Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001571.1 Hibiscus syriacus cultivar Beakdansim tig00003121_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: 126080
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:16646 original size:17 final size:16
Alignment explanation
Indices: 16620--16654 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
16610 TATTTAGACG
16620 AAAAATCATTAATTAC
1 AAAAATCATTAATTAC
16636 AAAACATCATTAATTAC
1 AAAA-ATCATTAATTAC
16653 AA
1 AA
16655 TGTTGAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATCATTAATTAC
Found at i:17656 original size:20 final size:21
Alignment explanation
Indices: 17616--17664 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
17606 ACACAATATA
17616 AATACAATAAAATAATTAAAAT
1 AATACAATAAAAT-ATTAAAAT
*
17638 AATACAATATAAT-TTAAAAT
1 AATACAATAAAATATTAAAAT
17658 AATACAA
1 AATACAA
17665 AATTGTACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 14 0.54
22 12 0.46
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (21 bp):
AATACAATAAAATATTAAAAT
Found at i:18576 original size:50 final size:51
Alignment explanation
Indices: 18479--18578 Score: 116
Period size: 50 Copynumber: 2.0 Consensus size: 51
18469 CTCTTTGTAA
* ** *
18479 TAAGGCGCGCCCTCTGCAACGCGCTATACGCTGATTTGGCATTACGTGGGG
1 TAAGGAGCGCCCTCTGCAACGCGCTATACGCTGACATGGCATCACGTGGGG
*
18530 TAAGGAGCGCCC-CTGCGACGCGCCT-TACGCTGACATGG-ATACACGTGGG
1 TAAGGAGCGCCCTCTGCAACGCG-CTATACGCTGACATGGCAT-CACGTGGG
18579 TATAACGCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
49 2 0.05
50 27 0.64
51 13 0.31
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.20
Consensus pattern (51 bp):
TAAGGAGCGCCCTCTGCAACGCGCTATACGCTGACATGGCATCACGTGGGG
Found at i:22344 original size:35 final size:34
Alignment explanation
Indices: 22259--22345 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
22249 AAAATAATTT
*
22259 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
22293 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
22331 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
22346 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:29933 original size:30 final size:31
Alignment explanation
Indices: 29882--29943 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
29872 CGATGAATAG
29882 CTGTTTCATACTGATAAACTATTAAGAACTAA
1 CTGTTTCATACTGA-AAACTATTAAGAACTAA
29914 CTGTTTCATACTG-AAACTATTAAGAACTAA
1 CTGTTTCATACTGAAAACTATTAAGAACTAA
29944 ATCTTGTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 17 0.57
32 13 0.43
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (31 bp):
CTGTTTCATACTGAAAACTATTAAGAACTAA
Found at i:35015 original size:123 final size:120
Alignment explanation
Indices: 34821--35045 Score: 301
Period size: 123 Copynumber: 1.9 Consensus size: 120
34811 CCATGATTGC
** * *
34821 ATTTTCAGGTAAGAAGAAAGCATCTAAGAAGAAAAGCACTGCTGCATTTGCAGCCTTGCGCGATG
1 ATTTTCAGGTAAGAAGAAAGCATCTAAGAAGAAAAGCACTGCCACATTTGCAGCCTTGCACGACG
*
34886 AGCTTGAAAACAAAGAGGGTGTGAAAGAAGATGAGGAAGAAGATGCTCCTTCATTTGG
66 AACTTGAAAACAAAGAGGGTGT--AA-AAGATGAGGAAGAAGATGCTCCTTCATTTGG
* * *
34944 ATTTTCAGGTAAGAAG-AAGTTATCTAAGAAGAAAAGCAGTGCCACATTTGCAGCCTTAG-ATGA
1 ATTTTCAGGTAAGAAGAAAG-CATCTAAGAAGAAAAGCACTGCCACATTTGCAGCCTT-GCACGA
**
35007 CGAACTTGAAAATGAAGAGGGTGTAAAAGATGAGGAAGA
64 CGAACTTGAAAACAAAGAGGGTGTAAAAGATGAGGAAGA
35046 TGTTACTTCA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
120 13 0.14
121 2 0.02
122 3 0.03
123 71 0.79
124 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (120 bp):
ATTTTCAGGTAAGAAGAAAGCATCTAAGAAGAAAAGCACTGCCACATTTGCAGCCTTGCACGACG
AACTTGAAAACAAAGAGGGTGTAAAAGATGAGGAAGAAGATGCTCCTTCATTTGG
