Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002846.1 Hibiscus syriacus cultivar Beakdansim tig00005858_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: 98313
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:3006 original size:29 final size:31
Alignment explanation
Indices: 2973--3044 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
2963 AAAATTTTGG
* *
2973 TTAGTGAGC-AAAATAT-AAATTTTGAAAGT
1 TTAGTGAGCTAAAATATAAAATTTGGAAAAT
*
3002 TTAGTG-GCTAAAGTATAAAATTTGGAAAAT
1 TTAGTGAGCTAAAATATAAAATTTGGAAAAT
*
3032 TTAGTGACCTAAA
1 TTAGTGAGCTAAA
3045 TGGTAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.06
29 12 0.33
30 17 0.47
31 5 0.14
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (31 bp):
TTAGTGAGCTAAAATATAAAATTTGGAAAAT
Found at i:3996 original size:10 final size:10
Alignment explanation
Indices: 3972--4006 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
3962 TTCATGTTTG
3972 AATCGAATCAA
1 AATCGAAT-AA
3983 AATCGAATAA
1 AATCGAATAA
3993 AATCGAATAA
1 AATCGAATAA
4003 AATC
1 AATC
4007 ATGAAAACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (10 bp):
AATCGAATAA
Found at i:4717 original size:21 final size:21
Alignment explanation
Indices: 4691--4732 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4681 CTTATGTTAT
4691 CGAACAAACATTGGTTTGCGA
1 CGAACAAACATTGGTTTGCGA
4712 CGAACAAACATTGGTTTGCGA
1 CGAACAAACATTGGTTTGCGA
4733 TGAGCCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (21 bp):
CGAACAAACATTGGTTTGCGA
Found at i:4963 original size:22 final size:23
Alignment explanation
Indices: 4923--4968 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
4913 TTCTATAGAA
4923 AATAGTATAGGAATTATTTTTAT
1 AATAGTATAGGAATTATTTTTAT
4946 AATAGTATAGG-ATTATTTTTAT
1 AATAGTATAGGAATTATTTTTAT
4968 A
1 A
4969 CTGTTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (23 bp):
AATAGTATAGGAATTATTTTTAT
Found at i:7983 original size:2 final size:2
Alignment explanation
Indices: 7976--8006 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7966 ACATGAACTC
7976 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 A
8007 CAAACATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8429 original size:23 final size:22
Alignment explanation
Indices: 8403--8445 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
8393 CACCGAAGTG
*
8403 CCACGTAGAAATGTCCATAAGGT
1 CCACATAGAAAT-TCCATAAGGT
*
8426 CCACATAGAAATTCCTTAAG
1 CCACATAGAAATTCCATAAG
8446 AATCATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (22 bp):
CCACATAGAAATTCCATAAGGT
Found at i:8936 original size:2 final size:2
Alignment explanation
Indices: 8929--8997 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
8919 CAGAGTCATC
8929 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
* *
8971 TA TA TA TA TA TA TA TA CA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8998 CATTTACCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13317 original size:4 final size:4
Alignment explanation
Indices: 13310--13349 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
13300 ATATATATAT
13310 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
13350 CATTTCCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:13760 original size:23 final size:23
Alignment explanation
Indices: 13727--13800 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
13717 CAGCTCGTAT
13727 AAATGCACCGAAGTGCCACGAAG
1 AAATGCACCGAAGTGCCACGAAG
* * * *
13750 GATTGCACCGAAGTGCCGA-GTAT
1 AAATGCACCGAAGTGCC-ACGAAG
*
13773 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGAAG
13796 AAATG
1 AAATG
13801 TCCATAAGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGAAG
Found at i:13814 original size:23 final size:22
Alignment explanation
Indices: 13788--13830 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
13778 CACCGAAGTG
*
13788 CCACGTAGAAATGTCCATAAGGA
1 CCACATAGAAAT-TCCATAAGGA
*
13811 CCACATAGAAATTCCTTAAG
1 CCACATAGAAATTCCATAAG
13831 AATCATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (22 bp):
