Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003477.1 Hibiscus syriacus cultivar Beakdansim tig00007350_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: 95861
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6309 original size:16 final size:17
Alignment explanation
Indices: 6278--6310 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6268 AAGTAAAAAT
*
6278 CTAAATTATAATCTAAA
1 CTAAATTATAAACTAAA
6295 CTAAA-TATAAACTAAA
1 CTAAATTATAAACTAAA
6311 GATGTTTTCT
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:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (17 bp):
CTAAATTATAAACTAAA
Found at i:7093 original size:27 final size:28
Alignment explanation
Indices: 7062--7117 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
7052 AAACCCCAGC
7062 TATAGCTAT-AAACCCTAGCCCTAGGGT
1 TATAGCTATAAAACCCTAGCCCTAGGGT
7089 TATAGCTATAAAACCCTAGCCCTAGGGT
1 TATAGCTATAAAACCCTAGCCCTAGGGT
7117 T
1 T
7118 CTTTCTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (28 bp):
TATAGCTATAAAACCCTAGCCCTAGGGT
Found at i:15733 original size:42 final size:42
Alignment explanation
Indices: 15686--15768 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
15676 ACTTCATCCG
15686 TTCTCTCCATCTATCCGAGTACAACAATAACAATAAACAAAA
1 TTCTCTCCATCTATCCGAGTACAACAATAACAATAAACAAAA
* *
15728 TTCTCTCGATCTATCCGAGTTCAACAATAACAATAAACAAA
1 TTCTCTCCATCTATCCGAGTACAACAATAACAATAAACAAA
15769 CTAGAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.25
Consensus pattern (42 bp):
TTCTCTCCATCTATCCGAGTACAACAATAACAATAAACAAAA
Found at i:16671 original size:31 final size:31
Alignment explanation
Indices: 16636--16703 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
16626 GATTAAATTT
* * *
16636 TAATTTGACATCTAAATTTTAGATAATATAC
1 TAATTTAACATCTAAATGTTAGATAAGATAC
*
16667 TAATTTAACCTCTAAATGTTAGATAAGATAC
1 TAATTTAACATCTAAATGTTAGATAAGATAC
16698 TAATTT
1 TAATTT
16704 TACCATTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
TAATTTAACATCTAAATGTTAGATAAGATAC
Found at i:22491 original size:19 final size:19
Alignment explanation
Indices: 22469--22505 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22459 TAATTTACGT
*
22469 TTATAGTTGTAAATATTTA
1 TTATAATTGTAAATATTTA
*
22488 TTATAATTTTAAATATTT
1 TTATAATTGTAAATATTT
22506 TATCTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTATAATTGTAAATATTTA
Found at i:23141 original size:23 final size:23
Alignment explanation
Indices: 23115--23159 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
23105 GTTATTCGTG
*
23115 TTCATTCGTTTGTTTGGTTAAAA
1 TTCATTCGTTTATTTGGTTAAAA
23138 TTCATTCGTTTATTTGGTTAAA
1 TTCATTCGTTTATTTGGTTAAA
23160 GTTAAACGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (23 bp):
TTCATTCGTTTATTTGGTTAAAA
Found at i:31139 original size:35 final size:34
Alignment explanation
Indices: 31075--31214 Score: 156
Period size: 36 Copynumber: 4.0 Consensus size: 34
31065 GAACAAGAAT
* * *
31075 AACGGAAGGAAACGTCGCACTTCCAATTCAAGTG
1 AACGGAAGGAAGCATCGCACTTCCGATTCAAGTG
*
31109 AACGGAAGGAAGCATCGGCACTTCCGATTCAAACTG
1 AACGGAAGGAAGCATC-GCACTTCCGATTC-AAGTG
* *
31145 AACGGAAGGAAGCATCGACACTTTCGATTTAAGTCG
1 AACGGAAGGAAGCATCG-CACTTCCGATTCAAGT-G
* *
31181 AACGGAAGG-AGACGTCGCACTTTCGATTCAAGTG
1 AACGGAAGGAAG-CATCGCACTTCCGATTCAAGTG
31215 TTCATTTTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
34 15 0.16
