Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001959.1 Hibiscus syriacus cultivar Beakdansim tig00003963_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: 54594
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:1547 original size:18 final size:17
Alignment explanation
Indices: 1524--1560 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1514 ATATAGAGAT
1524 AAAGAGGAGAGAGAAAAA
1 AAAGAGGA-AGAGAAAAA
*
1542 AAAGAGGAAGATAAAAA
1 AAAGAGGAAGAGAAAAA
1559 AA
1 AA
1561 GAAAAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (17 bp):
AAAGAGGAAGAGAAAAA
Found at i:1559 original size:15 final size:15
Alignment explanation
Indices: 1538--1620 Score: 57
Period size: 16 Copynumber: 5.5 Consensus size: 15
1528 AGGAGAGAGA
*
1538 AAAAAAAGAGGAAGAT
1 AAAAAAAGA-AAAGAT
1554 AAAAAAAGAAAAGAT
1 AAAAAAAGAAAAGAT
1569 AAAAGATAA-AAAA-A-
1 AAAA-A-AAGAAAAGAT
*
1583 AGAAAAAAGAAAA-AG
1 A-AAAAAAGAAAAGAT
* *
1598 AAGAAAAGAAAAAAT
1 AAAAAAAGAAAAGAT
1613 ACAAAAAA
1 A-AAAAAA
1621 AAATAAATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
13 2 0.04
14 17 0.30
15 16 0.29
16 19 0.34
17 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAAAAGAAAAGAT
Found at i:1559 original size:16 final size:16
Alignment explanation
Indices: 1524--1572 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
1514 ATATAGAGAT
*
1524 AAAGAGGAGAGAGAAAAA
1 AAAGAGGA-AGA-TAAAA
1542 AAAGAGGAAGATAAAA
1 AAAGAGGAAGATAAAA
*
1558 AAAGA-AAAGATAAAA
1 AAAGAGGAAGATAAAA
1573 GATAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 9 0.31
16 9 0.31
17 3 0.10
18 8 0.28
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.04
Consensus pattern (16 bp):
AAAGAGGAAGATAAAA
Found at i:1610 original size:30 final size:30
Alignment explanation
Indices: 1555--1620 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
1545 GAGGAAGATA
* *
1555 AAAAAAGAAAAGATAAAAGATAAAAAAAAG
1 AAAAAAGAAAAGATAAAAGAGAAAAAAAAC
*
1585 AAAAAAGAAAAAGA-AGAAA-AGAAAAAATAC
1 AAAAAAG-AAAAGATA-AAAGAGAAAAAAAAC
1615 AAAAAA
1 AAAAAA
1621 AAATAAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.05
Consensus pattern (30 bp):
AAAAAAGAAAAGATAAAAGAGAAAAAAAAC
Found at i:1611 original size:7 final size:7
Alignment explanation
Indices: 1555--1611 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
1545 GAGGAAGATA
1555 AAAAAAG
1 AAAAAAG
* *
1562 AAAAGAT
1 AAAAAAG
*
1569 AAAAGATAA
1 AAAA-A-AG
1578 AAAAAAG
1 AAAAAAG
1585 AAAAAAG
1 AAAAAAG
1592 -AAAAAG
1 AAAAAAG
1598 AAGAAAAG
1 AA-AAAAG
1606 AAAAAA
1 AAAAAA
1612 TACAAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
6 6 0.15
7 22 0.54
8 8 0.20
9 5 0.12
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:9724 original size:13 final size:13
Alignment explanation
Indices: 9708--9738 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9698 AATAACATTA
*
9708 CTAAATTTTAATT
1 CTAAATTTTAAAT
9721 CTAAATTTTAAAT
1 CTAAATTTTAAAT
9734 CTAAA
1 CTAAA
9739 CCATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (13 bp):
CTAAATTTTAAAT
Found at i:15727 original size:15 final size:15
Alignment explanation
Indices: 15709--15762 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
15699 GATAATGATG
15709 CTTGTGATGTTACAA
1 CTTGTGATGTTACAA
***
15724 CTTGTGATG-TAGGTT
1 CTTGTGATGTTA-CAA
*
15739 CTTGTGATGTTGCAA
1 CTTGTGATGTTACAA
15754 CTTGTGATG
1 CTTGTGATG
15763 ATGGTGCTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 2 0.07
15 27 0.90
16 1 0.03
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.43
Consensus pattern (15 bp):
CTTGTGATGTTACAA
Found at i:15745 original size:30 final size:30
Alignment explanation
Indices: 15688--15798 Score: 109
Period size: 30 Copynumber: 3.6 Consensus size: 30
15678 AATGGACTAG
*
15688 CAACTTGTGATGATAATGATGCTTGTGATGTTA
