Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002350.1 Hibiscus syriacus cultivar Beakdansim tig00004795_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: 75076
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1269 original size:28 final size:28
Alignment explanation
Indices: 1229--1284 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1219 AAGTACTCCT
1229 AACTAAATTGATGTAAGC-ATGACATCAA
1 AACTAAATTGATGT-AGCAATGACATCAA
*
1257 AACTAAATTGATGTAGCAATGTCATCAA
1 AACTAAATTGATGTAGCAATGACATCAA
1285 TTAATTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (28 bp):
AACTAAATTGATGTAGCAATGACATCAA
Found at i:2992 original size:27 final size:27
Alignment explanation
Indices: 2929--2992 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
2919 TGCTGGAAGT
* *
2929 AGCTGTTGAAAAGTTAGGGGGTTAGGA
1 AGCTGTTGAGAAGTTAGGCGGTTAGGA
*
2956 AGCTGTTGAGAAGTTAGGCGGTTAGGG
1 AGCTGTTGAGAAGTTAGGCGGTTAGGA
2983 AGCTGTTGAG
1 AGCTGTTGAG
2993 CTTCTGTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.06, G:0.42, T:0.27
Consensus pattern (27 bp):
AGCTGTTGAGAAGTTAGGCGGTTAGGA
Found at i:3222 original size:26 final size:27
Alignment explanation
Indices: 3174--3236 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
3164 TTAACAGAAG
*
3174 CTCAACAGCTCCCTAACCGCCTAACTT
1 CTCAACAGCTCCCTAACCACCTAACTT
* *
3201 CTCAACAGCT-TCTAACTACCTAACTT
1 CTCAACAGCTCCCTAACCACCTAACTT
3227 CTCAACAGCT
1 CTCAACAGCT
3237 ACTGCCAGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.29, C:0.40, G:0.06, T:0.25
Consensus pattern (27 bp):
CTCAACAGCTCCCTAACCACCTAACTT
Found at i:7210 original size:3 final size:3
Alignment explanation
Indices: 7198--7239 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
7188 TAAATATTAT
7198 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
7240 TAAAACTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:8184 original size:14 final size:14
Alignment explanation
Indices: 8165--8197 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
8155 TGGGGAGTAA
*
8165 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
8179 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
8193 TCCCT
1 TCCCT
8198 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:9880 original size:18 final size:18
Alignment explanation
Indices: 9832--9874 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
9822 GCCGGTTCGG
* *
9832 TTCGAATAGTTCAGCGGT
1 TTCGAACAGTTCAGCAGT
*
9850 TTTGAACAGTTCAGCAGT
1 TTCGAACAGTTCAGCAGT
9868 TTCGAAC
1 TTCGAAC
9875 GATTCACTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (18 bp):
TTCGAACAGTTCAGCAGT
Found at i:11930 original size:2 final size:2
Alignment explanation
Indices: 11877--11919 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11867 AACTCTAATT
11877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11919 T
1 T
11920 TAGAATATAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14601 original size:13 final size:13
Alignment explanation
Indices: 14583--14607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14573 CAACCCGACC
14583 CGACCCGTTGACT
1 CGACCCGTTGACT
14596 CGACCCGTTGAC
1 CGACCCGTTGAC
14608 CATTGACCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:20681 original size:147 final size:147
Alignment explanation
Indices: 20414--20711 Score: 587
Period size: 147 Copynumber: 2.0 Consensus size: 147
20404 TGGGGGGTGC
20414 ACCTTAGCTTAAGTTAAGGGCAAATCTTGTTTGATGTGCTTATAAATAAACTCAAACAAGAAGTA
1 ACCTTAGCTTAAGTTAAGGGCAAATCTTGTTTGATGTGCTTATAAATAAACTCAAACAAGAAGTA
