Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000732.1 Hibiscus syriacus cultivar Beakdansim tig00001420_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: 168431
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:116211 original size:19 final size:18
Alignment explanation
Indices: 116187--116233 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
116177 AACGCGATTT
*
116187 TCGCAACGAATTTGGAAAA
1 TCGCAACGAA-ATGGAAAA
116206 TCGCAACGCGAAATGGAAAA
1 TCGCAA--CGAAATGGAAAA
116226 TCGCAACG
1 TCGCAACG
116234 CGATTTTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 13 0.52
21 4 0.16
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.15
Consensus pattern (18 bp):
TCGCAACGAAATGGAAAA
Found at i:116224 original size:20 final size:20
Alignment explanation
Indices: 116199--116277 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
116189 GCAACGAATT
116199 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
**
116219 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** ** *
116239 TTCAGCTATCGCAACGCGAAC
1 TGGA-AAATCGCAACGCGAAA
116260 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
116278 TTTTCGCAAC
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 32 0.70
21 14 0.30
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:116253 original size:41 final size:41
Alignment explanation
Indices: 116205--116282 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
116195 AATTTGGAAA
116205 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAGCT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAGCT
*
116246 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTC
116283 GCAACGAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAGCT
Found at i:116305 original size:19 final size:19
Alignment explanation
Indices: 116281--116327 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
116271 AACGCGATTT
116281 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
116300 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
*
116319 TCACAACGA
1 TCGCAACGA
116328 CAACTGTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:116342 original size:94 final size:93
Alignment explanation
Indices: 116161--116376 Score: 328
Period size: 94 Copynumber: 2.3 Consensus size: 93
116151 GACCACGACC
116161 CGAACTGGAAAATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAACGCGAAATGGAAAA
1 CGAACTGGAAAATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAAC-CGAAATGGAAAA
* * * *
116226 TCGCAACGCGATTTTCAGCTATCGCAACG
65 TCACAACGCAACTGTCAGCTATCGCAACG
*
116255 CGAACTGGAAAATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAA-CGAATTTGGAAAA
1 CGAACTGGAAAATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAACCGAA-ATGGAAAA
116319 TCACAACGACAACTGT-AGACTATCGCAACG
65 TCACAACG-CAACTGTCAG-CTATCGCAACG
*
116349 CGAACTGAAAAATCGCAACGCGATTTTC
1 CGAACTGGAAAATCGCAACGCGATTTTC
116377 AACTATCGCA
Statistics
Matches: 113, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
92 4 0.04
93 16 0.14
94 93 0.82
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (93 bp):
CGAACTGGAAAATCGCAACGCGATTTTCGCAACGAATTTGGAAAATCGCAACCGAAATGGAAAAT
CACAACGCAACTGTCAGCTATCGCAACG
Found at i:116359 original size:41 final size:41
Alignment explanation
Indices: 116315--116393 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
116305 ACGAATTTGG
116315 AAAATCACAACGACAACTGT-AGACTATCGCAACGCGAACTGA
1 AAAATCACAACG-CAACTGTCA-ACTATCGCAACGCGAACTGA
* * * *
116357 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAA
1 AAAATCACAACGCAACTGTCAACTATCGCAACGCGAA