CCACATAGAAATTCCATAAGGA
Found at i:16544 original size:64 final size:63
Alignment explanation
Indices: 16476--16656 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 63
16466 TTGGAACACT
* ***
16476 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
16540 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * *
16604 AGAGTGCATCGATGCATGGAGAT-TGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAG-TGTGCATCGATGCATGAAATGCATTCGATGTT
16657 CAATTAATTC
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
64 54 0.55
65 44 0.44
66 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:16632 original size:19 final size:17
Alignment explanation
Indices: 16608--16654 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
16598 ATATTCAGAG
16608 TGCATCGATGCATGGAGA
1 TGCATCGATGCATGGA-A
*
16626 TTGCATCGGTGCATGGAA
1 -TGCATCGATGCATGGAA
16644 TGCATTCGATG
1 TGCA-TCGATG
16655 TTCAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 6 0.24
19 15 0.60
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:16696 original size:65 final size:64
Alignment explanation
Indices: 16498--16705 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
16488 GCACCAAGTG
* * *
16498 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCT-GATGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATAGATGCATCGATGCATGAC-TG
16562 -
64 A
* *
16562 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG-TGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATAGATGCATCGATGCAT-GACT
16624 GA
63 GA
* * * *
16626 TTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATAGATGCATCGATGCATGTACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCATAGATGCATCGATGCATG-ACT
16690 GA
63 GA
*
16692 TGCATCGGTGCATG
1 TGCATCGATGCATG
16706 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
63 13 0.11
64 42 0.34
65 61 0.50
66 6 0.05
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATAGATGCATCGATGCATGACTGA
Found at i:23142 original size:22 final size:21
Alignment explanation
Indices: 23100--23139 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23090 GAGTTTGTTT
*
23100 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
23121 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
23140 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:25132 original size:64 final size:63
Alignment explanation
Indices: 25064--25244 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
25054 TTGGAACACT
* ***
25064 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
25128 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
25192 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
25245 CAATTAATTC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
64 54 0.55
65 45 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:25216 original size:19 final size:19
Alignment explanation
Indices: 25192--25242 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
25182 GAAAATATTC
25192 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
25211 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
25230 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
25243 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:25218 original size:65 final size:65
Alignment explanation
Indices: 25085--25244 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
25075 TGCACCAAGT
* ***
25085 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
25149 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
25213 A
65 A
* *
25214 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
25245 CAATTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:25284 original size:65 final size:63
Alignment explanation
Indices: 25086--25293 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 63
25076 GCACCAAGTG
* * *
25086 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGAC-TGA
*
25150 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCAT-GACT
25212 GA
62 GA
* * * *