20479 GAAGTAATTGGGCACGAACCAACAACATCAACAGGTGAGAGTAAAAGATTTGCCAATATATTTGG
66 GAAGTAATTGGGCACGAACCAACAACATCAACAGGTGAGAGTAAAAGATTTGCCAATATATTTGG
20544 CATTGGCTTGCAAGGGA
131 CATTGGCTTGCAAGGGA
20561 ACCTTAGCTTAAGTTAAGGGCAAATCTTGTTTGATGTGCTTATAAATAAACTCAAACAAGAAGTA
1 ACCTTAGCTTAAGTTAAGGGCAAATCTTGTTTGATGTGCTTATAAATAAACTCAAACAAGAAGTA
*
20626 GAAGTAATTGGGCACGAACCAGCAACATCAACAGGTGAGAGTAAAAGATTTGCCAATATATTTGG
66 GAAGTAATTGGGCACGAACCAACAACATCAACAGGTGAGAGTAAAAGATTTGCCAATATATTTGG
20691 CATTGGCTTGCAAGGGA
131 CATTGGCTTGCAAGGGA
20708 ACCT
1 ACCT
20712 AGATCTTGTT
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 150 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (147 bp):
ACCTTAGCTTAAGTTAAGGGCAAATCTTGTTTGATGTGCTTATAAATAAACTCAAACAAGAAGTA
GAAGTAATTGGGCACGAACCAACAACATCAACAGGTGAGAGTAAAAGATTTGCCAATATATTTGG
CATTGGCTTGCAAGGGA
Found at i:23627 original size:24 final size:25
Alignment explanation
Indices: 23572--23628 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
23562 GTCCTTGTGT
*
23572 TTATGTTTATTTTTATTTTATGTTGC
1 TTAT-TTTACTTTTATTTTATGTTGC
23598 TT-TTTTACTTTTACTTTTAT-TTG-
1 TTATTTTACTTTTA-TTTTATGTTGC
23621 TTATTTTA
1 TTATTTTA
23629 AATATTGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 2 0.07
24 17 0.61
25 7 0.25
26 2 0.07
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (25 bp):
TTATTTTACTTTTATTTTATGTTGC
Found at i:26761 original size:3 final size:3
Alignment explanation
Indices: 26753--26813 Score: 86
Period size: 3 Copynumber: 19.3 Consensus size: 3
26743 AAAACCCCGG
*
26753 TTC TTC TTC TTC ATTC TTCC TTC TTC CTC TTC TTC TTTC TTC TTC TTC
1 TTC TTC TTC TTC -TTC TT-C TTC TTC TTC TTC TTC -TTC TTC TTC TTC
26801 TTC TTC TTC TTC T
1 TTC TTC TTC TTC T
26814 CTCACCCCCA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 44 0.83
4 9 0.17
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:26841 original size:32 final size:33
Alignment explanation
Indices: 26802--26879 Score: 122
Period size: 34 Copynumber: 2.4 Consensus size: 33
26792 TTCTTCTTCT
*
26802 TCTTCTTCTTCTCTC-ACCCCCATTAACCTCAC
1 TCTTCTTCTTCTCTCAACCCCCATTAACCCCAC
*
26834 TCTTCTTCTTCTCTCATACCCCTATTAACCCCAC
1 TCTTCTTCTTCTCTCA-ACCCCCATTAACCCCAC
26868 TCTTCTTCTTCT
1 TCTTCTTCTTCT
26880 TCTTCTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 15 0.36
34 27 0.64
ACGTcount: A:0.14, C:0.44, G:0.00, T:0.42
Consensus pattern (33 bp):
TCTTCTTCTTCTCTCAACCCCCATTAACCCCAC
Found at i:29571 original size:3 final size:3
Alignment explanation
Indices: 29563--29645 Score: 121
Period size: 3 Copynumber: 26.3 Consensus size: 3
29553 GGGTGTGAGG
29563 GAA GAA GAA GAAA GAA GAA GAA GAAA GAA GAAA GAA GAA GAA GAA GAA
1 GAA GAA GAA G-AA GAA GAA GAA G-AA GAA G-AA GAA GAA GAA GAA GAA
*
29611 GAA GAA GAA GAA GAA GAA GAG GAA GAA GAAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA G
29646 GAACAATGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
3 62 0.84
4 12 0.16
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29574 original size:37 final size:34
Alignment explanation
Indices: 29494--29573 Score: 133
Period size: 34 Copynumber: 2.4 Consensus size: 34
29484 GTGGGAGAAT
29494 AGAAGAAGAAGAGTGAAGTTAACAGGGGTGTGAG
1 AGAAGAAGAAGAGTGAAGTTAACAGGGGTGTGAG
* *
29528 AGAAGAAGAAGAGTGAGGTTAACGGGGGTGTGAG
1 AGAAGAAGAAGAGTGAAGTTAACAGGGGTGTGAG
*
29562 GGAAGAAGAAGA
1 AGAAGAAGAAGA
29574 AAGAAGAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.41, C:0.03, G:0.44, T:0.12
Consensus pattern (34 bp):
AGAAGAAGAAGAGTGAAGTTAACAGGGGTGTGAG
Found at i:31280 original size:3 final size:3
