Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007874.1 Hibiscus syriacus cultivar Beakdansim tig00110249_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: 91435
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2820 original size:38 final size:39
Alignment explanation
Indices: 2774--2859 Score: 122
Period size: 38 Copynumber: 2.3 Consensus size: 39
2764 AAAAATGGTG
* * * *
2774 CCCCCCTTTCTCATGGGATCAGAACCAAT-CAATAAAAT
1 CCCCCCTTTCTCATAGGATCAAAACCAATAAAAAAAAAT
2812 CCCCCCTTTCTCATAGGATCAAAACCAATAAAAAAAAAT
1 CCCCCCTTTCTCATAGGATCAAAACCAATAAAAAAAAAT
2851 -CCCCCTTTC
1 CCCCCCTTTC
2860 ATGGCTTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 36 0.84
39 7 0.16
ACGTcount: A:0.36, C:0.34, G:0.07, T:0.23
Consensus pattern (39 bp):
CCCCCCTTTCTCATAGGATCAAAACCAATAAAAAAAAAT
Found at i:3035 original size:3 final size:3
Alignment explanation
Indices: 3011--3064 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
3001 GGTCCTAAAA
* * * *
3011 AAT AA- AAT AAA AAT ATT AAT AAT AAT AAT AAT TAT AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3058 AA- AAT AA
1 AAT AAT AA
3065 AAAATCTGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20272 original size:20 final size:21
Alignment explanation
Indices: 20226--20286 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
20216 TTCCCCTGTG
20226 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
20249 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
20269 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
20287 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:41928 original size:230 final size:228
Alignment explanation
Indices: 41526--41975 Score: 783
Period size: 230 Copynumber: 2.0 Consensus size: 228
41516 GTAAATTATC
* *
41526 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* **
41591 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAATAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
41656 TGTGTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACCATTAAAAAAATTG
41721 AAACATAAATTACATAACTTTCAAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAAGTATA
*
41755 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
41820 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* * *
41885 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACCATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACCATTAAAAAAATT
41950 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
41976 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
229 41 0.20
230 168 0.80
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACCATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAAGTATA
Found at i:42064 original size:20 final size:19
Alignment explanation
Indices: 42041--42086 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
42031 CGATATACCA
42041 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
42061 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
42081 GGTAAA
1 GGTAAA
42087 TTTAAAAGTG
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:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:42232 original size:20 final size:19
Alignment explanation
Indices: 42209--42255 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
42199 CGATATAACA
42209 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
42229 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
42249 GGTAAAA
1 GGTAAAA
42256 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:42257 original size:17 final size:19
Alignment explanation
Indices: 42218--42260 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
42208 AGGTAAAAAT
42218 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
42238 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
42255 ATGATA
1 ATGATA
42261 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:44623 original size:33 final size:33
Alignment explanation
