Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001260.1 Hibiscus syriacus cultivar Beakdansim tig00002478_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: 107795
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6602 original size:2 final size:2
Alignment explanation
Indices: 6595--6630 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6585 TGATAAATAA
6595 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
6631 TTGAACTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8686 original size:23 final size:23
Alignment explanation
Indices: 8660--8703 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
8650 TTTCTTGTTG
8660 TTTCTTAAGCC-CTTCTAACTTAT
1 TTTCTTAAGCCTC-TCTAACTTAT
*
8683 TTTCTTGAGCCTCTCTAACTT
1 TTTCTTAAGCCTCTCTAACTT
8704 CAGGAGGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.48
Consensus pattern (23 bp):
TTTCTTAAGCCTCTCTAACTTAT
Found at i:9174 original size:19 final size:19
Alignment explanation
Indices: 9127--9174 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
9117 AAATAAGTGT
9127 TTAAATAC-T-TTAAAAAA
1 TTAAATACATATTAAAAAA
9144 TGATAAA-A-ATATTAAAAAA
1 T--TAAATACATATTAAAAAA
9163 TTAAATACATAT
1 TTAAATACATAT
9175 AACATATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
17 5 0.20
18 3 0.12
19 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
TTAAATACATATTAAAAAA
Found at i:9879 original size:19 final size:19
Alignment explanation
Indices: 9844--9885 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
9834 GAGATTATGG
9844 TTTTTATAAATATAATAATA
1 TTTTTATAAATATAATAA-A
9864 TTTTTATTAAA-A-AATAAA
1 TTTTTA-TAAATATAATAAA
9882 TTTT
1 TTTT
9886 AAAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 7 0.33
21 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTTATAAATATAATAAA
Found at i:10331 original size:29 final size:30
Alignment explanation
Indices: 10295--10360 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
10285 ATATATAATT
* *
10295 TTTAAAATATA-TTTTT-GAATATTTTTATA
1 TTTAAAATATAGTTTTTAAAATAATTTT-TA
*
10324 TTTAAAATTTAGTTTTTAAAATAATTTTTA
1 TTTAAAATATAGTTTTTAAAATAATTTTTA
10354 TTTAAAA
1 TTTAAAA
10361 AATTAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 10 0.31
30 14 0.44
31 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTAAAATATAGTTTTTAAAATAATTTTTA
Found at i:11727 original size:17 final size:19
Alignment explanation
Indices: 11705--11752 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
11695 AGTAATTAGT
11705 ATAATATTT-TAA-AAATA
1 ATAATATTTATAATAAATA
11722 ATAATAGTTTATAATAAATA
1 ATAATA-TTTATAATAAATA
*
11742 ATATTATTTAT
1 ATAATATTTAT
11753 TATATTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 6 0.22
18 3 0.11
19 8 0.30
20 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAATATTTATAATAAATA
Found at i:12691 original size:3 final size:3
Alignment explanation
Indices: 12677--12716 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
12667 AGGTCAACTT
12677 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12717 GCTAGGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:14463 original size:13 final size:13
Alignment explanation
Indices: 14445--14507 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
14435 TTGGTATTAT
14445 TTTTGAAAAGTGA
1 TTTTGAAAAGTGA
*
14458 TTTTGAAAGGT-A
1 TTTTGAAAAGTGA
*
14470 TTGTT-AGAAAGTGC
1 TT-TTGA-AAAGTGA
*
14484 TTCTGAAAAGTGA
1 TTTTGAAAAGTGA
*
14497 TTTTGTAAAGT
1 TTTTGAAAAGT
14508 TGAGTTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
12 4 0.10
13 32 0.82
14 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTGA
Found at i:14682 original size:23 final size:25
Alignment explanation
Indices: 14625--14682 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
14615 ATAATTCATT
*
14625 AATATTATGATATATAAAAATATCA
1 AATATTATTATATATAAAAATATCA
* *
14650 ACT-TAAATTATA-ATAAAAATAT-A
1 AATAT-TATTATATATAAAAATATCA
14673 AATATTATTA
1 AATATTATTA
14683 CATTTCATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
23 7 0.27
24 12 0.46
25 7 0.27
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (25 bp):
AATATTATTATATATAAAAATATCA
Found at i:22309 original size:4 final size:4
Alignment explanation
Indices: 22302--22332 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
22292 TATATATATA
22302 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
22333 AAAAGATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:23811 original size:29 final size:29
Alignment explanation
Indices: 23769--23825 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
23759 ATGGAAGCTG
23769 AAAGTGTAAAAACAATGTTTAATAGTTAA