25214 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGTACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATG-ACT
25278 GA
62 GA
*
25280 TGCATCGGTGCATG
1 TGCATCGATGCATG
25294 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
63 11 0.09
64 44 0.36
65 63 0.51
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGACTGA
Found at i:26706 original size:20 final size:20
Alignment explanation
Indices: 26681--26736 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 20
26671 CCTTTGAAGA
26681 GGTATCGATACCC-ACTATAG
1 GGTATCGATACCCAACTA-AG
26701 GGTATCGGTACTACCCTAACTAAG
1 GGTATC-G-A-TACCC-AACTAAG
26725 GGTATCGATACC
1 GGTATCGATACC
26737 TAGACGGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 6 0.19
21 5 0.16
22 2 0.06
23 6 0.19
24 8 0.26
25 4 0.13
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCCAACTAAG
Found at i:28031 original size:60 final size:60
Alignment explanation
Indices: 27963--28197 Score: 380
Period size: 60 Copynumber: 3.9 Consensus size: 60
27953 GCTTGTTCTG
*
27963 ATCTTCCATATTGGACTCTTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGTATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGTATGT
* *
28023 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTATACGGTAAGTCCTTATGGATGTCTGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGTATGT
* * * * *
28083 ATTTTTCATATTGGACTTCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGTTTGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGTATGT
* *
28143 ATCTTCCATAATGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATG
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATG
28198 CTTGTTTTGG
Statistics
Matches: 162, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 162 1.00
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (60 bp):
ATCTTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGTATGT
Found at i:29097 original size:31 final size:30
Alignment explanation
Indices: 29062--29134 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
29052 TACATGTCAT
*
29062 ATAATCACTTCAAATAACATGATATATATAC
1 ATAATCACTTCAAATAACATAATATATAT-C
* **
29093 ATAATCAATTTGAATAACATAATATATATC
1 ATAATCACTTCAAATAACATAATATATATC
29123 ATATTATCACTT
1 ATA--ATCACTT
29135 TTAATTTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 4 0.11
31 25 0.71
32 6 0.17
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.37
Consensus pattern (30 bp):
ATAATCACTTCAAATAACATAATATATATC
Found at i:51726 original size:29 final size:29
Alignment explanation
Indices: 51672--51727 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
51662 TTGTAATTAC
* * *
51672 TGTTTAGTCCCTTAAGTTTTTGTTTTTGT
1 TGTTTAGTCCCTTAAGATTATATTTTTGT
51701 TGTTTAG-CCCTTTAAGATTATATTTTT
1 TGTTTAGTCCC-TTAAGATTATATTTTT
51728 TCTATTTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (29 bp):
TGTTTAGTCCCTTAAGATTATATTTTTGT
Found at i:55629 original size:2 final size:2
Alignment explanation
Indices: 55620--55652 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
55610 ATAGAATCCG
55620 TA TA -A 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
55653 CAATAAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:57492 original size:31 final size:29
Alignment explanation
Indices: 57457--57531 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 29
57447 CCTTGAGGTA
57457 GTTTCTTTGGAAACACAAA-ATCTTTGAGTC
1 GTTTCTTT-GAAACA-AAACATCTTTGAGTC
57487 TGTTTCTCTTGAAACAAAACCATCTTTGAGTC
1 -GTTTCT-TTGAAACAAAA-CATCTTTGAGTC
*
57519 GTTTCCTTGAAAC
1 GTTTCTTTGAAAC
57532 GAATTTTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 10 0.25
31 17 0.43
32 13 0.32
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (29 bp):
GTTTCTTTGAAACAAAACATCTTTGAGTC
Found at i:57549 original size:97 final size:100
Alignment explanation
Indices: 57374--57595 Score: 269
Period size: 97 Copynumber: 2.2 Consensus size: 100
57364 AAAATTTACC
*
57374 ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAAAATCTTTGAGATTGTTTCAATTGAAACAAAT