Indices: 44576--44641 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
44566 AAATAGATGG
* *
44576 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
44609 AGTGATGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
44642 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGATGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:47646 original size:25 final size:25
Alignment explanation
Indices: 47612--47676 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
47602 TTATCATTAA
47612 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
47637 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
47662 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
47677 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:53813 original size:23 final size:23
Alignment explanation
Indices: 53787--53847 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
53777 TGAATTCAGC
*
53787 TGCATTATTGCATCAC-TTATTGA
1 TGCATTATTGCAGC-CTTTATTGA
*
53810 TGCATTATTGCAGCCTTTATTGT
1 TGCATTATTGCAGCCTTTATTGA
53833 TGCATTATTGCAGCC
1 TGCATTATTGCAGCC
53848 CTTCAAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (23 bp):
TGCATTATTGCAGCCTTTATTGA
Found at i:53819 original size:11 final size:12
Alignment explanation
Indices: 53787--53844 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 12
53777 TGAATTCAGC
53787 TGCATTATTGCA
1 TGCATTATTGCA
53799 T-CACTTATTG-A
1 TGCA-TTATTGCA
53810 TGCATTATTGCA
1 TGCATTATTGCA
* *
53822 -GCCTTTATTG-T
1 TG-CATTATTGCA
53833 TGCATTATTGCA
1 TGCATTATTGCA
53845 GCCCTTCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
11 18 0.50
12 18 0.50
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (12 bp):
TGCATTATTGCA
Found at i:54134 original size:21 final size:22
Alignment explanation
Indices: 54093--54149 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
54083 GGTAAAACAA
*
54093 AATTTTAGTTA-ATTAGTTTGTT
1 AATTTAAGTTATATTAG-TTGTT
54115 AATTTAAGTTATATTA-TTGTT
1 AATTTAAGTTATATTAGTTGTT
*
54136 AGTTTAAGTTATAT
1 AATTTAAGTTATAT
54150 CATATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 18 0.56
22 10 0.31
23 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (22 bp):
AATTTAAGTTATATTAGTTGTT
Found at i:54258 original size:44 final size:45
Alignment explanation
Indices: 54188--54273 Score: 131
Period size: 44 Copynumber: 1.9 Consensus size: 45
54178 GTTTGTTTGA
54188 TAGTTATATATTAAAAAAATAATTAATTAGTGTGTTAGTTAGTCGT
1 TAGTTATATATTAAAAAAATAATTAATTAGTGTG-TAGTTAGTCGT
* *
54234 TAGTTATATA-T-AAAAAATATTTAATTAGTTTGTAGTTAGT
1 TAGTTATATATTAAAAAAATAATTAATTAGTGTGTAGTTAGT
54274 TAAATAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 8 0.21
44 19 0.50
45 1 0.03
46 10 0.26
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (45 bp):
TAGTTATATATTAAAAAAATAATTAATTAGTGTGTAGTTAGTCGT
Found at i:54282 original size:44 final size:46
Alignment explanation
Indices: 54187--54283 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 46
54177 AGTTTGTTTG
**
54187 ATAGTTATATATTAAAAAAATAATTAATTAGTGTGTTAGTTAGTCG
1 ATAGTTATATATTAAAAAAATAATTAATTAGTGTGTTAGTTAGTAA
* * *
54233 TTAGTTATATA-T-AAAAAATATTTAATTAGTTTG-TAGTTAGTTAA
1 ATAGTTATATATTAAAAAAATAATTAATTAGTGTGTTAGTTAG-TAA
54277 ATAGTTA
1 ATAGTTA
54284 AGTTATACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
43 7 0.16
44 26 0.59
45 1 0.02
46 10 0.23
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.44
Consensus pattern (46 bp):
ATAGTTATATATTAAAAAAATAATTAATTAGTGTGTTAGTTAGTAA
Found at i:54406 original size:18 final size:17
Alignment explanation
Indices: 54387--54439 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 17
54377 ATTAGATTTA
54387 AATTAGTTTATTATTAT
1 AATTAGTTTATTATTAT
*
54404 AA--A--TTATTAGT-T
1 AATTAGTTTATTATTAT
54416 AATTAGTTTATTATTAT
1 AATTAGTTTATTATTAT
54433 AAATTAG
1 -AATTAG
54440 GGTAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
12 3 0.11
13 7 0.25
14 1 0.04
15 1 0.04
16 7 0.25
17 3 0.11
18 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.53