116394 ATGCAACGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 20 0.62
42 12 0.38
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (41 bp):
AAAATCACAACGCAACTGTCAACTATCGCAACGCGAACTGA
Found at i:116400 original size:21 final size:21
Alignment explanation
Indices: 116337--116400 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
116327 ACAACTGTAG
*
116337 ACTATCGCAACGCGAACTG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
116357 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
116378 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
116399 AC
1 AC
116401 GCGAATTTAT
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:117781 original size:32 final size:31
Alignment explanation
Indices: 117738--117810 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
117728 TATTTTGTCC
*
117738 ATATATATCATATTAGACATTTAATCAAACAT
1 ATATATATCATATTAAACATTTAATCAAAC-T
* * *
117770 ATATGTATCATATTAAATATTTTATCAAACT
1 ATATATATCATATTAAACATTTAATCAAACT
*
117801 ATAAATATCA
1 ATATATATCA
117811 AATAATTACT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 9 0.26
32 26 0.74
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.40
Consensus pattern (31 bp):
ATATATATCATATTAAACATTTAATCAAACT
Found at i:119565 original size:14 final size:14
Alignment explanation
Indices: 119546--119587 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
119536 TTTAGAAATA
119546 GTTTTTAGTGTTAG
1 GTTTTTAGTGTTAG
119560 GTTTTTAGTAGGTTA-
1 GTTTTTAGT--GTTAG
119575 -TTTTTAGTGTTAG
1 GTTTTTAGTGTTAG
119588 TCTGTTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 4 0.16
14 17 0.68
16 4 0.16
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (14 bp):
GTTTTTAGTGTTAG
Found at i:120224 original size:40 final size:40
Alignment explanation
Indices: 120152--120265 Score: 167
Period size: 40 Copynumber: 2.9 Consensus size: 40
120142 TCTTTGTCTT
*
120152 TGGGTGTTAGTGTGAGTTTTTGTTGTGGTTTGGGGCATATA
1 TGGGTGTTTGTGTGAG-TTTTGTTGTGGTTTGGGGCATATA
* *
120193 TGGGTGTTTGTGTGAGTTTTGTTGTGGTTTGGGGTATGTA
1 TGGGTGTTTGTGTGAGTTTTGTTGTGGTTTGGGGCATATA
* *
120233 TGGGTGTTTGTGTGTGTTTTGTTAT-GTTTGGGG
1 TGGGTGTTTGTGTGAGTTTTGTTGTGGTTTGGGG
120266 TATGTATTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
39 8 0.12
40 45 0.66
41 15 0.22
ACGTcount: A:0.08, C:0.01, G:0.41, T:0.50
Consensus pattern (40 bp):
TGGGTGTTTGTGTGAGTTTTGTTGTGGTTTGGGGCATATA
Found at i:128585 original size:23 final size:23
Alignment explanation
Indices: 128567--128627 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
128557 CTCGTATAAA
*
128567 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
128590 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
128613 TGCATCGTAGTGCCA
1 TGCACCGTAGTGCCA
128628 TATAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:128898 original size:29 final size:29
Alignment explanation
Indices: 128842--128898 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
128832 TTATCATACA
* *
128842 TTCACATATACACATAGTCTCATAGTTCT
1 TTCACATATACACATAGACACATAGTTCT
* *
128871 TTCACATATACATATAGACACATGGTTC
1 TTCACATATACACATAGACACATAGTTC
128899 ACTTACACGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (29 bp):
TTCACATATACACATAGACACATAGTTCT
Found at i:129581 original size:43 final size:42
Alignment explanation
Indices: 129457--129595 Score: 161
Period size: 43 Copynumber: 3.2 Consensus size: 42
129447 TTTTTAACAA
* * * * *
129457 AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTGTCAG
1 AAAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTC-T
* *
129500 AAAAACACCGCAATAGGTGTTGATGTTTTGCGACGTTTTTCT