1 ATCTTTGAGTCTGTTTCCCTTGAAACAAAAC--AAATCTTTGAGATCGTTTCAATTGAAACAAAT
* *
57439 TTTGTCTCCCTTGAGGTAGTTTCTTTGGAAACACAAA
64 TTTGTCTCCCTTGAGATAGCTTCTTTGGAAACACAAA
* * * *
57476 ATCTTTGAGTCTGTTTCTCTTGAAACAAAAC-CATCTTTGAG-TCGTTTC-CTTGAAACGAATTT
1 ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAATCTTTGAGATCGTTTCAATTGAAACAAATTT
* *
57538 TGTCTCTCTTGAGATAGCTTCTCTT-GAAGCATC---
66 TGTCTCCCTTGAGATAGCTTCT-TTGGAAACA-CAAA
*
57571 ATCTTTGAGTCGGTTTCCCTTGAAA
1 ATCTTTGAGTCTGTTTCCCTTGAAA
57596 ACATTATCCC
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
95 23 0.21
97 36 0.34
98 9 0.08
99 9 0.08
102 30 0.28
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (100 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAATCTTTGAGATCGTTTCAATTGAAACAAATTT
TGTCTCCCTTGAGATAGCTTCTTTGGAAACACAAA
Found at i:59629 original size:40 final size:40
Alignment explanation
Indices: 59585--59689 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 40
59575 GGACACTAAG
*
59585 TGTATATGGTGGGCACGACCTTATGTGTAATACATTTCGA
1 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
*
59625 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGG
1 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
*
59665 TGTATATGGTGGGCATGACCTTATG
1 TGTATATGGTGGGCACGACCTTATG
59690 CGTAGCACTA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (40 bp):
TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
Found at i:60733 original size:43 final size:43
Alignment explanation
Indices: 60684--60825 Score: 115
Period size: 43 Copynumber: 3.2 Consensus size: 43
60674 CGACCAGACC
60684 TCCTCATCACGTAGAAGCGGTGTCACCCCTAGATAACTAGTCA
1 TCCTCATCACGTAGAAGCGGTGTCACCCCTAGATAACTAGTCA
* * * ** *
60727 TCCTCATAACGTAGGAA-CTGTGTTATCATCCCTAAAGATGGCTTGTCA
1 TCCTCATCACGTA-GAAGC-G-G-TGTCACCCCT--AGATAACTAGTCA
* ** * * *
60775 TCCTCATCACGTAGGAGCCATGTCACCCCTAGACAACCAGTCG
1 TCCTCATCACGTAGAAGCGGTGTCACCCCTAGATAACTAGTCA
60818 TCCTCATC
1 TCCTCATC
60826 GTGTAGGAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
43 28 0.38
44 4 0.05
45 9 0.12
46 8 0.11
47 2 0.03
48 23 0.31
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (43 bp):
TCCTCATCACGTAGAAGCGGTGTCACCCCTAGATAACTAGTCA
Found at i:60784 original size:131 final size:130
Alignment explanation
Indices: 60507--60784 Score: 378
Period size: 130 Copynumber: 2.1 Consensus size: 130
60497 GGGTATTACA
* * * * * *
60507 CATGCCGTCCTTATCACATAGGAACTGTGTCATCCACTGACCAGACCTCCTCATCACGTAGGAGC
1 CATGCCATCCTCATCACATAAGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGAAGC
* * * *
60572 CGTGTCACCCTTAGATAACAGCCGTCCTCATCACCTAGGAACCGTGTTATCATCCTTAAAGATGG
66 CGTGTCACCCCTAGATAACAGCCATCCTCATAACCTAGGAACCGTGTTATCATCCCTAAAGATGG
*
60637 CATGCCATCCTCATCACTTAAGAACCGTGTCATCTC-CCGACCAGACCTCCTCATCACGTAGAAG
1 CATGCCATCCTCATCACATAAGAACCGTGTCATC-CACCGACCAGACCTCCTCATCACGTAGAAG
* * * *
60701 CGGTGTCACCCCTAGATAACTAGTCATCCTCATAACGTAGGAACTGTGTTATCATCCCTAAAGAT
65 CCGTGTCACCCCTAGATAAC-AGCCATCCTCATAACCTAGGAACCGTGTTATCATCCCTAAAGAT
60766 GG
129 GG
* *
60768 CTTGTCATCCTCATCAC
1 CATGCCATCCTCATCAC
60785 GTAGGAGCCA
Statistics
Matches: 129, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
130 73 0.57
131 56 0.43
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (130 bp):
CATGCCATCCTCATCACATAAGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGAAGC
CGTGTCACCCCTAGATAACAGCCATCCTCATAACCTAGGAACCGTGTTATCATCCCTAAAGATGG
Found at i:60799 original size:131 final size:130
Alignment explanation
Indices: 60545--60799 Score: 366
Period size: 131 Copynumber: 2.0 Consensus size: 130
60535 GTCATCCACT
* * * *
60545 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAACAGCCGTCCTCATCACCTAG
1 GACCAGACCTCCTCATCACGTAGAAGCCGTGTCACCCCTAGATAACAGCCATCCTCATAACCTAG
* * *
60610 GAACCGTGTTATCATCCTTAAAGATGGCATGCCATCCTCATCACTTAAGAACCGTGTCATCTCCC
66 GAACCGTGTTATCATCCCTAAAGATGGCATGCCATCCTCATCACGTAAGAACCATGTCATCTCCC
* * *
60675 GACCAGACCTCCTCATCACGTAGAAGCGGTGTCACCCCTAGATAACTAGTCATCCTCATAACGTA