Consensus pattern (17 bp):
AATTAGTTTATTATTAT
Found at i:54492 original size:21 final size:21
Alignment explanation
Indices: 54467--54506 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54457 GTTAATTAGT
*
54467 TTGTTAGTTTAAGTTATATTA
1 TTGTTACTTTAAGTTATATTA
54488 TTGTTACTTTAAGTTATAT
1 TTGTTACTTTAAGTTATAT
54507 CATATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTACTTTAAGTTATATTA
Found at i:57411 original size:16 final size:17
Alignment explanation
Indices: 57384--57416 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
57374 CTACGTGTAA
*
57384 GTGAACTATGTGCTAAT
1 GTGAACTATGTGATAAT
57401 GTGAA-TATGTGATAAT
1 GTGAACTATGTGATAAT
57417 TATAAAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
GTGAACTATGTGATAAT
Found at i:57677 original size:23 final size:24
Alignment explanation
Indices: 57644--57713 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
57634 AATCTTATAT
*
57644 GGCACTACGGTGC-ATTTCTACGC
1 GGCACTTCGGTGCAATTTCTACGC
* * *
57667 GGCACTTCGGTGCAAATTCTATGT
1 GGCACTTCGGTGCAATTTCTACGC
*
57691 GGCACTTCGGTGCAATTTATACG
1 GGCACTTCGGTGCAATTTCTACG
57714 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 12 0.31
24 27 0.69
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (24 bp):
GGCACTTCGGTGCAATTTCTACGC
Found at i:59646 original size:15 final size:15
Alignment explanation
Indices: 59622--59655 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
59612 CCGTAGGACC
59622 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
59637 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
59652 ACTA
1 ACTA
59656 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:59830 original size:27 final size:29
Alignment explanation
Indices: 59738--59836 Score: 168
Period size: 29 Copynumber: 3.5 Consensus size: 29
59728 TTTCATATGT
59738 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
59766 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
59795 TCATGTAGCTCATGTCATTTCTC-T-TGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
59822 TCATGTAGCTCATGT
1 TCATGTAGCTCATGT
59837 TCTCATATCA
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
27 18 0.26
28 8 0.12
29 42 0.62
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:61494 original size:172 final size:176
Alignment explanation
Indices: 61179--61531 Score: 585
Period size: 172 Copynumber: 2.0 Consensus size: 176
61169 TCTCCATGTC
61179 TCTTAACGTTCCCATGTTGCATCCTCTACTTTGTGATTCCTCCACAAGACTTTAACCAATTGAAT
1 TCTTAACGTTCCCATGTTGCATCCTCTACTTTGTGATTCCTCCACAAGACTTTAACCAATTGAAT
*
61244 AGTCTGTTCCTTAGTTGCTTGACTTCGTGAGCTAATATTTGAACATGTCTTCCTCATAAGTTAAT
66 AGTCTGTTCC-T--TTGCTTGACTTCGTGAGCTAATATTTGAACATGTCTTCCTCATAAGTAAAT
*
61309 CTGATCAAACTTCAATTTTCTTCCGGAGTCACAATGTGGGATGGAACATA
128 CTGATCAAACTTCAA-TTTCTTCAGGAGTCACAATGTGGGATGGAACATA
61359 TCTTAACGTTCCCATGTTGCAT-CTCTACTTTGTGATTCCTCCACAAGACTTTAA-CAATTGAAT
1 TCTTAACGTTCCCATGTTGCATCCTCTACTTTGTGATTCCTCCACAAGACTTTAACCAATTGAAT
61422 AGTCTTGTTCC-TTG-TTG-C-TCGTGAGCTAATATTTGAACATGTCTTCCTCATAAGTAAAATC
66 AGTC-TGTTCCTTTGCTTGACTTCGTGAGCTAATATTTGAACATGTCTTCCTCATAAGT-AAATC
61483 TGATC-AACTTCAATTTCTTCAGGAGTCACAATGTGGGATGGAACATA
129 TGATCAAACTTCAATTTCTTCAGGAGTCACAATGTGGGATGGAACATA
61530 TC
1 TC
61532 GATATTCCTA
Statistics
Matches: 169, Mismatches: 2, Indels: 13
0.92 0.01 0.07
Matches are distributed among these distances:
171 35 0.21
172 45 0.27
173 10 0.06
174 3 0.02
175 3 0.02
178 13 0.08
179 38 0.22
180 22 0.13
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (176 bp):
TCTTAACGTTCCCATGTTGCATCCTCTACTTTGTGATTCCTCCACAAGACTTTAACCAATTGAAT
AGTCTGTTCCTTTGCTTGACTTCGTGAGCTAATATTTGAACATGTCTTCCTCATAAGTAAATCTG
ATCAAACTTCAATTTCTTCAGGAGTCACAATGTGGGATGGAACATA
Found at i:65924 original size:32 final size:31
Alignment explanation
Indices: 65888--65963 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
65878 CGGGGCCGTG
*
65888 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
