Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004268.1 Hibiscus syriacus cultivar Beakdansim tig00009353_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: 78296
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:154 original size:27 final size:27
Alignment explanation
Indices: 102--154 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
92 AATTTATTTG
* * *
102 TCTCAAGTGAGAATGAAATGGTTTTTA
1 TCTCAAGGGAGAAGGAAATGGATTTTA
129 TCTCAAGGGAGAAGGAATAT-GATTTT
1 TCTCAAGGGAGAAGGAA-ATGGATTTT
155 CAAAGGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (27 bp):
TCTCAAGGGAGAAGGAAATGGATTTTA
Found at i:9080 original size:20 final size:20
Alignment explanation
Indices: 9055--9092 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9045 TGAAAAAATA
9055 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
9075 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
9093 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:15662 original size:20 final size:20
Alignment explanation
Indices: 15620--15662 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
15610 TTATTTTCAT
* *
15620 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
15640 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
15660 TTT
1 TTT
15663 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:17355 original size:21 final size:21
Alignment explanation
Indices: 17331--17374 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17321 CTTTGATGCT
17331 TTCTCT-TTGATTCTCTCTTGA
1 TTCTCTCTTGATTCT-TCTTGA
*
17352 TTCTCTCTTGATTCTTGTTGA
1 TTCTCTCTTGATTCTTCTTGA
17373 TT
1 TT
17375 GTTGTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.09, C:0.20, G:0.11, T:0.59
Consensus pattern (21 bp):
TTCTCTCTTGATTCTTCTTGA
Found at i:17374 original size:10 final size:11
Alignment explanation
Indices: 17331--17366 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
17321 CTTTGATGCT
17331 TTCTCT-TTGA
1 TTCTCTCTTGA
17341 TTCTCTCTTGA
1 TTCTCTCTTGA
17352 TTCTCTCTTGA
1 TTCTCTCTTGA
17363 TTCT
1 TTCT
17367 TGTTGATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:17734 original size:45 final size:46
Alignment explanation
Indices: 17646--17736 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
17636 TTGAAAAAGC
* *
17646 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
17692 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
17737 TTCGATGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:23531 original size:58 final size:57
Alignment explanation
Indices: 23428--23569 Score: 185
Period size: 58 Copynumber: 2.4 Consensus size: 57
23418 TAATGATGTA
* * * * * *
23428 ATTTTGTATTCATGTTTTGGTTCTTCTTCGGAGGGTAATGCCCCCATCTTGTTTCCTG
1 ATTTTGTATT-ATGTTTGGGTTCCTCTTCAGAGAGTAACGCCCCCATCATGTTTCCTG
* *
23486 ATATTTGTATTATGTTTGGGTTCCTCTTTAGAGAGTAACGTCCCCATCATGTTTCCTG
1 AT-TTTGTATTATGTTTGGGTTCCTCTTCAGAGAGTAACGCCCCCATCATGTTTCCTG
23544 ATTATTGTATTATGTTTGGGTTCCTC
1 ATT-TTGTATTATGTTTGGGTTCCTC
23570 ATCGGATGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
57 1 0.01
58 65 0.88
59 8 0.11
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.46
Consensus pattern (57 bp):
ATTTTGTATTATGTTTGGGTTCCTCTTCAGAGAGTAACGCCCCCATCATGTTTCCTG
Found at i:24468 original size:21 final size:21
Alignment explanation
Indices: 24425--24468 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
24415 TTACCGTACG
* *
24425 AATGACCAATCTTTTTATGAA
1 AATGACCAATCCTTTTATAAA
* *
24446 AATGATCAATCCTTTTCTAAA
1 AATGACCAATCCTTTTATAAA
24467 AA
1 AA
24469 ATGGAACATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (21 bp):
AATGACCAATCCTTTTATAAA
Found at i:25550 original size:14 final size:13
Alignment explanation