1 GACCAGACCTCCTCATCACGTAGAAGCCGTGTCACCCCTAGATAAC-AGCCATCCTCATAACCTA
* * * * *
60740 GGAACTGTGTTATCATCCCTAAAGATGGCTTGTCATCCTCATCACGTAGGAGCCATGTCA
65 GGAACCGTGTTATCATCCCTAAAGATGGCATGCCATCCTCATCACGTAAGAACCATGTCA
60800 CCCCTAGACA
Statistics
Matches: 109, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
130 43 0.39
131 66 0.61
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (130 bp):
GACCAGACCTCCTCATCACGTAGAAGCCGTGTCACCCCTAGATAACAGCCATCCTCATAACCTAG
GAACCGTGTTATCATCCCTAAAGATGGCATGCCATCCTCATCACGTAAGAACCATGTCATCTCCC
Found at i:61172 original size:23 final size:24
Alignment explanation
Indices: 61131--61190 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
61121 ACCAAAAATA
* *
61131 TTATTATATTATATGTATTGTT-T
1 TTATTATATTATATCTATTATTAT
61154 TTATTATTATTA-ATCTATTATTAT
1 TTATTA-TATTATATCTATTATTAT
*
61178 TTATAAT-TTATAT
1 TTATTATATTATAT
61191 TTTTTGTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.10
23 17 0.55
24 11 0.35
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (24 bp):
TTATTATATTATATCTATTATTAT
Found at i:62872 original size:29 final size:29
Alignment explanation
Indices: 62838--62894 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
62828 TTGTAATTAA
* *
62838 TGTTTAGTCCC-TTAAGTTTATGTTTTTGT
1 TGTTTAG-CCCTTTAAGATTATATTTTTGT
62867 TGTTTAGCCCTTTAAGATTATATTTTTG
1 TGTTTAGCCCTTTAAGATTATATTTTTG
62895 CTATTTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.56
Consensus pattern (29 bp):
TGTTTAGCCCTTTAAGATTATATTTTTGT
Found at i:65055 original size:27 final size:28
Alignment explanation
Indices: 65024--65080 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
65014 TTTTAAATTC
* *
65024 TATTTTAA-TTATTATTATTATTTTATA
1 TATTTTAATTTATTAGTATTAGTTTATA
*
65051 TA-TTTAATTTTTTAGTATTAGTTTATA
1 TATTTTAATTTATTAGTATTAGTTTATA
65078 TAT
1 TAT
65081 CAGTTTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (28 bp):
TATTTTAATTTATTAGTATTAGTTTATA
Found at i:66959 original size:3 final size:3
Alignment explanation
Indices: 66951--66992 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
66941 TATCTGCTCC
* *
66951 TGA TGA TGA TGA TGG TGA TAA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
66993 GAGTGAGAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:72755 original size:21 final size:21
Alignment explanation
Indices: 72730--72775 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
72720 ATGAAGTTGT
72730 GGATGATTTGGAGCCGTTTGG
1 GGATGATTTGGAGCCGTTTGG
72751 GGATGATTTGGAGCCGTTTGG
1 GGATGATTTGGAGCCGTTTGG
72772 GGAT
1 GGAT
72776 AAAATCTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.09, G:0.43, T:0.33
Consensus pattern (21 bp):
GGATGATTTGGAGCCGTTTGG
Found at i:72918 original size:20 final size:21
Alignment explanation
Indices: 72888--72927 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
72878 AGTCGTTGGA
*
72888 GCCTGATGGTATTGATACTAT
1 GCCTGATGGTATCGATACTAT
72909 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
72928 CTATGTGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:77352 original size:89 final size:90
Alignment explanation
Indices: 77182--77364 Score: 244
Period size: 89 Copynumber: 2.0 Consensus size: 90
77172 GGTAAGACCT
* * * *
77182 TACGGATCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTTCC
1 TACGAATCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTCTCA
* *
77247 TTTGTTGTATGCTTAGGCTAA-CCC
66 TTTGCTATATGCTTAGGCTAAGCCC
* *
77271 TACGAATCTAAGGATACCCTTGGGTAGGTCCATAGGCCCCAAGGAATATCCTTTGGTTGG-CTCT
1 TACGAATCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTCTC-
* * *
77335 ATTTGCTATGTGTTTAGGGTAAGCCC
65 ATTTGCTATATGCTTAGGCTAAGCCC
77361 TACG
1 TACG
77365 GACGCAGTCC
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
88 2 0.02
89 72 0.89
90 7 0.09
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (90 bp):
TACGAATCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTCTCA
TTTGCTATATGCTTAGGCTAAGCCC
Found at i:81021 original size:58 final size:58
Alignment explanation