Alignment explanation
Indices: 31269--31332 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
31259 TTTTTTTCCG
** * *
31269 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TCA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31314 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
31333 CAAATTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 44 0.86
4 3 0.06
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:34921 original size:16 final size:16
Alignment explanation
Indices: 34882--34921 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
34872 TTATTCATTT
*
34882 TGGGTAGATAACATGC
1 TGGGTAGATAACATGA
*
34898 TCGGGTAGATATCATGA
1 T-GGGTAGATAACATGA
34915 TGGGTAG
1 TGGGTAG
34922 GTGTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.28, C:0.10, G:0.35, T:0.28
Consensus pattern (16 bp):
TGGGTAGATAACATGA
Found at i:39402 original size:31 final size:31
Alignment explanation
Indices: 39367--39426 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
39357 CCTTGAGGCA
39367 GTTTCTC-TATAAATACAAA-ATCTTTGAGGTT
1 GTTTCTCTTA-AAATA-AAACATCTTTGAGGTT
39398 GTTTCTCTTAAAATAAAACCATCTTTGAG
1 GTTTCTCTTAAAATAAAA-CATCTTTGAG
39427 TCGTTTCCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.12
31 12 0.46
32 11 0.42
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (31 bp):
GTTTCTCTTAAAATAAAACATCTTTGAGGTT
Found at i:39500 original size:32 final size:31
Alignment explanation
Indices: 39386--39512 Score: 80
Period size: 32 Copynumber: 4.0 Consensus size: 31
39376 TAAATACAAA
* *
39386 ATCTTTGAGGTTGTTTCTCTTAAAATAAAACC
1 ATCTTTGA-GTTGTTTCTCTTAAAACAAAATC
* * * **
39418 ATCTTTGAGTCGTTTCCCTTGAAACGAATTTTC
1 ATCTTTGAGTTGTTTCTCTTAAAAC-AA-AATC
* *
39451 A-CTCTTGAGACAT-TTTCTCTTAAAACAAGATC
1 ATCT-TTGAG--TTGTTTCTCTTAAAACAAAATC
*
39483 ATCTTTGAGTTTGTTTCTCTGAAAA-AAAAT
1 ATCTTTGAG-TTGTTTCTCTTAAAACAAAAT
39513 GTTTTATCCC
Statistics
Matches: 71, Mismatches: 17, Indels: 15
0.69 0.17 0.15
Matches are distributed among these distances:
31 18 0.25
32 31 0.44
33 11 0.15
34 11 0.15
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (31 bp):
ATCTTTGAGTTGTTTCTCTTAAAACAAAATC
Found at i:39694 original size:36 final size:36
Alignment explanation
Indices: 39621--39695 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
39611 AACAAACATC
*
39621 TTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCA
1 TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
* *
39657 TTTGAGA-CAGTTTTCCTTTAAAC-AATCTTTGAGTCA
1 TTTGAGATCA-TTTCCCTTTAAACGAAT-TTTGACTCA
39693 TTT
1 TTT
39696 CTTTTGAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (36 bp):
TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
Found at i:39712 original size:63 final size:62
Alignment explanation
Indices: 39614--39731 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 62
39604 GAAACAAAAC
*
39614 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTGAGACAGTTTTCCTTT
* *
39676 AAACAATCTTTGAG-TCATTT-CTTTTGAAACAAAATTTTGTCTCTTTTGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCATTTGAGACAGTT
39732 GCTTTTGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
61 4 0.08
62 14 0.28
63 32 0.64
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (62 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTGAGACAGTTTTCCTTT
Found at i:39881 original size:40 final size:40
Alignment explanation
Indices: 39819--40151 Score: 210
Period size: 40 Copynumber: 7.9 Consensus size: 40
39809 CTTTATATGG
* * *
39819 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGA
1 CCAGACGTCCTCATCACGTAGGAACCGTGTCATCCCTAGA
** * * *
39859 CCAGATATCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGACGTCCTCATCACGTAGGAACCGTGTCATCCCTAG---A
* *
39902 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGACGTCCTCATCACGTAGGAACCGTGTCATC-CC--TAGA
* * *
39945 TGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGA
1 ---CCAGACGTCCTCATCACGTAGGAACCGTGTCATCCCTAGA
* * *
39988 CCAGATC-TCTTCATCACGTATGAGCCGTGTCA-CCCTAGATAA
1 CCAGA-CGTCCTCATCACGTAGGAACCGTGTCATCCCTAG---A
* *
40030 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGACGTCCTCATCACGTAGGAACCGTGTCATC-CC--TAGA
* * * *
40073 TGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATTCCC-CGA
1 ---CCAG-ACGTCCTCATCACGTAGGAACCGTGTCA-TCCCTAGA
* *
40116 CCAGATC-TCTTCATCACGTAGGAGCCGTGTCA-CCCT
1 CCAGA-CGTCCTCATCACGTAGGAACCGTGTCATCCCT
40152 TAGATGACCA
Statistics
Matches: 232, Mismatches: 36, Indels: 51
0.73 0.11 0.16
Matches are distributed among these distances:
38 3 0.01
39 6 0.03
40 85 0.37
41 2 0.01
42 26 0.11
43 37 0.16
44 3 0.01
45 2 0.01
46 65 0.28
47 3 0.01
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (40 bp):
CCAGACGTCCTCATCACGTAGGAACCGTGTCATCCCTAGA
Found at i:39962 original size:46 final size:45
Alignment explanation
Indices: 39815--40108 Score: 226
Period size: 46 Copynumber: 6.8 Consensus size: 45
39805 ACTCCTTTAT
* *
39815 ATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATC-CC-CAG
1 ATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTTAG
*** * *
39858 A---CCAGATATCCTCATCACGTAGGAGCCGTGTCA--ACCATAG
1 ATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTTAG
** *
39898 ATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAG
1 ATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACC-TTAG
* *
39944 ATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATC-CC-CAG
1 ATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTTAG
* * * *
39987 A---CCAGATC-TCTTCATCACGTATGAGCCGTGTCA-C-CC-TAG
1 ATGGCCAG-CCGTCCTCATCACGTAGGAACCGTGTCATCACCTTAG
** *
40026 ATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAG
1 ATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACC-TTAG
* * * *
40072 ATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCAT
1 ATGGCCAG-CCGTCCTCATCACGTAGGAACCGTGTCAT
40109 TCCCCGACCA
Statistics
Matches: 198, Mismatches: 35, Indels: 33
0.74 0.13 0.12
Matches are distributed among these distances:
39 8 0.04
40 55 0.28
41 2 0.01
42 25 0.13
43 32 0.16
44 2 0.01
45 5 0.03
46 68 0.34
47 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (45 bp):
ATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTTAG
Found at i:40045 original size:82 final size:85
Alignment explanation
Indices: 39948--40107 Score: 236
Period size: 82 Copynumber: 1.9 Consensus size: 85
39938 CTTTAGATGG
* *
39948 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATC-CC-CAGA-CCAGATCTCTTCATCACGTATG
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTCAGAGCCAGAACTCTTCATCACGTATG
40010 AGCCGTGTCACCCTAGATAA
66 AGCCGTGTCACCCTAGATAA
* *
40030 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACC-TCAGA--GCCAGAACTCTTCATCACGT
40095 ATGAGCCGTGTCA
63 ATGAGCCGTGTCA
40108 TTCCCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
82 32 0.47
83 2 0.03
85 3 0.04
88 31 0.46
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (85 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTCAGAGCCAGAACTCTTCATCACGTATG
AGCCGTGTCACCCTAGATAA
Found at i:40113 original size:129 final size:128
Alignment explanation