Found at i:35420 original size:12 final size:12
Alignment explanation
Indices: 35403--35437 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
35393 CTGAAACTTC
35403 GAAGAACAAGAA
1 GAAGAACAAGAA
*
35415 GAAGAATAAGAA
1 GAAGAACAAGAA
35427 GAAGAACAAGA
1 GAAGAACAAGA
35438 GTGGAAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.66, C:0.06, G:0.26, T:0.03
Consensus pattern (12 bp):
GAAGAACAAGAA
Found at i:35658 original size:13 final size:12
Alignment explanation
Indices: 35634--35676 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
35624 CTGCTGCTGC
35634 AAAGAAAAGGAA
1 AAAGAAAAGGAA
35646 AAAGAAGAAGGAA
1 AAAGAA-AAGGAA
*
35659 AAGGAAAAAGAGAA
1 AAAG-AAAAG-GAA
35673 AAAG
1 AAAG
35677 GCTGCTGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.23
13 12 0.46
14 8 0.31
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGGAA
Found at i:40091 original size:16 final size:17
Alignment explanation
Indices: 40066--40098 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40056 GGGTCTGCTG
*
40066 GTGGACTGATG-TGTTT
1 GTGGAATGATGATGTTT
40082 GTGGAATGATGATGTTT
1 GTGGAATGATGATGTTT
40099 TTGAGGTAAA
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:0.18, C:0.03, G:0.36, T:0.42
Consensus pattern (17 bp):
GTGGAATGATGATGTTT
Found at i:72212 original size:19 final size:20
Alignment explanation
Indices: 72168--72212 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
72158 AGTTTTTCAT
*
72168 AATAACAATATAATTTGATC
1 AATAACAATATAATTTGATA
72188 AA-AACACA-ATAATTTGA-A
1 AATAACA-ATATAATTTGATA
72206 AATAACA
1 AATAACA
72213 TTTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 2 0.09
19 17 0.77
20 3 0.14
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.27
Consensus pattern (20 bp):
AATAACAATATAATTTGATA
Found at i:72642 original size:21 final size:21
Alignment explanation
Indices: 72616--72655 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72606 CAGAACCCCA
*
72616 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
72637 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
72656 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:72684 original size:19 final size:20
Alignment explanation
Indices: 72638--72697 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
72628 TTCCCCTGTG
72638 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
72661 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
72680 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
72698 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:76537 original size:22 final size:21
Alignment explanation
Indices: 76495--76534 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
76485 GAGTTTGTTT
*
76495 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
76516 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
76535 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:79665 original size:23 final size:22
Alignment explanation
Indices: 79621--79665 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
79611 AATCTCATAG
* *
79621 GGGAACCGATTCTCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
79643 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
79666 AAATTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:80829 original size:24 final size:24
Alignment explanation
Indices: 80780--80838 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
80770 TACGCGTAAG
* *
80780 TGAACCATGTG-TTTATATGTATA
1 TGAACTATGTGATTTATATGTAGA
80803 TGAGA-TATGTGATTTATATG-ACGA
1 TGA-ACTATGTGATTTATATGTA-GA
80827 TGAACTATGTGA
1 TGAACTATGTGA
80839 AAGAACTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (24 bp):
TGAACTATGTGATTTATATGTAGA
