Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003471.1 Hibiscus syriacus cultivar Beakdansim tig00007342_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: 93915
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:403 original size:30 final size:32
Alignment explanation
Indices: 369--428 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
359 GGTTTTGAAT
*
369 ATTAAAAATTTAAGTATTAAA-ACG-AATTAA
1 ATTAAAAATTTAAGTACTAAATACGTAATTAA
* *
399 ATTAATAATTTGAGTACTAAATACGTAATT
1 ATTAAAAATTTAAGTACTAAATACGTAATT
429 TACTCTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 3 0.12
32 4 0.16
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (32 bp):
ATTAAAAATTTAAGTACTAAATACGTAATTAA
Found at i:590 original size:36 final size:36
Alignment explanation
Indices: 549--617 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
539 TATAATTAAA
549 ATTAATCAT-TGTGATACGGATAT-AATAATTTATGAC
1 ATTAAT-ATATGTGATACGGATATGAA-AATTTATGAC
*
585 ATTAATATATGTGATACTGATATGAAAATTTAT
1 ATTAATATATGTGATACGGATATGAAAATTTAT
618 AACGTTGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 2 0.07
36 26 0.87
37 2 0.07
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (36 bp):
ATTAATATATGTGATACGGATATGAAAATTTATGAC
Found at i:838 original size:2 final size:2
Alignment explanation
Indices: 831--864 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
821 AAACTTAAAA
831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
865 TGTACATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1001 original size:2 final size:2
Alignment explanation
Indices: 985--1035 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
975 TCATCTTTTC
985 AT AT CAT AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1026 AT -T AT A- AT AT
1 AT AT AT AT AT AT
1036 TTTTAAATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.09
2 38 0.86
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1020 original size:23 final size:22
Alignment explanation
Indices: 985--1035 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
975 TCATCTTTTC
985 ATATCATATTATATATATATATAT
1 ATAT-ATATTATATATATAT-TAT
1009 ATATATATTATATATATATTAT
1 ATATATATTATATATATATTAT
1031 A-ATAT
1 ATATAT
1036 TTTTAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.15
22 4 0.15
23 15 0.56
24 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATATATTATATATATATTAT
Found at i:1335 original size:23 final size:23
Alignment explanation
Indices: 1294--1337 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1284 ATTTTTTTAA
*
1294 TCAAAATAAAAATATTTTAAATT
1 TCAAAATAAAAATAATTTAAATT
1317 TCAAAATAATAAA-AATTTAAA
1 TCAAAATAA-AAATAATTTAAA
1338 AAATACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (23 bp):
TCAAAATAAAAATAATTTAAATT
Found at i:1669 original size:2 final size:2
Alignment explanation
Indices: 1662--1686 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1652 TGACATTACG
1662 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1687 TTCAGTGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8704 original size:32 final size:32
Alignment explanation
Indices: 8635--8705 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
8625 TTATTGGTGT
*
8635 GTTGTTTATCGATTGTGGCATCAATTTTAATC
1 GTTGTTGATCGATTGTGGCATCAATTTTAATC
* * *
8667 TTTGTTGATCGATTGTGGTATCAATTTTAATG
1 GTTGTTGATCGATTGTGGCATCAATTTTAATC
8699 GTTGTTG
1 GTTGTTG
8706 CTGACAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.20, C:0.08, G:0.23, T:0.49
Consensus pattern (32 bp):
GTTGTTGATCGATTGTGGCATCAATTTTAATC
Found at i:11751 original size:6 final size:6
Alignment explanation
Indices: 11742--11814 Score: 132
Period size: 6 Copynumber: 12.5 Consensus size: 6
11732 TACATATATG
11742 TATGTA TATGTA TA--TA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
11788 TATGTA TATGTA TATGTA TATGTA TAT
1 TATGTA TATGTA TATGTA TATGTA TAT
11815 ATAACTATTT
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.06
6 61 0.94
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATGTA
Found at i:12982 original size:13 final size:15
Alignment explanation
Indices: 12960--13005 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
12950 TTCTCCATTA
*
12960 TTTATGGTTTTA-AG
1 TTTATAGTTTTAGAG
12974 -TTATAG-TTTAGAG
1 TTTATAGTTTTAGAG
*
12987 TTTATAGTTTTAGGG
1 TTTATAGTTTTAGAG
13002 TTTA
1 TTTA
13006 AATTTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.15
13 7 0.26
14 6 0.22
15 10 0.37
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (15 bp):
TTTATAGTTTTAGAG
Found at i:23429 original size:37 final size:37