65920 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
65951 GAGCCTACCTAAG
1 GGGCCTACCTAAG
65964 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:65947 original size:63 final size:63
Alignment explanation
Indices: 65841--65963 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
65831 ACCTAAGGGA
* * ** *
65841 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
65904 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
65964 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:68850 original size:19 final size:19
Alignment explanation
Indices: 68828--68910 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
68818 CTAGGCGGCT
*
68828 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
68847 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
68866 CGGCTCGGCT--G---AAA
1 CGGCTCGGCTCAGCTCAAA
*
68880 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
68899 CGGCTCGGCTCA
1 CGGCTCGGCTCA
68911 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
16 1 0.02
17 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.35, G:0.30, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:68857 original size:14 final size:14
Alignment explanation
Indices: 68852--68918 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
68842 TCAAACGGCT
*
68852 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
68866 CGGCTCGGCTGAAA
1 CGGCTCGGCTCAAA
68880 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
68898 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
68913 CGGCTC
1 CGGCTC
68919 CTCAGGCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.19, C:0.36, G:0.30, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:68881 original size:33 final size:33
Alignment explanation
Indices: 68834--68918 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
68824 GGCTCGGCTT
*
68834 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
68867 GGCTCGGCTGAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
68900 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
68919 CTCAGGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.20, C:0.35, G:0.29, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:71014 original size:32 final size:31
Alignment explanation
Indices: 70978--71053 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
70968 CGGGGCCGTG
*
70978 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
71010 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
71041 GAGCCTACCTAAG
1 GGGCCTACCTAAG
71054 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:71037 original size:63 final size:63
Alignment explanation
Indices: 70931--71053 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
70921 ACCTAAGGGA
* * ** *
70931 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
70994 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
71054 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:73942 original size:19 final size:19
Alignment explanation
Indices: 73920--74002 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
73910 CTAGGCGGCT
*
73920 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
73939 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
73958 CGGCTCGGCT--G---AAA
1 CGGCTCGGCTCAGCTCAAA
*
73972 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
73991 CGGCTCGGCTCA
1 CGGCTCGGCTCA
74003 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
16 1 0.02
17 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.35, G:0.30, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:73949 original size:14 final size:14
Alignment explanation
Indices: 73944--74010 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
73934 TCAAACGGCT
*
73944 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
73958 CGGCTCGGCTGAAA
1 CGGCTCGGCTCAAA
73972 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
73990 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
