Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005255.1 Hibiscus syriacus cultivar Beakdansim tig00011891_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: 90817
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2024 original size:180 final size:182
Alignment explanation
Indices: 1562--2239 Score: 1195
Period size: 180 Copynumber: 3.7 Consensus size: 182
1552 GTAAATTTGC
1562 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTT
1 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC-ATATCGACACTTT
1627 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGA-TTAAAAAAG
65 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAG
*
1691 TGTCGACA-TTACACATCGGAACCCATAATTATAATGTAAGAGATAATTTAGT
130 TGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTAGT
*
1743 AATATAACCGATAT-AATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTT
1 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC-ATATCGACACTTT
1807 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAG
65 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAG
1872 TGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTAGT
130 TGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTAGT
1925 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC-TATCGACACTTTT
1 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCATATCGACACTTTT
1989 TAATATTGTGTCGGTACTTTATGTCCATA-TGGAAGAAAAATGTGTCGATACGATTTAAAAAAGT
66 TAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGT
* * * *
2053 ATCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGT
131 GTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTAGT
* *
2105 AATATAACCGGTATACATATACCGGTTTTATGCGCGAATAGGTCTACAACATATATCGACACTTT
1 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAAC-CATATCGACACTTT
* * *
2170 ATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAG
65 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAG
2235 TGTCG
130 TGTCG
2240 GTAATTTTAA
Statistics
Matches: 478, Mismatches: 13, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
180 237 0.50
181 72 0.15
182 96 0.20
183 73 0.15
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (182 bp):
AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCATATCGACACTTTT
TAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGT
GTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTAGT
Found at i:2230 original size:363 final size:362
Alignment explanation
Indices: 1562--2239 Score: 1216
Period size: 363 Copynumber: 1.9 Consensus size: 362
1552 GTAAATTTGC
1562 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTT
1 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC-ATATCGACACTTT
1627 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTAAAAAAGT
65 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTAAAAAAGT
* *
1692 GTCGACATTACACATCGGAACCCATAATTATAATGTAAGAGATAATTTAGTAATATAACCGATAT
130 ATCGACATTACACATCGGAACCCAGAATTATAATGTAAGAGATAATTTAGTAATATAACCGATAT
* *
1757 AATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGG
195 AATATACCGGTTTTATGCGCGAATAGGTCTACAACATATATCGACACTTTATAATATTGTGTCGG
* *
1822 TACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACAC
260 TACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACAC
1887 ATCGGAACCCATAATTATAATGTAATAGATAATTTAGT
325 ATCGGAACCCATAATTATAATGTAATAGATAATTTAGT
1925 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC-TATCGACACTTTT
1 AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCATATCGACACTTTT
1989 TAATATTGTGTCGGTACTTTATGTCCATA-TGGAAGAAAAATGTGTCGATACGATTTAAAAAAGT
66 TAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGA-TTAAAAAAGT
* * * *
2053 ATCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTA
130 ATCGACA-TTACACATCGGAACCCAGAATTATAATGTAAGAGATAATTTAGTAATATAACCGATA
2118 TACATATACCGGTTTTATGCGCGAATAGGTCTACAACATATATCGACACTTTATAATATTGTGTC
194 TA-ATATACCGGTTTTATGCGCGAATAGGTCTACAACATATATCGACACTTTATAATATTGTGTC
2183 GGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
258 GGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
2240 GTAATTTTAA
Statistics
Matches: 302, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
360 24 0.08
361 58 0.19
362 54 0.18
363 166 0.55
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (362 bp):
AATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCATATCGACACTTTT
TAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTAAAAAAGTA
TCGACATTACACATCGGAACCCAGAATTATAATGTAAGAGATAATTTAGTAATATAACCGATATA
ATATACCGGTTTTATGCGCGAATAGGTCTACAACATATATCGACACTTTATAATATTGTGTCGGT
ACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACA
TCGGAACCCATAATTATAATGTAATAGATAATTTAGT
Found at i:5084 original size:21 final size:22
Alignment explanation
Indices: 5038--5084 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
5028 AAATTACATA
*
5038 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGAAC
* *
5060 -CTTTTTATAAAAGTAT-GAAC
1 ACTTTTAAAAAAAGTATCGAAC
5080 ACTTT
1 ACTTT
5085 CAATATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGAAC
Found at i:5132 original size:22 final size:23
Alignment explanation
Indices: 5102--5173 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
5092 ATAGGTAAAC
*
5102 ATATGATGTAATAGGTAGC-CTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
5124 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
5147 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
5170 ATAT
1 ATAT
5174 TGTAAAATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 16 0.39
23 25 0.61
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5816 original size:18 final size:18
Alignment explanation
Indices: 5795--5831 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5785 GTAATTGGAG
5795 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5813 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5831 T
1 T
5832 ATATATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5839 original size:24 final size:24