Alignment explanation
Indices: 23353--23429 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
23343 TTTTTATATT
*
23353 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
23390 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
23427 TTT
1 TTT
23430 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:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:24060 original size:2 final size:2
Alignment explanation
Indices: 24049--24083 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
24039 ATGTTGGTTG
24049 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
24084 TCTTTCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25200 original size:20 final size:21
Alignment explanation
Indices: 25177--25217 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25167 TATTATATGT
**
25177 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
25197 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
25218 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:26141 original size:18 final size:18
Alignment explanation
Indices: 26120--26158 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
26110 CTGTTTTTTT
26120 TTTCT-TCTCAGTTCTCTG
1 TTTCTGTCTCAG-TCTCTG
*
26138 TTTCTGTCTCTGTCTCTG
1 TTTCTGTCTCAGTCTCTG
26156 TTT
1 TTT
26159 TTTTTCAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.03, C:0.26, G:0.13, T:0.59
Consensus pattern (18 bp):
TTTCTGTCTCAGTCTCTG
Found at i:26607 original size:3 final size:3
Alignment explanation
Indices: 26599--26700 Score: 186
Period size: 3 Copynumber: 33.7 Consensus size: 3
26589 TTAATATATT
*
26599 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
26647 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
26693 TAA TAA TA
1 TAA TAA TA
26701 TGGATAAAAA
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 93 0.97
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27258 original size:117 final size:115
Alignment explanation
Indices: 27018--27701 Score: 972
Period size: 117 Copynumber: 5.9 Consensus size: 115
27008 TAGAATTATG
* * *
27018 CAAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTC--A-GATGAGTTCTT
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* *
27079 CTCATTATGAACTTCTCCGGAAAAGATAATCCATCAAGTGATGAATTCAAA
66 CTCATTATGAACTCCTCTGGAAAA-ATAATCCATCAAGTGATGAATTCAAA
27130 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* *
27195 CTTATTATGAACCTCCTCTGGCAACAATAATCCATCAAGTGATGAATTCAAA
66 CTCATTATGAA-CTCCTCTGG-AAAAATAATCCATCAAGTGATGAATTCAAA
27247 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
** * * * * *
27309 CTCATTATGAACTCGAACTGGAAAAATTGATCTATCAAGTGATGGATTTAAG
66 CTCATTATGAACTC-CTCTGGAAAAA-TAATCCATCAAGTGATGAATTCAAA
*
27361 C-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
*
27425 CTCATTATGAACCTCCTCTGGCAACAATAATCCATCAAGTGATGAATTCAAA
66 CTCATTATGAA-CTCCTCTGG-AAAAATAATCCATCAAGTGATGAATTCAAA
27477 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* ** * * *
27542 CTTATTATGAACTCGAACTGGAAAAATTGATCCATCAAATGATGGATTC-AA
66 CTCATTATGAACTC-CTCTGGAAAAA-TAATCCATCAAGTGATGAATTCAAA
**
27593 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
*
27658 CTCATTATGAACCTCCTCTGAAAAAAAATAATCCATCAAGTGAT
66 CTCATTATGAA-CTCCTCTG--GAAAAATAATCCATCAAGTGAT
27702 AGATTTGAAT
Statistics
Matches: 512, Mismatches: 41, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
112 6 0.01
113 94 0.18
114 46 0.09
115 3 0.01
116 153 0.30
117 202 0.39
118 8 0.02
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (115 bp):
CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
CTCATTATGAACTCCTCTGGAAAAATAATCCATCAAGTGATGAATTCAAA
Found at i:27368 original size:230 final size:230
Alignment explanation
Indices: 27018--27701 Score: 1115
Period size: 230 Copynumber: 3.0 Consensus size: 230
27008 TAGAATTATG
* * *
27018 CAAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
27082 ATTATGAACTTC--TCCGGAAAAGA-TAATCCATCAAGTGATGAATTCAAACAAAAAGGTTGAAC
66 ATTATGAAC-TCGAACTGGAAAA-ATTGATCCATCAAGTGATGGATTCAAGC-AAAAGGTTGAAC
*
27144 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTTATTATGAACCT
128 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACCT
27209 CCTCTGGCAACAATAATCCATCAAGTGATGAATTCAAA
193 CCTCTGGCAACAATAATCCATCAAGTGATGAATTCAAA
27247 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
27312 ATTATGAACTCGAACTGGAAAAATTGATCTATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
66 ATTATGAACTCGAACTGGAAAAATTGATCCATCAAGTGATGGATTCAAGCAAAAGGTTGAACAAA
*
27377 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACCTCCT
131 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACCTCCT
27442 CTGGCAACAATAATCCATCAAGTGATGAATTCAAA
196 CTGGCAACAATAATCCATCAAGTGATGAATTCAAA
27477 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
* * *
27542 CTTATTATGAACTCGAACTGGAAAAATTGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAAC
63 CTCATTATGAACTCGAACTGGAAAAATTGATCCATCAAGTGATGGATTCAAGCAAAAGGTTGAAC
27607 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACCT
128 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACCT
** *
27672 CCTCTGAAAAAAAATAATCCATCAAGTGAT
193 CCTCTG-GCAACAATAATCCATCAAGTGAT
27702 AGATTTGAAT
Statistics
Matches: 426, Mismatches: 21, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
229 8 0.02
230 228 0.54
231 28 0.07
232 1 0.00
233 141 0.33
234 20 0.05
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (230 bp):
CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCGAACTGGAAAAATTGATCCATCAAGTGATGGATTCAAGCAAAAGGTTGAACAAA
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACCTCCT
CTGGCAACAATAATCCATCAAGTGATGAATTCAAA
Found at i:28609 original size:84 final size:83
Alignment explanation
Indices: 28435--28644 Score: 357
Period size: 84 Copynumber: 2.5 Consensus size: 83
28425 TATTTTTACC
* *
28435 AACCAGATTAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
28500 CAATGATTGGTTCTGCCA
66 CAATGATTGGTTCTGCCA
*
28518 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCAAAT
* * *
28583 TCGATGATTGGTTCTGTCT
65 TCAATGATTGGTTCTGCCA
28602 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
28645 GAGTCTCTTT
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
83 42 0.35
84 77 0.65
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
CAATGATTGGTTCTGCCA
Found at i:29451 original size:16 final size:17
Alignment explanation
Indices: 29413--29457 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
29403 AATATAAAAG
*
29413 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
29431 AATAAATTGAATCTC-A
1 AATAAATTGAATCTCAA
29447 AATAAATTGAA
1 AATAAATTGAA
29458 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:29798 original size:7 final size:7
Alignment explanation
Indices: 29786--29815 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29776 CTTGACCCCC
29786 CTTTTTT
1 CTTTTTT
29793 CTTTTTT
1 CTTTTTT
29800 CTTTTTT
1 CTTTTTT
29807 -TTTTTT
1 CTTTTTT
29813 CTT
1 CTT
29816 CAAGCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
CTTTTTT
Found at i:29810 original size:13 final size:14
Alignment explanation
Indices: 29786--29815 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
29776 CTTGACCCCC
29786 CTTTTTTCTTTTTT
1 CTTTTTTCTTTTTT
29800 CTTTTTT-TTTTTT
1 CTTTTTTCTTTTTT
29813 CTT
1 CTT
29816 CAAGCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
CTTTTTTCTTTTTT
Found at i:42043 original size:18 final size:18
Alignment explanation
Indices: 42011--42082 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 18
42001 GGTATATTTG
42011 TTTTTTTTTCTTTCTCTGT
1 TTTTTTTTTC-TTCTCTGT
*
42030 TTTTTTTTTCTTCTCAGT
1 TTTTTTTTTCTTCTCTGT
42048 TCTCTGTTTCTGTCTCTGTCTCTGT
1 T-T-T-TTT-T-T-TCT-TCTCTGT
42073 TTTTTTTTTC
1 TTTTTTTTTC
42083 AGGTTGGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
18 8 0.18
19 13 0.30
20 2 0.05
21 4 0.09
22 4 0.09
23 2 0.05
24 4 0.09
25 7 0.16
ACGTcount: A:0.01, C:0.19, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTTTTTTTCTTCTCTGT
Found at i:42521 original size:3 final size:3
Alignment explanation
Indices: 42515--42603 Score: 133
Period size: 3 Copynumber: 29.7 Consensus size: 3
42505 ATTTAATATT
* * *
42515 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAG TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
42563 TAT TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42604 TGGATAAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:43944 original size:17 final size:16
Alignment explanation
Indices: 43914--43947 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43904 AAACCATCAA
*
43914 TTTTTGTTTGTTTTAG
1 TTTTTGTTTATTTTAG
43930 TTTTTGTTTAATTTTAG
1 TTTTTGTTT-ATTTTAG
43947 T
1 T
43948 ACCCATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (16 bp):
TTTTTGTTTATTTTAG
Found at i:50061 original size:2 final size:2
Alignment explanation
Indices: 50048--50112 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
50038 TCATGCATAC
*
50048 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50090 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