1 CAACTTGTGATG---ATGGTGCTTGTGATGTTA
* *
15721 CAACTTGTGATG-TAGGTTCTTGTGATGTTG
1 CAACTTGTGATGAT-GGTGCTTGTGATGTTA
* *
15751 CAACTTGTGATGATGGTGCTTATGATGTTG
1 CAACTTGTGATGATGGTGCTTGTGATGTTA
*
15781 CATCCTT-TGATGATGGTG
1 CA-ACTTGTGATGATGGTG
15799 TGATCCTTGT
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.01
30 52 0.75
31 4 0.06
33 12 0.17
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.41
Consensus pattern (30 bp):
CAACTTGTGATGATGGTGCTTGTGATGTTA
Found at i:17334 original size:44 final size:41
Alignment explanation
Indices: 17259--17345 Score: 131
Period size: 41 Copynumber: 2.0 Consensus size: 41
17249 CATATGGGAA
17259 AGCAGCAACAATCACAAGATAAAAACCTATTAAGA-ATATGT
1 AGCAGCAACAATCACAAGATAAAAACCTATTAA-ACATATGT
17300 AGCAGCAACAATCACAAGATAAAAAAACCCTATTAAACATATGT
1 AGCAGCAACAATCACAAGAT--AAAAA-CCTATTAAACATATGT
17344 AG
1 AG
17346 TATCAACATA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
41 20 0.48
43 6 0.14
44 16 0.38
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.18
Consensus pattern (41 bp):
AGCAGCAACAATCACAAGATAAAAACCTATTAAACATATGT
Found at i:22094 original size:48 final size:48
Alignment explanation
Indices: 22040--22131 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
22030 TTCGACTTGA
* *
22040 ATTCTGTTCTGATA-CATTACCTGAATTATGTTCTGATTTCTGATCTGG
1 ATTCTGTTATGATATC-TCACCTGAATTATGTTCTGATTTCTGATCTGG
* * *
22088 ATTCTGTTATGATATCTCATCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTATGATATCTCACCTGAATTATGTTCTGATTTCTGAT
22132 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
48 37 0.97
49 1 0.03
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (48 bp):
ATTCTGTTATGATATCTCACCTGAATTATGTTCTGATTTCTGATCTGG
Found at i:22095 original size:24 final size:24
Alignment explanation
Indices: 22060--22131 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
22050 GATACATTAC
* *
22060 CTGAATTATGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * *
22084 CTGGATTCTGTTATGATATCTCAT
1 CTGAATTCTGTTATGATTTCTGAT
*
22108 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
22132 ATCTCCGTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:23458 original size:3 final size:3
Alignment explanation
Indices: 23450--23475 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23440 TGTGAATCTA
23450 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
23476 ATGGAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:26559 original size:31 final size:31
Alignment explanation
Indices: 26521--26675 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
26511 CCCGAAGGAC
* * *
26521 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
26552 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
26583 CAGT-CGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
26613 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
26644 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
26675 C
1 C
26676 CCTCGACCCT
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 27 0.24
31 85 0.75
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:26627 original size:61 final size:62
Alignment explanation
Indices: 26521--26675 Score: 242
Period size: 61 Copynumber: 2.5 Consensus size: 62
26511 CCCGAAGGAC
* * *
26521 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
*
26583 CAGT-CGTATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
*
26644 CAGTCCATATGTCCCGAAGAACATAGGTAAAC
1 CAGTCCATATGTTCCGAAGAACATAGGTAAAC
26676 CCTCGACCCT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
61 55 0.65
62 30 0.35
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:26917 original size:23 final size:24
Alignment explanation
Indices: 26891--26937 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