Found at i:81077 original size:103 final size:103
Alignment explanation
Indices: 80951--81176 Score: 364
Period size: 103 Copynumber: 2.2 Consensus size: 103
80941 GTCGAGGGTC
* * * *
80951 TATGTGGTCATTCAGGATATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
81016 TTGATCCTTGGCATATGTATATGATTCATAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCATAAGGAATGA
81054 TATGTGGTCCTTCAGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
81119 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCATAAGGAATGA
81157 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
81177 TATTATATGG
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 1 0.01
103 113 0.99
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCATAAGGAATGA
Found at i:81218 original size:23 final size:23
Alignment explanation
Indices: 81185--81252 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
81175 ATTATTATAT
* *
81185 GGCACTACGGTGTAATTGTACGC
1 GGCACTACGGTGCAATTATACGC
* * *
81208 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTATACGC
*
81231 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
81253 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:84435 original size:64 final size:64
Alignment explanation
Indices: 84346--84540 Score: 318
Period size: 64 Copynumber: 3.0 Consensus size: 64
84336 GGAGCGTCTG
* * * *
84346 TCAACAAACAACTTTACAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTTTAC
1 TCAACAAACAATTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTAC
* *
84410 TCAACAAACTATTTTCCAGTTTCATTCAGAGTCAATTTCAATTTCACAGCGAAGGATATTGTAC
1 TCAACAAACAATTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTAC
* *
84474 TCAACAAACAATTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGAATATTGAAC
1 TCAACAAACAATTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTAC
84538 TCA
1 TCA
84541 CAATTTGCTC
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 121 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (64 bp):
TCAACAAACAATTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTAC
Found at i:84786 original size:43 final size:43
Alignment explanation
Indices: 84738--84858 Score: 199
Period size: 43 Copynumber: 2.8 Consensus size: 43
84728 TGAAGGGGTC
*
84738 ATCCACGATTTCAACTCCACGATGGAGGATATCGTACCAAC-G
1 ATCCACAATTTCAACTCCACGATGGAGGATATCGTACCAACAG
*
84780 AATCCACAATTTCAACTCCACGATAGAGGATATCGTACCAACAG
1 -ATCCACAATTTCAACTCCACGATGGAGGATATCGTACCAACAG
*
84824 ATCCACAATTTCAACTCCACAATGGAGGATATCGT
1 ATCCACAATTTCAACTCCACGATGGAGGATATCGT
84859 GCCCATACAT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
43 72 0.99
44 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
ATCCACAATTTCAACTCCACGATGGAGGATATCGTACCAACAG
Found at i:84871 original size:43 final size:41
Alignment explanation
Indices: 84737--84888 Score: 169
Period size: 43 Copynumber: 3.6 Consensus size: 41
84727 ATGAAGGGGT
* * *
84737 CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCAA
1 CATCCACAATTTCAACTCCACAATGGAGGATATCGTCCCAA
* * *
84778 CGAATCCACAATTTCAACTCCACGATAGAGGATATCGTACCAA
1 C--ATCCACAATTTCAACTCCACAATGGAGGATATCGTCCCAA
84821 CAGATCCACAATTTCAACTCCACAATGGAGGATATCGTGCCCATA
1 C--ATCCACAATTTCAACTCCACAATGGAGGATATCGT-CCCA-A
** *
84866 CATCCACGGTTTCAACTTCACAA
1 CATCCACAATTTCAACTCCACAA
84889 CGAAGGGAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.01
43 91 0.94
44 3 0.03
45 2 0.02
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (41 bp):
CATCCACAATTTCAACTCCACAATGGAGGATATCGTCCCAA
Found at i:85181 original size:43 final size:43
Alignment explanation
Indices: 85120--85214 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
85110 GCCATCTATA
* *
85120 ATTTCAACTCCACGACGGAGGATATCGTACCCACGA-ATCCATG