50113 ATTTTAGAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55312 original size:162 final size:162
Alignment explanation
Indices: 55045--55359 Score: 432
Period size: 162 Copynumber: 1.9 Consensus size: 162
55035 GTAACAATAT
** * * * *
55045 AAAGATTTCATGATTGTTTGACGTTTTTAGGTCAAACGTAAAGACTCCAGAAATACACGGCGTTT
1 AAAGATTTCATGATTACTTGACGTCTTCAGGCCAAACGTAAAGACTCCAGAAATACACGACGTTT
* * * * *
55110 TCAAATTTAGGAGAGACACGTGGAGTGCACGACATCTTCAGTCCATACAGAAGCATTCGAGAATA
66 TCAAATCTAGGAAAGACACGTGGAGTGCACGACATCTTCAGTCCATACAAAAGCACTCGAAAATA
55175 CACAATGTCTTCAGCTTTACTTCAGTCCATAA
131 CACAATGTCTTCAGCTTTACTTCAGTCCATAA
* * * * **
55207 AAAGATTTCATGGTTACTTGATGTCTTCAGGCCAAACGTAAAGACTCCGGGAATGTACGACGTTT
1 AAAGATTTCATGATTACTTGACGTCTTCAGGCCAAACGTAAAGACTCCAGAAATACACGACGTTT
**
55272 TCAGGTCTAGGAAAGACACGTGGAGTGCACGACATCTTCAGTCCATACAAAAGCACTCGAAAATA
66 TCAAATCTAGGAAAGACACGTGGAGTGCACGACATCTTCAGTCCATACAAAAGCACTCGAAAATA
* **
55337 CGCGGTGTCTTCAGCTTTACTTC
131 CACAATGTCTTCAGCTTTACTTC
55360 GACAGCAACA
Statistics
Matches: 131, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
162 131 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (162 bp):
AAAGATTTCATGATTACTTGACGTCTTCAGGCCAAACGTAAAGACTCCAGAAATACACGACGTTT
TCAAATCTAGGAAAGACACGTGGAGTGCACGACATCTTCAGTCCATACAAAAGCACTCGAAAATA
CACAATGTCTTCAGCTTTACTTCAGTCCATAA
Found at i:58598 original size:48 final size:48
Alignment explanation
Indices: 58546--58665 Score: 231
Period size: 48 Copynumber: 2.5 Consensus size: 48
58536 ACATATATAT
58546 TACAAATACTAAATCAATATGTTGATCTAATTATCTTAACATTTCTAC
1 TACAAATACTAAATCAATATGTTGATCTAATTATCTTAACATTTCTAC
58594 TACAAATACTAAATCAATATGTTGATCTAATTATCTTAACATTTCTAC
1 TACAAATACTAAATCAATATGTTGATCTAATTATCTTAACATTTCTAC
58642 TACAAATACTAAATCAATAATGTT
1 TACAAATACTAAATCAAT-ATGTT
58666 AAAATTATAA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
48 66 0.93
49 5 0.07
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (48 bp):
TACAAATACTAAATCAATATGTTGATCTAATTATCTTAACATTTCTAC
Found at i:64182 original size:12 final size:12
Alignment explanation
Indices: 64165--64248 Score: 63
Period size: 12 Copynumber: 7.2 Consensus size: 12
64155 AAGAAAAATG
*
64165 AAAAATGATGAA
1 AAAAATGAAGAA
*
64177 AAAAATGAAAAGA
1 AAAAATGAAGA-A
64190 AAAAATGAAGAA
1 AAAAATGAAGAA
*
64202 AAGGAAA--AATAA
1 AA--AAATGAAGAA
64214 AAAAATGAAGAA
1 AAAAATGAAGAA
*
64226 AAGAA--AAG-A
1 AAAAATGAAGAA
64235 AAAAATGAA-AA
1 AAAAATGAAGAA
64246 AAA
1 AAA
64249 TGAAAAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
9 5 0.09
10 6 0.11
11 6 0.11
12 26 0.46
13 11 0.19
14 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAAATGAAGAA
Found at i:64192 original size:24 final size:22
Alignment explanation
Indices: 64172--64300 Score: 111
Period size: 23 Copynumber: 5.7 Consensus size: 22
64162 ATGAAAAATG
64172 ATGAAAAAAATGAAAAGAAAAA
1 ATGAAAAAAATGAAAAGAAAAA
* * *
64194 ATGAAGAAAAGGAAAAATAAAAAA
1 ATGAAAAAAATG-AAAA-GAAAAA
*
64218 ATGAAGAAAA-GAAAAGAAAAA
1 ATGAAAAAAATGAAAAGAAAAA
64239 ATGAAAAAAATGAAAAATGAAAAA
1 ATGAAAAAAATG-AAAA-GAAAAA
* *
64263 AAG-AAAAAGTGAAAA-AAGAAGA
1 ATGAAAAAAATGAAAAGAA-AA-A
* *
64285 AAGAGAAAAATGAAAA
1 ATGAAAAAAATGAAAA
64301 ATAAAAAAAG
Statistics
Matches: 90, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.02
21 16 0.18
22 23 0.26
23 26 0.29
24 23 0.26
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (22 bp):
ATGAAAAAAATGAAAAGAAAAA
Found at i:64240 original size:45 final size:47
Alignment explanation
Indices: 64157--64309 Score: 165
Period size: 45 Copynumber: 3.3 Consensus size: 47
64147 TTCGCTTGAA
* *
64157 GAAAAATGAAAAATGATGAAAAAAATGAAAAGAAAAAATGAAGAAAAG
1 GAAAAATGAAAAA-AATGAAAAAAATGAAAAGAAAAAATGAAAAAAAG
* *
64205 GAAAAAT-AAAAAAATGAAGAAAA-GAAAAGAAAAAATGAAAAAAAT
1 GAAAAATGAAAAAAATGAAAAAAATGAAAAGAAAAAATGAAAAAAAG
* * * *
64250 GAAAAATGAAAAAAA-G-AAAAAGTGAAAA-AAGAAGAAAGAGAAAAAT
1 GAAAAATGAAAAAAATGAAAAAAATGAAAAGAA-AA-AATGAAAAAAAG
64296 GAAAAAT-AAAAAAA
1 GAAAAATGAAAAAAA
64310 GAGAAAATTA
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
44 6 0.06
45 42 0.45
46 33 0.35
47 5 0.05
48 7 0.08
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.08
Consensus pattern (47 bp):
GAAAAATGAAAAAAATGAAAAAAATGAAAAGAAAAAATGAAAAAAAG
Found at i:64245 original size:6 final size:7
Alignment explanation
Indices: 64157--64307 Score: 73
Period size: 7 Copynumber: 20.9 Consensus size: 7
64147 TTCGCTTGAA
64157 GAAAAAT
1 GAAAAAT
64164 GAAAAAT
1 GAAAAAT
**
64171 GATGAA-
1 GAAAAAT
64177 -AAAAAT
1 GAAAAAT
64183 G-AAAA-
1 GAAAAAT
64188 GAAAAAAT
1 G-AAAAAT
*