Alignment explanation
Indices: 5787--5833 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5777 TTTCATATGT
* *
5787 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
5811 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
5834 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:6131 original size:39 final size:39
Alignment explanation
Indices: 6088--6173 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
6078 TCCGATGCTC
*
6088 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
6127 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
6166 ATCAAAAT
1 ATCAAAAT
6174 ATACAACTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:6610 original size:23 final size:23
Alignment explanation
Indices: 6576--6648 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
6566 ATAGGTAAAC
*
6576 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
6599 ATATAATTTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
6622 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
6645 ATAT
1 ATAT
6649 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:7382 original size:333 final size:333
Alignment explanation
Indices: 6694--7690 Score: 1899
Period size: 333 Copynumber: 3.0 Consensus size: 333
6684 ACTTTTTTCC
*
6694 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAATATATTAATTTAGTAATTAT
1 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
* *
6759 AGGCGTCTAATGATTTA-TTTTTTCATTACGATATATATTATGATTAAATTAAAAATTCTAAATA
66 AGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
6823 TTATTTTATAAAATATCAAAACAATCAAATAATTTCTTGTGCAAATGAAATTATTAAATTAATAT
131 TTATTTTATAAAATATCAAAACAATCAAATAATTT-TTGTGCAAATGAAATTATTAAATTAATAT
6888 TGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAA
195 TGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAA
6953 GTATCGATCCTTTTTATAAAAAGTATGGACAC-TTCAATATAATATAATGTAATAGGTAAATTTG
260 GTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAATTTG
7017 CAATGCTCA
325 CAATGCTCA
7026 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
1 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
7091 AGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
66 AGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
7156 TTATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAATGAAATTATTAAATTAATATT
131 TTATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAATGAAATTATTAAATTAATATT
7221 GTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAG
196 GTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAG
7286 TATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
261 TATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
7351 AATGCTCA
326 AATGCTCA
7359 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
1 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
*
7424 AGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
66 AGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
*
7489 ATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATAT
131 TTATTTTATAAAATATCAAAACAATCAAATAA-TTTTTGTGCAAATGAAATTATTAAATTAATAT
7554 TGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAA
195 TGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAA
* *
7619 ATATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAATTTG
260 GTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAATTTG
7684 CAATGCT
325 CAATGCT
7691 ATCGGTATAA
Statistics
Matches: 655, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
332 207 0.32
333 281 0.43
334 167 0.25
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (333 bp):
CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
AGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
TTATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAATGAAATTATTAAATTAATATT
GTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAG
TATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
AATGCTCA
Found at i:12261 original size:23 final size:23
Alignment explanation
Indices: 12228--12288 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
12218 CTAGTATAAA
12228 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* * *
12251 TGCACCAAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
12274 TGCATCGAAGTGCCA
1 TGCACCGAAGTGCCA
12289 TATAAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:12776 original size:2 final size:2
Alignment explanation
Indices: 12771--12798 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12761 TATCTTATTC
12771 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
12799 CCGCAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13739 original size:20 final size:20
Alignment explanation
Indices: 13711--13768 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
13701 TTTCCCTTGA
13711 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
* *
13731 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATACATTC--T-AC
13754 ATGTGCATCGATACA
1 A-GTGCATCGATACA
13769 CTACCCATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.50
22 1 0.03
23 3 0.10
24 11 0.37
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:13848 original size:64 final size:63
Alignment explanation
Indices: 13756--13917 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
13746 TCTTTAACAT
* * * *
13756 GTGCATCGATACACTACCCATGCATCGATACACAAATCACCTTCGATGTTT-TAATTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCAATTTTAA-GGG
* * * ** * *
13820 GTGCATCGATGCACTCCTTATACATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCAATTTTAAGGG
*
13884 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
13918 CTGAACAATT
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 2 0.03
64 68 0.85
65 10 0.12
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCAATTTTAAGGG
Found at i:14969 original size:24 final size:24
Alignment explanation
Indices: 14937--14999 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
14927 GTTACTCTTC
* *
