Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005662.1 Hibiscus syriacus cultivar Beakdansim tig00013237_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: 70815
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:231 original size:68 final size:72
Alignment explanation
Indices: 100--244 Score: 201
Period size: 68 Copynumber: 2.1 Consensus size: 72
90 CGCTGGTCTT
** *
100 TCATTGTCAAGTCTTGGTGTGTTTCTGTTTTTCTGTCATGTAATAAATAATATCTCTTGGTTCTC
1 TCATTGTCAAGTCTTGGTACGTTTCTG-TTTTCTGTCATGTAATAAATAATATCTCTTGGTTCTA
165 ACCTAGAG
65 ACCTAGAG
173 TCATTGTCAAGTCTT-GTACGTTTCTG-TTTCTG-CATGT-A-AAATAAATATCTCTTGGTTCTA
1 TCATTGTCAAGTCTTGGTACGTTTCTGTTTTCTGTCATGTAATAAAT-AATATCTCTTGGTTCTA
*
233 ACCTAGGG
65 ACCTAGAG
241 TCAT
1 TCAT
245 GAAAATGCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
67 4 0.06
68 28 0.42
69 5 0.07
70 6 0.09
72 9 0.13
73 15 0.22
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (72 bp):
TCATTGTCAAGTCTTGGTACGTTTCTGTTTTCTGTCATGTAATAAATAATATCTCTTGGTTCTAA
CCTAGAG
Found at i:4064 original size:13 final size:13
Alignment explanation
Indices: 4048--4084 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
4038 TGGCCCCATC
4048 CCGTCTCCCCCGG
1 CCGTCTCCCCCGG
4061 CCGTCTCCCCCGG
1 CCGTCTCCCCCGG
4074 CCGTCTCCCCC
1 CCGTCTCCCCC
4085 CTTGTGTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.00, C:0.65, G:0.19, T:0.16
Consensus pattern (13 bp):
CCGTCTCCCCCGG
Found at i:14562 original size:27 final size:26
Alignment explanation
Indices: 14507--14565 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
14497 TTTTGTGTGG
* *
14507 ATTTAATCTTTATTATTTTGAATTTA
1 ATTTAATCTTTATTATTTTCAATTAA
* *
14533 ATTTAATCTTTTATTTTTTTCAGTTAA
1 ATTTAATC-TTTATTATTTTCAATTAA
14560 ATTTAA
1 ATTTAA
14566 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
ATTTAATCTTTATTATTTTCAATTAA
Found at i:14840 original size:20 final size:20
Alignment explanation
Indices: 14784--14887 Score: 111
Period size: 20 Copynumber: 5.2 Consensus size: 20
14774 GCAATTTTCC
*
14784 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
14804 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
14824 TACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
* * *
14844 GACTATCGCAACGAGATTCT
1 GACTATCGCAATGCGATTAT
* *
14864 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
14884 GACT
1 GACT
14888 GTCGTAACAC
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 71 0.97
21 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:18036 original size:11 final size:12
Alignment explanation
Indices: 18009--18036 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17999 TGGTATCAAG
18009 AAAAAGGCAATC
1 AAAAAGGCAATC
18021 AAAAAGGCAATC
1 AAAAAGGCAATC
18033 AAAA
1 AAAA
18037 TCAAAATCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAAGGCAATC
Found at i:18363 original size:140 final size:140
Alignment explanation
Indices: 18111--18380 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
18101 AAACGTTGTA
* *
18111 TTATGTGTAAACTTTTAATATTTTGAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
18176 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
18241 TATGTGTATT
131 TATGTGTATT
18251 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
18316 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGTGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
18381 CGCAACGCGA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:18466 original size:54 final size:53
Alignment explanation
Indices: 18379--18594 Score: 229
Period size: 54 Copynumber: 3.9 Consensus size: 53
18369 GAATTTGACT
*