1 AAAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
* * *
129542 CACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTTTGCT
1 -AAAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTT-CT
129586 AAAAACGCCG
1 AAAAACGCCG
129596 GTAAAGGTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 79 0.98
44 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
AAAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
Found at i:130020 original size:21 final size:21
Alignment explanation
Indices: 129996--130044 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
129986 GCTGATATGT
129996 TGCTTCTCTCTGTGCTGCCAC
1 TGCTTCTCTCTGTGCTGCCAC
* *
130017 TGCTTCTCTTTGTGCTGCCGC
1 TGCTTCTCTCTGTGCTGCCAC
130038 TGCTTCT
1 TGCTTCT
130045 TTCTCTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.02, C:0.35, G:0.20, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTGCCAC
Found at i:139726 original size:42 final size:42
Alignment explanation
Indices: 139680--139770 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 42
139670 TTTGTAATCC
*
139680 AAACGCCGTAATCGT-TATACTCTATCGCGGCGTTTTCA-TAAT
1 AAACGCCG-AATAGTGTATACTCTATCGCGGCGTTTTCACT-AT
* * * *
139722 AAACGCC-ACTAGTGTCTACTCTATTGCGGCGTTTTTACTAT
1 AAACGCCGAATAGTGTATACTCTATCGCGGCGTTTTCACTAT
139763 AAACGCCG
1 AAACGCCG
139771 CTATTGCTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
40 4 0.10
41 29 0.71
42 8 0.20
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (42 bp):
AAACGCCGAATAGTGTATACTCTATCGCGGCGTTTTCACTAT
Found at i:140706 original size:154 final size:154
Alignment explanation
Indices: 140395--140698 Score: 585
Period size: 154 Copynumber: 2.0 Consensus size: 154
140385 TACATCAGCT
140395 AAATTTACTGATATATGTAGCTTTATCTATTTAACAACAATCATACATTTTAATTAACCCACAAG
1 AAATTTACTGATATATGTAGCTTTATCTATTTAACAACAATCATACATTTTAATTAACCCACAAG
140460 TTATGCAGAATAAAACCTAACAACAAAATAAATTAAAATTGATAAACATTAAATTAAATGTATGG
66 TTATGCAGAATAAAACCTAACAAC-AAATAAATTAAAATTGATAAACATTAAATTAAATGTATGG
140525 TTGAACCTATTGCGACATTTGTAAA
130 TTGAACCTATTGCGACATTTGTAAA
140550 AAATTTACTGATATATGTAGC-TTATCTATTTAACAACAATCATACATTTTAATTAACCCACAAG
1 AAATTTACTGATATATGTAGCTTTATCTATTTAACAACAATCATACATTTTAATTAACCCACAAG
140614 TTATGCAGAATAAAACCTAACAAC-AATAAATTAAAATTGATAAACATTAAATTAAATGTATGGT
66 TTATGCAGAATAAAACCTAACAACAAATAAATTAAAATTGATAAACATTAAATTAAATGTATGGT
140678 TGAACCTATTGCGACATTTGT
131 TGAACCTATTGCGACATTTGT
140699 TGTAAAAAAA
Statistics
Matches: 149, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
152 61 0.41
154 67 0.45
155 21 0.14
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (154 bp):
AAATTTACTGATATATGTAGCTTTATCTATTTAACAACAATCATACATTTTAATTAACCCACAAG
TTATGCAGAATAAAACCTAACAACAAATAAATTAAAATTGATAAACATTAAATTAAATGTATGGT
TGAACCTATTGCGACATTTGTAAA
Found at i:143421 original size:20 final size:20
Alignment explanation
Indices: 143393--143442 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
143383 TGAAGGTATA
143393 TATCGATGCACTACACAATG
1 TATCGATGCACTACACAATG
*
143413 TATCAATGCACTACACAATG
1 TATCGATGCACTACACAATG
143433 TATCGATGCA
1 TATCGATGCA
143443 TCCCTTAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (20 bp):
TATCGATGCACTACACAATG
Found at i:146763 original size:2 final size:2
Alignment explanation
Indices: 146756--146795 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
146746 ATTACACATC
146756 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
146796 GTATTACATA
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:146943 original size:23 final size:23
Alignment explanation