1 AAAGTGTAAAAACAATGTTTAATAGTTAA
23798 AAAGTGTAAAAACAATGTTTAATAGTTA
1 AAAGTGTAAAAACAATGTTTAATAGTTA
23826 CATTAAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.32
Consensus pattern (29 bp):
AAAGTGTAAAAACAATGTTTAATAGTTAA
Found at i:26434 original size:12 final size:12
Alignment explanation
Indices: 26417--26447 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
26407 TTCTTTACTA
26417 TTTTTATTTATC
1 TTTTTATTTATC
*
26429 TTTTTAATTATC
1 TTTTTATTTATC
26441 TTTTTAT
1 TTTTTAT
26448 ATATTCATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTATTTATC
Found at i:35148 original size:36 final size:36
Alignment explanation
Indices: 34971--35171 Score: 167
Period size: 36 Copynumber: 5.5 Consensus size: 36
34961 TTTTATAGCA
* * *
34971 ATATAATATA-ATTTTTGAAAAT-GTTTTTAAAATAT
1 ATATAATATATAGTTTTG-AAATCATTTTGAAAATAT
* * ** * **
35006 ATGTACTATATAGTTTCAAAAACATTCCGAAAATAT
1 ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
* ** *
35042 ATATAGTATATAGTTTT-AAATTTTTTTTTTTGAAAACAT
1 ATATAATATATAGTTTTGAAA----TCATTTTGAAAATAT
*
35081 ATATAATGTATAGTTTTTGAAAATGCA-TTTGAAAATAT
1 ATATAATATATAG-TTTTG-AAAT-CATTTTGAAAATAT
35119 ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
1 ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
35155 ATATAATATATAGTTTT
1 ATATAATATATAGTTTT
35172 TTTTTTTAAA
Statistics
Matches: 130, Mismatches: 25, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
35 16 0.12
36 59 0.45
37 5 0.04
38 23 0.18
39 20 0.15
40 4 0.03
42 3 0.02
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
Found at i:35219 original size:40 final size:41
Alignment explanation
Indices: 35175--35251 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
35165 TAGTTTTTTT
35175 TTTTAAAAAAAACAT-TTTTGGAAAATTATATAATATATAG
1 TTTTAAAAAAAACATATTTTGGAAAATTATATAATATATAG
**
35215 TTTTAAAAAAAACATATTTTGGAATCTTATATAATAT
1 TTTTAAAAAAAACATATTTTGGAAAATTATATAATAT
35252 TCTTAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 15 0.44
41 19 0.56
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (41 bp):
TTTTAAAAAAAACATATTTTGGAAAATTATATAATATATAG
Found at i:36555 original size:11 final size:11
Alignment explanation
Indices: 36539--36583 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
36529 ATATTTTTCT
36539 TATTTATTTAA
1 TATTTATTTAA
*
36550 TATTTATTTAT
1 TATTTATTTAA
36561 TATTTATTTAA
1 TATTTATTTAA
36572 T-TTTAATTTAA
1 TATTT-ATTTAA
36583 T
1 T
36584 TTCTTTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 3 0.10
11 28 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:36568 original size:15 final size:15
Alignment explanation
Indices: 36538--36703 Score: 62
Period size: 12 Copynumber: 11.5 Consensus size: 15
36528 AATATTTTTC
*
36538 TTATTTATTTAATAT
1 TTATTTATTTATTAT
36553 TTATTTA-TTATTTAT
1 TTATTTATTTA-TTAT
36568 TTAATTTTAATTTA--AT
1 TT-A-TTT-ATTTATTAT
* *
36584 TTCTTTGATTTATTGT
1 TTATTT-ATTTATTAT
36600 TT-TTTA--TATTAT
1 TTATTTATTTATTAT
36612 TTACTTT-TATTATTA-
1 TTA-TTTAT-TTATTAT
36627 TTA-TTA-TTATTA-
1 TTATTTATTTATTAT
36639 TTA-TTA-TTATTA-
1 TTATTTATTTATTAT
36651 TTA-TTA-TTATTA-
1 TTATTTATTTATTAT
36663 TTA-TTATTATTATTATT
1 TTATTTA-T-TTATTA-T
*
36680 TTGATTTATTTAATAT
1 TT-ATTTATTTATTAT
*
36696 TTTTTTAT
1 TTATTTAT
36704 CATCTAACAT
Statistics
Matches: 124, Mismatches: 7, Indels: 40
0.73 0.04 0.23
Matches are distributed among these distances:
12 43 0.35
13 2 0.02
14 15 0.12
15 29 0.23
16 16 0.13
17 10 0.08
18 3 0.02
19 6 0.05
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTTATTTATTAT
Found at i:36624 original size:3 final size:3
Alignment explanation
Indices: 36618--36679 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
36608 TTATTTACTT
36618 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36666 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
36680 TTGATTTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:37775 original size:17 final size:17
Alignment explanation
Indices: 37755--37787 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37745 CTCACTAACC
*
37755 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
37772 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
37788 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:38442 original size:19 final size:19
Alignment explanation
Indices: 38408--38452 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
38398 ATTTAGACAT
38408 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
38426 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
38445 TTTGCATT
1 TTTGCATT
