 124 0.22
396 199 0.35
397 209 0.37
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (395 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
GTATAATGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG
AAAAA
Found at i:6843 original size:19 final size:19
Alignment explanation
Indices: 6811--6858 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
6801 AATTATTCAC
6811 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
6829 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
6848 ATACAAAATTA
1 ATACAAAATTA
6859 ACTCGACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:8785 original size:21 final size:21
Alignment explanation
Indices: 8745--8809 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
8735 CCCCTTATTC
* *
8745 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
8766 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
8787 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
8808 CT
1 CT
8810 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:11067 original size:20 final size:20
Alignment explanation
Indices: 11040--11086 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
11030 TCCGGTTTCA
11040 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
11059 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
11080 TTTTACC
1 TTTTACC
11087 TGTTATATCG
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:11234 original size:20 final size:20
Alignment explanation
Indices: 11208--11253 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
11198 CACTTTTAAA
11208 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
11227 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
11248 TTTACC
1 TTTACC
11254 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:14487 original size:5 final size:5
Alignment explanation
Indices: 14443--14483 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
14433 CCGCCGCCGT
* * *
14443 CCCGT CCCGG CCCGG CCCGG CCCGG CCCGG CACGG CTCGG C
1 CCCGG CCCGG CCCGG CCCGG CCCGG CCCGG CCCGG CCCGG C
14484 TCGGGTCGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.02, C:0.56, G:0.37, T:0.05
Consensus pattern (5 bp):
CCCGG
Found at i:14498 original size:6 final size:6
Alignment explanation
Indices: 14487--14549 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
14477 GCTCGGCTCG
* *
14487 GGTCGA GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
14535 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
14550 AGTACGTGTC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.03, C:0.16, G:0.51, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:20027 original size:5 final size:5
Alignment explanation
Indices: 20017--20070 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
20007 CCGTCCGTCT
* * * * * *
20017 CGGCA CGGCA CGGCA CGGCA CGACA CGGCT CGGCT CGGCT CGGCT CGGCT
1 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA
20067 CGGC
1 CGGC
20071 TCGTGGTCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.11, C:0.41, G:0.39, T:0.09
Consensus pattern (5 bp):
CGGCA
Found at i:20032 original size:10 final size:10
Alignment explanation
Indices: 20015--20070 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
20005 GTCCGTCCGT
20015 CTCGGCACGG
1 CTCGGCACGG
*
20025 CACGGCACGG
1 CTCGGCACGG
* *
20035 CACGACACGG
1 CTCGGCACGG
*
20045 CTCGGCTCGG
1 CTCGGCACGG
*
20055 CTCGGCTCGG
1 CTCGGCACGG
20065 CTCGGC
1 CTCGGC
20071 TCGTGGTCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.11, C:0.41, G:0.38, T:0.11
Consensus pattern (10 bp):
CTCGGCACGG
Found at i:20037 original size:15 final size:15
Alignment explanation
Indices: 20015--20070 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
20005 GTCCGTCCGT
20015 CTCGGCACGGCACGG
1 CTCGGCACGGCACGG
* *
20030 CACGGCACGACACGG
1 CTCGGCACGGCACGG
* *
20045 CTCGGCTCGGCTCGG
1 CTCGGCACGGCACGG
*
20060 CTCGGCTCGGC
1 CTCGGCACGGC
20071 TCGTGGTCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.11, C:0.41, G:0.38, T:0.11
Consensus pattern (15 bp):
CTCGGCACGGCACGG
Found at i:20071 original size:5 final size:5
Alignment explanation
Indices: 20042--20073 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
20032 CGGCACGACA
20042 CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CG
1 CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CG
20074 TGGTCGTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.41, G:0.41, T:0.19
Consensus pattern (5 bp):
CGGCT
Found at i:20082 original size:6 final size:6
Alignment explanation
Indices: 20071--20161 Score: 164