26881 ATATACTTGT
*
26891 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
26914 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
26938 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:27601 original size:21 final size:21
Alignment explanation
Indices: 27571--27615 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27561 ATTCTATCGT
* *
27571 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
27592 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
27613 TTG
1 TTG
27616 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:30789 original size:31 final size:31
Alignment explanation
Indices: 30751--30906 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
30741 CCCGAAGGAC
* * *
30751 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
30782 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
30813 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
30844 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
30875 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
30906 C
1 C
30907 CCTTGACCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:31148 original size:23 final size:24
Alignment explanation
Indices: 31122--31168 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
31112 ATATACTTGT
*
31122 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
31145 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
31169 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:31832 original size:21 final size:21
Alignment explanation
Indices: 31802--31846 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31792 ATTCTATCGT
* *
31802 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
31823 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
31844 TTG
1 TTG
31847 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:33228 original size:24 final size:24
Alignment explanation
Indices: 33174--33246 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
33164 ATACATTACC
* * *
33174 TGAATTCTGTTCTGATTTTTTATC
1 TGAATTCTGTTATGATTTCTTATA
* * *
33198 TGGATTCTGTTATGATATCTGATA
1 TGAATTCTGTTATGATTTCTTATA
*
33222 TGAATTCTGTTTTGATTTCTTATA
1 TGAATTCTGTTATGATTTCTTATA
33246 T
1 T
33247 CTTCGTTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.55
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTTATA
Found at i:34100 original size:44 final size:45
Alignment explanation
Indices: 34034--34139 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 45
34024 CCTTGTCTCG
* *
34034 TCCATCACATAAAGAGTGGGATCAACATCACTC-ATTTGCTCGAT
1 TCCATCACATAAGGAGTGGGATCAACATCACCCTATTTGCTCGAT
** * * *
34078 TTTATCACATAAGGAGTTGGATCAACATTACCCTTTTTGCTCGAT
1 TCCATCACATAAGGAGTGGGATCAACATCACCCTATTTGCTCGAT
34123 TCCATCACATAAGGAGT
1 TCCATCACATAAGGAGT
34140 AAGATCAGCA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
44 27 0.52
45 25 0.48
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (45 bp):
TCCATCACATAAGGAGTGGGATCAACATCACCCTATTTGCTCGAT
Found at i:34146 original size:45 final size:44
Alignment explanation
Indices: 34034--34152 Score: 139
Period size: 45 Copynumber: 2.7 Consensus size: 44
34024 CCTTGTCTCG
* * *
34034 TCCATCACATAAAGAGTGGGATCAACATCACTCATTTGCTCGAT
1 TCCATCACATAAGGAGTAGGATCAACATCACCCATTTGCTCGAT
** * * *
34078 TTTATCACATAAGGAGTTGGATCAACATTACCCTTTTTGCTCGAT
1 TCCATCACATAAGGAGTAGGATCAACATCACCC-ATTTGCTCGAT
* *
34123 TCCATCACATAAGGAGTAAGATCAGCATCA
1 TCCATCACATAAGGAGTAGGATCAACATCA
34153 TCTCGCTTGA
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
44 27 0.44
45 34 0.56
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (44 bp):
TCCATCACATAAGGAGTAGGATCAACATCACCCATTTGCTCGAT
Found at i:34297 original size:37 final size:35
Alignment explanation
Indices: 34201--34354 Score: 161