Indices: 80927--81041 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
80917 AAGAAAATAG
80927 AGTTTGGTTGCTTAGAAAATGGAAAATGCCAATAGCATGATGTTACATCAAACTCTCT
1 AGTTTGGTTGCTTAGAAAATGGAAAATGCCAATAGCATGATGTTACATCAAACTCTCT
* * * *
80985 AGTTTTGTTTCTTAGAAAATGG-AAATGGTCAGTAGCATGATGTTACATCAAACTCTC
1 AGTTTGGTTGCTTAGAAAATGGAAAAT-GCCAATAGCATGATGTTACATCAAACTCTC
81042 AACGTGCTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 4 0.08
58 48 0.92
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (58 bp):
AGTTTGGTTGCTTAGAAAATGGAAAATGCCAATAGCATGATGTTACATCAAACTCTCT
Found at i:89134 original size:15 final size:15
Alignment explanation
Indices: 89114--89145 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
89104 AAAATCTTTC
*
89114 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
89129 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
89144 TT
1 TT
89146 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:90408 original size:35 final size:35
Alignment explanation
Indices: 90343--90410 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
90333 AACATCTACC
*
90343 AAACTTTACCAAACTTTAAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTAAAAAACAGTTTTCAAAG
*
90378 AAACATTTACCAAACTTT-AAAAATAGTTTTCAA
1 AAAC-TTTACCAAACTTTAAAAAACAGTTTTCAA
90411 GGTTGGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (35 bp):
AAACTTTACCAAACTTTAAAAAACAGTTTTCAAAG
Found at i:93569 original size:89 final size:89
Alignment explanation
Indices: 93469--93756 Score: 426
Period size: 89 Copynumber: 3.3 Consensus size: 89
93459 CATTTCTTAT
*
93469 CAATCTACTTACCATTTATCCCATAAGCTCGTAAGCTTA-TTTACCAATATATTTACCATTTGTT
1 CAATATACTTACCA-TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
93533 CCATAAGCTCATAAGCTTATTTTAC
65 CCATAAGCTCATAAGCTTATTTTAC
93558 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
1 CAATATACTTACCA-TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTT
93623 CCATAAGCTCATAAGCTTA-TTTAC
65 CCATAAGCTCATAAGCTTATTTTAC
* * * * *
93647 CAATA-ACTTACCA-TATTCAATAAGATCGTAAGCTTATTTTATC-ATATACTTACCATTTG-TC
1 CAATATACTTACCATTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTTC
*
93708 CATAAGCTCGTAAGCTTATTTTAC
66 CATAAGCTCATAAGCTTATTTTAC
* * *
93732 CAATACACTTGCCATTATTCCATAA
1 CAATATACTTACCATTATCCCATAA
93757 ACCATTTTCA
Statistics
Matches: 186, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
84 19 0.10
85 25 0.13
86 33 0.18
87 9 0.05
88 8 0.04
89 48 0.26
90 44 0.24
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (89 bp):
CAATATACTTACCATTATCCCATAAGCTCGTAAGCTTATTTTACCAATATATTTACCATTTGTTC
CATAAGCTCATAAGCTTATTTTAC
Found at i:93572 original size:45 final size:45
Alignment explanation
Indices: 93469--93756 Score: 385
Period size: 45 Copynumber: 6.6 Consensus size: 45
93459 CATTTCTTAT
* *
93469 CAATCTACTTACCATTTATCCCATAAGCTCGTAAGCTTA-TTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
93513 CAATATATTTACCATTTGTTCCATAAGCTCATAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
93558 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
93603 CAATATATTTACCATTTGTTCCATAAGCTCATAAGCTTA-TTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
93647 CAATA-ACTTACCA--TATTCAATAAGATCGTAAGCTTATTTTAT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
93689 C-ATATACTTACCATTT-GTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
93732 CAATACACTTGCCA-TTATTCCATAA
1 CAATATACTTACCATTTATTCCATAA
93757 ACCATTTTCA
Statistics
Matches: 211, Mismatches: 26, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
41 22 0.10
42 13 0.06
43 33 0.16
44 62 0.29
45 81 0.38
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:98249 original size:17 final size:18
Alignment explanation
Indices: 98222--98255 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
98212 GTTAAATTTT
98222 AAACGAAAAACTAAGATG
1 AAACGAAAAACTAAGATG
98240 AAAC-AAAAACTAAGAT
1 AAACGAAAAACTAAGAT
98256 ATAGGTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (18 bp):
AAACGAAAAACTAAGATG
Done.