64196 GAAGAAAAG
1 G-A-AAAAT
64205 GAAAAAT
1 GAAAAAT
*
64212 AAAAAAAT
1 -GAAAAAT
*
64220 GAAGAAAA
1 GAA-AAAT
64228 G-AAAA-
1 GAAAAAT
64233 GAAAAAAT
1 G-AAAAAT
64241 GAAAAAAAT
1 G--AAAAAT
64250 GAAAAAT
1 GAAAAAT
*
64257 GAAAAAAA
1 G-AAAAAT
64265 GAAAAAGT
1 GAAAAA-T
*
64273 GAAAAAA
1 GAAAAAT
*
64280 GAAGAAAGA
1 GAA-AAA-T
64289 GAAAAAT
1 GAAAAAT
64296 GAAAAAT
1 GAAAAAT
64303 -AAAAA
1 GAAAAA
64308 AAGAGAAAAT
Statistics
Matches: 115, Mismatches: 13, Indels: 33
0.71 0.08 0.20
Matches are distributed among these distances:
5 5 0.04
6 12 0.10
7 48 0.42
8 33 0.29
9 17 0.15
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.09
Consensus pattern (7 bp):
GAAAAAT
Found at i:64280 original size:9 final size:8
Alignment explanation
Indices: 64158--64301 Score: 103
Period size: 8 Copynumber: 18.5 Consensus size: 8
64148 TCGCTTGAAG
64158 AAAAATGA
1 AAAAATGA
64166 AAAATGATGAA
1 AAAA--ATG-A
64177 AAAAATG-
1 AAAAATGA
64184 -AAAA-GA
1 AAAAATGA
64190 AAAAATGA
1 AAAAATGA
*
64198 AGAAAA-GG
1 A-AAAATGA
*
64206 AAAAATAA
1 AAAAATGA
64214 AAAAATGA
1 AAAAATGA
64222 AGAAAA-G-
1 A-AAAATGA
64229 -AAAA-GA
1 AAAAATGA
64235 AAAAATGAA
1 AAAAATG-A
64244 AAAAATG-
1 AAAAATGA
64251 AAAAATGA
1 AAAAATGA
*
64259 AAAAAAGA
1 AAAAATGA
*
64267 AAAAGTGA
1 AAAAATGA
64275 AAAAA-GA
1 AAAAATGA
*
64282 AGAAA-GA
1 AAAAATGA
64289 GAAAAATGA
1 -AAAAATGA
64298 AAAA
1 AAAA
64302 TAAAAAAAGA
Statistics
Matches: 110, Mismatches: 10, Indels: 32
0.72 0.07 0.21
Matches are distributed among these distances:
5 6 0.05
6 4 0.04
7 27 0.25
8 44 0.40
9 21 0.19
10 3 0.03
11 5 0.05
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (8 bp):
AAAAATGA
Found at i:64301 original size:23 final size:23
Alignment explanation
Indices: 64229--64316 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
64219 TGAAGAAAAG
*
64229 AAAAGAAAAAATGAAAAAAATGAA
1 AAAAGAAAAAA-GAGAAAAATGAA
*
64253 AAATGAAAAAA-AGAAAAAGTGAA
1 AAAAGAAAAAAGAGAAAAA-TGAA
*
64276 AAAAGAAGAAAGAGAAAAATGAA
1 AAAAGAAAAAAGAGAAAAATGAA
64299 AAATA-AAAAAAGAGAAAA
1 AAA-AGAAAAAAGAGAAAA
64317 TTAAAGGGGG
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
22 6 0.11
23 32 0.57
24 18 0.32
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (23 bp):
AAAAGAAAAAAGAGAAAAATGAA
Found at i:64301 original size:37 final size:36
Alignment explanation
Indices: 64177--64307 Score: 110
Period size: 37 Copynumber: 3.5 Consensus size: 36
64167 AAATGATGAA
64177 AAAAATG-AAAAGAAAAAATGAAGAAAAGGAAAAATAA-
1 AAAAATGAAAAAG-AAAAATGAA-AAAAGGAAAAA-AAG
*
64214 AAAAATGAAGAAA-AGAAAA-GAAAAAATGAAAAAAATG
1 AAAAATGAA-AAAGA-AAAATGAAAAAAGGAAAAAAA-G
*
64251 AAAAATGAAAAAAAGAAAAAGTGAAAAAA-GAAGAAAGAG
1 AAAAATG--AAAAAGAAAAA-TGAAAAAAGGAA-AAAAAG
*
64290 AAAAATGAAAAATAAAAA
1 AAAAATGAAAAAGAAAAA
64308 AAGAGAAAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
35 2 0.03
36 10 0.12
37 28 0.35
38 12 0.15
39 17 0.21
40 11 0.14
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (36 bp):
AAAAATGAAAAAGAAAAATGAAAAAAGGAAAAAAAG
Found at i:64309 original size:16 final size:15
Alignment explanation
Indices: 64184--64317 Score: 109
Period size: 16 Copynumber: 8.7 Consensus size: 15
64174 GAAAAAAATG
64184 AAAAGAAAAAATGAAGA
1 AAAAG-AAAAATGAA-A
*
64201 AAAGGAAAAAT-AAA
1 AAAAGAAAAATGAAA
* *
64215 AAAATGAAGAA--AAG
1 AAAA-GAAAAATGAAA
64229 AAAAGAAAAAATGAAA
1 AAAAG-AAAAATGAAA
64245 AAAATGAAAAATGAAA
1 AAAA-GAAAAATGAAA
64261 AAAAGAAAAAGTG-AA
1 AAAAGAAAAA-TGAAA
64276 AAAAGAAGAAA-GAGAA
1 AAAAGAA-AAATGA-AA
*
64292 AAATGAAAAAT-AAA
1 AAAAGAAAAATGAAA
64306 AAAAGAGAAAAT
1 AAAAGA-AAAAT
64318 TAAAGGGGGT
Statistics
Matches: 98, Mismatches: 8, Indels: 24
0.75 0.06 0.18
Matches are distributed among these distances:
13 1 0.01
14 22 0.22
15 31 0.32
16 39 0.40
17 5 0.05
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAATGAAA
Found at i:64403 original size:45 final size:44
Alignment explanation
Indices: 64319--64403 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 44
64309 AGAGAAAATT
* * *
64319 AAAGGGGGTTCAAGATGAAAACCCAAAAAGGGTGTCTTGAAACC
1 AAAGGAGGTTCAAGATGAAAACCCAAAAAGGGCGGCTTGAAACC
* **
64363 AAAGGAGGTCTCAAGTTGAAAACCCGCAAAGGGCGGCTTGA
1 AAAGGAGGT-TCAAGATGAAAACCCAAAAAGGGCGGCTTGA
64404 GTTTTGTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 8 0.24
45 26 0.76
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (44 bp):
AAAGGAGGTTCAAGATGAAAACCCAAAAAGGGCGGCTTGAAACC
Found at i:65735 original size:55 final size:55
Alignment explanation
Indices: 65676--66221 Score: 687
Period size: 55 Copynumber: 10.0 Consensus size: 55