Indices: 39808--40162 Score: 552
Period size: 128 Copynumber: 2.8 Consensus size: 128
39798 AACCATAACT
* * * *
39808 CCTTTATATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATATCCTCAT
1 CCTTTAGATGGCCAGACGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
*
39873 CACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 CACGTAGGAGCCGTGTC-ACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
*
39937 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
1 CCTTTAGATGGCCAGACGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
*
40002 CACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 CACGTAGGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
* * * *
40065 CCTTTAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTC
1 CCTTTAGATGGCCAG-ACGTCCTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTC
*
40128 ATCACGTAGGAGCCGTGTCACCCTTAGATGACCAG
64 ATCACGTAGGAGCCGTGTCACCC-TAGATAACCAG
40163 ACCTCTTCAT
Statistics
Matches: 211, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
128 117 0.55
129 94 0.45
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (128 bp):
CCTTTAGATGGCCAGACGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
CACGTAGGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
Found at i:40179 original size:43 final size:43
Alignment explanation
Indices: 39869--40189 Score: 223
Period size: 46 Copynumber: 7.5 Consensus size: 43
39859 CCAGATATCC
* * * *
39869 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCACCCTTAGATGACCAGACC-TCT
* * * *
39912 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAG-CCGTCC
1 TCATCACGTAGGAGCCGTG---TCACCCTTAGATGACCAGACC-TCT
* * * *
39958 TCATCATGTAGGAACCGTGTCATCCC---CA-GACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-CCCTTAGATGACCAGACCTCT
* * *
39998 TCATCACGTATGAGCCGTGTCACCC-TAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCACCCTTAGATGACCAGACC-TCT
* * * *
40040 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTG---TCACCCTTAGATGACCAGACCTCT
* **** *
40086 TCATCACGTATGAGCCGTGTCA---TTCCCCGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCACCCTTAGATGACCAGACCTCT
40126 TCATCACGTAGGAGCCGTGTCACCCTTAGATGACCAGACCTCT
1 TCATCACGTAGGAGCCGTGTCACCCTTAGATGACCAGACCTCT
** *
40169 TCATTGCGTAGGAGCAGTGTC
1 TCATCACGTAGGAGCCGTGTC
40190 GTCCCCACCA
Statistics
Matches: 218, Mismatches: 43, Indels: 34
0.74 0.15 0.12
Matches are distributed among these distances:
39 3 0.01
40 59 0.27
41 4 0.02
42 24 0.11
43 55 0.25
44 2 0.01
45 5 0.02
46 65 0.30
47 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.25
Consensus pattern (43 bp):
TCATCACGTAGGAGCCGTGTCACCCTTAGATGACCAGACCTCT
Found at i:40367 original size:3 final size:3
Alignment explanation
Indices: 40356--40416 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
40346 TTTTTTTCCG
** * *
40356 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TCA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40401 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
40417 CAAATTTTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:48218 original size:22 final size:22
Alignment explanation
Indices: 48170--48239 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
48160 AATTCTTTTC
48170 TTTATTATCTCATAAA-TA-TTAT
1 TTTATTATCT--TAAATTATTTAT
*
48192 CTTATTATCTTAAATTATTTATT
1 TTTATTATCTTAAATTATTTA-T
*
48215 TTATATTAT-TT-ATTTATTTAT
1 TT-TATTATCTTAAATTATTTAT
48236 TTTA
1 TTTA
48240 ATTTTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
20 6 0.15
21 5 0.12
22 20 0.49
23 4 0.10
24 6 0.15