35 33 0.36
36 44 0.48
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (34 bp):
AACGGAAGGAAGCATCGCACTTCCGATTCAAGTG
Found at i:31609 original size:29 final size:29
Alignment explanation
Indices: 31566--31648 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
31556 CTCACCTAAC
31566 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
31596 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
31625 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
31649 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:34283 original size:176 final size:176
Alignment explanation
Indices: 33989--34340 Score: 654
Period size: 176 Copynumber: 2.0 Consensus size: 176
33979 CCTCGATCGG
*
33989 ATCTCATGGCTTTGATCTTTCTACCGCTTTCTCTTCCACTGCTGCTTTGAACTTCTTGAAGACTT
1 ATCTCATGGCTTTGATCTTTCTACCGCTTTCTCTTCCACTACTGCTTTGAACTTCTTGAAGACTT
34054 CAAAAACTTCTGACTTCTGTTTCAAGAAATATACCCAGGTTTTTCTTGAAAAATCATCAATGAAA
66 CAAAAACTTCTGACTTCTGTTTCAAGAAATATACCCAGGTTTTTCTTGAAAAATCATCAAT-AAA
34119 GAAGAAAATAGTTAATATTACCGAGAGAGCTCGACTTGATC-GTCCA
130 GAAGAAAATAGTTAATATTACCGAGAGAGCTCGACTTGATCGGTCCA
34165 ATCTCATGGCTTTGATCTTTCTACCGCTTTCTCTTTCCACTACTGCTTTGAACTTCTTGAAGACT
1 ATCTCATGGCTTTGATCTTTCTACCGCTTTCTC-TTCCACTACTGCTTTGAACTTCTTGAAGACT
34230 TC-AAAACTTCTGACTTCTGTTTCAAGAAATATACCCAGGTTTTTCTTGAAAAATCATCAATAAA
65 TCAAAAACTTCTGACTTCTGTTTCAAGAAATATACCCAGGTTTTTCTTGAAAAATCATCAATAAA
*
34294 GAAGAAAATAGTTACTATTACCGAGAGAGCTCGACTTGATCGGTCCA
130 GAAGAAAATAGTTAATATTACCGAGAGAGCTCGACTTGATCGGTCCA
34341 CACACATCGG
Statistics
Matches: 172, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
175 43 0.25
176 97 0.56
177 32 0.19
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (176 bp):
ATCTCATGGCTTTGATCTTTCTACCGCTTTCTCTTCCACTACTGCTTTGAACTTCTTGAAGACTT
CAAAAACTTCTGACTTCTGTTTCAAGAAATATACCCAGGTTTTTCTTGAAAAATCATCAATAAAG
AAGAAAATAGTTAATATTACCGAGAGAGCTCGACTTGATCGGTCCA
Found at i:35175 original size:34 final size:35
Alignment explanation
Indices: 35137--35202 Score: 125
Period size: 34 Copynumber: 1.9 Consensus size: 35
35127 TTGATTCTTC
35137 ACGGCCTCGTGTTAAGCTTTCTCC-TTCTCATTCT
1 ACGGCCTCGTGTTAAGCTTTCTCCTTTCTCATTCT
35171 ACGGCCTCGTGTTAAGCTTTCTCCTTTCTCAT
1 ACGGCCTCGTGTTAAGCTTTCTCCTTTCTCAT
35203 AGTTGTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 24 0.77
35 7 0.23
ACGTcount: A:0.12, C:0.32, G:0.15, T:0.41
Consensus pattern (35 bp):
ACGGCCTCGTGTTAAGCTTTCTCCTTTCTCATTCT
Found at i:36559 original size:29 final size:29
Alignment explanation
Indices: 36516--36598 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
36506 CTCACCTAAC
36516 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
36546 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
36575 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
36599 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:37559 original size:15 final size:16
Alignment explanation
Indices: 37527--37558 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
37517 ATTAAAGGAC
37527 TTAAATAAATCAAATT
1 TTAAATAAATCAAATT
37543 TTAAA-AAAT-AAATT
1 TTAAATAAATCAAATT
37557 TT
1 TT
37559 TGATAGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATAAATCAAATT
Found at i:45433 original size:18 final size:19
Alignment explanation
Indices: 45403--45445 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
45393 TATTCTCTTA
*