65666 AACAAACTCA
*
65676 TTTTATGAAGATTGTTCGAGTTCTATAATCTCTGAAGGAATAGAGAGCGGACCCG
1 TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
*
65731 TTTTATGAAGATTGTTTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
1 TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
*
65786 TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCA
1 TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
* * *
65841 TTTTATGAAGATTGTTCGAGTTTTATACTCTCTGAAGGACTAGAGAGCGGACTCG
1 TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
* * *
65896 TTTTATAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGATAGAGGACCCG
1 TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
* *
65951 TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGAGAGCGGACTCG
1 TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
* * * * * *
66006 TTTGT-TAAAGATTGTTCGAGTTC--TACTCCCTGAAGCAAGAGGGAGC-AAGCCCG
1 TTT-TATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-CCCG
* * * *
66059 TTTGT-TGAGGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGAGAACAGACCCG
1 TTT-TATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
* * * * *
66114 TTTGT-TGAAGATTGTTCGAG-TCTTATACTCCCTGAATGAATAGGGAGCAGACACG
1 TTT-TATGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCG
* * * * *
66169 -TTTACTGAAGATTGGTCGAG-TCTTATACTCCCTGAAGGGATAGGGAGCAGACC
1 TTTTA-TGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACC
66222 TGTCATTCGA
Statistics
Matches: 437, Mismatches: 46, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
52 1 0.00
53 43 0.10
54 4 0.01
55 387 0.89
56 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (55 bp):
TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
Found at i:67893 original size:22 final size:22
Alignment explanation
Indices: 67876--67942 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
67866 CTCGTATAAA
67876 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
67898 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
67920 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
67942 T
1 T
67943 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:68203 original size:30 final size:31
Alignment explanation
Indices: 68162--68221 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
68152 TAGACATAGT
*
68162 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
68192 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
68222 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:68278 original size:29 final size:28
Alignment explanation
Indices: 68236--68306 Score: 115
Period size: 29 Copynumber: 2.5 Consensus size: 28
68226 TTTTCTGCAC
*
68236 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATA-CA
*
68265 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
68293 ATTCATGTCATGTA
1 ATTCATGTCATGTA
68307 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 15 0.38
29 25 0.62
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:68765 original size:70 final size:71
Alignment explanation
Indices: 68610--68766 Score: 235
Period size: 71 Copynumber: 2.2 Consensus size: 71
68600 TTTTCTCATG
* * *
68610 GGGGAATCGGTTCCCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATAC
1 GGGGTATCGGTTCCCCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATAC
*
68675 GATGAG
66 GATGAA
* * *
68681 GGGGTATCGGTTCCCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC
1 GGGGTATCGGTTCCCCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATAC
*
68745 GTTGAA
66 GATGAA
68751 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
68767 TTGAATGGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 22 0.28
71 56 0.72
ACGTcount: A:0.17, C:0.31, G:0.26, T:0.26
Consensus pattern (71 bp):
GGGGTATCGGTTCCCCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATAC
GATGAA
Found at i:68776 original size:21 final size:21
Alignment explanation
Indices: 68746--68788 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
68736 ATTCATTTCG
* *
68746 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
68767 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
68788 T
1 T
68789 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:74824 original size:22 final size:22
Alignment explanation
Indices: 74807--74873 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
74797 CTCGTATAAA
74807 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
74829 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
74851 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
74873 T