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATTATCTTAAATTATTTAT
Found at i:55690 original size:31 final size:31
Alignment explanation
Indices: 55655--55715 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
55645 TCGCGAGCCT
* *
55655 AAAATTTTCAAGCTCGACTCGAACTCGAAAG
1 AAAATATTCAAACTCGACTCGAACTCGAAAG
*
55686 AAAATATTGAAACTCGACTCGAACTCGAAA
1 AAAATATTCAAACTCGACTCGAACTCGAAA
55716 AGGCTCGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (31 bp):
AAAATATTCAAACTCGACTCGAACTCGAAAG
Found at i:55794 original size:12 final size:12
Alignment explanation
Indices: 55777--55809 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
55767 GCTCGATTGA
55777 AGCTCGATTTTG
1 AGCTCGATTTTG
55789 AGCTCGATTTTG
1 AGCTCGATTTTG
55801 AGCTCGATT
1 AGCTCGATT
55810 CAAGCTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:55817 original size:11 final size:12
Alignment explanation
Indices: 55763--55818 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
55753 AGCTCGAGAC
55763 TCAAGCTCGA-T
1 TCAAGCTCGATT
*
55774 TGAAGCTCGATT
1 TCAAGCTCGATT
**
55786 TTGAGCTCGATT
1 TCAAGCTCGATT
**
55798 TTGAGCTCGA-T
1 TCAAGCTCGATT
55809 TCAAGCTCGA
1 TCAAGCTCGA
55819 ACTCGAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
11 18 0.46
12 21 0.54
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (12 bp):
TCAAGCTCGATT
Found at i:55833 original size:29 final size:29
Alignment explanation
Indices: 55791--55853 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
55781 CGATTTTGAG
*
55791 CTCGATTTTGAGCTCGATTCAAGCTCGAA
1 CTCGAATTTGAGCTCGATTCAAGCTCGAA
55820 CTCGAATTTGAGCTCGATTCAAGCTCGAA
1 CTCGAATTTGAGCTCGATTCAAGCTCGAA
55849 CTCGA
1 CTCGA
55854 TTCAAGCTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (29 bp):
CTCGAATTTGAGCTCGATTCAAGCTCGAA
Found at i:55854 original size:17 final size:17
Alignment explanation
Indices: 55832--55868 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
55822 CGAATTTGAG
55832 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
55849 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
55866 CTC
1 CTC
55869 AAACTCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:55877 original size:29 final size:29
Alignment explanation
Indices: 55801--55864 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
55791 CTCGATTTTG
**
55801 AGCTCGATTCAAGCTCGAACTCGAATTTG
1 AGCTCGATTCAAGCTCGAACTCGAATTCA
55830 AGCTCGATTCAAGCTCGAACTCG-ATTCA
1 AGCTCGATTCAAGCTCGAACTCGAATTCA
55858 AGCTCGA
1 AGCTCGA
55865 ACTCAAACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 10 0.30
29 23 0.70
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (29 bp):
AGCTCGATTCAAGCTCGAACTCGAATTCA
Found at i:56276 original size:34 final size:31
Alignment explanation
Indices: 56235--56326 Score: 116
Period size: 30 Copynumber: 2.9 Consensus size: 31
56225 CCAGTTAAGC
56235 TTACTTACAAAAAGATGGCATCAACATGTCAAGT
1 TTACTTACAAAAAGATGG---CAACATGTCAAGT
* *
56269 TTACTTAC-AAGAGATTGCAACATGTCAAGT
1 TTACTTACAAAAAGATGGCAACATGTCAAGT
*
56299 TTACTTAC-AAAAGATTGCAACATGTCAA
1 TTACTTACAAAAAGATGGCAACATGTCAA
56327 CCAGTTAGCT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 40 0.73
33 7 0.13
34 8 0.15
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (31 bp):
TTACTTACAAAAAGATGGCAACATGTCAAGT
Found at i:56292 original size:30 final size:30
Alignment explanation
Indices: 56256--56326 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
56246 AAGATGGCAT
*
56256 CAACATGTCAAGTTTACTTACAAGAGATTG
1 CAACATGTCAAGTTTACTTACAAAAGATTG
56286 CAACATGTCAAGTTTACTTACAAAAGATTG