38453 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:41916 original size:84 final size:81
Alignment explanation
Indices: 41828--42726 Score: 804
Period size: 84 Copynumber: 10.8 Consensus size: 81
41818 GTTCAAGGCC
* * *
41828 AGAAGGGCTATCTGCCCACCAAGACCTTCGAGTTCGACTACGCTCAAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTC-AGCTCCAAGGCACATCATT
* * *
41893 TGCAGTATAGCTTAGGTT
64 TGCAGCATAACTTAAGTT
* * * * * * * *
41911 GAGAAGAGCTATCTGC--CAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACAT
1 -AGAAGGGTTATCTGCAACAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* * *
41973 TTACAGCATAACTCAAGGCT
63 TTGCAGCATAACTTAA-GTT
* * * *
41993 AGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATCT
1 AGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
42058 GCAGAATAGCTTAAGTCG
65 GCAGCATAACTTAAGT-T
* * * *
42076 AGAAGGGCTATCTGC--CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTT
1 AGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
* *
42139 GCAGTATAACTTAAGTCA
65 GCAGCATAACTTAAGT-T
*
42157 AGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGC-AAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
42222 TGCAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGT-T
* * * * *
42241 AGAAGGGTTATCTGCCAACTAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATATCA
1 AGAAGGGTTATCTG-CAAC-AAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCA
* * * *
42305 TTTACAGCACAACTCAAGGCT
62 TTTGCAGCATAACTTAA-GTT
* * *
42326 AGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
42391 GCAGCATAACTTAAGTCG
65 GCAGCATAACTTAAGT-T
* * * * *
42409 AGAAGGGTTATCTGCCAACTAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATATCA
1 AGAAGGGTTATCTG-CAAC-AAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCA
* * *
42473 TTTACAGCATAACTCAAGGCT
62 TTTGCAGCATAACTTAA-GTT
* * *
42494 AGAAGGGTTATCTGTCACCAAAGACCTTCTAGTTCGACTACGCTCAGCTCCAAGGCATATCATTT
1 AGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
42559 GCGGCACAGCTTAAGTCT
65 GCAGCATAACTTAAGT-T
* * * * *** *
42577 AGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTTCGGGGGTACATCAT
1 AGAAGGGTTATCTG-CAAC-AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * *
42642 TTACAGCATAACTCAAGGCT
63 TTGCAGCATAACTTAA-GTT
* * *
42662 AGGAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
42727 ACAACATAGC
Statistics
Matches: 662, Mismatches: 125, Indels: 57
0.78 0.15 0.07
Matches are distributed among these distances:
80 34 0.05
81 93 0.14
82 9 0.01
83 134 0.20
84 240 0.36
85 149 0.23
86 3 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (81 bp):
AGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
CAGCATAACTTAAGTT
Found at i:42389 original size:168 final size:167
Alignment explanation
Indices: 41820--42736 Score: 1242
Period size: 168 Copynumber: 5.5 Consensus size: 167
41810 GCAGCTTAGT
* * ** *
41820 TCAAGGCCAGAAGGGCTATCTGCCCACC-AAGACCTTCGAGTTCGACTACGCTCAAGCTCCAAGG
1 TCAAGGCTAGAAGGGTTATCTG-TTACCAAAGACCTTTGAGTTCGACTACGCTC-AGCTCCAAGG
* * * * *
41884 CACATCATTTGCAGTATAGCTTAGGTTGAGAAGAGCTATCTG-C--CAAAGACCCTTAAGTTCGA
64 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCCTTAAGTTCGA
*
41946 TTACACTCAGCTTCAAGGGCATAACATTTACAGCATAAC
129 TTACACTCAGCTTCAAGGGCATATCATTTACAGCATAAC
*
41985 TCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
1 TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
* * * ** *
42050 CATCATCTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGACT
66 CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCCTTAAGTTCGATT
** * * *
42112 ACGTTCAGCTTCGAA-GGCACATCATTTGCAGTATAAC
131 ACACTCAGCTTC-AAGGGCATATCATTTACAGCATAAC
* * * * *
42149 TTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 TCAAGGCTAGAAGGGTTATCTG-TTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
*
42214 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGA
65 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCCTTAAGTTCGA
*
42279 TTACACTCAGCTTCAAGGGCATATCATTTACAGCACAAC
129 TTACACTCAGCTTCAAGGGCATATCATTTACAGCATAAC
*
42318 TCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
1 TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
*
42383 CATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGAT
66 CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCCTTAAGTTCGAT
42448 TACACTCAGCTTCAAGGGCATATCATTTACAGCATAAC
130 TACACTCAGCTTCAAGGGCATATCATTTACAGCATAAC
*
42486 TCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCT-AGTTCGACTACGCTCAGCTCCAAGGC
1 TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTT-TGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * * * *
42550 ATATCATTTGCGGCACAGCTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGA-CCTTCGAGTTTG
65 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCCTT-AAGTTCG
** * *
42614 ATTACACTCAGCTTCGGGGGTACATCATTTACAGCATAAC
128 ATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAAC
* * *
42654 TCAAGGCTAGGAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
1 TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
* *
42719 CATCATTTACAACATAGC
66 CATCATTTGCAGCATAGC
42737 CTAAAGCAAG
Statistics
Matches: 672, Mismatches: 69, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
164 115 0.17
165 122 0.18
166 1 0.00
167 4 0.01
168 365 0.54
169 65 0.10
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (167 bp):
TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCCTTAAGTTCGATT
ACACTCAGCTTCAAGGGCATATCATTTACAGCATAAC
Found at i:43359 original size:38 final size:36
Alignment explanation
Indices: 43254--43453 Score: 190
Period size: 36 Copynumber: 5.5 Consensus size: 36
43244 TTTTATAGCA
* * *
43254 ATATAATATA-ATTTTTGAAAAT-GTTTTTAAAATAT
1 ATATAATATATAGTTTT-AAAATCATTTTGAAAATAT
* * * * **
43289 ATGTACTATATAGTTTCAAAAACATTCCGAAAATAT
1 ATATAATATATAGTTTTAAAATCATTTTGAAAATAT
* ** *
43325 ATATAGTATATAGTTTTAAAATTTTTTTTTGAAAACAT
1 ATATAATATATAGTTTTAAAA--TCATTTTGAAAATAT
*
43363 ATATAATGTATAGTTTTTGAAAATGCA-TTTGAAAATAT
1 ATATAATATATAG-TTTT-AAAAT-CATTTTGAAAATAT
*
43401 ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
1 ATATAATATATAGTTTTAAAATCATTTTGAAAATAT
43437 ATATAATATATAGTTTT
1 ATATAATATATAGTTTT
43454 TTTTTTAAAA
Statistics
Matches: 132, Mismatches: 25, Indels: 15
0.77 0.15 0.09
Matches are distributed among these distances:
35 14 0.11
36 63 0.48
37 4 0.03
38 43 0.33
39 4 0.03
40 4 0.03
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (36 bp):
ATATAATATATAGTTTTAAAATCATTTTGAAAATAT
Found at i:43501 original size:40 final size:41
Alignment explanation
Indices: 43456--43532 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
43446 ATAGTTTTTT
43456 TTTTAAAAAAAACAT-TTTTGGAAAATTATATAATATATAG
1 TTTTAAAAAAAACATATTTTGGAAAATTATATAATATATAG
**
43496 TTTTAAAAAAAACATATTTTGGAATCTTATATAATAT
1 TTTTAAAAAAAACATATTTTGGAAAATTATATAATAT
43533 TCTTAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 15 0.44
41 19 0.56
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (41 bp):
TTTTAAAAAAAACATATTTTGGAAAATTATATAATATATAG
Found at i:43505 original size:41 final size:41
Alignment explanation
Indices: 43317--43532 Score: 143
Period size: 38 Copynumber: 5.4 Consensus size: 41
43307 AAAACATTCC
* *** *
43317 GAAAATATATATAGTATATAGTTTT---AAAATTTTTTTTT
1 GAAAATATATATAATATATAGTTTTAAAAAAAACATTTTTG
* * ** **
43355 GAAAACATATATAATGTATAGTTTTTGAAAATGCA--TTT-
1 GAAAATATATATAATATATAGTTTTAAAAAAAACATTTTTG
* *
43393 GAAAATATATATAATATATAGTTTT---GAAATCA-TTTT-
1 GAAAATATATATAATATATAGTTTTAAAAAAAACATTTTTG
43429 GAAAATATATATAATATATAGTTTTTTTTTTAAAAAAAACATTTTTG
1 GAAAATATATATAATATATAG------TTTTAAAAAAAACATTTTTG
43476 GAAAAT-TATATAATATATAGTTTTAAAAAAAACATATTTTG
1 GAAAATATATATAATATATAGTTTTAAAAAAAACAT-TTTTG
**
43517 GAATCT-TATATAATAT
1 GAAAATATATATAATAT
43533 TCTTAAATCA
Statistics
Matches: 146, Mismatches: 16, Indels: 29
0.76 0.08 0.15
Matches are distributed among these distances:
35 4 0.03
36 24 0.16
38 45 0.31
39 3 0.02
40 15 0.10
41 22 0.15
42 4 0.03
45 5 0.03
46 18 0.12
47 6 0.04
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (41 bp):
GAAAATATATATAATATATAGTTTTAAAAAAAACATTTTTG
Found at i:44841 original size:11 final size:11
Alignment explanation
Indices: 44825--44869 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
44815 ATATTTTTCT
44825 TATTTATTTAA
1 TATTTATTTAA
*
44836 TATTTATTTAT
1 TATTTATTTAA
44847 TATTTATTTAA
1 TATTTATTTAA
44858 T-TTTAATTTAA
1 TATTT-ATTTAA
44869 T
1 T
44870 TTCTTTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 3 0.10
11 28 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:44854 original size:15 final size:15
Alignment explanation
Indices: 44824--44947 Score: 50
Period size: 15 Copynumber: 8.1 Consensus size: 15
44814 AATATTTTTC
*
44824 TTATTTATTTAATAT
1 TTATTTATTTATTAT
44839 TTATTTA-TTATTTAT
1 TTATTTATTTA-TTAT
44854 TTAATTTTAATTTA--AT
1 TT-A-TTT-ATTTATTAT
* *
44870 TTCTTTGATTTATTGT
1 TTATTT-ATTTATTAT
44886 TT-TTTA--TATTAT
1 TTATTTATTTATTAT
44898 TTACTTT-TATTATTA-
1 TTA-TTTAT-TTATTAT
44913 TTA-TTATTATTATTATT
1 TTATTTA-T-TTATTA-T
*
44930 TTGATTTATTTAATAT
1 TT-ATTTATTTATTAT
44946 TT
1 TT
44948 TTTTTATCAT
Statistics
Matches: 85, Mismatches: 6, Indels: 35
0.67 0.05 0.28
Matches are distributed among these distances:
12 7 0.08
13 2 0.02
14 15 0.18
15 26 0.31
16 16 0.19
17 10 0.12
18 3 0.04
19 6 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTTATTTATTAT
Found at i:44910 original size:3 final size:3
Alignment explanation
Indices: 44904--44929 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44894 TTATTTACTT
44904 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
44930 TTGATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:45824 original size:5 final size:5
Alignment explanation
Indices: 45814--45851 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
45804 TTCAAGCCAC
45814 TTTTA TTTTA -TTTA TTTT- TTTTA TCTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTT
45852 TGAGTCTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.27
5 17 0.57
6 5 0.17
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:46093 original size:29 final size:29
Alignment explanation
Indices: 46038--46093 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
46028 ATTTTACCTT
*
46038 TTTATATTATATTCTTATACTATTAATAA
1 TTTATATTATAGTCTTATACTATTAATAA
46067 TTTATATTAT-GT-TTATACATATATAAT
1 TTTATATTATAGTCTTATAC-TAT-TAAT
46094 CTTTACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 4 0.17
29 14 0.58
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTATATTATAGTCTTATACTATTAATAA
Found at i:46407 original size:22 final size:20
Alignment explanation
Indices: 46356--46407 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 20
46346 TAATTTTGGT
* *
46356 ATTTATATTTTTTACATTTA
1 ATTTATATCTTTTAAATTTA
46376 ATTTTCATATCTTTTAAATTCATA
1 A-TTT-ATATCTTTTAAATT--TA
46400 ATTTATAT
1 ATTTATAT
46408 TTATGCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 16 0.62
23 3 0.12
24 3 0.12
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATATCTTTTAAATTTA
Found at i:46426 original size:16 final size:16
Alignment explanation
Indices: 46401--46449 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
46391 AAATTCATAA
46401 TTTA-TATTTATGCTT
1 TTTATTATTTATGCTT
46416 TTTATTATTTAT-CTT
1 TTTATTATTTATGCTT
* *
46431 TTTTTTATTAATG-TT
1 TTTATTATTTATGCTT
46446 TTTA
1 TTTA
46450 ATTTTAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 22 0.76
16 7 0.24
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTATTATTTATGCTT
Found at i:51425 original size:47 final size:48
Alignment explanation
Indices: 51339--51491 Score: 145
Period size: 47 Copynumber: 3.2 Consensus size: 48
51329 ACGGGTAAAG
* * * *
51339 TCCAATAATTGAATTACAGGTT-AGTACATCATTATCGGATGATAAAT-
1 TCCAATAATCGAATTACAGGTTGA-TGCATCCTTAACGGATGATAAATA
* *
51386 TCCAATAATCGACTTACAGATTGATGCATCCTTAACGGATGATAAATA
1 TCCAATAATCGAATTACAGGTTGATGCATCCTTAACGGATGATAAATA
* * * * *
51434 T-CAATAACCGAATTATAGGTTGGTGCATCCTT-ATGAGATGAT-AATG
1 TCCAATAATCGAATTACAGGTTGATGCATCCTTAACG-GATGATAAATA
*
51480 TCCAATCATCGA
1 TCCAATAATCGA
51492 GTAATCATAT
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
46 6 0.07
47 79 0.91
48 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (48 bp):
TCCAATAATCGAATTACAGGTTGATGCATCCTTAACGGATGATAAATA
Found at i:52186 original size:20 final size:19
Alignment explanation
Indices: 52133--52182 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
52123 CCCAAACCCT
* *
52133 AAATATAAACCCTATTCTC
1 AAATATTAACCCTAATCTC
*
52152 AAATATTGACCCTAATCTC
1 AAATATTAACCCTAATCTC
52171 AAATATTAACCC
1 AAATATTAACCC
52183 CTAAATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (19 bp):
AAATATTAACCCTAATCTC
Found at i:60629 original size:17 final size:18
Alignment explanation
Indices: 60607--60642 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
60597 CTTAATATAA
60607 AAATATTTAT-TTAAATT
1 AAATATTTATCTTAAATT
*
60624 AAATATTTTTCTTAAATT
1 AAATATTTATCTTAAATT
60642 A
1 A
60643 TTGTCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATATTTATCTTAAATT
Found at i:69794 original size:17 final size:17
Alignment explanation
Indices: 69758--69808 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
69748 TGTGCTGATC
69758 TTAAAATTTAATATTT-TT
1 TTAAAATTT--TATTTATT
69776 TT-AAATATTTATTTATT
1 TTAAAAT-TTTATTTATT
69793 TTAAAATTTTATTTAT
1 TTAAAATTTTATTTAT
69809 ACTAATTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 17 0.57
18 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTAAAATTTTATTTATT
Found at i:71409 original size:20 final size:19
Alignment explanation
Indices: 71389--71444 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
71379 TATTTAGATA
71389 AATTTATTAATAATTTTAT
1 AATTTATTAATAATTTTAT
71408 AATCTT-TTAATAAATTTTAT
1 AAT-TTATTAAT-AATTTTAT
*
71428 AA-TTATTTTATAATTTT