18379 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCACAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAAC-CAAAA
*
18433 ATCGCAACGCGAATTTGACTATCGCAACTCGAATTTG-TCTATCGCAACGCAAATTTGA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAT-TATCGCAAC-CAAA----A
* * * * * *
18491 CTATCACAATGCGAATTTGATTATCGCAACG-GTTATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGCGAATTTGACTATCGCAACGCG-AATTTGATTATCGCAACCA-AAA
* *
18547 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGAGTATCGCAAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAAC
18595 GCGAATTTGA
Statistics
Matches: 136, Mismatches: 15, Indels: 22
0.79 0.09 0.13
Matches are distributed among these distances:
53 1 0.01
54 89 0.65
55 1 0.01
56 1 0.01
58 1 0.01
59 2 0.01
60 41 0.30
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (53 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACCAAAA
Found at i:18480 original size:74 final size:74
Alignment explanation
Indices: 18359--18499 Score: 237
Period size: 74 Copynumber: 1.9 Consensus size: 74
18349 TCATTTGAAT
* * *
18359 ATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCAC
18424 AACTCAAAA
66 AACTCAAAA
* *
18433 ATCGCAACGCGAATTTGACTATCGCAACTCGAATTTGTCTATCGCAACGCAAATTTGACTATCAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCAC
18498 AA
66 AA
18500 TGCGAATTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCAC
AACTCAAAA
Found at i:18551 original size:74 final size:74
Alignment explanation
Indices: 18351--18617 Score: 215
Period size: 74 Copynumber: 3.5 Consensus size: 74
18341 TTACACATTC
* * * *
18351 ATTTGAATATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTG
1 ATTTGAGTATCGCAACGCGAATTTGACTATCGCAACGAGAA----A--ATCGCAACGCAAATTTG
* *
18416 ATTATCACAACTC-A
60 ACTATCACAACGCGA
* ***
18430 A----A-AATCGCAACGCGAATTTGACTATCGCAACTCGAATTTGTCTATCGCAACGCAAATTTG
1 ATTTGAGTATCGCAACGCGAATTTGACTATCGCAA--CG-A---GAAAATCGCAACGCAAATTTG
*
18490 ACTATCACAATGCGA
60 ACTATCACAACGCGA
* * * *
18505 ATTTGATTATCGCAACG-GTTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGAGTAT
1 ATTTGAGTATCGCAACGCG-AATTTGACTATCGCAACGAGAAAATCGCAACGCAAATTTGACTAT
*
18569 CGCAACGCGA
65 CACAACGCGA
*
18579 ATTTGAGTATCGCAACGCGAATTTGATTATCGCAACGAG
1 ATTTGAGTATCGCAACGCGAATTTGACTATCGCAACGAG
18618 TATTTGACTA
Statistics
Matches: 152, Mismatches: 22, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
74 115 0.76
75 4 0.03
76 2 0.01
77 1 0.01
78 2 0.01
79 3 0.02
80 25 0.16
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (74 bp):
ATTTGAGTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCAACGCAAATTTGACTATC
ACAACGCGA
Found at i:18551 original size:94 final size:94
Alignment explanation
Indices: 18359--18679 Score: 357
Period size: 94 Copynumber: 3.4 Consensus size: 94
18349 TCATTTGAAT
* * *
18359 ATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGC
* ** * * * * *
18424 AACTCAAAAATCG-C-AACGCGAATTTGAC--T
66 AAC-GAGTATTTGACTATCGC-AA--CGACAAA
* * * *
18453 ATCGCAACTCGAATTTGTCTATCGCAACGCAAATTTGACTATCACAATGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGC
*
18518 AACG-GTTATTTGACTATCGCAACGAGAAA
66 AACGAG-TATTTGACTATCGCAACGACAAA
* * *
18547 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGC
18612 AACGAGTATTTGACTATCGCAACGACAAA
66 AACGAGTATTTGACTATCGCAACGACAAA
* * *
18641 ATCGCAAAGCGTATTAGACTATCGCAACGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACT
18680 TTCGCGTTGC
Statistics
Matches: 192, Mismatches: 29, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
92 2 0.01
93 8 0.04
94 177 0.92
95 5 0.03
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGC
AACGAGTATTTGACTATCGCAACGACAAA