1 CAACATGTCAAGTTTACTTACAAAAGATTG
56316 CAACATGTCAA
1 CAACATGTCAA
56327 CCAGTTAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (30 bp):
CAACATGTCAAGTTTACTTACAAAAGATTG
Found at i:58470 original size:21 final size:22
Alignment explanation
Indices: 58431--58476 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
58421 CATAATTATA
* *
58431 TTAAGAGTTTAGGGTTTAGGAT
1 TTAAGAGTATAGGGCTTAGGAT
*
58453 TTAAGA-TATAGGGCTTAGGGT
1 TTAAGAGTATAGGGCTTAGGAT
58474 TTA
1 TTA
58477 GGGTTTGGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.28, C:0.02, G:0.30, T:0.39
Consensus pattern (22 bp):
TTAAGAGTATAGGGCTTAGGAT
Found at i:58488 original size:6 final size:7
Alignment explanation
Indices: 58437--58493 Score: 62
Period size: 7 Copynumber: 8.3 Consensus size: 7
58427 TATATTAAGA
58437 GTTTAGG
1 GTTTAGG
58444 GTTTAGG
1 GTTTAGG
* *
58451 ATTTAAG
1 GTTTAGG
* *
58458 ATATAGG
1 GTTTAGG
*
58465 GCTTAGG
1 GTTTAGG
58472 GTTTAGG
1 GTTTAGG
58479 GTTT-GG
1 GTTTAGG
58485 GTTTAGG
1 GTTTAGG
58492 GT
1 GT
58494 GTAATCTAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 6 0.15
7 35 0.85
ACGTcount: A:0.19, C:0.02, G:0.39, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Found at i:58495 original size:130 final size:123
Alignment explanation
Indices: 58336--58666 Score: 437
Period size: 130 Copynumber: 2.6 Consensus size: 123
58326 GATTAAGTGT
** *
58336 TTAGGGTTTAGGGCTTAAGGTTTAGGGTGTAATCTAACATGTGTTTAATTAAATGAGCTTTTATT
1 TTAGGGTTTAGGG-TTTGGGTTTAGGGTGTAATCTAACATGTGCTTAATTAAATGAGCTTTTATT
* * *
58401 TTTCTTTTAGTACCCTATCACATAATTATATTAAGAGTTTAGGGTTTAGGATTTAAGATATAGGG
65 TTTCTTTTAGTACCCTATCACATAATTAGATTAAGAGCTTAGGGCTTAGG------GAT-TAGGG
*
58466 C
123 A
* *
58467 TTAGGGTTTAGGGTTTGGGTTTAGGGTGTAATCTAACACGTGCTTAATTAAATAAGCTTTTATTT
1 TTAGGGTTTAGGGTTTGGGTTTAGGGTGTAATCTAACATGTGCTTAATTAAATGAGCTTTTATTT
**
58532 TTCTTTTAAAACCCTATCACATAATTAGATTAAGAGCTTAGGGCTTAGGGATTAGGGA
66 TTCTTTTAGTACCCTATCACATAATTAGATTAAGAGCTTAGGGCTTAGGGATTAGGGA
** * *
58590 TTAGAATTTAGGGTTTAGGGTTTAGGATGTAATCTAACATGTGGTTAATTAAATGAGCTTTTATT
1 TTAGGGTTTAGGGTTT-GGGTTTAGGGTGTAATCTAACATGTGCTTAATTAAATGAGCTTTTATT
*
58655 TTTGTTTTAGTA
65 TTTCTTTTAGTA
58667 ATATACAATG
Statistics
Matches: 179, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
123 19 0.11
124 56 0.31
130 91 0.51
131 13 0.07
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (123 bp):
TTAGGGTTTAGGGTTTGGGTTTAGGGTGTAATCTAACATGTGCTTAATTAAATGAGCTTTTATTT
TTCTTTTAGTACCCTATCACATAATTAGATTAAGAGCTTAGGGCTTAGGGATTAGGGA
Found at i:63183 original size:18 final size:18
Alignment explanation
Indices: 63133--63185 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
63123 CAAAGTAAAA
* * *
63133 TATTATTGTATTAAATTT
1 TATTATTATATAAAATAT
* *
63151 TATATAATATTTAAAATAT
1 TAT-TATTATATAAAATAT
63170 TATTATTATATAAAAT
1 TATTATTATATAAAAT
63186 TAAAAATTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TATTATTATATAAAATAT
Found at i:68086 original size:2 final size:2
Alignment explanation
Indices: 68079--68111 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
68069 TACTTGATTA
68079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
68112 AAATTTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69444 original size:10 final size:11
Alignment explanation
Indices: 69418--69442 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
69408 CAAAATCATT
69418 AAAATTAAAAA
1 AAAATTAAAAA
69429 AAAATTAAAAA
1 AAAATTAAAAA
69440 AAA
1 AAA
69443 TTGGAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATTAAAAA
Done.