14937 GGAGGTAATGTCTGAAGAAATTAT
1 GGAGGTAATGTCCGAAGAAACTAT
14961 GGAGGTAATGTCCGAAGAAACTAT
1 GGAGGTAATGTCCGAAGAAACTAT
14985 GGAGGTAATGTCCGA
1 GGAGGTAATGTCCGA
15000 GCTTTATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.24
Consensus pattern (24 bp):
GGAGGTAATGTCCGAAGAAACTAT
Found at i:16904 original size:16 final size:15
Alignment explanation
Indices: 16885--16918 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
16875 AAAAAAAATC
16885 AAAATCAAAAATTGAA
1 AAAATCAAAAA-TGAA
*
16901 AAAATGAAAAATGAA
1 AAAATCAAAAATGAA
16916 AAA
1 AAA
16919 TGAGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (15 bp):
AAAATCAAAAATGAA
Found at i:16911 original size:23 final size:22
Alignment explanation
Indices: 16868--16931 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
16858 AATTTATTTT
* *
16868 AAAAATTAAAAAAAATCAAAATC
1 AAAAATT-GAAAAAATAAAAATC
*
16891 AAAAATTGAAAAAATGAAAAATG
1 AAAAATTGAAAAAAT-AAAAATC
16914 AAAAA-TGAGAAAAATAAA
1 AAAAATTGA-AAAAATAAA
16932 TAAGGATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATTGAAAAAATAAAAATC
Found at i:16966 original size:2 final size:2
Alignment explanation
Indices: 16959--16991 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16949 ATGTGATAAT
16959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16992 GTTTCTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20367 original size:25 final size:25
Alignment explanation
Indices: 20320--20369 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20310 TTTTGCTCTA
* * *
20320 CCTAAAATGTTATAAGTTTATCCCT
1 CCTAAAATGTTAGAAGGTCATCCCT
*
20345 CCTAAAATTTTAGAAGGTCATCCCT
1 CCTAAAATGTTAGAAGGTCATCCCT
20370 ATTATAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (25 bp):
CCTAAAATGTTAGAAGGTCATCCCT
Found at i:22675 original size:3 final size:3
Alignment explanation
Indices: 22669--22697 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
22659 TTTGTGACAT
22669 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22698 ATATATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:22954 original size:31 final size:29
Alignment explanation
Indices: 22907--22964 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
22897 AATAAAATAA
* *
22907 AAAATAAATGAAAGTTTAGATATTAAAAC
1 AAAATAAATAAAAGTTTAGATACTAAAAC
*
22936 AAAATAAAATAAATAGTTTATATACTAAA
1 AAAAT-AAATAAA-AGTTTAGATACTAAA
22965 TATGTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 6 0.25
31 13 0.54
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.29
Consensus pattern (29 bp):
AAAATAAATAAAAGTTTAGATACTAAAAC
Found at i:36075 original size:6 final size:6
Alignment explanation
Indices: 36059--36106 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
36049 GGTCGCATCT
*
36059 CATAGG TATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG
1 CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG
36107 TACATGCATC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (6 bp):
CATAGG
Found at i:36843 original size:2 final size:2
Alignment explanation
Indices: 36836--36866 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
36826 TCAGAACACT
36836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36867 GCATGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42530 original size:7 final size:7
Alignment explanation
Indices: 42518--42547 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
42508 GTCAAAGAAA
42518 GTCAACG
1 GTCAACG
42525 GTCAACG
1 GTCAACG
42532 GTCAACG
1 GTCAACG
42539 GTCAACG
1 GTCAACG
42546 GT
1 GT
42548 TCGGTCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:49159 original size:22 final size:22
Alignment explanation
Indices: 49132--49179 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
49122 AACGATCAAC
*
49132 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAAAGGTCCGGTCGGGTCG
* *
49154 GGTCAAAGGTCGGGTCGGGTCT
1 GGTCAAAGGTCCGGTCGGGTCG
49176 GGTC
1 GGTC
49180 GGTCGGGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.10, C:0.23, G:0.46, T:0.21
Consensus pattern (22 bp):
GGTCAAAGGTCCGGTCGGGTCG
Found at i:49185 original size:14 final size:15
Alignment explanation
Indices: 49139--49188 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 15
49129 AACGGTCAAC
*
49139 GGTCCGGTCGGGTCG
1 GGTCTGGTCGGGTCG
*
49154 GGTCAAAGGTCGGGTCG
1 GGTC--TGGTCGGGTCG
49171 GGTCTGGTC-GGTCG
1 GGTCTGGTCGGGTCG
49185 GGTC
1 GGTC
49189 AGACCGGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.29
15 8 0.26
17 14 0.45
ACGTcount: A:0.06, C:0.22, G:0.50, T:0.22
Consensus pattern (15 bp):
GGTCTGGTCGGGTCG
Found at i:49211 original size:19 final size:20
Alignment explanation
Indices: 49187--49253 Score: 97
Period size: 19 Copynumber: 3.5 Consensus size: 20
49177 GTCGGTCGGG
49187 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
49206 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
*
49225 TC-GAACCGATCAAACCGG-
1 TCAGAACCGGTCAAACCGGT
49243 TCAGAACCGGT
1 TCAGAACCGGT
49254 TGAAAACCGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.07
19 41 0.93
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.15
Consensus pattern (20 bp):
TCAGAACCGGTCAAACCGGT
Found at i:49215 original size:10 final size:9
Alignment explanation
Indices: 49185--49273 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
49175 TGGTCGGTCG
*
49185 GGTCAGACC
1 GGTCAAACC
49194 GGTCAAACC
1 GGTCAAACC
*
49203 GGTTCAGACC
1 GG-TCAAACC
49213 GGTCAAACC
1 GGTCAAACC
*
49222 GGTTCGAACC
1 GG-TCAAACC
*
49232 GATCAAACC
1 GGTCAAACC
49241 GGTCAGAACC
1 GGTCA-AACC
*
49251 GGTTGAAAACC
1 GG-T-CAAACC
*
49262 GGTTAAACC
1 GGTCAAACC
49271 GGT
1 GGT
49274 TTCCAGCAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
9 36 0.55
10 22 0.33
11 7 0.11
12 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:49272 original size:20 final size:21
Alignment explanation
Indices: 49236--49274 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49226 CGAACCGATC
49236 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