Indices: 146917--146975 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
146907 CGTATAAATA
146917 CACCGAAGTGCCACGTAAAATTG
1 CACCGAAGTGCCACGTAAAATTG
* *
146940 CACC-ATAGTGCCGCGTAGAATTG
1 CACCGA-AGTGCCACGTAAAATTG
*
146963 CACCGTAGTGCCA
1 CACCGAAGTGCCA
146976 TATAAGATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAAAATTG
Found at i:149759 original size:24 final size:24
Alignment explanation
Indices: 149723--149771 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
149713 GCTACTTTTG
149723 GGTGCCCCCTTTTTTAATTCATTC
1 GGTGCCCCCTTTTTTAATTCATTC
*
149747 GGTGCCCCTTTTTTTAATTCATTC
1 GGTGCCCCCTTTTTTAATTCATTC
149771 G
1 G
149772 ATGCATTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.27, G:0.14, T:0.47
Consensus pattern (24 bp):
GGTGCCCCCTTTTTTAATTCATTC
Found at i:152178 original size:21 final size:21
Alignment explanation
Indices: 152138--152179 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
152128 TTCACTTGTG
**
152138 TATTCTTTCTAACATTGCTCT
1 TATTCTTTCTAACAAGGCTCT
152159 TATTCTTTCTAACAAGGCTCT
1 TATTCTTTCTAACAAGGCTCT
152180 AGAATCAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.48
Consensus pattern (21 bp):
TATTCTTTCTAACAAGGCTCT
Found at i:152479 original size:80 final size:80
Alignment explanation
Indices: 152346--152506 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
152336 GTCAAAATGA
*
152346 ACCAATTCTAGAACACTTTTGCCTCTAGAATTTGACGTGTTGAATTTCAACCAGTGCTACTTACT
1 ACCAATTCTAGAACACTTTTGCCTCTAGAATTTGACGTGTTAAATTTCAACCAGTGCTACTTACT
152411 TGTTATACAATGCTC
66 TGTTATACAATGCTC
152426 ACCAATTCTAGAACACTTTTGCCTCTAGAATTTGACGTGTTAAATTTCAACCAGTGCTACTTACT
1 ACCAATTCTAGAACACTTTTGCCTCTAGAATTTGACGTGTTAAATTTCAACCAGTGCTACTTACT
152491 TGTTATACAATGCTC
66 TGTTATACAATGCTC
152506 A
1 A
152507 TATAAGTAAG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (80 bp):
ACCAATTCTAGAACACTTTTGCCTCTAGAATTTGACGTGTTAAATTTCAACCAGTGCTACTTACT
TGTTATACAATGCTC
Found at i:154843 original size:16 final size:16
Alignment explanation
Indices: 154824--154858 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
154814 TTATCAATAG
154824 AAAATATAAAAAAATT
1 AAAATATAAAAAAATT
* *
154840 AAAATATATAATAATT
1 AAAATATAAAAAAATT
154856 AAA
1 AAA
154859 TTTTTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAAAAAAATT
Found at i:156375 original size:190 final size:191
Alignment explanation
Indices: 156052--156429 Score: 722
Period size: 190 Copynumber: 2.0 Consensus size: 191
156042 CCAAAAATTC
156052 AATAAGCACAAGTCTAAAATATTATATTTAAACATATAAAAAATGTATATAAATAAATTTGAGAT
1 AATAAGCACAAGTCTAAAATATTATATTTAAACATATAAAAAATGTATATAAATAAATTTGAGAT
156117 TTGAGAATATAATAAAAAAAATTTGTTGATATTGAGATGTCAAAAATAAATTTTAAACTTAATAG
66 TTGAGAATATAATAAAAAAAATTTGTTGATATTGAGATGTCAAAAATAAATTTTAAACTTAATAG
156182 GTTTATATATATACACAAAAATTAAAAATAA-TTTAAATACTAAAATCTACATATTTTTAA
131 GTTTATATATATACACAAAAATTAAAAATAATTTTAAATACTAAAATCTACATATTTTTAA
* *
156242 AATAAGCGCATGTCTAAAATATTATATTTAAACATATAAAAAATGTATATAAATAAATTTGAGAT
1 AATAAGCACAAGTCTAAAATATTATATTTAAACATATAAAAAATGTATATAAATAAATTTGAGAT
*
156307 TTGAGAATATAATAATAAAAATTTGTTGATATTGAGATGTCAAAAATAAATTTTAAACTTAATAG
66 TTGAGAATATAATAAAAAAAATTTGTTGATATTGAGATGTCAAAAATAAATTTTAAACTTAATAG
156372 GTTTATATATATACACAAAAATTAAAAATAATTTTAAATACTAAAATCTACATATTTT
131 GTTTATATATATACACAAAAATTAAAAATAATTTTAAATACTAAAATCTACATATTTT
156430 AGAGGTAAGT
Statistics
Matches: 184, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
190 158 0.86
191 26 0.14
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.36
Consensus pattern (191 bp):
AATAAGCACAAGTCTAAAATATTATATTTAAACATATAAAAAATGTATATAAATAAATTTGAGAT