1 ATTTCAACTCCACGACGGAGGATATCATACCCAC-ACATCCACG
*
85163 ATTTCAACTCCACGACGGAGGATATCATGCCCACACATCCACG
1 ATTTCAACTCCACGACGGAGGATATCATACCCACACATCCACG
*
85206 GTTTCAACT
1 ATTTCAACT
85215 TCATGACGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 1 0.02
43 46 0.98
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (43 bp):
ATTTCAACTCCACGACGGAGGATATCATACCCACACATCCACG
Found at i:85505 original size:66 final size:66
Alignment explanation
Indices: 85392--85550 Score: 212
Period size: 66 Copynumber: 2.4 Consensus size: 66
85382 ACTTAACTTG
* * * * *
85392 GATTTCAACTTCTCGATGAAGGATATCCAATTCAAGGTTCAATTTCACGACGAAGGGGACA-TCT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGACATTC-
85456 AC
65 AC
* * * * *
85458 GATTTCAACTTCACGACGAATGATATCCAATTCTAGGCTCAACTTCACAATGAATGGGTCATTCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGACATTCA
85523 C
66 C
85524 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
85551 GTGATCATTT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 79 0.98
67 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (66 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGACATTCA
C
Found at i:85803 original size:84 final size:84
Alignment explanation
Indices: 85554--86340 Score: 842
Period size: 84 Copynumber: 9.4 Consensus size: 84
85544 GGATATCGTG
* * * *
85554 ATCATTTGCAGCTTAGCTCAAGGCAAGAAGGGCTATCT-TCTAACAAAAGACCTTCGAGTTCGAT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTC-AACCAAAGACCTTCGAGTTCGAT
*
85618 TACACTCAGCTCAAAGGCAC
65 TATACTCAGCTCAAAGGCAC
* * * *
85638 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTCAA-CAAAGACCTTTGAGTTCGATT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATT
85702 ATACTCAGCTCAAAGGCAC
66 ATACTCAGCTCAAAGGCAC
* * * * * * * * *
85721 ATCATTTGCAGTATAGCTTAAGTCGAGAAGTGCTATCTGCCAACCAAAGACCTTCGAGTTTGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATT
** *
85786 ACGCTCAGCTCCAAGGCAC
66 ATACTCAGCTCAAAGGCAC
* * * * *
85805 GTCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACATTCGAGTTCGATT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATT
85870 ATACTCAGCTCAAAGGCAC
66 ATACTCAGCTCAAAGGCAC
* * * * * * * *
85889 ATCATTTGCAGTATAGCTTAAGTCGAGAAGTGCTATCTGTCAACCAAAAACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATT
* *
85954 ATGCTCAGCTCCAAGGCAC
66 ATACTCAGCTCAAAGGCAC
* ** *
85973 GTCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTACCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATT
* * *
86038 ACACTTAGCTCTAAGGCAC
66 ATACTCAGCTCAAAGGCAC
* * * * *
86057 GTCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAATACCTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATT
* *
86122 ATATTCAGCTCAAAGGCAT
66 ATACTCAGCTCAAAGGCAC
* * * * * * * * * *
86141 ATCATTTGCAGTATAGCTTAAGTCGAGAAGAGTTATCTGTC-ATCAAATACCTTCGAGATCCGAT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAG-TTCGAT
* * * *
86205 TTTATTCAGCTCCAAGGTAC
65 TATACTCAGCTCAAAGGCAC
* * * * * * *
86225 GTCATTTGCAGCATAACTCAAGTCTAGAAGGGTTATGTATCAACAAAAGACCTTTTGAGTTCGAT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACC-TTCGAGTTCGAT
* ** *
86290 TATACTCAGCTTAAAGATAT
65 TATACTCAGCTCAAAGGCAC
*
86310 ATCTTTTGCAGCATAACTCAAGGCTAGAAGG
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGG
86341 ATTATCTACC
Statistics
Matches: 580, Mismatches: 118, Indels: 9
0.82 0.17 0.01
Matches are distributed among these distances:
83 84 0.14
84 435 0.75
85 56 0.10
86 5 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATT
ATACTCAGCTCAAAGGCAC
Found at i:86067 original size:252 final size:251
Alignment explanation
Indices: 85555--86375 Score: 1043