Indices: 25497--25546 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
25487 GATAAAATAC
25497 ATTTATATAT-AT
1 ATTTATATATAAT
*
25509 ATATATATATAAT
1 ATTTATATATAAT
25522 ATGTTATATATTAAT
1 AT-TTATATA-TAAT
25537 ATTTATATAT
1 ATTTATATAT
25547 TAATTCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 9 0.27
13 5 0.15
14 13 0.39
15 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
ATTTATATATAAT
Found at i:29902 original size:28 final size:29
Alignment explanation
Indices: 29870--29939 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
29860 ATCTTATGTA
* *
29870 ATTTAAATAATTTATGTT-TATAATTTAT
1 ATTTAAATAATTAATGTTAAATAATTTAT
29898 ATTTAAATAATTAATGTTCAAATAATTTAT
1 ATTTAAATAATTAATGTT-AAATAATTTAT
29928 ATTTAAATAATT
1 ATTTAAATAATT
29940 GATAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 17 0.45
30 21 0.55
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTTAAATAATTAATGTTAAATAATTTAT
Found at i:29907 original size:15 final size:15
Alignment explanation
Indices: 29870--29939 Score: 90
Period size: 15 Copynumber: 4.8 Consensus size: 15
29860 ATCTTATGTA
29870 ATTTAAATAATTTAT
1 ATTTAAATAATTTAT
*
29885 GTTT--ATAATTTAT
1 ATTTAAATAATTTAT
*
29898 ATTTAAATAATTAAT
1 ATTTAAATAATTTAT
* *
29913 GTTCAAATAATTTAT
1 ATTTAAATAATTTAT
29928 ATTTAAATAATT
1 ATTTAAATAATT
29940 GATAAAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
13 12 0.27
15 33 0.73
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTAAATAATTTAT
Found at i:36457 original size:13 final size:13
Alignment explanation
Indices: 36432--36466 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
36422 CTATTTTCGG
36432 AAAATTAATTTTA
1 AAAATTAATTTTA
*
36445 AAAAGTTAATTTAA
1 AAAA-TTAATTTTA
36459 AAAATTAA
1 AAAATTAA
36467 AGATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
AAAATTAATTTTA
Found at i:36493 original size:14 final size:13
Alignment explanation
Indices: 36450--36499 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
36440 TTTTAAAAAG
* *
36450 TTAATTTAAAAAA
1 TTAAATTAATAAA
36463 TTAAAGATTAATAAA
1 TT-AA-ATTAATAAA
36478 TTAAATTAATTAAA
1 TTAAATTAA-TAAA
36492 TTAAATTA
1 TTAAATTA
36500 TTATAAACGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 7 0.22
14 16 0.50
15 9 0.28
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
TTAAATTAATAAA
Found at i:38957 original size:3 final size:3
Alignment explanation
Indices: 38949--39001 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
38939 CCTTTTATCT
38949 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38995 TT- TTA TT
1 TTA TTA TT
39002 TCTTACTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:39081 original size:30 final size:31
Alignment explanation
Indices: 39047--39116 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
39037 ATATATATTA
39047 TATTT-TATTTTTTAATCA-TTTTATTATTTT
1 TATTTCTATTTTTT-ATCATTTTTATTATTTT
* * *
39077 TATTTCT-TTTTTTTTTATTTTTATTTTTTT
1 TATTTCTATTTTTTATCATTTTTATTATTTT
39107 TATTTCTATT
1 TATTTCTATT
39117 ACTTTGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 2 0.06
30 29 0.85
31 3 0.09
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (31 bp):
TATTTCTATTTTTTATCATTTTTATTATTTT
Found at i:39089 original size:21 final size:20
Alignment explanation
Indices: 39065--39107 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
39055 TTTTTAATCA
39065 TTTTATTATTTTTATTTCTTT
1 TTTTATTATTTTTATTT-TTT
*
39086 TTTTTTTATTTTTATTTTTT
1 TTTTATTATTTTTATTTTTT
39106 TT
1 TT
39108 ATTTCTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTATTATTTTTATTTTTT
Found at i:39116 original size:15 final size:15
Alignment explanation