Period size: 6 Copynumber: 15.2 Consensus size: 6
20061 TCGGCTCGGC
*
20071 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
*
20119 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGA TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
20162 AATACGTGTC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.02, C:0.16, G:0.48, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:20461 original size:22 final size:22
Alignment explanation
Indices: 20436--20490 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
20426 TCAGGAGTTA
* *
20436 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
20458 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
20480 CGGGAGTTATA
1 CAGGAGTTATA
20491 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:23026 original size:15 final size:15
Alignment explanation
Indices: 23008--23041 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22998 ATTTTAAACT
*
23008 TAATTTAATATAAAA
1 TAATTTAATACAAAA
*
23023 TAATTTATTACAAAA
1 TAATTTAATACAAAA
23038 TAAT
1 TAAT
23042 AATAAAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATTTAATACAAAA
Found at i:25626 original size:22 final size:23
Alignment explanation
Indices: 25570--25626 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 23
25560 TGATCCTTGC
* *
25570 CATATGTATATGATTCTTAAGGA
1 CATATCTATATGGTTCTTAAGGA
* * *
25593 -ATTTCTACATGGTTCTTAGGGA
1 CATATCTATATGGTTCTTAAGGA
25615 CATAT-TATATGG
1 CATATCTATATGG
25627 CACTTCGTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (23 bp):
CATATCTATATGGTTCTTAAGGA
Found at i:25661 original size:23 final size:23
Alignment explanation
Indices: 25625--25692 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
25615 CATATTATAT
*
25625 GGCACTTCGTTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
25648 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
25671 GGCACTTCAGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
25693 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:30430 original size:23 final size:23
Alignment explanation
Indices: 30394--30461 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
30384 CATATTATAT
*
30394 GGCACTTCGTTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * **
30417 GGCACTACGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACGC
*
30440 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
30462 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:31953 original size:16 final size:16
Alignment explanation
Indices: 31934--32004 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 16
31924 AGAATATAAT
31934 AAATAAAAATTAAAAA
1 AAATAAAAATTAAAAA
*
31950 AAATAAGAA-TAAAAA
1 AAATAAAAATTAAAAA
31965 TAAATCTAAAAATTTATTAAAA
1 -AAA--TAAAAA-TTA--AAAA
*
31987 AAATAGAAAGTTAAAAA
1 AAATA-AAAATTAAAAA
32004 A
1 A
32005 TTACCTTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
15 6 0.14
16 11 0.25
17 5 0.11
18 5 0.11
19 5 0.11
20 5 0.11
21 3 0.07
22 4 0.09
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (16 bp):
AAATAAAAATTAAAAA
Found at i:31955 original size:23 final size:22
Alignment explanation
Indices: 31920--31965 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
31910 ATGTCGCCAT
* *
31920 TTAAAGAATATAATAAATAAAAA
1 TTAAAAAAAATAA-AAATAAAAA
*
31943 TTAAAAAAAATAAGAATAAAAA
1 TTAAAAAAAATAAAAATAAAAA
31965 T
1 T
31966 AAATCTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (22 bp):
TTAAAAAAAATAAAAATAAAAA
Found at i:41070 original size:14 final size:14
Alignment explanation
Indices: 41030--41062 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41020 AGACTGTTTG
*
41030 TTTTACTGAAAATA
1 TTTTTCTGAAAATA
41044 TTTTTCTGAAAATA
1 TTTTTCTGAAAATA
41058 TTTTT
1 TTTTT
41063 TGTAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTTTCTGAAAATA
Found at i:41080 original size:35 final size:34
Alignment explanation
Indices: 41036--41104 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
41026 TTTGTTTTAC
*
41036 TGAAAATATTTTTCT-GAAAATATTTTTTGTAAAA
1 TGAAAATATTTTT-TGGAAAATATTTTTTGAAAAA
41070 TGAAATATATTTTTTGGAAAATATTTTTTGAAAAA
1 TGAAA-ATATTTTTTGGAAAATATTTTTTGAAAAA
41105 CGTTTTACGG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.46
Consensus pattern (34 bp):
TGAAAATATTTTTTGGAAAATATTTTTTGAAAAA
Found at i:41081 original size:21 final size:20
Alignment explanation
Indices: 41050--41091 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
41040 AATATTTTTC
*
41050 TGAAAATATTTTTTGTAAAA
1 TGAAAATATTTTTTGGAAAA
41070 TGAAATATATTTTTTGGAAAA
1 TGAAA-ATATTTTTTGGAAAA
41091 T
1 T
41092 ATTTTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAAATATTTTTTGGAAAA
Found at i:41104 original size:14 final size:14
Alignment explanation
Indices: 41070--41104 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41060 TTTTGTAAAA
*
41070 TGAAATATATTTTT
1 TGAAAAATATTTTT
*
41084 TGGAAAATATTTTT
1 TGAAAAATATTTTT
41098 TGAAAAA
1 TGAAAAA
41105 CGTTTTACGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (14 bp):
TGAAAAATATTTTT
Found at i:41272 original size:14 final size:14
Alignment explanation
Indices: 41253--41300 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
41243 ATAATTTATT
41253 TATTATTATTAAAA
1 TATTATTATTAAAA
* *
41267 TATTATTTTTATAA
1 TATTATTATTAAAA
* *
41281 TTTTATTAATAAAAA
1 TATTATT-ATTAAAA
41296 TATTA
1 TATTA
41301 AGATTAGTAC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATTATTAAAA
Found at i:41425 original size:23 final size:24
Alignment explanation
Indices: 41375--41426 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
41365 GTACTATATT
*
41375 ATATTTTAAAAAATATTAATTAAT
1 ATATTTTAAAAAATATTAATTAAA
* * *
41399 ATATTTT-AAATATCTTTATTAAA
1 ATATTTTAAAAAATATTAATTAAA
41422 ATATT
1 ATATT
41427 ATTATATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTTTAAAAAATATTAATTAAA
Found at i:41467 original size:23 final size:26
Alignment explanation
Indices: 41421--41504 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
41411 TCTTTATTAA
41421 AATATTATTATATTAAATACATAAAT
1 AATATTATTATATTAAATACATAAAT
*
41447 AATATTATTA-ATTATTAATA-ATTTAAT
1 AATATTATTATATTA--AATACA-TAAAT
* *
41474 AATATTATTCTATGAAATTA-ATAAAT
1 AATATTATTATATTAAA-TACATAAAT
41500 AATAT
1 AATAT
41505 ACATTTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
25 4 0.08
26 22 0.45
27 20 0.41
28 3 0.06
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (26 bp):
AATATTATTATATTAAATACATAAAT
Found at i:41478 original size:53 final size:52
Alignment explanation
Indices: 41417--41536 Score: 147
Period size: 53 Copynumber: 2.3 Consensus size: 52
41407 AATATCTTTA
* *
41417 TTAA-AATATTATTATATTAAA-TACATAAATAATAT-TATTAATTATTAATAAT
1 TTAATAATATTATTATATGAAATTA-ATAAATAATATACATT--TTATTAATAAT
*
41469 TTAATAATATTATTCTATGAAATTAATAAATAATATACATTTTATTAATAAT
1 TTAATAATATTATTATATGAAATTAATAAATAATATACATTTTATTAATAAT
*
41521 TTATTATATATTATTA
1 TTAATA-ATATTATTA
41537 AAATAAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
52 20 0.34
53 34 0.58
54 5 0.08
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (52 bp):
TTAATAATATTATTATATGAAATTAATAAATAATATACATTTTATTAATAAT
Found at i:41605 original size:23 final size:22
Alignment explanation
Indices: 41562--41628 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
41552 ATCTTATATC
* *
41562 ATTATAATA-TAATTAAGTATTTT
1 ATTATAATATTAA--AAATATTAT
41585 ATTATAATATTTAAAAATATTAT
1 ATTATAATA-TTAAAAATATTAT
* *
41608 ATTATATTATTAGAAATATTA
1 ATTATAATATTAAAAATATTA
41629 ATAAATGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 11 0.29
23 24 0.63
25 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
ATTATAATATTAAAAATATTAT
Found at i:41714 original size:82 final size:82
Alignment explanation
Indices: 41527--41723 Score: 176
Period size: 83 Copynumber: 2.4 Consensus size: 82
41517 TAATTTATTA
* * * * * *
41527 TATATTATTA-AAATAAAAATATAA-TATCTTATATCATTATAATATAATTAAGTATTTTATTAT
1 TATATTATTAGAAATATAAATAAAATTATTTTAAAT-ATT-TTA-ATAATTAAGTATTTTATTAA
41590 AATATTTAAAAATATTATAT
63 AATATTTAAAAATATTATAT
*
41610 TATATTATTAGAAATATTAAT-AAATGTATTTTAAATATTTTAATAATTAA-TATTTTTATTAAA
1 TATATTATTAGAAATATAAATAAAAT-TATTTTAAATATTTTAATAATTAAGTA-TTTTATTAAA
*
41673 ATGATATT-AAAATATTTTAT
64 AT-AT-TTAAAAATATTATAT
*
41693 TA-A-TATTA-AATTCATAAAATAAAATTATTTT
1 TATATTATTAGAAAT-AT-AAATAAAATTATTTT
41724 GAGTGTTTAT
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
80 3 0.03
81 9 0.09
82 29 0.31
83 33 0.35
84 13 0.14
85 8 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (82 bp):
TATATTATTAGAAATATAAATAAAATTATTTTAAATATTTTAATAATTAAGTATTTTATTAAAAT
ATTTAAAAATATTATAT
Found at i:50500 original size:17 final size:17
Alignment explanation
Indices: 50478--50517 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
50468 AAGCATGTTC
50478 GGGTAGATTATCATGTG
1 GGGTAGATTATCATGTG
50495 GGGTAGATTATCATGTG
1 GGGTAGATTATCATGTG
50512 GGGTAG
1 GGGTAG
50518 GATTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.05, G:0.40, T:0.33
Consensus pattern (17 bp):
GGGTAGATTATCATGTG
Found at i:53429 original size:106 final size:106
Alignment explanation
Indices: 53205--53922 Score: 1183
Period size: 106 Copynumber: 6.8 Consensus size: 106
53195 AACCATGAGC
* * * *