Period size: 252 Copynumber: 3.3 Consensus size: 251
85545 GATATCGTGA
* * * *
85555 TCATTTGCAGCTTAGCTCAAGGCAAGAAGGGCTATCT-TCTAACAAAAGACCTTCGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATC-AACAAAAGACCTTCGAGTTCGATT
* * * * * * * * *
85619 ACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTCAACAA
65 ATACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGTTATCTGTCAACAA
* * * * * * * *
85684 AGACCTTTGAGTTCGATTATACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGA
130 AAACCTTCGAGTTCGATTATACTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGTCTAGA
* * * * *
85749 AGTGCTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACG
195 AGGGCTATCTACCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACG
*
85806 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACATTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGATTA
* *
85871 TACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGTGCTATCTGTCAACCAA
66 TACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGTTATCTGTCAA-CAA
* * *
85936 AAACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCTAGA
130 AAACCTTCGAGTTCGATTATACTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGTCTAGA
*
86001 AGGGCTATCTACCAACCAAAGACCTTCGAGTTCGACTACACTTAGCTCTAAGGCACG
195 AGGGCTATCTACCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACG
*
86058 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAATACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGATTA
* * *
86123 TATTCAGCTCAAAGGCATATCATTTGCAGTATAGCTTAAGTCGAGAAGAGTTATCTGTCATCAAA
66 TACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGTTATCTGTCAACAAA
* * * * *
86188 TACCTTCGAGATCCGATTTTATTCAGCTCCAAGGTACGTCATTTGCAGCATAACTCAAGTCTAGA
131 AACCTTCGAG-TTCGATTATACTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGTCTAGA
* * * * * * * ** **
86253 AGGGTTATGTATCAACAAAAGACCTTTTGAGTTCGATTATACTCAGCT-TAAAGATATA
195 AGGGCTATCTACCAACCAAAGACC-TTCGAGTTCGACTACACTCAGCTCT-AAGGCACG
* * * * * *
86311 TCTTTTGCAGCATAACTCAAGGCTAGAAGGATTATCTACCAACATCAAGACTTTTGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACA-AAAGACCTTCGAGTTCGATT
86376 TCATTCATCT
Statistics
Matches: 498, Mismatches: 66, Indels: 9
0.87 0.12 0.02
Matches are distributed among these distances:
251 121 0.24
252 297 0.60
253 64 0.13
254 16 0.03
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (251 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGATTA
TACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGTTATCTGTCAACAAA
AACCTTCGAGTTCGATTATACTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGTCTAGAA
GGGCTATCTACCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACG
Found at i:96007 original size:65 final size:63
Alignment explanation
Indices: 95905--96053 Score: 221
Period size: 65 Copynumber: 2.3 Consensus size: 63
95895 TGAACTTGTA
* *
95905 ATGTTTTAAGTTTGTTG-GA-TAAAATTATTATGTTTTATGGTTATTGGATATTAAAATAATT
1 ATGTTTTAAGTTTGTTGATATTAAAATTATTATGTTTTATGGTTACTGGATATTAAAATAATT
* *
95966 ATGTTTTTAAGTTTGTTGTATATTAAAATTATTATGTTTTATGTTTACTGGATATTGAAATAATT
1 ATG-TTTTAAGTTTGTTG-ATATTAAAATTATTATGTTTTATGGTTACTGGATATTAAAATAATT
96031 ATGTTTTAAGTTTGTTGGATATT
1 ATGTTTTAAGTTTGTT-GATATT
96054 GGAATTGTTA
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
61 3 0.04
62 14 0.18
64 19 0.24
65 43 0.54
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.53
Consensus pattern (63 bp):
ATGTTTTAAGTTTGTTGATATTAAAATTATTATGTTTTATGGTTACTGGATATTAAAATAATT
Found at i:96054 original size:32 final size:32
Alignment explanation
Indices: 95905--96079 Score: 194
Period size: 32 Copynumber: 5.5 Consensus size: 32
95895 TGAACTTGTA
95905 ATGTTTTAAGTTTGTTGG--A-TAAAATTATT