1 AATTTA-TTAATAATTTT
71445 TTAAACTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 2 0.06
19 14 0.44
20 16 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTATTAATAATTTTAT
Found at i:71421 original size:31 final size:31
Alignment explanation
Indices: 71381--71448 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
71371 TTTTAGAGTA
71381 TTTAGATAAA-TTTATTAATAATTTTATAATCT
1 TTTA-ATAAATTTTA-TAATAATTTTATAATCT
* *
71413 TTTAATAAATTTTATAATTATTTTATAATTT
1 TTTAATAAATTTTATAATAATTTTATAATCT
71444 TTTAA
1 TTTAA
71449 ACTTTATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTAATAAATTTTATAATAATTTTATAATCT
Found at i:71442 original size:11 final size:11
Alignment explanation
Indices: 71391--71447 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
71381 TTTAGATAAA
*
71391 TTTATTAATAAT
1 TTTA-TAATTAT
71403 TTTATAATCT-T
1 TTTATAAT-TAT
*
71414 TTAATAA--AT
1 TTTATAATTAT
71423 TTTATAATTAT
1 TTTATAATTAT
71434 TTTATAATT-T
1 TTTATAATTAT
71444 TTTA
1 TTTA
71448 AACTTTATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
9 7 0.18
10 5 0.13
11 22 0.58
12 4 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTATAATTAT
Found at i:71445 original size:20 final size:19
Alignment explanation
Indices: 71395--71444 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
71385 GATAAATTTA
71395 TTAATAATTTTATAATCTT
1 TTAATAATTTTATAATCTT
71414 TTAATAAATTTTATAAT-TAT
1 TTAAT-AATTTTATAATCT-T
*
71434 TTTATAATTTT
1 TTAATAATTTT
71445 TTAAACTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATAATTTTATAATCTT
Found at i:71525 original size:13 final size:13
Alignment explanation
Indices: 71507--71531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71497 TATACTTTAT
71507 TTAAAAAAATATA
1 TTAAAAAAATATA
71520 TTAAAAAAATAT
1 TTAAAAAAATAT
71532 TATATGAATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAAAATATA
Found at i:72229 original size:31 final size:32
Alignment explanation
Indices: 72170--72238 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
72160 TCAATAAAGT
*
72170 TTAAAAAATTATAAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAAATACTTAATAAATTTA
* *
72202 TTAAAAGATTATAAAATTA-TTAATAAATTTA
1 TTAAAAAATTATAAAAATACTTAATAAATTTA
72233 TCTAAA
1 T-TAAA
72239 TACTATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 12 0.36
32 21 0.64
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (32 bp):
TTAAAAAATTATAAAAATACTTAATAAATTTA
Found at i:72233 original size:20 final size:19
Alignment explanation
Indices: 72169--72233 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
72159 GTCAATAAAG
*
72169 TTTAAAAAATTA-TAAAAA
1 TTTATAAAATTATTAAAAA
*
72187 TACTTATTAAATTTATTAAAAGA
1 T--TTA-TAAAATTATTAAAA-A
72210 -TTATAAAATTATTAATAAA
1 TTTATAAAATTATTAA-AAA
72229 TTTAT
1 TTTAT
72234 CTAAATACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
18 1 0.03
19 12 0.32
20 12 0.32
21 6 0.16
22 5 0.14
23 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTATAAAATTATTAAAAA
Found at i:72246 original size:31 final size:31
Alignment explanation
Indices: 72170--72254 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
72160 TCAATAAAGT
* * * *
72170 TTAAAAAATTATAAAAATACTTATTAAATTTA
1 TTAAAAGACTATAAAATTA-TTAATAAATTTA
*
72202 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAGACTATAAAATTATTAATAAATTTA
* *
72233 TCT-AAATACTATAAAATAATTA
1 T-TAAAAGACTATAAAATTATTA
72255 TTATATTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.61
32 18 0.39
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAAAGACTATAAAATTATTAATAAATTTA
Found at i:75074 original size:16 final size:16
Alignment explanation
Indices: 75053--75083 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
75043 ATAAATAAGT
75053 GAACATAAACGAACAC
1 GAACATAAACGAACAC
75069 GAACATAAACGAACA
1 GAACATAAACGAACA
75084 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:75170 original size:16 final size:16
Alignment explanation
Indices: 75149--75203 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
75139 CATTTAATAA
* *
75149 ATAAACGAACACAAAT
1 ATAAACGAACACGAAC
75165 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
75181 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
75197 ATAAACG
1 ATAAACG
75204 TTGGAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:76735 original size:24 final size:24
Alignment explanation
Indices: 76698--76753 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
76688 TATTAGGTTA
* * *
76698 AACATAAATGAACGTACATAAACG
1 AACATAACTAAACGCACATAAACG
*
76722 AACATAACTAAACGCATATAAACG
1 AACATAACTAAACGCACATAAACG
76746 AACATAAC