45403 TTTT-TTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
45421 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
45439 TTTTATT
1 TTTTATT
45446 ACTATCTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:49464 original size:20 final size:20
Alignment explanation
Indices: 49439--49485 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
49429 GTTGAATGTG
* *
49439 GAAAAAAACAGCAATTCGAAC
1 GAAAAAAAGA-CAATTCGAAA
*
49460 GAAAAAAAGACTATTCGAAA
1 GAAAAAAAGACAATTCGAAA
49480 GAAAAA
1 GAAAAA
49486 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.11
Consensus pattern (20 bp):
GAAAAAAAGACAATTCGAAA
Found at i:54234 original size:15 final size:15
Alignment explanation
Indices: 54214--54243 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54204 TATTCAAGTA
54214 ACACAAGACTATGAT
1 ACACAAGACTATGAT
54229 ACACAAGACTATGAT
1 ACACAAGACTATGAT
54244 GATACAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
ACACAAGACTATGAT
Found at i:65205 original size:19 final size:19
Alignment explanation
Indices: 65183--65220 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
65173 TGTTATTAAA
65183 AGTTAAATATTGAT-TATTT
1 AGTTAAAT-TTGATGTATTT
*
65202 AGTTAAGTTTGATGTATTT
1 AGTTAAATTTGATGTATTT
65221 GATGAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (19 bp):
AGTTAAATTTGATGTATTT
Found at i:68740 original size:3 final size:3
Alignment explanation
Indices: 68732--68796 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
68722 GCAAAAATTG
*
68732 TAA TAA TAA -AA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
68777 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
68797 CGGAAAAAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 8 0.14
3 48 0.86
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:68748 original size:11 final size:11
Alignment explanation
Indices: 68732--68796 Score: 87
Period size: 11 Copynumber: 5.8 Consensus size: 11
68722 GCAAAAATTG
68732 TAATAATAAAA
1 TAATAATAAAA
68743 TAATAATAAAA
1 TAATAATAAAA
*
68754 TAATAATATAA
1 TAATAATAAAA
*
68765 TGATAATAATAA
1 TAATAATAA-AA
68777 TAATAATAATAA
1 TAATAATAA-AA
68789 TAA-AATAA
1 TAATAATAA
68797 CGGAAAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
11 33 0.67
12 16 0.33
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:69155 original size:87 final size:87
Alignment explanation
Indices: 68996--69375 Score: 517
Period size: 87 Copynumber: 4.3 Consensus size: 87
68986 CGTCTAAGGG
* * * * * * * * *
68996 TGACATGGCTCCTACGTGATGAGGAAATCTGGTCATTTTTAGGGATGATAACTCGGTTCCTACGT
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCA-TCTAAAGG-TGATAACACGGTTCCTACGT
* *
69061 AATGAGGACGACTGGTTATCAGGT
64 GATGAGGACGGCTGGTTATCAGGT
69085 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
69150 TGAGGACGGCTGGTTATCAGGT
66 TGAGGACGGCTGGTTATCAGGT
69172 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
69237 TGAGGACGGCTGGTTATCAGGT
66 TGAGGACGGCTGGTTATCAGGT
* * *
69259 TAACGCGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCT--A--AA-GGTGATAACACGGTTCCTA
* *
69324 CGTGATAAGGACGGCTGGTTATCCTAATGT
61 CGTGATGAGGACGGCTGGTTAT-C--AGGT
*
69354 TGACACGGCTCCTACGTGATGA
1 TGACACGGCTCTTACGTGATGA
69376 GGAAGTCTGG
Statistics
Matches: 264, Mismatches: 19, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
87 164 0.62
88 5 0.02
89 31 0.12
91 2 0.01
92 39 0.15