74005 CGGCTC
1 CGGCTC
74011 CTCAGGCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.19, C:0.36, G:0.30, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:73973 original size:33 final size:33
Alignment explanation
Indices: 73926--74010 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
73916 GGCTCGGCTT
*
73926 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
73959 GGCTCGGCTGAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
73992 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
74011 CTCAGGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.20, C:0.35, G:0.29, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:76362 original size:29 final size:29
Alignment explanation
Indices: 76319--76399 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
76309 TTTCATATGT
76319 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
76347 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
76376 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
76400 ATATCACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 37 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:78093 original size:21 final size:21
Alignment explanation
Indices: 78067--78108 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
78057 CCAGAGTTTG
78067 TGCAGCCTGAGGCACCCATCT
1 TGCAGCCTGAGGCACCCATCT
78088 TGCAGCCTGAGGCACCCATCT
1 TGCAGCCTGAGGCACCCATCT
78109 ACTCTCCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.24, T:0.19
Consensus pattern (21 bp):
TGCAGCCTGAGGCACCCATCT
Found at i:78562 original size:14 final size:13
Alignment explanation
Indices: 78526--78653 Score: 128
Period size: 14 Copynumber: 10.1 Consensus size: 13
78516 AAATTTAATA
78526 ATAAATCATTATT
1 ATAAATCATTATT
*
78539 ATCAA-C-TTATT
1 ATAAATCATTATT
78550 ACTAAATCATTA-T
1 A-TAAATCATTATT
78563 -T--ATCATTATT
1 ATAAATCATTATT
78573 ATTAAATCATTATT
1 A-TAAATCATTATT
*
78587 AT-AATGATTATT
1 ATAAATCATTATT
78599 ACTAAATCATTATT
1 A-TAAATCATTATT
*
78613 AT-AATGATTATT
1 ATAAATCATTATT
78625 ACTAAATCATTATT
1 A-TAAATCATTATT
78639 ATCAAATCATTATT
1 AT-AAATCATTATT
78653 A
1 A
78654 AATTATCAAA
Statistics
Matches: 96, Mismatches: 6, Indels: 25
0.76 0.05 0.20
Matches are distributed among these distances:
9 7 0.07
10 1 0.01
11 7 0.07
12 25 0.26
13 11 0.11
14 45 0.47
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (13 bp):
ATAAATCATTATT
Found at i:78587 original size:26 final size:26
Alignment explanation
Indices: 78527--78653 Score: 165
Period size: 26 Copynumber: 5.0 Consensus size: 26
78517 AATTTAATAA
78527 TAAATCATTATTATCAA-C-TTATTAC
1 TAAATCATTATTAT-AATCATTATTAC
*
78552 TAAATCATTA-T-T-ATCATTATTAT
1 TAAATCATTATTATAATCATTATTAC
*
78575 TAAATCATTATTATAATGATTATTAC
1 TAAATCATTATTATAATCATTATTAC
*
78601 TAAATCATTATTATAATGATTATTAC
1 TAAATCATTATTATAATCATTATTAC
78627 TAAATCATTATTATCAAATCATTATTA
1 TAAATCATTATTAT--AATCATTATTA
78654 AATTATCAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 17 0.19
24 2 0.02
25 11 0.12
26 49 0.54
28 10 0.11
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (26 bp):
TAAATCATTATTATAATCATTATTAC
Found at i:78660 original size:19 final size:20
Alignment explanation
Indices: 78635--78688 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
78625 ACTAAATCAT
78635 TATTATCAAATCATTATTAA
1 TATTATCAAATCATTATTAA
*
78655 -ATTATCAAACCATTA--AA
1 TATTATCAAATCATTATTAA
78672 TATTA--AAATCATTATTA
1 TATTATCAAATCATTATTA
78689 TCAAATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 8 0.28
17 2 0.07
18 5 0.17
19 14 0.48
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (20 bp):
TATTATCAAATCATTATTAA
Found at i:78696 original size:14 final size:14
Alignment explanation
Indices: 78564--78699 Score: 95
Period size: 14 Copynumber: 9.5 Consensus size: 14
78554 AATCATTATT
*
78564 ATCATTATTATTAA
1 ATCATTATTATCAA
78578 ATCATTATTAT--A
1 ATCATTATTATCAA
*
78590 ATGATTATTA-CTAA
1 ATCATTATTATC-AA