Found at i:18551 original size:114 final size:114
Alignment explanation
Indices: 18351--18635 Score: 385
Period size: 114 Copynumber: 2.5 Consensus size: 114
18341 TTACACATTC
* *
18351 ATTTGAATATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTG
* *
18416 ATTATCACAACTCAAAAATCGCAACGCGAATTTGACTATCGCAACTCGA
66 ACTATCACAACTCAAAAATCGCAACGCGAATTTGACTATCGCAACGCGA
* * * * * *
18465 ATTTGTCTATCGCAACGCAAATTTGACTATCACAATGCGAATTTGATTATCGCAACG-GTTATTT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCG-AATTT
* * *
18529 GACTATCGCAAC-GAGAAAATCGCAACGCGAATTTGAGTATCGCAACGCGA
65 GACTATCACAACTCA-AAAATCGCAACGCGAATTTGACTATCGCAACGCGA
* * * *
18579 ATTTGAGTATCGCAACGCGAATTTGATTATCGCAACGAGTATTTGACTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
18636 ACAAAATCGC
Statistics
Matches: 147, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
113 2 0.01
114 145 0.99
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (114 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTG
ACTATCACAACTCAAAAATCGCAACGCGAATTTGACTATCGCAACGCGA
Found at i:18636 original size:20 final size:20
Alignment explanation
Indices: 18351--18635 Score: 299
Period size: 20 Copynumber: 14.8 Consensus size: 20
18341 TTACACATTC
* *
18351 ATTTGAATATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
18371 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
18391 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
18411 ATTTGATTATCACAACTC-A
1 ATTTGACTATCGCAACGCGA
*
18430 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
18445 ATTTGACTATCGCAACTCGA
1 ATTTGACTATCGCAACGCGA
* *
18465 ATTTGTCTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
* *
18485 ATTTGACTATCACAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
18505 ATTTGATTATCGCAACG-GTT
1 ATTTGACTATCGCAACGCG-A
*
18525 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
18545 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
18559 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
18579 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
18599 ATTTGATTATCGCAACGAGT
1 ATTTGACTATCGCAACGCGA
18619 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
18636 ACAAAATCGC
Statistics
Matches: 223, Mismatches: 28, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
14 20 0.09
15 3 0.01
16 1 0.00
18 1 0.00
19 4 0.02
20 193 0.87
21 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:18703 original size:20 final size:20
Alignment explanation
Indices: 18678--18731 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
18668 CGCGAATTGA
*
18678 CTTTCGCGTTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
*
18698 CTTTCGCATTGCGATTTTGA
1 CTTTCGCATTGCGATTTTGT
* *
18718 GTTTAGCATTGCGA
1 CTTTCGCATTGCGA
18732 AAGTGTACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:18890 original size:14 final size:14
Alignment explanation
Indices: 18830--18891 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
18820 CACAAATAAG
*
18830 AATTATTTACACATC
1 AATT-TTTACAAATC
**
18845 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
18860 AACTTTTACAAATC
1 AATTTTTACAAATC
*
18874 AATTTTTATAAATC
1 AATTTTTACAAATC
18888 AATT
1 AATT
18892 AAACAAACAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:20902 original size:18 final size:19
Alignment explanation
Indices: 20879--20924 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
20869 GAAACTTAAA
20879 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
20897 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
20917 ATCGCAAC
1 ATCGCAAC
20925 GAGAGAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
20 15 0.60