1 T
74874 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:75134 original size:30 final size:31
Alignment explanation
Indices: 75093--75152 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
75083 TAGACATAGT
*
75093 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
75123 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
75153 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:75209 original size:29 final size:28
Alignment explanation
Indices: 75167--75237 Score: 115
Period size: 29 Copynumber: 2.5 Consensus size: 28
75157 TTTTCTGCAC
*
75167 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATA-CA
*
75196 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
75224 ATTCATGTCATGTA
1 ATTCATGTCATGTA
75238 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 15 0.38
29 25 0.62
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:75685 original size:68 final size:69
Alignment explanation
Indices: 75541--75692 Score: 218
Period size: 69 Copynumber: 2.2 Consensus size: 69
75531 TTTTCTCATG
* * *
75541 GGGGAATCGGTT-CCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
*
75605 TGAG
66 TGAA
* * * *
75609 GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGT
1 GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
75673 TGAA
66 TGAA
75677 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
75693 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
68 33 0.44
69 42 0.56
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
TGAA
Found at i:75702 original size:21 final size:21
Alignment explanation
Indices: 75672--75714 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
75662 ATTCATTTCG
* *
75672 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
75693 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
75714 T
1 T
75715 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:78803 original size:39 final size:39
Alignment explanation
Indices: 78740--78839 Score: 128
Period size: 39 Copynumber: 2.6 Consensus size: 39
78730 TGTTTCTGCA
* **
78740 TGGCCTAAAGACGTCATGTTCTCCTAGAGTCTTATCCAT
1 TGGCCTGAAGACGTCATGCACTCCTAGAGTCTTATCCAT
* * *
78779 TGGCCTGAAGACGTCGTGCACTCCTGGAGTCTTATTCAT
1 TGGCCTGAAGACGTCATGCACTCCTAGAGTCTTATCCAT
* *
78818 TGACCTGAAGACGGCATGCACT
1 TGGCCTGAAGACGTCATGCACT
78840 TATGGAGTCT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (39 bp):
TGGCCTGAAGACGTCATGCACTCCTAGAGTCTTATCCAT
Found at i:78846 original size:39 final size:39
Alignment explanation
Indices: 78766--78889 Score: 135
Period size: 39 Copynumber: 3.2 Consensus size: 39
78756 TGTTCTCCTA
* * * *
78766 GAGTCTTATCCATTGGCCTGAAGACGTCGTGCACTCCTG
1 GAGTCTTATTCATTGGCCTGAAGACGCCATGCACTCATG
* * *
78805 GAGTCTTATTCATTGACCTGAAGACGGCATGCACTTATG
1 GAGTCTTATTCATTGGCCTGAAGACGCCATGCACTCATG
* *
78844 GAGTCTTTATGT--TTGGCCTGAAGACACCATGCAATCATG
1 GAGTC-TTAT-TCATTGGCCTGAAGACGCCATGCACTCATG
78883 GAGTCTT
1 GAGTCTT
78890 TATTTTGTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.03
39 65 0.90
40 4 0.06
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (39 bp):
GAGTCTTATTCATTGGCCTGAAGACGCCATGCACTCATG
Found at i:83786 original size:22 final size:23
Alignment explanation
Indices: 83758--83846 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 23
83748 TTTAGGATTT
83758 ATATTATATAATTAATATA-AAA
1 ATATTATATAATTAATATATAAA
*
83780 ATATTATAT-ATT-ATATATATA
1 ATATTATATAATTAATATATAAA
*
83801 AT-TAATATAA--AATATATAAA
1 ATATTATATAATTAATATATAAA
*
83821 ATAATATATATATATATATATATAAA
1 ATATTATATA-AT-TA-ATATATAAA
83847 TAATAGGGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
20 20 0.38
21 13 0.25
22 10 0.19
25 1 0.02
26 9 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTATATAATTAATATATAAA
Found at i:83796 original size:2 final size:2
Alignment explanation
Indices: 83780--83844 Score: 56
Period size: 2 Copynumber: 36.5 Consensus size: 2
83770 TAATATAAAA
*
83780 AT AT -T AT AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
83816 AT A- AA AT A- 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 AT AT A
83845 AATAATAGGG
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
1 8 0.15
2 45 0.85
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:83842 original size:44 final size:40
Alignment explanation
Indices: 83771--83851 Score: 117
Period size: 44 Copynumber: 1.9 Consensus size: 40
83761 TTATATAATT
*
83771 AATATAAAAATATTATATATTATATATATAATTAATATAA
1 AATATAAAAATATTATATATTATATATATAAATAATATAA
83811 AATATATAAAATAATATATATATATATATATATAAATAATA