78604 ATCATTATTAT--A
1 ATCATTATTATCAA
*
78616 ATGATTATTA-CTAA
1 ATCATTATTATC-AA
78630 ATCATTATTATCAA
1 ATCATTATTATCAA
78644 ATCATTATTAAATTATCAA
1 ATC---ATT--ATTATCAA
* * *
78663 ACCATTAAATATTAAA
1 ATCATT-ATTA-TCAA
78679 ATCATTATTATCAA
1 ATCATTATTATCAA
78693 ATCATTA
1 ATCATTA
78700 CTAAATCATA
Statistics
Matches: 98, Mismatches: 10, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
12 20 0.20
14 46 0.47
15 8 0.08
16 11 0.11
17 3 0.03
19 10 0.10
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.43
Consensus pattern (14 bp):
ATCATTATTATCAA
Found at i:78719 original size:49 final size:49
Alignment explanation
Indices: 78528--78720 Score: 171
Period size: 49 Copynumber: 3.9 Consensus size: 49
78518 ATTTAATAAT
* * * *
78528 AAATCATTATTATCAACTTATTACTAAATCATTATTATCATT-ATTATT-
1 AAATCATTATTATCAAATCATTACTAAATCA-TATAATCATTAAATATTA
* * * * *
78576 AAATCATTATTAT-AATGATTATTACTAAATCATTATTAT-AATGATTATTA
1 AAATCATTATTATCAA--ATCATTACTAAATCA-TATAATCATTAAATATTA
* * *
78626 CTAAATCATTATTATCAAATCATTATTAAATTATCA-AACCATTAAATATTA
1 --AAATCATTATTATCAAATCATTACTAAATCAT-ATAATCATTAAATATTA
*
78677 AAATCATTATTATCAAATCATTACTAAATCATATAATTATTAAA
1 AAATCATTATTATCAAATCATTACTAAATCATATAATCATTAAA
78721 AAATCCTATG
Statistics
Matches: 121, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
47 2 0.02
48 16 0.13
49 65 0.54
50 2 0.02
51 21 0.17
52 13 0.11
53 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (49 bp):
AAATCATTATTATCAAATCATTACTAAATCATATAATCATTAAATATTA
Found at i:78736 original size:27 final size:27
Alignment explanation
Indices: 78706--78759 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
78696 ATTACTAAAT
78706 CATATAATTATTAAAAAATCCTATGTG
1 CATATAATTATTAAAAAATCCTATGTG
78733 CATATAATTATTAAAAAATCCTATGTG
1 CATATAATTATTAAAAAATCCTATGTG
78760 TTTTGATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (27 bp):
CATATAATTATTAAAAAATCCTATGTG
Found at i:78992 original size:14 final size:15
Alignment explanation
Indices: 78973--79002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
78963 ATCATTACTT
78973 AATCATT-AATATTA
1 AATCATTAAATATTA
78987 AATCATTAAATATTA
1 AATCATTAAATATTA
79002 A
1 A
79003 TAATAAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AATCATTAAATATTA
Found at i:78995 original size:21 final size:21
Alignment explanation
Indices: 78977--79039 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
78967 TTACTTAATC
*
78977 ATTAATATTAAATCATTAAAT
1 ATTAATAATAAATCATTAAAT
*
78998 ATTAATAATAAATCGTTATTAAT
1 ATTAATAATAAATCATTA--AAT
* *
79021 AATAATTACTAAATCATTA
1 ATTAA-TAATAAATCATTA
79040 TTAAATCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 16 0.47
23 7 0.21
24 11 0.32
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTAATAATAAATCATTAAAT
Found at i:79044 original size:11 final size:11
Alignment explanation
Indices: 78931--79210 Score: 117
Period size: 11 Copynumber: 23.4 Consensus size: 11
78921 ATTATTAATG
78931 ATTAAATCATT
1 ATTAAATCATT
78942 ATTACAATTTCATT
1 ATTA-AA--TCATT
78956 ATTACTAATCATT
1 ATTA--AATCATT
78969 ACTT-AATCATTAAT
1 A-TTAAATCA-T--T
78983 ATTAAATCATT
1 ATTAAATCATT
* *
78994 A--AATATTAAT
1 ATTAA-ATCATT
* *
79004 AATAAATCGTT
1 ATTAAATCATT
*
79015 ATTAATAATAATT
1 ATT-A-AATCATT
*
79028 ACTAAATCATT
1 ATTAAATCATT
79039 ATTAAATCATT
1 ATTAAATCATT
79050 ATTATCAAATCATT
1 A-T-T-AAATCATT
*
79064 ATTATAATGATT
1 ATTA-AATCATT
79076 ATTACTAAATCATT
1 A-T--TAAATCATT
*
79090 ATTATAATGATT
1 ATTA-AATCATT
79102 ATTATCAAATCATT
1 A-T-T-AAATCATT
*
79116 ACTAAATCATT
1 ATTAAATCATT
*
79127 GTTAAATCATT
1 ATTAAATCATT
79138 ATT--ATCATT
1 ATTAAATCATT
79147 ATTACCAAATCATT
1 ATT---AAATCATT
*
79161 ACTAAATCATCAAAT
1 ATTAAATCAT----T
79176 CATTAAAT-ATT
1 -ATTAAATCATT
*
79187 A--AAATTATT
1 ATTAAATCATT
79196 ATTAAATCATT
1 ATTAAATCATT
79207 ATTA
1 ATTA
79211 TGGTTAATTG
Statistics
Matches: 208, Mismatches: 23, Indels: 76
0.68 0.07 0.25
Matches are distributed among these distances:
8 4 0.02
9 15 0.07
10 6 0.03
11 74 0.36
12 24 0.12
13 21 0.10
14 50 0.24
15 8 0.04
16 6 0.03
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (11 bp):
ATTAAATCATT
Found at i:79053 original size:14 final size:14
Alignment explanation
Indices: 79036--79116 Score: 89
Period size: 14 Copynumber: 6.1 Consensus size: 14
79026 TTACTAAATC
79036 ATTATTAAATCATT
1 ATTATTAAATCATT
*
79050 ATTATCAAATCATT
1 ATTATTAAATCATT
*
79064 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
79076 ATTACTAAATCATT
1 ATTATTAAATCATT
*
79090 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
79102 ATTATCAAATCATT
1 ATTATTAAATCATT
79116 A
1 A
79117 CTAAATCATT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
12 20 0.36
13 2 0.04
14 34 0.61
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:79420 original size:60 final size:60
Alignment explanation
Indices: 79335--79451 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
79325 TTACATAAAT
79335 TCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATAATTACTA
1 TCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATAATTACTA
*
79395 TCAAATCATTAAATATTATTAATAATTTCATTATTACTAATCATTACTAAATAATTA
1 TCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATAATTA
79452 TTATAATTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (60 bp):
TCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATAATTACTA
Found at i:82351 original size:2 final size:2
Alignment explanation
Indices: 82344--82370 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
82334 TTCTCTACAA
82344 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
82371 AATTTAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82846 original size:19 final size:17
Alignment explanation
Indices: 82805--82857 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 17
82795 TAAATTAAAA
*
82805 AATATATATTTTAAACAAT
1 AATATAT-TTTTAAAC-AC
82824 AATAAATATTTTTAAACAC
1 AAT--ATATTTTTAAACAC
82843 AATAT-TTTTTAAACA
1 AATATATTTTTAAACA
82858 GAAATAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.32
17 2 0.06
19 7 0.23
20 8 0.26
21 4 0.13
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATATTTTTAAACAC
Found at i:83077 original size:17 final size:18
Alignment explanation
Indices: 83055--83088 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
83045 CCTGTTCGTG
83055 TAAACAAAAT-TTTTATT
1 TAAACAAAATATTTTATT
83072 TAAACAAAATATTTTAT
1 TAAACAAAATATTTTAT
83089 ACAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAACAAAATATTTTATT
Found at i:83350 original size:26 final size:25
Alignment explanation
Indices: 83309--83407 Score: 86
Period size: 24 Copynumber: 4.2 Consensus size: 25
83299 TTATATAATA
*
83309 TAATATATAACTTAAACTAACAAAC
1 TAATATATAACCTAAACTAACAAAC
83334 TAATATAATAACCTAAACTAACAAA-
1 TAATAT-ATAACCTAAACTAACAAAC
* *
83359 T-ATA-AT---TTATACTAACAAAC
1 TAATATATAACCTAAACTAACAAAC
* * *
83379 TAAT-TAAACCCTAAACTAATAAAC
1 TAATATATAACCTAAACTAACAAAC
83403 TAATA
1 TAATA
83408 ATTTCATATA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
19 11 0.19
20 1 0.02
21 3 0.05
22 2 0.03
24 18 0.31
25 7 0.12
26 17 0.29
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (25 bp):
TAATATATAACCTAAACTAACAAAC
Found at i:83376 original size:45 final size:43
Alignment explanation
Indices: 83313--83433 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 43
83303 ATAATATAAT
* *
83313 ATATAACTTAAACTAACAAACTAATATAATAACCTAAACTAACAA
1 ATATAATTTATACTAACAAACTAAT-TAA-AACCTAAACTAACAA
* *
83358 ATATAATTTATACTAACAAACTAATTAAACCCTAAACTAATAA
1 ATATAATTTATACTAACAAACTAATTAAAACCTAAACTAACAA
* *
83401 ACTAATAATTTCATA-TAATAAACTAATTTAAAC
1 A-T-ATAATTT-ATACTAACAAACTAATTAAAAC
83434 AATAAAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
43 14 0.21
44 4 0.06
45 45 0.68
46 3 0.05
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (43 bp):
ATATAATTTATACTAACAAACTAATTAAAACCTAAACTAACAA
Found at i:84493 original size:22 final size:23