93 1 0.00
95 22 0.08
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (87 bp):
TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
TGAGGACGGCTGGTTATCAGGT
Found at i:69190 original size:41 final size:41
Alignment explanation
Indices: 69056--69280 Score: 175
Period size: 41 Copynumber: 5.2 Consensus size: 41
69046 ACTCGGTTCC
* * *
69056 TACGTAATGAGGACGACTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTAACACGGCTCT
* * ** * *
69097 TACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATC---AGGT--TAACACGGCTCT
*
69143 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTAACACGGCTCT
* * ** * *
69184 TACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATC---AGGT--TAACACGGCTCT
*
69230 TACGTGATGAGGACGGCTGGTTATCAGGTTAACGCGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTAACACGGCTCT
69271 TACGTGATGA
1 TACGTGATGA
69281 AGAGATCTGG
Statistics
Matches: 141, Mismatches: 29, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
40 2 0.01
41 65 0.46
43 8 0.06
44 8 0.06
46 56 0.40
47 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (41 bp):
TACGTGATGAGGACGGCTGGTTATCAGGTTAACACGGCTCT
Found at i:83756 original size:3 final size:3
Alignment explanation
Indices: 83748--83804 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
83738 GCAAAAATTG
83748 TAA TAA TAA -AA TAA TAA TAAA TAA TAA T-A TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
83791 TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA
83805 CGGAAAAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.16
3 38 0.78
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:83764 original size:11 final size:11
Alignment explanation
Indices: 83748--83804 Score: 82
Period size: 11 Copynumber: 5.3 Consensus size: 11
83738 GCAAAAATTG
83748 TAATAATAAAA
1 TAATAATAAAA
83759 TAATAAT-AAA
1 TAATAATAAAA
*
83769 TAATAATATAA
1 TAATAATAAAA
83780 T-ATAATAATAA
1 TAATAATAA-AA
83791 TAATAATAAAA
1 TAATAATAAAA
83802 TAA
1 TAA
83805 CGGAAAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 16 0.39
11 18 0.44
12 7 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:83786 original size:26 final size:25
Alignment explanation
Indices: 83749--83804 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
83739 CAAAAATTGT
83749 AATAATAAAATAATAATAAATAATAA
1 AATAATAAAATAATAAT-AATAATAA
* *
83775 TATAATATAATAATAATAATAATAA
1 AATAATAAAATAATAATAATAATAA
83800 AATAA
1 AATAA
83805 CGGAAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
AATAATAAAATAATAATAATAATAA
Found at i:86898 original size:21 final size:21
Alignment explanation
Indices: 86854--86898 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
86844 ACAATACCTA
* *
86854 ATTAAATTTAATGCATGCTTG
1 ATTAAATTTAATGCATACTCG
*
86875 ATTATATTTAATGCATACTCG
1 ATTAAATTTAATGCATACTCG
86896 ATT
1 ATT
86899 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (21 bp):
ATTAAATTTAATGCATACTCG
Found at i:93265 original size:2 final size:2
Alignment explanation
Indices: 93258--93285 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
93248 ATCTGACCTA
93258 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
93286 TTGAGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94519 original size:20 final size:20
Alignment explanation
Indices: 94494--94536 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