Indices: 39064--39116 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
39054 TTTTTTAATC
*
39064 ATTT-TATTATTTTT
1 ATTTCTATTTTTTTT
*
39078 ATTTCTTTTTTTTTT
1 ATTTCTATTTTTTTT
*
39093 ATTTTTATTTTTTTT
1 ATTTCTATTTTTTTT
39108 ATTTCTATT
1 ATTTCTATT
39117 ACTTTGTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 4 0.12
15 29 0.88
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTCTATTTTTTTT
Found at i:39116 original size:21 final size:21
Alignment explanation
Indices: 39071--39116 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39061 ATCATTTTAT
*
39071 TATTTTTATTTCTTTTTTTTT
1 TATTTTTATTTCTTTTTTTTC
39092 TATTTTTATTT-TTTTTATTTC
1 TATTTTTATTTCTTTTT-TTTC
39113 TATT
1 TATT
39117 ACTTTGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (21 bp):
TATTTTTATTTCTTTTTTTTC
Found at i:39138 original size:2 final size:2
Alignment explanation
Indices: 39131--39173 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
39121 TGTTTATACG
39131 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
39173 T
1 T
39174 TTTTTTTCCT
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:39297 original size:7 final size:7
Alignment explanation
Indices: 39213--39358 Score: 55
Period size: 7 Copynumber: 19.6 Consensus size: 7
39203 ATATACTCTC
39213 TTTTATT
1 TTTTATT
39220 TATTTAATT
1 T-TTT-ATT
39229 TATTTAATT
1 T-TTT-ATT
39238 TTTTA-T
1 TTTTATT
*
39244 CTTTATT
1 TTTTATT
39251 GTATTTATT
1 -T-TTTATT
39260 TTTT-TAT
1 TTTTAT-T
* *
39267 TTCTAGT
1 TTTTATT
* *
39274 TTCTAGT
1 TTTTATT
* *
39281 TTCTAGT
1 TTTTATT
39288 TTTTATT
1 TTTTATT
39295 TTTTATT
1 TTTTATT
*
39302 TTTT-TA
1 TTTTATT
* *
39308 TTATATA
1 TTTTATT
39315 TTTTATT
1 TTTTATT
*
39322 TTTTCCTT
1 TTTT-ATT
*
39330 TTTCTTTT
1 TTT-TATT
39338 TCTTTATAT
1 T-TTTAT-T
39347 TTTTATT
1 TTTTATT
39354 ATTTT
1 -TTTT
39359 TTCCTTTATT
Statistics
Matches: 113, Mismatches: 13, Indels: 25
0.75 0.09 0.17
Matches are distributed among these distances:
6 10 0.09
7 53 0.47
8 26 0.23
9 24 0.21
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (7 bp):
TTTTATT
Found at i:39324 original size:33 final size:31
Alignment explanation
Indices: 39294--39358 Score: 76
Period size: 34 Copynumber: 2.0 Consensus size: 31
39284 TAGTTTTTAT
*
39294 TTTTTATTTTTTTATTATATATTTTATTTTTTCC
1 TTTTTATTTTTCT-TTATAT-TTTTATTTTTT-C
*
39328 TTTTTCTTTTTCTTTATATTTTTATTATTTT
1 TTTTTATTTTTCTTTATATTTTTATT-TTTT
39359 TTCCTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 7 0.25
33 10 0.36
34 11 0.39
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTTATTTTTCTTTATATTTTTATTTTTTC
Found at i:39332 original size:35 final size:35
Alignment explanation
Indices: 39293--39370 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
39283 CTAGTTTTTA
39293 TTTTTTATTTT-TTTATTATATATT-TTATTTTTTCC
1 TTTTTTATTTTCTTTA-TAT-TATTATTATTTTTTCC
*
39328 TTTTTCT-TTTTCTTTATATTTTTATTATTTTTTCC
1 TTTTT-TATTTTCTTTATATTATTATTATTTTTTCC
*
39363 TTTATTAT
1 TTTTTTAT
39371 ATTTATCCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
34 4 0.11
35 28 0.76
36 5 0.14
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (35 bp):
TTTTTTATTTTCTTTATATTATTATTATTTTTTCC
Found at i:39409 original size:15 final size:16
Alignment explanation
Indices: 39391--39423 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39381 TTTAACTTCA
39391 TTTTATTTTCTTT-TC
1 TTTTATTTTCTTTATC
*
39406 TTTTCTTTTCTTTATC
1 TTTTATTTTCTTTATC
39422 TT
1 TT
39424 ATCTTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTTTCTTTATC
Found at i:40554 original size:17 final size:17
Alignment explanation
Indices: 40534--40566 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40524 CTCACTAACC
*
40534 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