Alignment explanation
Indices: 84459--84511 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
84449 TTCAGTATTT
84459 GTCCC-AAAGGACCACTGGATAC
1 GTCCCGAAAGGACCACTGGATAC
84481 GTCCCGAAA-GACCACTGGATAC
1 GTCCCGAAAGGACCACTGGATAC
84503 GTCCCGAAA
1 GTCCCGAAA
84512 ACTAATATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.13
Consensus pattern (23 bp):
GTCCCGAAAGGACCACTGGATAC
Found at i:85069 original size:24 final size:24
Alignment explanation
Indices: 85037--85155 Score: 114
Period size: 24 Copynumber: 5.4 Consensus size: 24
85027 TACACCATGT
85037 ATCGATGCATCCCTTGACGGGTGC
1 ATCGATGCATCCCTTGACGGGTGC
***
85061 ATCGATGCA---C-T-ACCCATGC
1 ATCGATGCATCCCTTGACGGGTGC
85080 ATCGATGCATCCCTTGACGGGTGC
1 ATCGATGCATCCCTTGACGGGTGC
***
85104 ATCGATGCA---C-T-ACCCATGC
1 ATCGATGCATCCCTTGACGGGTGC
85123 ATCGATGCATCCCTTGACGGGTGC
1 ATCGATGCATCCCTTGACGGGTGC
85147 ATCGATGCA
1 ATCGATGCA
85156 CTACCCATGC
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
19 28 0.38
20 2 0.03
21 2 0.03
22 2 0.03
23 2 0.03
24 37 0.51
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (24 bp):
ATCGATGCATCCCTTGACGGGTGC
Found at i:85082 original size:19 final size:19
Alignment explanation
Indices: 85058--85174 Score: 81
Period size: 19 Copynumber: 5.6 Consensus size: 19
85048 CCTTGACGGG
85058 TGCATCGATGCACTACCCA
1 TGCATCGATGCACTACCCA
***
85077 TGCATCGATGCATCCCTTGACGGG
1 TGCATCGATGCA---C-T-ACCCA
85101 TGCATCGATGCACTACCCA
1 TGCATCGATGCACTACCCA
***
85120 TGCATCGATGCATCCCTTGACGGG
1 TGCATCGATGCA---C-T-ACCCA
85144 TGCATCGATGCACTACCCA
1 TGCATCGATGCACTACCCA
*
85163 TGCATCGGTGCA
1 TGCATCGATGCA
85175 TAAATCCTAT
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
19 39 0.52
20 2 0.03
21 2 0.03
22 2 0.03
23 2 0.03
24 28 0.37
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCACTACCCA
Found at i:85089 original size:43 final size:43
Alignment explanation
Indices: 85014--85175 Score: 288
Period size: 43 Copynumber: 3.7 Consensus size: 43
85004 ATTGAAGGTA
* *
85014 TGCATTGATGCACTACACCATGTATCGATGCATCCCTTGACGGG
1 TGCATCGATGCACTAC-CCATGCATCGATGCATCCCTTGACGGG
85058 TGCATCGATGCACTACCCATGCATCGATGCATCCCTTGACGGG
1 TGCATCGATGCACTACCCATGCATCGATGCATCCCTTGACGGG
85101 TGCATCGATGCACTACCCATGCATCGATGCATCCCTTGACGGG
1 TGCATCGATGCACTACCCATGCATCGATGCATCCCTTGACGGG
*
85144 TGCATCGATGCACTACCCATGCATCGGTGCAT
1 TGCATCGATGCACTACCCATGCATCGATGCAT
85176 AAATCCTATT
Statistics
Matches: 115, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
43 100 0.87
44 15 0.13
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.25
Consensus pattern (43 bp):
TGCATCGATGCACTACCCATGCATCGATGCATCCCTTGACGGG
Found at i:85229 original size:16 final size:16
Alignment explanation
Indices: 85208--85251 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
85198 TTTAAACAGG
*
85208 TGCATCGATGCACTTA
1 TGCATCGATGCACTAA
85224 TGCATCGATGCACTAA
1 TGCATCGATGCACTAA
85240 TGGCATTCGATG
1 T-GCA-TCGATG
85252 TTCATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 16 0.64
17 3 0.12
18 6 0.24
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (16 bp):
TGCATCGATGCACTAA
Found at i:91322 original size:18 final size:18
Alignment explanation
Indices: 91299--91333 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
91289 GTTCAGTATT
91299 TGTCCCAAAGAACCACTA
1 TGTCCCAAAGAACCACTA
* *
91317 TGTCCCGAAGGACCACT
1 TGTCCCAAAGAACCACT
91334 GGATACGTCT
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:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGAACCACTA
Found at i:91352 original size:22 final size:21
Alignment explanation
Indices: 91321--91372 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 21
91311 CCACTATGTC
91321 CCGAAGGACCACTGGATACGT
1 CCGAAGGACCACTGGATACGT
*
91342 CTCGAATGACCACTGGATACGT
1 C-CGAAGGACCACTGGATACGT
91364 CCGAAGGAC
1 CCGAAGGAC
91373 TAATATACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (21 bp):
CCGAAGGACCACTGGATACGT
Done.