53205 ACGAAGAAAATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTC-
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
53269 A-ATA-AACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* * *
53308 GCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
53373 ACAAACAACTTCTCAATTTCTGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
53414 ACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
53479 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
53520 ACGAAGGATATTGGACTCTAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
53585 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
53626 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
53691 ACAAACAACTTCTCAATTTCTGAGCCAATTTCAACTTCACA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
53732 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * * * * *
53797 ATAAACAATTTCCCAATTTCAAAGTCAATTTCAACTTCATA
66 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
53838 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
53903 ATAAACAACTT-TCAACTTCA
66 ACAAACAACTTCTCAATTTCA
53923 CGACGGAGGA
Statistics
Matches: 579, Mismatches: 33, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
103 57 0.10
104 1 0.00
105 9 0.02
106 512 0.88
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
Found at i:54470 original size:84 final size:84
Alignment explanation
Indices: 54010--54461 Score: 526
Period size: 84 Copynumber: 5.4 Consensus size: 84
54000 AGGCTATCTG
** * * * * ** * * *
54010 CCAAAGACCCCCGAGTTCGATTACACTCAGCTCCGAGGTACATCATTTGCAACATAGCTCAAGGC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTC
* * * * *
54075 AAAAAGGGCTATTTGCCAT
66 GAGAAGGGTTATCTGCCAA
* * * * *
54094 CCAAAGACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCATATCATTTGCAGTATAACTTAAGT
54159 CGAGAAGGGTTATCTGCCAA
65 CGAGAAGGGTTATCTGCCAA
* * *
54179 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATTATTTGCAGTACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTC
*
54244 GAGAAGGGTTATCTGTCAA
66 GAGAAGGGTTATCTGCCAA
* * *
54263 CCAAAGACCTTCGGGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTC
* * *
54328 TAGAGGGGTTGTCTGCCAA
66 GAGAAGGGTTATCTGCCAA
* * * * * * * *
54347 CAAAAGACCTTTGAATTCGACTACGCTTAGCTCCAAGGCATATCCTTTACAGCATAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTC
54412 GAGAAGGGTTATCTGCCAA
66 GAGAAGGGTTATCTGCCAA
* *
54431 CCGAAGACCTTCGAGTTCGATTACACTCAGC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGC
54462 ACAGAGGCAA
Statistics
Matches: 316, Mismatches: 51, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
84 249 0.79
85 67 0.21
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTC
GAGAAGGGTTATCTGCCAA
Found at i:58914 original size:16 final size:16
Alignment explanation
Indices: 58893--58926 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
58883 TTACTATTCA
*
58893 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
58909 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
58925 CG
1 CG
58927 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:59697 original size:15 final size:16
Alignment explanation
Indices: 59677--59708 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
59667 TGGCAGATCC
59677 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
59692 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
59708 A
1 A
59709 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:64514 original size:13 final size:13
Alignment explanation
Indices: 64493--64527 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
64483 GTCTTGCCGG
64493 TCATCTCTAATCC
1 TCATCTCTAATCC
*
64506 TCATTTCTAATCC
1 TCATCTCTAATCC
64519 TCATCTCTA
1 TCATCTCTA
64528 TTTTAACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (13 bp):
TCATCTCTAATCC
Found at i:64730 original size:21 final size:22
Alignment explanation
Indices: 64692--64737 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
64682 TACAAAAAGA
64692 TTAATATTATTATTTATCTAATT
1 TTAATATTATTATTTATCT-ATT
64715 TTAATA-TATT-TTTATCTATT
1 TTAATATTATTATTTATCTATT
64735 TTA
1 TTA
64738 TAATTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 4 0.17
23 6 0.26
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAATATTATTATTTATCTATT
Found at i:70589 original size:28 final size:29
Alignment explanation
Indices: 70548--70613 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
70538 TCAATGTATG
* * *
70548 TATTTGGTTTCAGTTTAGT-GTCAACGTT
1 TATTTCGTTCCAGTTTAGTACTCAACGTT
*
70576 TATTTCGTTCCAGTTTAGTACTTAACGTT
1 TATTTCGTTCCAGTTTAGTACTCAACGTT
70605 TCATTTCGT