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:20993 original size:20 final size:20
Alignment explanation
Indices: 20968--21015 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
20958 GCGATTCTCT
20968 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
20988 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
21008 TGTTGCGA
1 CGTTGCGA
21016 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:22995 original size:20 final size:20
Alignment explanation
Indices: 22923--22986 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
22913 GAAACTTAAA
* **
22923 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
22943 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
22963 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
22983 ATCG
1 ATCG
22987 TAATGCGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:23649 original size:20 final size:20
Alignment explanation
Indices: 23617--23723 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
23607 GAAAATCGTT
* *
23617 TTGCGATAATCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
* * *
23637 TTGTGACAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
23657 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
23677 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
23697 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCG
23717 TTGCGAT
1 TTGCGAT
23724 TTACATATTC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:23741 original size:40 final size:40
Alignment explanation
Indices: 23617--23747 Score: 120
Period size: 40 Copynumber: 3.3 Consensus size: 40
23607 GAAAATCGTT
* * * * * * *
23617 TTGCGATAATCAGCATCGCGTTGTGACAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCATTGCGATAGTCAGAATCGCA
* * *
23657 TTGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCATTGCGATAGTCAGAATCGCA
* * * *
23697 TTGCGATAGTCATAATCGCATTGCGAT-TTACATATTCGCA
1 TTGCGATAGTCAGAATCGCATTGCGATAGT-CAGAATCGCA
23737 TTGCGATAGTC
1 TTGCGATAGTC
23748 GGAAAATCAC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 76 0.99
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (40 bp):
TTGCGATAGTCAGAATCGCATTGCGATAGTCAGAATCGCA
Found at i:26769 original size:118 final size:119
Alignment explanation
Indices: 26671--26887 Score: 262
Period size: 118 Copynumber: 1.8 Consensus size: 119
26661 ATTATATTTT
26671 ATAATATTTTA-AATTAAGACCATTAATTTAT-ATATTTTTACAA-TTTAATCATTGAGGTTTAA
1 ATAATA-TTTAGAATTAAGACCATTAATTT-TGATA-TTTTACAATTTTAATCATTGAGGTTTAA
* ** * *
26733 TATTTTAATTTTAAATAATA-TTTTAGGATTATTTACACTAATAATACCTAGATTCC
63 AATAATAATTTTAAATAATATTTTTAGAATTATTTACACTAATAATAACTAGATTCC
* *** * * *
26789 ATGATATTTAGAATTAAGATTTTTAATTTTGATATTTTACAATTTTAATCCTTTAGTTTTAAAAT
1 ATAATATTTAGAATTAAGACCATTAATTTTGATATTTTACAATTTTAATCATTGAGGTTTAAAAT
*
26854 AATAATTTTAAATATTATTTTTAGAATTATTTAC
66 AATAATTTTAAATAATATTTTTAGAATTATTTAC
26888 TATTATAGTA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
117 13 0.16
118 55 0.66
119 15 0.18
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (119 bp):
ATAATATTTAGAATTAAGACCATTAATTTTGATATTTTACAATTTTAATCATTGAGGTTTAAAAT
AATAATTTTAAATAATATTTTTAGAATTATTTACACTAATAATAACTAGATTCC
Found at i:28191 original size:46 final size:47
Alignment explanation
Indices: 28096--28191 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 47
28086 CTTAATTTAC
* *
28096 TTTATTTTCCTAATAAATGCATGCAAACTAGAAATCACGCGGTTAGA
1 TTTATTTTCCAAATAAATGCATGCAAACTAGAAATCACGAGGTTAGA
* * *
28143 TTTATTTCTCCAAATAAA-GCATG-GAACTAGATA-CATGAGGTTAGGA
1 TTTATTT-TCCAAATAAATGCATGCAAACTAGAAATCACGAGGTTA-GA
28189 TTT
1 TTT
28192 TTATGATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