49257 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
49275 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:53148 original size:18 final size:18
Alignment explanation
Indices: 53117--53151 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53107 ACTGAATATT
*
53117 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
53135 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
53152 CCTTAAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:59613 original size:9 final size:8
Alignment explanation
Indices: 59585--59620 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
59575 ATGTCATAAC
59585 TTAAAATT
1 TTAAAATT
59593 TTAAAATT
1 TTAAAATT
59601 TTAAAATTT
1 TTAAAA-TT
59610 TTAAAATT
1 TTAAAATT
59618 TTA
1 TTA
59621 TTTCCTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTAAAATT
Found at i:59613 original size:17 final size:16
Alignment explanation
Indices: 59585--59620 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
59575 ATGTCATAAC
59585 TTAAAATTTTAAAATT
1 TTAAAATTTTAAAATT
59601 TTAAAATTTTTAAAATT
1 TTAAAA-TTTTAAAATT
59618 TTA
1 TTA
59621 TTTCCTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAATTTTAAAATT
Found at i:59948 original size:36 final size:38
Alignment explanation
Indices: 59872--59949 Score: 92
Period size: 36 Copynumber: 2.1 Consensus size: 38
59862 AACAAGTTAG
* *
59872 AAAATATTTATATATTTTCTTTAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAATTAAAAATCAT
59910 AAAAT-TTT-TATATTTGT-TTTACAAAATTAAAAAT-AT
1 AAAATATTTATATATTT-TCTTTA-AAAATTAAAAATCAT
59946 AAAA
1 AAAA
59950 AGGTTAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
36 17 0.47
37 14 0.39
38 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (38 bp):
AAAATATTTATATATTTTCTTTAAAAATTAAAAATCAT
Found at i:60144 original size:21 final size:20
Alignment explanation
Indices: 60058--60215 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
60048 AAATGACCAA
**
60058 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
60077 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
60097 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
60117 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
60138 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
60159 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
60179 CCAAAATCGCAACGTGAATAT
1 -CAAAATCGCAACGCGATTTT
*
60200 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
60216 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:60225 original size:20 final size:20
Alignment explanation
Indices: 60202--60375 Score: 208
Period size: 20 Copynumber: 8.7 Consensus size: 20
60192 GTGAATATGA
* *
60202 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
60222 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
60242 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
60262 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
60282 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
60302 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* ***
60322 AAATCGCAACG-ATAATAAAT
1 AAATCGCAACGCGT-ATCCGT
60342 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
60363 AAATCGCAACGCG
1 AAATCGCAACGCG
60376 ATATTTAAAG
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 112 0.86
21 16 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:60266 original size:60 final size:60
Alignment explanation
Indices: 60182--60373 Score: 240
Period size: 60 Copynumber: 3.2 Consensus size: 60
60172 CGATTTTCCA
* ** * * *
60182 AAATCGCAACGTGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGTGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* *** *
60242 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* * **
60302 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATAAATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGTGTATCCGTAAATCGCAACGCGAATAAAT-AAATCGCAACGCGTATCCGT
60363 AAATCGCAACG
1 AAATCGCAACG
60374 CGATATTTAA
Statistics
Matches: 111, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 82 0.74
61 29 0.26
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGTGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
Found at i:60797 original size:33 final size:33
Alignment explanation
Indices: 60758--60828 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
60748 TTCACTTAGA
*
60758 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
60791 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
60824 TTTCA
1 TTTCA
60829 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:60952 original size:20 final size:20
Alignment explanation
Indices: 60908--61017 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
60898 TGCAGAAGAG
*
60908 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
60929 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
60949 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
60970 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
60984 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
61003 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
61018 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:60965 original size:41 final size:38
Alignment explanation
Indices: 60901--61017 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
60891 TTCAATTTGC
* *
60901 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
60939 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
60980 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
61013 AGAAT
1 AGAAT
61018 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:60987 original size:14 final size:14
Alignment explanation
Indices: 60968--61024 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
60958 GAGAAATGAA
60968 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
60982 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
61001 AATCGCAACGAGAG
1 AATCGCAACGAGAG
61015 AATCGCAACG
1 AATCGCAACG