94484 TAATTGATTC
94494 AATCAGACCACCGCACCGTT
1 AATCAGACCACCGCACCGTT
94514 AATCAGACCACCGCACCGTT
1 AATCAGACCACCGCACCGTT
94534 AAT
1 AAT
94537 TTTAATAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.14, T:0.16
Consensus pattern (20 bp):
AATCAGACCACCGCACCGTT
Found at i:95199 original size:93 final size:92
Alignment explanation
Indices: 95041--95224 Score: 284
Period size: 93 Copynumber: 2.0 Consensus size: 92
95031 AATAATTTTA
*
95041 AAATAAATTTCGGTTCGATTAATGTTAAAGAAAAAATTGGTTAATTGATTCGGTTAATAATTTTC
1 AAATAAATTTCAGTTCGATTAATGTTAAAGAAAAAATTGGTTAATTGATTCGGTTAATAATTTTC
95106 AAATAAATTTCAATTCGATTAACGGTC
66 AAATAAATTTCAATTCGATTAACGGTC
95133 AAAT-AATTTCAGTTCGA-TAATGGTTTAAAGAAAAAAATTGGTTAATTTGATTCGGTT-ATAAT
1 AAATAAATTTCAGTTCGATTAAT-G-TTAAAG-AAAAAATTGGTTAA-TTGATTCGGTTAATAAT
**
95195 TTTCAAATAAATTTCGGTTCGATTAACGGT
62 TTTCAAATAAATTTCAATTCGATTAACGGT
95225 TAAGGTAAAA
Statistics
Matches: 85, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
90 4 0.05
91 13 0.15
92 10 0.12
93 47 0.55
94 11 0.13
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (92 bp):
AAATAAATTTCAGTTCGATTAATGTTAAAGAAAAAATTGGTTAATTGATTCGGTTAATAATTTTC
AAATAAATTTCAATTCGATTAACGGTC
Found at i:95217 original size:67 final size:71
Alignment explanation
Indices: 95131--95298 Score: 177
Period size: 74 Copynumber: 2.4 Consensus size: 71
95121 CGATTAACGG
* * *
95131 TCAAAT-AATTTCAGTTCGATAATGGTTTAAAG-AAAAA-AATT-GGTTAAT-TTGATTCGGTT-
1 TCAAATAAATTTCGGTTCGATAACGG-TTAAAGTAAAAATAATTAGGTTAATATTAATTCGGTTA
95190 ATAATTT
65 ATAATTT
* ** *
95197 TCAAATAAATTTCGGTTCGATTAACGGTTAAGGTAAAAATAATTATTTTATTCGATTAATTCGGT
1 TCAAATAAATTTCGGTTCGA-TAACGGTTAAAGTAAAAATAATTAGGTTAAT--ATTAATTCGGT
95262 TAATAATTT
63 TAATAATTT
*
95271 TCAAATAAATTTCGATTCGATTAACGGT
1 TCAAATAAATTTCGGTTCGA-TAACGGT
95299 CAAAATTTCA
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
66 6 0.07
67 17 0.20
68 10 0.12
69 4 0.05
70 4 0.05
73 10 0.12
74 34 0.40
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (71 bp):
TCAAATAAATTTCGGTTCGATAACGGTTAAAGTAAAAATAATTAGGTTAATATTAATTCGGTTAA
TAATTT
Found at i:95486 original size:161 final size:167
Alignment explanation
Indices: 95088--95497 Score: 610
Period size: 161 Copynumber: 2.5 Consensus size: 167
95078 TGGTTAATTG
*
95088 ATTCGGTTAATAATTTTCAAATAAATTTCAATTCGATTAACGGTCAAATAATTTCAGTTCGA-TA
1 ATTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCAGTTCGATTA
*
95152 ATGGTTTAAAGAAAAAAATTGGTTAATTTGATTCGGTTATAATTTTCAAATAAATTTCGGTTCGA
66 ATGG-TTAAAGAAAAAAATTGGTTAATTTGAGTCGGTTATAATTTTCAAATAAATTTCGGTTCGA
* *
95217 TTAACGGTTAAGGTAAAAATAATTATTTTATTCGATTA
130 TTAACGGATAAGATAAAAATAATTATTTTATTCGATTA
95255 ATTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTC-AA-AATTTCAGTTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCAGTTCGATTA
* *
95318 ATGGTTAAAGAAAAAACTTGGTTGATTTG-GTCGGTTAATAA-TTTCAAATAAATTTCGGTTCGA
66 ATGGTTAAAGAAAAAAATTGGTTAATTTGAGTCGGTT-ATAATTTTCAAATAAATTTCGGTTCGA
95381 TTAA-GGATAA-ATAAAAATAATTTATTTTATTC-AGTTA
130 TTAACGGATAAGATAAAAATAA-TTATTTTATTCGA-TTA
* * **
95418 ATTCGGTT-A-AATTTTCAAATAAA-TTGGGTT-GATTAACGGTCAAATAATTTTGGTTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCAGTTCGATTA
95479 ATGGTTAAAGAAAAAAATT
66 ATGGTTAAAGAAAAAAATT
95498 CGTTTAATAA
Statistics
Matches: 226, Mismatches: 11, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