Period size: 36 Copynumber: 4.2 Consensus size: 35
34191 AAATCATTTC
34201 TCTTAAAACAAAAGTTTCATCTCACTTGAGTTTGTTTT
1 TCTTAAAAC-AAA-TTTCATCTCACTTGAGTTTG-TTT
*
34239 TCTAAAAACAAATTTCATCTCACTTGAGTTTGTTT
1 TCTTAAAACAAATTTCATCTCACTTGAGTTTGTTT
** *
34274 ATCTTAAAACAAAGTTTTTTCTCACTTTA-TATTGTTT
1 -TCTTAAAACAAA-TTTCATCTCACTTGAGT-TTGTTT
*
34311 TCTTATAAACAAA-TTCTGTCTCACTTGAGATTT-TTT
1 TCTTA-AAACAAATTTC-ATCTCACTTGAG-TTTGTTT
34347 TCTTAAAA
1 TCTTAAAA
34355 AAACAAAAGA
Statistics
Matches: 101, Mismatches: 8, Indels: 17
0.80 0.06 0.13
Matches are distributed among these distances:
35 8 0.08
36 54 0.53
37 30 0.30
38 9 0.09
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.46
Consensus pattern (35 bp):
TCTTAAAACAAATTTCATCTCACTTGAGTTTGTTT
Found at i:34321 original size:73 final size:73
Alignment explanation
Indices: 34201--34354 Score: 183
Period size: 73 Copynumber: 2.1 Consensus size: 73
34191 AAATCATTTC
34201 TCTTAAAACAAAAGTTTCATCTCACTTGAGTTTGTTTTTCTAAAAACAAATT-TCATCTCACTTG
1 TCTTAAAACAAAAGTTTCATCTCACTTGAGTTTGTTTTTCTAAAAACAAATTCT-ATCTCACTTG
34265 AG-TTTGTTT
65 AGATTT-TTT
** * * *
34274 ATCTTAAAAC-AAAGTTTTTTCTCACTTTA-TATTG-TTTTCTTATAAACAAATTCTGTCTCACT
1 -TCTTAAAACAAAAGTTTCATCTCACTTGAGT-TTGTTTTTC-TAAAAACAAATTCTATCTCACT
34336 TGAGATTTTTT
63 TGAGATTTTTT
34347 TCTTAAAA
1 TCTTAAAA
34355 AAACAAAAGA
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
72 14 0.20
73 44 0.62
74 13 0.18
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.46
Consensus pattern (73 bp):
TCTTAAAACAAAAGTTTCATCTCACTTGAGTTTGTTTTTCTAAAAACAAATTCTATCTCACTTGA
GATTTTTT
Found at i:34818 original size:23 final size:24
Alignment explanation
Indices: 34769--34820 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
34759 CACAACAACC
*
34769 AAAAAAGTATTCACAATCGAACCAG
1 AAAAAAGTAATCACAATCGAA-CAG
* *
34794 AAAAAATTAATCACAATCTAA-AG
1 AAAAAAGTAATCACAATCGAACAG
34817 AAAA
1 AAAA
34821 TACAAGGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
25 18 0.75
ACGTcount: A:0.60, C:0.15, G:0.08, T:0.17
Consensus pattern (24 bp):
AAAAAAGTAATCACAATCGAACAG
Found at i:37907 original size:5 final size:5
Alignment explanation
Indices: 37897--37947 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
37887 ATAAACAATT
37897 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
37947 T
1 T
37948 AGGGGAATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TTAAA
Found at i:38867 original size:25 final size:26
Alignment explanation
Indices: 38825--38876 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
38815 TATATCAATT
38825 TAAACTATAATAAAAATAAAAATATA
1 TAAACTATAATAAAAATAAAAATATA
* *
38851 TAAA-TATAATTATAATAAAAATATA
1 TAAACTATAATAAAAATAAAAATATA
38876 T
1 T
38877 TTTATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAACTATAATAAAAATAAAAATATA
Found at i:38868 original size:31 final size:32
Alignment explanation
Indices: 38812--38873 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
38802 TTATTATATG
* *
38812 AAATATATCAATTTAAACTATAATAAAAATAA
1 AAATATATAAATATAAACTATAATAAAAATAA
*
38844 AAATATATAAATAT-AATTATAATAAAAATA
1 AAATATATAAATATAAACTATAATAAAAATA
38874 TATTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (32 bp):
AAATATATAAATATAAACTATAATAAAAATAA
Found at i:40188 original size:225 final size:223
Alignment explanation
Indices: 39852--40298 Score: 616
Period size: 225 Copynumber: 2.0 Consensus size: 223
39842 ACATAATCGG
*
39852 TTAATTACTTGAAACATTATCAACCATAATAACATAACAGATAATGCTTATGTACGTAATAGGTA
1 TTAATTACTTGAAACATTATCAACCATAATAACATAAAAGATAAT-CTTATGTACGTAATAGGTA
* * * *
39917 GCGTTTTTTAAAGTTGATGAGGCTTTAGAAATCCAACGATAACAAAATAGGTTAATTATTTGATT
65 ACGTTTTTTAAAGTTGAAGAGGCCTTAGAAATCCAACGATAACAAAATAGGTTAATTATTTAATT
* * * *
39982 TGTTATCAATATTATCAACATATTAGGTAGCACCTAAAATGTTA-CTAAAGTTTAAGCTGATGGG