61025 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:61000 original size:33 final size:33
Alignment explanation
Indices: 60960--61040 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
60950 CGCAACGAGA
60960 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
60993 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
61026 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
61041 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:63075 original size:93 final size:93
Alignment explanation
Indices: 62779--63244 Score: 895
Period size: 93 Copynumber: 5.1 Consensus size: 93
62769 TAGATTGCTT
*
62779 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
62844 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
62872 AGTAAATTTGTTCGGTTGCTG-CAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
62936 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
62963 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
63028 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
63056 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
63121 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
63149 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
63214 TTTGTCTTTGTTTTGTC-TTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
63240 AGTAA
1 AGTAA
63245 TGCAATCCAT
Statistics
Matches: 370, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
91 54 0.15
92 94 0.25
93 222 0.60
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:63412 original size:19 final size:19
Alignment explanation
Indices: 63292--63406 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
63282 TAGTTTACTT
* *
63292 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
63312 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
63331 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
63350 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
63364 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
63383 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
63402 TCGCA
1 TCGCA
63407 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 55 0.66
20 13 0.16
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:63424 original size:19 final size:19
Alignment explanation
Indices: 63402--63536 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
63392 GAAACCAAAA
*
63402 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
63421 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
63437 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
63454 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
63470 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
63487 TCGCGTTGCGACTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
63506 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
63526 TCGTGTTGCGA
1 TCGCGTTGCGA
63537 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 44 0.47
20 12 0.13
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:63443 original size:14 final size:14
Alignment explanation
Indices: 63424--63480 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
63414 TTTCATTTCG
63424 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
63438 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
63455 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
63471 CGTTGCGATT
1 CGTTGCGATT
63481 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:63449 original size:33 final size:33
Alignment explanation
Indices: 63407--63497 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
63397 CAAAATCGCA
*
63407 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
63440 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
63473 TTGCGATTTTCATTTCGCGTTGCGA
1 TTGCGATTTTCATTTCGCGTTGCGA
63498 CTTTGGTTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:65478 original size:14 final size:14
Alignment explanation
Indices: 65459--65494 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
65449 ATTGTTTAAT
65459 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
65473 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
65487 TGATTTGT
1 TGATTTGT
65495 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:65669 original size:20 final size:19
Alignment explanation
Indices: 65601--65679 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
65591 AAAAATGACT
65601 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
65620 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
65634 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
65653 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
65673 ATCGCAA
1 ATCGCAA
65680 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.38
20 16 0.31
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:65750 original size:19 final size:19
Alignment explanation
Indices: 65726--65904 Score: 173
Period size: 19 Copynumber: 10.4 Consensus size: 19
65716 GATTCTCTCG
65726 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
65745 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
65764 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
65778 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
65797 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
65811 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
65830 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
65844 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
65864 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
65878 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
65897 TTGCGATT
1 TTGCGATT
65905 CTCTCGTTGC
Statistics
Matches: 131, Mismatches: 8, Indels: 42
0.72 0.04 0.23
Matches are distributed among these distances:
14 29 0.22
16 23 0.18
17 20 0.15
18 3 0.02
19 44 0.34
20 12 0.09
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:65761 original size:52 final size:52
Alignment explanation
Indices: 65704--65904 Score: 222
Period size: 52 Copynumber: 3.9 Consensus size: 52