1 AATATA-AAAAT-AT-TATATAT-TATATATATAAATAATA
83852 GGGGGCGGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
40 6 0.17
41 5 0.14
42 2 0.06
43 7 0.19
44 16 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (40 bp):
AATATAAAAATATTATATATTATATATATAAATAATATAA
Found at i:83844 original size:14 final size:13
Alignment explanation
Indices: 83757--83851 Score: 77
Period size: 12 Copynumber: 8.2 Consensus size: 13
83747 GTTTAGGATT
83757 TATAT-TATATAA
1 TATATATATATAA
83769 T-TA-ATATA-AA
1 TATATATATATAA
*
83779 AATAT-TATAT-A
1 TATATATATATAA
83790 T-TATATATATAA
1 TATATATATATAA
*
83802 T-TA-ATATAAAA
1 TATATATATATAA
*
83813 TATATA-AAATAA
1 TATATATATATAA
83825 TATATATATAT-A
1 TATATATATATAA
*
83837 TATATATAAATAA
1 TATATATATATAA
83850 TA
1 TA
83852 GGGGGCGGGG
Statistics
Matches: 66, Mismatches: 7, Indels: 19
0.72 0.08 0.21
Matches are distributed among these distances:
10 5 0.08
11 26 0.39
12 28 0.42
13 7 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATATATATATAA
Found at i:86664 original size:2 final size:2
Alignment explanation
Indices: 86657--86696 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
86647 GAATTTATGC
86657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86697 CTGCATTATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90960 original size:37 final size:38
Alignment explanation
Indices: 90898--90985 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 38
90888 TTTATTTTGT
*
90898 TCGGG-TCGGGTGTTTTAAGTATGATATTCGGGTCGAG
1 TCGGGTTCGGGTTTTTTAAGTATGATATTCGGGTCGAG
* * *
90935 TC-GGTTCGTGTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTTCGGGTTTTTTAAGTATGATATTCGGGTCGAG
90972 TCGGGTTCGGGTTT
1 TCGGGTTCGGGTTT
90986 AGGGTGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 2 0.05
37 32 0.73
38 10 0.23
ACGTcount: A:0.11, C:0.11, G:0.38, T:0.40
Consensus pattern (38 bp):
TCGGGTTCGGGTTTTTTAAGTATGATATTCGGGTCGAG
Found at i:91180 original size:27 final size:28
Alignment explanation
Indices: 91150--91204 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
91140 TTTTGTTCGG
91150 GTCGGGTCGAG-TTTTTTAAGTGTGATA
1 GTCGGGTCGAGTTTTTTTAAGTGTGATA
*
91177 GTCGGGTCGGGTTTTTTTAAGTGTGATA
1 GTCGGGTCGAGTTTTTTTAAGTGTGATA
91205 TTCTGGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.16, C:0.07, G:0.35, T:0.42
Consensus pattern (28 bp):
GTCGGGTCGAGTTTTTTTAAGTGTGATA
Found at i:91184 original size:253 final size:240
Alignment explanation
Indices: 90725--91270 Score: 745
Period size: 253 Copynumber: 2.2 Consensus size: 240
90715 TTTATTTTGG
* * * * *
90725 TCGGGTTAAAGGTGAAAAAAACCAGATCGACCCGAAAATATATATAATTTAGGTCGGGTCGGGTT
1 TCGGGTTTAGGGTGAAAAAAACCGGATCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATT
** *
90790 AAGTCGCTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTTGGGTCGGGTTGGATTTC
66 AAGTCAATGTTTTTATTAAATAAAAATAATTTTTTATTATTTC--G--GGGTCGGGTCGGATTTC
* * *
90855 TAATTCATATATTCGGGTTGGGTCGGATGAAATTTTATTTTGTTCGGGTCGGGTGTTTTAAGTAT
127 TAATTCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTGTTTTAAGTAT
* **
90920 GATATTCGGGTCGAGTCGGTTCGTGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGT
192 GATA-----GTCGGGTCGG---GT-TTTTTTAAGTGTGATATTCGGGTCAAGTCGGGT
* *
90978 TCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATT
1 TCGGGTTTAGGGTGAAAAAAACCGGATCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATT
91043 AAGTCAATGTTTTTATTAAATAAAAATAATTTTTTATTATTTC-GGGTCGGGTCGGATTTCTAAT
66 AAGTCAATGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGGTCGGGTCGGATTTCTAAT
*
91107 TCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTG
131 TCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGT---G--TTTTAAGTA
*
91172 TGATAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCTGGTCAAGTCGGGT
191 TGATAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAAGTCGGGT
91222 TC-GGTTTAGGGTGAAAAAAACCGGATCGACCCGAAAAATATATATAATT
1 TCGGGTTTAGGGTGAAAAAAACCGGATCGACCCG-AAAATATATATAATT
91271 TTTCCTTATA
Statistics
Matches: 268, Mismatches: 19, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
243 30 0.11
244 47 0.18
245 2 0.01
248 76 0.28
251 1 0.00
253 112 0.42
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.36
Consensus pattern (240 bp):
TCGGGTTTAGGGTGAAAAAAACCGGATCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATT
AAGTCAATGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGGTCGGGTCGGATTTCTAAT
TCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTGTTTTAAGTATGATA
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAAGTCGGGT
Done.