1 T-ATTTCGT
70614 AACTCAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 17 0.53
29 8 0.25
30 7 0.22
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (29 bp):
TATTTCGTTCCAGTTTAGTACTCAACGTT
Found at i:71294 original size:29 final size:29
Alignment explanation
Indices: 71251--71310 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
71241 AATTTGAGTT
71251 ACGAAATGAAAATTAGACACCAAACTAGA
1 ACGAAATGAAAATTAGACACCAAACTAGA
* *
71280 ACGAAAT-AAACATTAGGCACTAAACTAGA
1 ACGAAATGAAA-ATTAGACACCAAACTAGA
71309 AC
1 AC
71311 CAAAAGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.15
Consensus pattern (29 bp):
ACGAAATGAAAATTAGACACCAAACTAGA
Found at i:71490 original size:50 final size:53
Alignment explanation
Indices: 71380--71493 Score: 137
Period size: 50 Copynumber: 2.2 Consensus size: 53
71370 CATTTTAATA
* * * *
71380 TGATAAATTCT-AATAAAAAATATTATATTTTATTAAAACTCATCACGTCGACG
1 TGATAAATT-TAAATAAAAAATATTATATGTGAGTAAAACTCATCACGTCAACG
* *
71433 TGATAAATTTAAATAAAAAATA-T-TATGTGAGT-AAACTTATCATGTCAACG
1 TGATAAATTTAAATAAAAAATATTATATGTGAGTAAAACTCATCACGTCAACG
71483 TGATAAATTTA
1 TGATAAATTTA
71494 TCTTGTACTA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
50 26 0.48
51 6 0.11
52 2 0.04
53 20 0.37
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (53 bp):
TGATAAATTTAAATAAAAAATATTATATGTGAGTAAAACTCATCACGTCAACG
Found at i:88259 original size:20 final size:21
Alignment explanation
Indices: 88223--88283 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
88213 TTTTGGTGCA
*
88223 GAGGGAA-TCGATACCCCC-AT
1 GAGGGAACT-GATTCCCCCTAT
*
88243 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACTGATTCCCCCTAT
*
88264 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACTGATTCCCCC
88284 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 15 0.44
21 3 0.09
22 1 0.03
23 15 0.44
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACTGATTCCCCCTAT
Found at i:88292 original size:21 final size:21
Alignment explanation
Indices: 88266--88305 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
88256 CCCCCTTTGA
*
88266 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
88287 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
88306 TAAGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:89945 original size:12 final size:12
Alignment explanation
Indices: 89928--89961 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
89918 AGATGAGCAT
*
89928 GAGCAGCCCGAG
1 GAGCAGCACGAG
89940 GAGCAGCACGAG
1 GAGCAGCACGAG
89952 GAGCAAGCAC
1 GAGC-AGCAC
89962 AACAAACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.32, C:0.29, G:0.38, T:0.00
Consensus pattern (12 bp):
GAGCAGCACGAG
Found at i:91815 original size:21 final size:21
Alignment explanation
Indices: 91789--91846 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
91779 CATTAGTGCA
*
91789 GATGCATGGATGCACTGTAGG
1 GATGCATGGATGCACTGCAGG
91810 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
91831 GATGCATGGATGCACT
1 GATGCATGGATGCACT
91847 TTGACACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.22
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:91985 original size:30 final size:30
Alignment explanation
Indices: 91928--91987 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
91918 AACTTTGAAT
91928 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
91958 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
91988 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:93307 original size:19 final size:20
Alignment explanation
Indices: 93264--93311 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
93254 TCTAAATCCT
*
93264 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
93284 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
93303 TTTTCAAAA
1 TTTTCAAAA
93312 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:94843 original size:30 final size:30
Alignment explanation
Indices: 94786--94844 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
94776 AACTTTGAAT
94786 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
94816 AAATTCAATTCAAGTCCAAAAACATTTTG
1 AAATTCAATTCAAATCCAAAAACATTTTG
94845 TCTTACATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:103014 original size:37 final size:37
Alignment explanation
Indices: 102938--103014 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
102928 TTTTTATATT
*
102938 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
102975 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
103012 TTT
1 TTT
103015 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Done.