45 8 0.19
46 13 0.31
47 12 0.29
48 9 0.21
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (47 bp):
TTTATTTTCCAAATAAATGCATGCAAACTAGAAATCACGAGGTTAGA
Found at i:28539 original size:20 final size:20
Alignment explanation
Indices: 28500--28556 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
28490 TTTCATTTTA
*
28500 CATTCACATCTTTGCATTTG
1 CATTCACATCTTTACATTTG
* *
28520 CATTCGCATCTTTACGTTTG
1 CATTCACATCTTTACATTTG
* *
28540 TATTTACAT-TTT-CATTT
1 CATTCACATCTTTACATTT
28557 TTTACATTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 23 0.77
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (20 bp):
CATTCACATCTTTACATTTG
Found at i:28562 original size:15 final size:15
Alignment explanation
Indices: 28542--28584 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
28532 TACGTTTGTA
*
28542 TTTACATTTTCATTT
1 TTTACATTTGCATTT
28557 TTTACATTTGCATTT
1 TTTACATTTGCATTT
28572 TTTACATTTGCAT
1 TTTACATTTGCAT
28585 ATTTGCATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTACATTTGCATTT
Found at i:28907 original size:42 final size:42
Alignment explanation
Indices: 28838--28921 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
28828 AGAGATGATT
* * * * * * *
28838 GATCAAGTAAAAAAGTTGCAGGGTGATTCAAATGAACAAATG
1 GATCAAGAAAAAAAATTCCAAGATGATTAAAAAGAACAAATG
*
28880 GATCAAGAAAAAAAATTCCAAGATGATTAAAAAGAGCAAATG
1 GATCAAGAAAAAAAATTCCAAGATGATTAAAAAGAACAAATG
28922 ACAAAACTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.19
Consensus pattern (42 bp):
GATCAAGAAAAAAAATTCCAAGATGATTAAAAAGAACAAATG
Found at i:30196 original size:97 final size:97
Alignment explanation
Indices: 30030--30217 Score: 349
Period size: 97 Copynumber: 1.9 Consensus size: 97
30020 GAAGTAATCG
*
30030 GAGACTGACCCATATGTTTAAAAAGGAATGGGGCAGATGTAACCCAGAAGACACCTCAGACACCT
1 GAGACTGACCCATAGGTTTAAAAAGGAATGGGGCAGATGTAACCCAGAAGACACCTCAGACACCT
30095 ATATCAGATTTTCTGAAAACAAGTGACGTATT
66 ATATCAGATTTTCTGAAAACAAGTGACGTATT
* *
30127 GAGACTGGCCCATAGGTTTAAAAAGGAATGGGGTAGATGTAACCCAGAAGACACCTCAGACACCT
1 GAGACTGACCCATAGGTTTAAAAAGGAATGGGGCAGATGTAACCCAGAAGACACCTCAGACACCT
30192 ATATCAGATTTTCTGAAAACAAGTGA
66 ATATCAGATTTTCTGAAAACAAGTGA
30218 GGTAGGGGGA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 88 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (97 bp):
GAGACTGACCCATAGGTTTAAAAAGGAATGGGGCAGATGTAACCCAGAAGACACCTCAGACACCT
ATATCAGATTTTCTGAAAACAAGTGACGTATT
Found at i:33310 original size:33 final size:31
Alignment explanation
Indices: 33273--33348 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
33263 GAGGGGCATT
*
33273 TTGAAGGTCTATATTATCAATGATTGTGACATC
1 TTGAAGGTCTATATCATC-ATG-TTGTGACATC
* * *
33306 TTGAA-GACTCACATCATCATGTTGTGACATT
1 TTGAAGGTCT-ATATCATCATGTTGTGACATC
33337 TTGAAGGTCTAT
1 TTGAAGGTCTAT
33349 TTTGATCATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
31 15 0.43
32 9 0.26
33 11 0.31
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (31 bp):
TTGAAGGTCTATATCATCATGTTGTGACATC
Found at i:35290 original size:137 final size:137
Alignment explanation
Indices: 35136--35930 Score: 1092
Period size: 137 Copynumber: 5.8 Consensus size: 137
35126 TCGTGTCCAT
* * * ** * * * *
35136 CAACATCATCCTTAGATAGCCATACGTCCTTATCACGAAGGAACTGTGTTATCTCAAATATCTTC
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
*
35201 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAT
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
35266 GAAGGAG
131 GAAGGAG
* *
35273 CAACATCATTCTTAGATAACCAGATATCCTCATCATGAAAGAACGGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
*
35338 -AAGATGGCCAGACGTTCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