1 ATGTTTTAAGTTTGTTGGATATTAAAATTATT
* * * *
95934 ATGTTTTATGGTTATTGGATATTAAAATAATT
1 ATGTTTTAAGTTTGTTGGATATTAAAATTATT
*
95966 ATGTTTTTAAGTTTGTTGTATATTAAAATTATT
1 ATG-TTTTAAGTTTGTTGGATATTAAAATTATT
* ** * *
95999 ATGTTTTATGTTTACTGGATATTGAAATAATT
1 ATGTTTTAAGTTTGTTGGATATTAAAATTATT
** *
96031 ATGTTTTAAGTTTGTTGGATATTGGAATTGTT
1 ATGTTTTAAGTTTGTTGGATATTAAAATTATT
*
96063 ATATTTTAAGTTTGTTG
1 ATGTTTTAAGTTTGTTG
96080 AGTTTTGGAA
Statistics
Matches: 120, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.12
31 1 0.01
32 77 0.64
33 27 0.22
ACGTcount: A:0.29, C:0.01, G:0.17, T:0.53
Consensus pattern (32 bp):
ATGTTTTAAGTTTGTTGGATATTAAAATTATT
Found at i:96088 original size:32 final size:32
Alignment explanation
Indices: 95905--96108 Score: 114
Period size: 32 Copynumber: 6.4 Consensus size: 32
95895 TGAACTTGTA
* * *
95905 ATGTTTTAAGTTTGTTGGATA---AAATTATT
1 ATGTTTTAAGTTTGTTGGATATTGGAAGTGTT
* * * * * *
95934 ATGTTTTATGGTTATTGGATATT-AAAATAATT
1 ATGTTTTAAGTTTGTTGGATATTGGAAGT-GTT
* ** * *
95966 ATGTTTTTAAGTTTGTTGTATATTAAAATTATT
1 ATG-TTTTAAGTTTGTTGGATATTGGAAGTGTT
* ** * *
95999 ATGTTTTATGTTTACTGGATATT-GAAATAATT
1 ATGTTTTAAGTTTGTTGGATATTGGAAGT-GTT
*
96031 ATGTTTTAAGTTTGTTGGATATTGGAATTGTT
1 ATGTTTTAAGTTTGTTGGATATTGGAAGTGTT
* *
96063 ATATTTTAAGTTTGTT-GAGTTTTGGAAGTGTT
1 ATGTTTTAAGTTTGTTGGA-TATTGGAAGTGTT
* *
96095 GTGTTCTAAGTTTG
1 ATGTTTTAAGTTTG
96109 ATGGTTATAA
Statistics
Matches: 141, Mismatches: 26, Indels: 13
0.78 0.14 0.07
Matches are distributed among these distances:
29 18 0.13
31 9 0.06
32 84 0.60
33 26 0.18
34 4 0.03
ACGTcount: A:0.27, C:0.01, G:0.19, T:0.52
Consensus pattern (32 bp):
ATGTTTTAAGTTTGTTGGATATTGGAAGTGTT
Found at i:100027 original size:2 final size:2
Alignment explanation
Indices: 100022--100064 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
100012 AATTTATAAA
100022 AT 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 AT
100064 A
1 A
100065 AATTTATAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:101449 original size:25 final size:24
Alignment explanation
Indices: 101421--101469 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
101411 CGTGATTACA
101421 AGAAAATATA-ATTAGTAAATTATGT
1 AGAAAA-ATAGATTA-TAAATTATGT
101446 AGAAAAATAGTATTATAAATTATG
1 AGAAAAATAG-ATTATAAATTATG
101470 AAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.14
25 15 0.68
26 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (24 bp):
AGAAAAATAGATTATAAATTATGT
Found at i:103598 original size:7 final size:7
Alignment explanation
Indices: 103586--103616 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
103576 AGAATAGCAC
103586 CGGTCAA
1 CGGTCAA
103593 CGGTCAA
1 CGGTCAA
103600 CGGTCAA
1 CGGTCAA
103607 CGGTCAA
1 CGGTCAA
103614 CGG
1 CGG
103617 GTTTGACCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:103647 original size:18 final size:18
Alignment explanation
Indices: 103626--103677 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
103616 GGTTTGACCC
103626 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
103644 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
103662 GGTCGGGTAAACGGGT
1 GGTCGGGTAAACGGGT
103678 AAACGGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.15, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:103720 original size:11 final size:10
Alignment explanation
Indices: 103690--103741 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
103680 ACGGGTCGTG
103690 ACCGGTC-AA
1 ACCGGTCAAA
103699 ACCGGTCAAA
1 ACCGGTCAAA
103709 ACCGGTTCAAA
1 ACCGG-TCAAA
*
103720 ACCGGT-TAA
1 ACCGGTCAAA
103729 ACCGGTCAAA
1 ACCGGTCAAA
103739 ACC
1 ACC