159 11 0.05
160 7 0.03
161 46 0.20
162 11 0.05
163 27 0.12
164 32 0.14
165 40 0.18
166 8 0.04
167 44 0.19
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (167 bp):
ATTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCAGTTCGATTA
ATGGTTAAAGAAAAAAATTGGTTAATTTGAGTCGGTTATAATTTTCAAATAAATTTCGGTTCGAT
TAACGGATAAGATAAAAATAATTATTTTATTCGATTA
Found at i:95623 original size:146 final size:150
Alignment explanation
Indices: 95427--95804 Score: 420
Period size: 155 Copynumber: 2.5 Consensus size: 150
95417 AATTCGGTTA
*
95427 AATTTTCAAATAAATTGGGTT-GATTAACGGTCAAATAATTTTGGTTCGATTAATGGTTAAAGAA
1 AATTTTCAAATAAATTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATGGTTAAAGAA
*
95491 AAAAATTCGTTTAATAATTTTCAAAT-AATTTCGGTTTAATTAAT-G-TTA-AAGAAA-A-AA-A
66 AAAAATTCGGTTAATAA-TTTCAAATAAATTT-GG-TTAATT--TGGTTTATAAGAAATATAACA
95549 TT-C-ATTAATTTGGTTCACTTAAT
126 TTACGATTAATTTGGTTCACTTAAT
* * *
95572 AATTTTCAAATAAATTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAACGGTTAAATAT
1 AATTTTCAAATAAATTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATGGTTAAAGAA
***** **
95637 TTCGGTTCGGTTAATAATTTCAAATAAATTTGGTTAATTTGGTTTATTTGAAATTATTAATCGAT
66 AAAAATTCGGTTAATAATTTCAAATAAATTTGGTTAATTTGGTTTATAAGAAA-TA-TAA-C-AT
* **
95702 TAACGGTTAATTTGGTTCGGTTAAT
127 T-ACGATTAATTTGGTTCACTTAAT
* * *
95727 AATTTTCAAATAATTTCGGTTCGATTAAAGGTCAAATAATTTCGGTTCGATTAAT-GTT-AAGAA
1 AATTTTCAAATAAATTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATGGTTAAAGAA
95790 AAAAATTCGGTTAAT
66 AAAAATTCGGTTAAT
95805 TTGGTTTGAT
Statistics
Matches: 192, Mismatches: 26, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
142 1 0.01
143 1 0.01
144 9 0.05
145 34 0.18
146 56 0.29
147 1 0.01
149 2 0.01
152 3 0.02
153 13 0.07
154 4 0.02
155 68 0.35
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (150 bp):
AATTTTCAAATAAATTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATGGTTAAAGAA
AAAAATTCGGTTAATAATTTCAAATAAATTTGGTTAATTTGGTTTATAAGAAATATAACATTACG
ATTAATTTGGTTCACTTAAT
Found at i:95644 original size:25 final size:26
Alignment explanation
Indices: 95577--95650 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 26
95567 TTAATAATTT
*
95577 TCAAATAAATTCGGTTCGATTAACGG
1 TCAAATAATTTCGGTTCGATTAACGG
*
95603 TCAAATAATTTTGGTTCGATTAACGG
1 TCAAATAATTTCGGTTCGATTAACGG
* *
95629 TTAAAT-ATTTCGGTTCGGTTAA
1 TCAAATAATTTCGGTTCGATTAA
95651 TAATTTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 14 0.33
26 29 0.67
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (26 bp):
TCAAATAATTTCGGTTCGATTAACGG
Found at i:95747 original size:38 final size:39
Alignment explanation
Indices: 95635--95747 Score: 94
Period size: 38 Copynumber: 3.0 Consensus size: 39
95625 ACGGTTAAAT
95635 ATTTCGGTTCGGTTAATAA-TTTCAAATAAATTT-GGTTA
1 ATTT-GGTTCGGTTAATAATTTTCAAATAAATTTCGGTTA
*** * ** *
95673 ATTTGGTTTATTTGA-AATTATT--AATCGATTAACGGTTA
1 ATTTGGTTCGGTTAATAATT-TTCAAATAAATT-TCGGTTA
95711 ATTTGGTTCGGTTAATAATTTTCAAAT-AATTTCGGTT
1 ATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTT
95748 CGATTAAAGG
Statistics
Matches: 55, Mismatches: 13, Indels: 14
0.67 0.16 0.17
Matches are distributed among these distances:
36 8 0.15
37 8 0.15
38 29 0.53
39 7 0.13
40 3 0.05
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (39 bp):
ATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTA
Done.