*
35402 GAAAGAG
131 GAAGGAG
* * *
35409 CAACATCATTCTTAGATAACCAAATATCCTTATCATGAAAGAACAGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
*
35474 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCGTCCACCGATCAGAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
*
35539 AAAGGAG
131 GAAGGAG
**
35546 CAACATCATTCTTAGATAACCAGATATCCTCATCGTGAAAGAACAGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
* *
35611 AAAGATGGCCAGACGTCCTCATCAAGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
*
35676 GAATGAG
131 GAAGGAG
* * * * * *
35683 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTCTCTCAAATATATTT
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
* * * * * *
35748 AAAGATGGCTAAACGTCCTCATCACGAAAGACCAATGTCATCCACTGACCAGAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
*
35813 GTAGGAG
131 GAAGGAG
* * * * ** * **
35820 CTGA-GTCATCCTCAGATAACCAGACGTCTTCATCAC-AAAGGAACCTTGTTATCTCAAATATCT
1 C-AACATCATTCTTAGATAACCAGATATCCTCATCACGAAA-GAACAGTGTTATCTCAAATATCT
* * ** *
35883 TCAAAGATGGTCAGACGTCCTCATCGTGAAGGAACAATGTCATACACC
64 TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACC
35931 AGTTTGATCT
Statistics
Matches: 588, Mismatches: 67, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
136 132 0.22
137 455 0.77
138 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (137 bp):
CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
GAAGGAG
Found at i:37194 original size:118 final size:118
Alignment explanation
Indices: 37072--37322 Score: 265
Period size: 118 Copynumber: 2.1 Consensus size: 118
37062 TAGGGTTAAA
* * * *
37072 TTACATTATTAGTAATTATATTTTATAATATTTTGAATTAAGACCATTAATTTAT-ATATTTTTA
1 TTACATTA-TAGTAACTAGATTTCATAATATTTAGAATTAAGACCATTAATTT-TGATA-TTTTA
* **
37136 CAA-TTTAATCATTGAGGTTTAATATTTTAATTTTAAATAATA-TTTTAGAATTAT
63 CAATTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
* * * * * ***
37190 TTACACTAATAATACCTAGATTTCATGATATTTAGAATTAGGATTTTTAATTTTGATATTTTACA
1 TTACA-TTATAGTAACTAGATTTCATAATATTTAGAATTAAGACCATTAATTTTGATATTTTACA
* * * *
37255 ATTTTAATCCTTTAGTTTTAAAATAATAATTTTAAATATTATTTTTAGAATTAT
65 ATTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
37309 TTACTATTATAGTA
1 TTAC-ATTATAGTA
37323 CTTTGCATAT
Statistics
Matches: 107, Mismatches: 21, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
117 9 0.08
118 73 0.68
119 24 0.22
120 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (118 bp):
TTACATTATAGTAACTAGATTTCATAATATTTAGAATTAAGACCATTAATTTTGATATTTTACAA
TTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
Found at i:43376 original size:31 final size:31
Alignment explanation
Indices: 43333--43396 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
43323 CAGTTACGTC
43333 GGGGACCATATTGCAAACT-GACTAAATGTTG
1 GGGGACCATATTGCAAA-TGGACTAAATGTTG
*
43364 GGGGACCTTATTGCAAATGGACTAAATGTTG
1 GGGGACCATATTGCAAATGGACTAAATGTTG
43395 GG
1 GG
43397 TACCGTATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (31 bp):
GGGGACCATATTGCAAATGGACTAAATGTTG
Found at i:45033 original size:31 final size:31
Alignment explanation
Indices: 44995--45066 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
44985 TTACATCAGA
*
44995 GACCATATTGCAAACGGAATAAATGTTGAGG
1 GACCATATTGCAAACGGAATAAATCTTGAGG
* * * *
45026 GACCATATTACAAATGGACTAAATCTTGGGG
1 GACCATATTGCAAACGGAATAAATCTTGAGG
45057 GACCATATTG
1 GACCATATTG
45067 TAAGTTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (31 bp):
GACCATATTGCAAACGGAATAAATCTTGAGG
Found at i:46223 original size:20 final size:20
Alignment explanation
Indices: 46198--46250 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