TTGAGAATATAATAAAAAAAATTTGTTGATATTGAGATGTCAAAAATAAATTTTAAACTTAATAG
GTTTATATATATACACAAAAATTAAAAATAATTTTAAATACTAAAATCTACATATTTTTAA
Found at i:156909 original size:109 final size:109
Alignment explanation
Indices: 156718--156936 Score: 438
Period size: 109 Copynumber: 2.0 Consensus size: 109
156708 CAAAATTTTG
156718 AAGCAAATTACAGTTTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGA
1 AAGCAAATTACAGTTTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGA
156783 CCGTCCGATCCTTTTGAAGGATCATTGGACGATTGTATCAATCC
66 CCGTCCGATCCTTTTGAAGGATCATTGGACGATTGTATCAATCC
156827 AAGCAAATTACAGTTTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGA
1 AAGCAAATTACAGTTTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGA
156892 CCGTCCGATCCTTTTGAAGGATCATTGGACGATTGTATCAATCC
66 CCGTCCGATCCTTTTGAAGGATCATTGGACGATTGTATCAATCC
156936 A
1 A
156937 TCATCAGTTT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (109 bp):
AAGCAAATTACAGTTTGTGAACTTTAGGCTAAGGTGGGGTTCTCGTTCCAGTGGGCGGAGTATGA
CCGTCCGATCCTTTTGAAGGATCATTGGACGATTGTATCAATCC
Found at i:164838 original size:30 final size:28
Alignment explanation
Indices: 164775--164862 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 28
164765 CAACCACCAT
* ****
164775 AGGTCGCCATGCACTCCCAGCGACCTCTT
1 AGGTCGCCATGCAC-CCCGGCGACCAAGG
164804 AGGTCGCCATGCATGCCCCGGCGACCAAGG
1 AGGTCGCCATGCA--CCCCGGCGACCAAGG
* *
164834 AGGTCGCCATGCACTCGGGCGACCAAGG
1 AGGTCGCCATGCACCCCGGCGACCAAGG
164862 A
1 A
164863 TTCATGCATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
28 14 0.28
29 13 0.26
30 22 0.44
31 1 0.02
ACGTcount: A:0.20, C:0.36, G:0.30, T:0.14
Consensus pattern (28 bp):
AGGTCGCCATGCACCCCGGCGACCAAGG
Found at i:165132 original size:28 final size:28
Alignment explanation
Indices: 165073--165156 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
165063 AGCAGGGGAT
* **
165073 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCG-GAGTGCATGGCGACCTACGAG
* *
165102 GTCGCCGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGAGTGCATGGCGACCTACGAG
*
165130 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGC-CGGAGTGCATGGCGACCTACG
165157 GCCACTGTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 21 0.46
29 25 0.54
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (28 bp):
GTCGCCGGAGTGCATGGCGACCTACGAG
Found at i:165482 original size:22 final size:23
Alignment explanation
Indices: 165440--165482 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
165430 AAAATTGGAG
*
165440 TTTTTTAAATAAATATTTTTACT
1 TTTTTTAAATAAATAATTTTACT
165463 TTTTTTAAATAAA-AATTTTA
1 TTTTTTAAATAAATAATTTTA
165483 AATTATCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTTAAATAAATAATTTTACT
Found at i:165736 original size:20 final size:20
Alignment explanation
Indices: 165711--165752 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
165701 TAAGATAAAC
165711 AATATCAAACATAATCTT-AA
1 AATATCAAACAT-ATCTTGAA
165731 AATATCAAACATATCTTGAA
1 AATATCAAACATATCTTGAA
165751 AA
1 AA
165753 GGTCCAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (20 bp):
AATATCAAACATATCTTGAA
Found at i:167228 original size:30 final size:31
Alignment explanation
Indices: 167181--167240 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
167171 AAAAAAAATA
167181 AGAATGAGTGAAAGCTTAGAAAAGC-TAGAG
1 AGAATGAGTGAAAGCTTAGAAAAGCATAGAG
* *
167211 AGAATCGAG-GAATGCTTAGCAAAGCATAGA
1 AGAAT-GAGTGAAAGCTTAGAAAAGCATAGA
167241 ATAGTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.17
Consensus pattern (31 bp):
AGAATGAGTGAAAGCTTAGAAAAGCATAGAG
Done.