103742 AGTTTCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:105290 original size:14 final size:15
Alignment explanation
Indices: 105244--105292 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
105234 ATTATTCTTA
105244 TAATT-AATATTGATT
1 TAATTGAATATTGA-T
* *
105259 TAATTTAA-ATTAAT
1 TAATTGAATATTGAT
105273 TAATTGAATATTGA-
1 TAATTGAATATTGAT
105287 TAATTG
1 TAATTG
105293 TTGAATGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 14 0.48
15 13 0.45
16 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (15 bp):
TAATTGAATATTGAT
Found at i:107302 original size:2 final size:2
Alignment explanation
Indices: 107295--107363 Score: 54
Period size: 2 Copynumber: 35.0 Consensus size: 2
107285 CAAATTCATA
* * * *
107295 AT AT AT AT AT AT AT AT AT CAGT -T TT A- AT -T AT AT TT AA AT TT
1 AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT
*
107336 AT AA 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
107364 CGCTTTTAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
1 3 0.06
2 48 0.91
3 1 0.02
4 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:113706 original size:18 final size:18
Alignment explanation
Indices: 113683--113726 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
113673 GAGGGATTAT
113683 CAGTGGTCCTTCGAGACA
1 CAGTGGTCCTTCGAGACA
* *
113701 CAGTGGTCTTTCGGGACA
1 CAGTGGTCCTTCGAGACA
113719 CAGTGGTC
1 CAGTGGTC
113727 ATTCAGGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (18 bp):
CAGTGGTCCTTCGAGACA
Found at i:113735 original size:18 final size:17
Alignment explanation
Indices: 113683--113736 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
113673 GAGGGATTAT
*
113683 CAGTGGTCCTTCGAGACA
1 CAGTGGTCATTCG-GACA
*
113701 CAGTGGTCTTTCGGGACA
1 CAGTGGTCATTC-GGACA
113719 CAGTGGTCATTCAGGACA
1 CAGTGGTCATTC-GGACA
113737 AATTTCTACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 31 0.97
19 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (17 bp):
CAGTGGTCATTCGGACA
Found at i:117120 original size:2 final size:2
Alignment explanation
Indices: 117113--117137 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
117103 TACAAATTCC
117113 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
117138 CTAACTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:120114 original size:19 final size:19
Alignment explanation
Indices: 120090--120142 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
120080 CGAATGCAAT
*
120090 TAGTGCATCGATGTATAAG
1 TAGTGCATCGATGCATAAG
120109 TAGTGCATCGATGCATAAG
1 TAGTGCATCGATGCATAAG
* *
120128 GAGTGCATTGATGCA
1 TAGTGCATCGATGCA
120143 CCCCCTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (19 bp):
TAGTGCATCGATGCATAAG
Found at i:120225 original size:24 final size:24
Alignment explanation
Indices: 120198--120251 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
120188 TGGGTAGTGT
120198 ATCGATGCACATGTTAAGGGATGC
1 ATCGATGCACATGTTAAGGGATGC
120222 ATCGATGCACATGTTAAGGGATGC
1 ATCGATGCACATGTTAAGGGATGC
120246 ATCGAT
1 ATCGAT
120252 ACACTGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (24 bp):
ATCGATGCACATGTTAAGGGATGC
Found at i:121131 original size:18 final size:18
Alignment explanation
Indices: 121024--121123 Score: 146
Period size: 18 Copynumber: 5.6 Consensus size: 18
121014 AAGGGACTAT
121024 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
* *
121042 TAGTGGTCCTTCGGTACA
1 CAGTGGTCCTTCGGGACA
*
121060 CAATGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
121078 CAGTAGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
121096 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
* *
121114 TAATGGTCCT
1 CAGTGGTCCT
121124 ACGAGACAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Done.