46188 ATCTTATTCC
46198 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
46218 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCCCA
46238 CTGGTAATCTTAC
1 CTGGTAATCTTAC
46251 CTTTCGTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:48874 original size:14 final size:16
Alignment explanation
Indices: 48855--48886 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
48845 TCATATTATC
48855 TATTTAAA-TTAT-AA
1 TATTTAAAGTTATCAA
48869 TATTTAAAGTTATCAA
1 TATTTAAAGTTATCAA
48885 TA
1 TA
48887 GATGAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TATTTAAAGTTATCAA
Found at i:56381 original size:12 final size:12
Alignment explanation
Indices: 56366--56426 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
56356 TGAATTATGT
56366 TCTGATTTCTGA
1 TCTGATTTCTGA
*
56378 TCTGGA-TTCTGT
1 TCT-GATTTCTGA
*
56390 TCTGATATCTGA
1 TCTGATTTCTGA
* *
56402 TCTGAATTCTGT
1 TCTGATTTCTGA
* *
56414 TTTAATTTCTGA
1 TCTGATTTCTGA
56426 T
1 T
56427 ATCTCTGTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (12 bp):
TCTGATTTCTGA
Found at i:56390 original size:24 final size:24
Alignment explanation
Indices: 56355--56426 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
56345 GCTACATGAC
*
56355 CTGAATTATGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
56379 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
56403 CTGAATTCTGTTTTAATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
56427 ATCTCTGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:59707 original size:11 final size:11
Alignment explanation
Indices: 59693--59724 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
59683 CAAGAATTAA
59693 TGAATGATGAT
1 TGAATGATGAT
*
59704 TGAAGGATGAT
1 TGAATGATGAT
59715 TGAATGATGA
1 TGAATGATGA
59725 ATAGATGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (11 bp):
TGAATGATGAT
Found at i:59847 original size:36 final size:35
Alignment explanation
Indices: 59752--59860 Score: 132
Period size: 35 Copynumber: 3.1 Consensus size: 35
59742 GGTGGTTATT
* * * *
59752 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
* *
59787 TAGGCGTGCAATGGTA-ATGAAAGATGGTGATGTTA
1 TAGGCGTGAAATGG-AGATGGAAGATGGTGATGTTA
59822 TAGGCGTGAAAATGGAGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGAGATGGAAGATGGTGATGTTA
59857 TAGG
1 TAGG
59861 TAGTATCTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 41 0.65
36 22 0.35
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.27
Consensus pattern (35 bp):
TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
Found at i:64112 original size:15 final size:15
Alignment explanation
Indices: 64092--64134 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
64082 AAAGGAAATA
64092 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
64107 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
64122 GAAATGGAAAGAA
1 GAAATGGAAAGAA
64135 ATGTTATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:64376 original size:36 final size:35
Alignment explanation
Indices: 64285--64393 Score: 132
Period size: 35 Copynumber: 3.1 Consensus size: 35
64275 GGTGGTTATT
* * * * *
64285 TAGGCGTGAAATGGTGATAGAAGATGGTAAAGATA
1 TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
*
64320 TAGGCGTGCAATGGTA-ATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGG-AGATGGAAGATGGTGATGTTA
64355 TAGGCGTGAAAATGGAGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGAGATGGAAGATGGTGATGTTA
64390 TAGG
1 TAGG
64394 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.33, C:0.04, G:0.38, T:0.26
Consensus pattern (35 bp):
TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
Done.