65694 TGCGTTTATA
65704 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
65756 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * * *
65806 -TCTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
65855 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
65905 CTCTCGTTGC
Statistics
Matches: 123, Mismatches: 13, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
45 9 0.07
46 5 0.04
47 17 0.14
49 7 0.06
50 5 0.04
51 2 0.02
52 47 0.38
53 19 0.15
54 5 0.04
55 6 0.05
56 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:65783 original size:14 final size:14
Alignment explanation
Indices: 65764--65851 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
65754 TCATTTCGCA
65764 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
65778 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
65795 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
65811 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
65828 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
65844 TTGCGATT
1 TTGCGATT
65852 TTCATTTCCG
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.33
16 14 0.23
17 14 0.23
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:65901 original size:67 final size:67
Alignment explanation
Indices: 65745--65937 Score: 309
Period size: 67 Copynumber: 2.9 Consensus size: 67
65735 TCATTTCGCA
65745 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTCTCT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTCTCT
65809 CG
66 CG
*
65811 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTCTC-
65876 T-G
65 TCG
* * * **
65878 TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGTGTTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAT
65938 AGTCAAATGC
Statistics
Matches: 119, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
66 48 0.40
67 70 0.59
68 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.46
Consensus pattern (67 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTCTCT
CG
Found at i:65926 original size:33 final size:33
Alignment explanation
Indices: 65745--65918 Score: 305
Period size: 33 Copynumber: 5.2 Consensus size: 33
65735 TCATTTCGCA
65745 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
65778 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
65811 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
65844 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
65878 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
65911 TTGCGATT
1 TTGCGATT
65919 GTAATTTCCG
Statistics
Matches: 134, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
32 1 0.01
33 103 0.77
34 29 0.22
35 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:65926 original size:100 final size:99
Alignment explanation
Indices: 65745--65926 Score: 303
Period size: 100 Copynumber: 1.8 Consensus size: 99
65735 TCATTTCGCA
65745 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* *
65810 GTTGCGATTTTCATTTCGCATTGCGATTCTCTCG
66 GTTGCGATTGTAATTTCGCATTGCGATTCTCTCG
* *
65844 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATTCTC
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
65908 TCGTTGCGATTGTAATTTC
64 TCGTTGCGATTGTAATTTC
65927 CGTGTTGCGA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
99 15 0.19
100 61 0.79
101 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (99 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
GTTGCGATTGTAATTTCGCATTGCGATTCTCTCG
Found at i:67149 original size:12 final size:12
Alignment explanation
Indices: 67132--67156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67122 TCTTCGGGGA
67132 CTTTTTCTTCTT
1 CTTTTTCTTCTT
67144 CTTTTTCTTCTT
1 CTTTTTCTTCTT
67156 C
1 C
67157 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:67365 original size:24 final size:24
Alignment explanation
Indices: 67331--67377 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
67321 CTGAAACATC
67331 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
67355 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
67378 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:68086 original size:20 final size:20
Alignment explanation
Indices: 68058--68287 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
68048 AAATTTCAGT
* * *
68058 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
68078 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
68098 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
68118 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
68138 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
68158 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
68178 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
68198 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
68218 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
68238 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
68258 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
68278 GTTGCGATTT
1 GTTGCGATTT
68288 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:68304 original size:21 final size:21
Alignment explanation
Indices: 68274--68356 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
68264 ATTTTCATAT
*
68274 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
68295 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
68316 TCGCATTGCAATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
68337 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
68357 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:68529 original size:26 final size:26
Alignment explanation
Indices: 68496--68553 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
68486 TTTTCTCTTT
68496 ATTTTAACCCCTGAACTTCATATAAA
1 ATTTTAACCCCTGAACTTCATATAAA
68522 ATTTTAACCCCTGAACTTCATATAAA
1 ATTTTAACCCCTGAACTTCATATAAA
68548 ATTTTA
1 ATTTTA
68554 TTTATGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (26 bp):
ATTTTAACCCCTGAACTTCATATAAA
Done.