1 AACATAAC
76754 CGAACGTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.55, C:0.20, G:0.09, T:0.16
Consensus pattern (24 bp):
AACATAACTAAACGCACATAAACG
Found at i:77012 original size:19 final size:19
Alignment explanation
Indices: 76988--77024 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
76978 CCCTTGTTGG
76988 AGGGAATTGAAATTTGACA
1 AGGGAATTGAAATTTGACA
77007 AGGGAATTGAAATTTGAC
1 AGGGAATTGAAATTTGAC
77025 CATACTACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (19 bp):
AGGGAATTGAAATTTGACA
Found at i:77447 original size:213 final size:209
Alignment explanation
Indices: 77188--77576 Score: 586
Period size: 214 Copynumber: 1.8 Consensus size: 209
77178 ATTCGGGTTA
* * *
77188 GGTCGAGTTCGAGTTTAGGGTGAAAAATACCAACCCGAAAAAATATATAATTTTACCTTATATGT
1 GGTCGAGTTCGAGTTTAGGGTGAAAAAAACCAACCCGAAAAAATATATAATTCTACCTTATATAT
* *
77253 TTAGGAATAATTACAATAATACCCCTCTCTCTAT-ATATTTTTTCAATTAAGT-AACTGTTTTTA
66 TTAGGAATAATTACAATAATACCCCTCTATATATAATATTTTTTCAATTAAGTCAA-TGTTTTTA
77316 -TGAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGGTCAGATTTCTAATTCATA
130 TTG-AATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGGTCAGATTTCTAATTCATA
77380 TATTCGGGTTGGGTCG
194 TATTCGGGTTGGGTCG
* *
77396 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACCGACCCGAAAAAATATATAATTCTACCTTA
1 GGTCGAGTTCGAGTTTAGGGTGAAAAAAACC--A---ACCCGAAAAAATATATAATTCTACCTTA
* *
77461 TATATTTATGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCAATGTT
61 TATATTTAGGAATAATTACAATAATACCCCTCTATATATAATATTTTTTCAATTAAGTCAATGTT
* * *
77526 TTTATTGAATAAAAATAATTTTTTATTATTTTGTGTCGTGTCGGGTCGGGT
126 TTTATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGGT
77577 TTATAATTCA
Statistics
Matches: 161, Mismatches: 12, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
208 28 0.17
210 1 0.01
213 62 0.39
214 66 0.41
215 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (209 bp):
GGTCGAGTTCGAGTTTAGGGTGAAAAAAACCAACCCGAAAAAATATATAATTCTACCTTATATAT
TTAGGAATAATTACAATAATACCCCTCTATATATAATATTTTTTCAATTAAGTCAATGTTTTTAT
TGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGGTCAGATTTCTAATTCATATA
TTCGGGTTGGGTCG
Found at i:78011 original size:17 final size:18
Alignment explanation
Indices: 77989--78035 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
77979 TATGGAATTG
*
77989 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
78006 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
78024 GATTCCAATTCC
1 GATTCCAATTCC
78036 CTCATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:78738 original size:19 final size:19
Alignment explanation
Indices: 78693--78738 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
78683 ATATGGATTT
*
78693 CATTCCCAGGGGAATCTCA
1 CATTCCCCGGGGAATCTCA
78712 CATTCCCCGGGGAATCTCA
1 CATTCCCCGGGGAATCTCA
78731 CATTCCCC
1 CATTCCCC
78739 ATCCAAACGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (19 bp):
CATTCCCCGGGGAATCTCA
Found at i:82259 original size:2 final size:2
Alignment explanation
Indices: 82247--82278 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
82237 ATCTAGTTGA
*
82247 AT AT AT GT 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
82279 CATGTTCTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87279 original size:3 final size:3
Alignment explanation
Indices: 87271--87297 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
87261 AATCAAAAGC
87271 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
87298 TGATAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:91433 original size:2 final size:2
Alignment explanation
Indices: 91426--91456 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
91416 TGTGCATTCC
91426 TA TA TA 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 TA TA TA T
91457 GTTCTTTACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:91994 original size:37 final size:36
Alignment explanation
Indices: 91929--92007 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
91919 CTTTATGCTA
* *
91929 CCAACGGCTATAAGGGAGAAGAGTCATCTCTTCATT
1 CCAACGGCTACAAGGGAGAAGAGTCATCTCTTCACT
91965 CCAACGGCTAGCAAGGGA-AATGA-TACATCTCTTCACT
1 CCAACGGCTA-CAAGGGAGAA-GAGT-CATCTCTTCACT
92002 CCAACG
1 CCAACG
92008 ATTACATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
36 13 0.34
37 25 0.66
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (36 bp):
CCAACGGCTACAAGGGAGAAGAGTCATCTCTTCACT
Found at i:92095 original size:35 final size:34
Alignment explanation
Indices: 92046--92159 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 34
92036 CTTTAATGAG
* *
92046 AAGAGTTATGTTGCTTCACCAAATGATACCTTTC