130 TGTTAGCAATATTATCAACATATTAGGTAGCACCTAAAATATTATC-AAAGTTTAACCTGATAGG
40046 GCCTTAGAAATCCGACGATAACAAAATAGA
194 GCCTTAGAAATCCGACGATAACAAAATAGA
* *
40076 TTAATTAC-TGAAACATTATCAACCATAATAACATAATAAG-TAGCAT-TTATTTAATGTAATAG
1 TTAATTACTTGAAACATTATCAACCATAATAACATAA-AAGATA--ATCTTATGT-ACGTAATAG
* * * * *
40138 GTAACGTCTTTTTAAATTTGACAG-GGCCTTAGAAATTCGACGATAACAAAATATGTTAATTTTT
62 GTAACGT-TTTTTAAAGTTGA-AGAGGCCTTAGAAATCCAACGATAACAAAATAGGTTAATTATT
* *
40202 TAATTTGTTAGCAATATTATCAACATATTAGGTAGCGCCTAAAATATTATCAAAGTTTCACCTGA
125 TAATTTGTTAGCAATATTATCAACATATTAGGTAGCACCTAAAATATTATCAAAGTTTAACCTGA
*
40267 TAGGGCCTTAGAAATCCGATGATAACAAAATA
190 TAGGGCCTTAGAAATCCGACGATAACAAAATA
40299 TGTTAAATAC
Statistics
Matches: 197, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
223 35 0.18
224 24 0.12
225 136 0.69
226 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (223 bp):
TTAATTACTTGAAACATTATCAACCATAATAACATAAAAGATAATCTTATGTACGTAATAGGTAA
CGTTTTTTAAAGTTGAAGAGGCCTTAGAAATCCAACGATAACAAAATAGGTTAATTATTTAATTT
GTTAGCAATATTATCAACATATTAGGTAGCACCTAAAATATTATCAAAGTTTAACCTGATAGGGC
CTTAGAAATCCGACGATAACAAAATAGA
Found at i:40349 original size:108 final size:108
Alignment explanation
Indices: 40160--40426 Score: 381
Period size: 108 Copynumber: 2.5 Consensus size: 108
40150 TAAATTTGAC
* * * *
40160 AGGGCCTTAGAAATTCGACGATAACAAAATATGTTAATTTTTTAATTTGTTAGCAATATTATCAA
1 AGGGCCTTAGAAATCCGATGATAACAAAATATGTTAATTTCTTATTTTGTTAGCAATATTATCAA
* *
40225 CATATTAGGTAGCGCCTAAAATATTATCAAAGTTTCACCTGAT
66 CATATTAGGTAGCGCCTAAAATATTACCAAAGTTTAACCTGAT
* * **
40268 AGGGCCTTAGAAATCCGATGATAACAAAATATGTTAAATACTTATTTTGTTATTAATATTATCAA
1 AGGGCCTTAGAAATCCGATGATAACAAAATATGTTAATTTCTTATTTTGTTAGCAATATTATCAA
* * *
40333 CATATTAGGTATCGCCTAAAATATTACCAATGTTTAAGCTGAT
66 CATATTAGGTAGCGCCTAAAATATTACCAAAGTTTAACCTGAT
* * * *
40376 TGGGCCTTCGAAATCCCATGACAACAAAATATGTTAATTTCTTATTTTGTT
1 AGGGCCTTAGAAATCCGATGATAACAAAATATGTTAATTTCTTATTTTGTT
40427 GTAAATAAAT
Statistics
Matches: 140, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 140 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (108 bp):
AGGGCCTTAGAAATCCGATGATAACAAAATATGTTAATTTCTTATTTTGTTAGCAATATTATCAA
CATATTAGGTAGCGCCTAAAATATTACCAAAGTTTAACCTGAT
Found at i:45358 original size:21 final size:21
Alignment explanation
Indices: 45332--45371 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45322 TAGAACCCCA
*
45332 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
45353 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
45372 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:45401 original size:21 final size:23
Alignment explanation
Indices: 45353--45403 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
45343 ATTCCCCTGT
45353 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
45376 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
45397 GGGGGGA
1 GGGGGGA
45404 TCAATTCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:49246 original size:22 final size:21
Alignment explanation
Indices: 49206--49245 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
49196 GAGTTTGTTT
49206 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
49227 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
49246 ATAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:52621 original size:14 final size:17
Alignment explanation
Indices: 52596--52632 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
52586 AGTTTTATGG
52596 AAAACAACATTT-AT-A
1 AAAACAACATTTAATCA
52611 AAAACAA-ATTTAATCA
1 AAAACAACATTTAATCA
52627 AAAACA
1 AAAACA
52633 TCAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 9 0.45
16 7 0.35
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAACAACATTTAATCA
Done.