1 AAGAGTCATGTTGCTTCACCAAATGATGCCTTTC
* *
92080 TAAGAGTCATTTTGCTTCACCAAATGATGTCTTTCC
1 -AAGAGTCATGTTGCTTCACCAAATGATGCCTTT-C
* * * *
92116 GAGAGTCATGATGCTTCAGCAAAGGATGCC-TTC
1 AAGAGTCATGTTGCTTCACCAAATGATGCCTTTC
92149 AAGAGTCATGT
1 AAGAGTCATGT
92160 CTTTTCACAA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
33 10 0.15
34 2 0.03
35 53 0.80
36 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (34 bp):
AAGAGTCATGTTGCTTCACCAAATGATGCCTTTC
Found at i:92274 original size:34 final size:34
Alignment explanation
Indices: 92140--92277 Score: 86
Period size: 33 Copynumber: 4.0 Consensus size: 34
92130 TTCAGCAAAG
* * * *
92140 GATGCCTTCAAGAGTCATGTCTTTTCA-CAAAAC
1 GATGCCCTCAAAAGTCACGTCTTTTCACCAAAAA
* * ** *
92173 GGTGCCCTCAAAAGTCATGTCTCCTCACTCCAAAA
1 GATGCCCTCAAAAGTCACGTCTTTTCAC-CAAAAA
* * *
92208 G--GCCCTCTAAAGGTCATGCCTCTTTAT-TCCAAAAA
1 GATGCCCTC-AAAAGTCA--CGTCTTT-TCACCAAAAA
*
92243 GATGCCTTCAAAAGTCACGTCTTTTCACCAAAAA
1 GATGCCCTCAAAAGTCACGTCTTTTCACCAAAAA
92277 G
1 G
92278 TGTTTCCAGA
Statistics
Matches: 78, Mismatches: 18, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
33 29 0.37
34 21 0.27
35 11 0.14
36 11 0.14
37 6 0.08
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.27
Consensus pattern (34 bp):
GATGCCCTCAAAAGTCACGTCTTTTCACCAAAAA
Found at i:96415 original size:188 final size:186
Alignment explanation
Indices: 96039--96522 Score: 464
Period size: 188 Copynumber: 2.6 Consensus size: 186
96029 GATTCAAAGT
* * * *
96039 AATAAGGACGATAACAAAAATAAGTTGAAAGTTGAAAATGTTATCAATCGTGGTAAGAAATTTGG
1 AATAAGGACGATAA-AAAAATAAGTTGAAAGCTGAAAATATTATCAATCGTGATAAGAAATATGG
* * * *
96104 TTACGCCTATAATTGTTAGCGTTCGATAAGAAAGTAAGTTGAGATCGGGTTTATTATAAGTTGCT
65 TTACGCCCATAATTGTTAGCGTTCAATAAAAAAGTAAGTTGAGATCGGGCTTATTATAAGTTGCT
* * * *
96169 TTAATAAATCTGGATTCGACCAAAATGTTATCAATGTTTAATAAATGGGTTTATCAA
130 TTAACAAATCTGGATTCGACCAAAATGTTATCAATGTTTAAGAAATGAGTTCATCAA
* * *
96226 AATAAAGACGATAATAAAATAAGTTGGAAA-CTGGAAATATTATCAATCGTGATAAGAAATATGG
1 AATAAGGACGATAAAAAAATAAGTT-GAAAGCTGAAAATATTATCAATCGTGATAAGAAATATGG
* * * *
96290 TTGA-GCCCATGATTGTTAGTGTTCAATAAAAAAAAGTAAGTTGAGATTGGGCTTGTTATAAGTT
65 TT-ACGCCCATAATTGTTAGCGTTCAAT--AAAAAAGTAAGTTGAGATCGGGCTTATTATAAGTT
* * * * *
96354 GCTTTAACAAATTTTGTTTCTACCAAAAATGTTA-CTAGA-GTTT-AGCAATGAGTTCATCAA
127 GCTTTAACAAATCTGGATTCGACC-AAAATGTTATC-A-ATGTTTAAGAAATGAGTTCATCAA
* * * * * * * *
96414 AATAAGGATGGTAACAAAATAAGCTAAAAGCTGAATATATTGTTAATCGT-AGTAAGAAAT-TCG
1 AATAAGGACGATAAAAAAATAAGTTGAAAGCTGAAAATATTATCAATCGTGA-TAAGAAATAT-G
* * * * *
96477 ATTGCGCCCATGAA-TGTTAGCAG-TCAATAAGAAACTAGGTTGAGAT
64 GTTACGCCCAT-AATTGTTAGC-GTTCAATAAAAAAGTAAGTTGAGAT
96523 TAGATTTGTT
Statistics
Matches: 243, Mismatches: 41, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
186 75 0.31
187 23 0.09
188 128 0.53
189 16 0.07
190 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (186 bp):
AATAAGGACGATAAAAAAATAAGTTGAAAGCTGAAAATATTATCAATCGTGATAAGAAATATGGT
TACGCCCATAATTGTTAGCGTTCAATAAAAAAGTAAGTTGAGATCGGGCTTATTATAAGTTGCTT
TAACAAATCTGGATTCGACCAAAATGTTATCAATGTTTAAGAAATGAGTTCATCAA
Found at i:106477 original size:139 final size:140
Alignment explanation
Indices: 106216--106591 Score: 460
Period size: 139 Copynumber: 2.7 Consensus size: 140
106206 TTTCAACATG
* *
106216 TTGTAACCTAAAATGTTAAATGCGGTTCAATACTTATTTTATGACAAGTATCAATACTTGTAACT
1 TTGTAACGTAAAATGTTAAATGTGGTTCAATACTTATTTTATGACAAGTATCAATACTTGTAACT
* * * * *
106281 AAGTATTGATACTTAGTTACAACCTAAAGTGTTATCCACTCCAACTTAAAATTTTATATCTTAGG
66 AAGTATCGATACTTAGTTACAACCTAAAATATTATACACTCCAACTTAAAATGTTATAT-TT-GG
106346 T-ACATTTTCGA
129 TAACATTTTCGA
* * * *
106357 TTGT-ACGT-AAATGTTAAATGTAGTTCAATAGTTATTTCATGACAAGTATCAATACTTGTTACT
1 TTGTAACGTAAAATGTTAAATGTGGTTCAATACTTATTTTATGACAAGTATCAATACTTGTAACT
* * *
106420 AAATATCGATACTTAGTTACAACCTAAAATATTATACAGTCTAA-TCTAAAATGTTATATTTGGT
66 AAGTATCGATACTTAGTTACAACCTAAAATATTATACACTCCAACT-TAAAATGTTATATTTGGT
*
106484 AATATTTTCGA
130 AACATTTTCGA
* ** * *
106495 TTGTAACTTAAAATGTTAAATGTGGTTTGATACTTATTTTACGA-AATGTATCAATACTTGAAAC
1 TTGTAACGTAAAATGTTAAATGTGGTTCAATACTTATTTTATGACAA-GTATCAATACTTGTAAC
* * *
106559 TGAGT-TCGATACTTAGTTATAATCT-AAATATTA
65 TAAGTATCGATACTTAGTTACAACCTAAAATATTA
106592 CTCCCTCCGT
Statistics
Matches: 202, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
137 3 0.01
138 24 0.12
139 122 0.60
140 49 0.24
141 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (140 bp):
TTGTAACGTAAAATGTTAAATGTGGTTCAATACTTATTTTATGACAAGTATCAATACTTGTAACT
AAGTATCGATACTTAGTTACAACCTAAAATATTATACACTCCAACTTAAAATGTTATATTTGGTA
ACATTTTCGA
Done.