40551 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
40567 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:44769 original size:84 final size:84
Alignment explanation
Indices: 44626--45356 Score: 817
Period size: 84 Copynumber: 8.8 Consensus size: 84
44616 TTTAAGATAA
* * *
44626 CATTTGCGGCATAACTTAAGTCGAGAAGGGTTATCCGCCAACCAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
*
44691 GCTCAGCTCCAAGGCACAT
66 ACTCAGCTCCAAGGCACAT
* * * **
44710 CGTTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
* * * *
44775 AGTCAGCTTCGAGGGCATAT
66 ACTCAGC-TCCAAGGCACAT
** * * * * *
44795 CATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
*
44859 GCTCAGCTCCAAGGCACAT
66 ACTCAGCTCCAAGGCACAT
* * **
44878 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A--AAAGACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
* * * *
44940 ACTCAGTTTCGAGGGCACAA
66 ACTCAG-CTCCAAGGCACAT
* * *
44960 CATTTGCGGCATAACTTAAGTCGAGAA-GGTTTTCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
45024 ACTCAGCTCCAAGGCACAT
66 ACTCAGCTCCAAGGCACAT
* * * * * *
45043 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGATTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
* *
45108 GCTCAGCTCCAAGGCATAT
66 ACTCAGCTCCAAGGCACAT
* * * *
45127 CATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTT-AAGTTCGATTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA-CCTTCGAGTTCGATTA
* *
45187 CACTCAGCTTCAAGGGCATAT
65 CACTCAGCTCCAA-GGCACAT
* * * * * *
45208 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
45272 ACTCAGCTCCAAGGCACAT
66 ACTCAGCTCCAAGGCACAT
* * **
45291 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
45352 ACTCA
66 ACTCA
45357 ACTTCGAGGT
Statistics
Matches: 536, Mismatches: 97, Indels: 32
0.81 0.15 0.05
Matches are distributed among these distances:
80 51 0.10
81 74 0.14
82 35 0.07
83 115 0.21
84 222 0.41
85 39 0.07
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (84 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
ACTCAGCTCCAAGGCACAT
Found at i:45256 original size:164 final size:164
Alignment explanation
Indices: 44626--45405 Score: 800
Period size: 165 Copynumber: 4.7 Consensus size: 164
44616 TTTAAGATAA
* * *
44626 CATTTGCGGCATAACTTAAGTCGAGAAGGGTTATCCGCCAACCAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACCCTTGAGTTCGATTAC
* *
44691 GCTCAGCTCCAAGGCACATCGTTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAA
63 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA-CAAA
* * * *
44756 GACCCCCGAGTTCGATTACAGTCAGCTTCGAGGGCATAT
127 GACCCCCGAGTTCGATTACACTCAGC-TCCAAGGCACAT
** * * * *
44795 CATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGA-CCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG--ACCAAAGACCCTT-GAGTTCGATTAC
*
44859 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A-AAAG
63 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAG
* * * *
44922 ACCCCCGAGTTCGATTACACTCAGTTTCGAGGGCACAA
128 ACCCCCGAGTTCGATTACACTCAG-CTCCAAGGCACAT
* * *
44960 CATTTGCGGCATAACTTAAGTCGAGAA-GGTTTTCTGCCAACCAAAGA-CCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACCCTT-GAGTTCGATTA
* * * * *
45023 CACTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAA
62 CACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAC-AA
*** ** *
45088 AGACCTTTGAGTTCGATTATGCTCAGCTCCAAGGCATAT
126 AGACCCCCGAGTTCGATTACACTCAGCTCCAAGGCACAT
* * * *
45127 CATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCTTAAGTTCGATTACACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTTGAGTTCGATTACACT
* * * * * * * * *
45191 CAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGAC
66 CAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAGAC
***
45256 CTTTGAGTTCGATTACACTCAGCTCCAAGGCACAT
130 CCCCGAGTTCGATTACACTCAGCTCCAAGGCACAT
* * **
45291 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTTGAGTTCGATTACACT
* * * * * * * * *
45355 CAACTTCGAGGTCATATCATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
66 CAGCTCCAAGG-CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
45406 TTGTCAATAA
Statistics
Matches: 532, Mismatches: 69, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
163 2 0.00
164 176 0.33
165 181 0.34
166 1 0.00
167 36 0.07
168 106 0.20
169 30 0.06
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCCTTGAGTTCGATTACACT
CAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACC
CCCGAGTTCGATTACACTCAGCTCCAAGGCACAT
Found at i:47064 original size:9 final size:8
Alignment explanation
Indices: 47036--47099 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
47026 ATATATTTTA
47036 TTTTATTT
1 TTTTATTT
* **
47044 TTTAATCA
1 TTTTATTT
47052 TTTTATTAT
1 TTTTATT-T
47061 TTTTA-TT
1 TTTTATTT
*
47068 TCTT-TTT
1 TTTTATTT
*
47075 TTTTATTA
1 TTTTATTT
47083 TTTTATTT
1 TTTTATTT
47091 CTTTTATTT
1 -TTTTATTT
47100 CTATTACTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
7 9 0.21
8 20 0.48
9 13 0.31
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTATTT
Found at i:47077 original size:14 final size:15
Alignment explanation
Indices: 47054--47101 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
47044 TTTAATCATT
47054 TTATTATTTTTATTTC
1 TTATT-TTTTTATTTC
*
47070 TT-TTTTTTTATTATT
1 TTATTTTTTTATT-TC
47085 TTATTTCTTTTATTTC
1 TTATTT-TTTTATTTC
47101 T
1 T
47102 ATTACTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.30
15 5 0.19
16 7 0.26
17 7 0.26
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTTTTTATTTC
Found at i:47082 original size:23 final size:23
Alignment explanation
Indices: 47033--47105 Score: 87
Period size: 23 Copynumber: 3.1 Consensus size: 23
47023 TATATATATT
*
47033 TTATTTTATTT-TTTAATCATTTTA
1 TTATTTTATTTCTTTTAT--TTTTA
47057 TTATTTTTATTTCTTTT-TTTTTA
1 TTA-TTTTATTTCTTTTATTTTTA
*
47080 TTATTTTATTTCTTTTATTTCTA
1 TTATTTTATTTCTTTTATTTTTA
47103 TTA
1 TTA
47106 CTTTGTTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
22 13 0.30
23 16 0.36
24 3 0.07
25 9 0.20
26 3 0.07
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTTTATTTCTTTTATTTTTA
Found at i:47085 original size:17 final size:17
Alignment explanation
Indices: 47033--47098 Score: 61
Period size: 16 Copynumber: 4.1 Consensus size: 17
47023 TATATATATT
*
47033 TTATTTTATTT-TTTAA
1 TTATTTTATTTCTTTTA
*
47049 TCATTTTATTAT-TTTTA
1 TTATTTTATT-TCTTTTA
*
47066 TT-TCTT-TTT-TTTTA
1 TTATTTTATTTCTTTTA
47080 TTATTTTATTTCTTTTA
1 TTATTTTATTTCTTTTA
47097 TT
1 TT
47099 TCTATTACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
14 8 0.20
15 5 0.12
16 15 0.37
17 13 0.32
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTATTTCTTTTA
Found at i:47086 original size:31 final size:31
Alignment explanation
Indices: 47031--47104 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
47021 CATATATATA
47031 TTTTATTT-TATTTTTTAATCATTTTATTAT-
1 TTTTATTTCTATTTTTTAATCATTTTATT-TC
* * *
47061 TTTTATTTCTTTTTTTTTATTATTTTATTTC
1 TTTTATTTCTATTTTTTAATCATTTTATTTC
47092 TTTTATTTCTATT
1 TTTTATTTCTATT
47105 ACTTTGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 9 0.24
31 29 0.76
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTATTTCTATTTTTTAATCATTTTATTTC
Found at i:47363 original size:5 final size:5
Alignment explanation
Indices: 47353--47427 Score: 57
Period size: 5 Copynumber: 14.8 Consensus size: 5
47343 ATTTAACTTC
* * *
47353 ATTTT ATTTT ATTTT A-TTT -TTTT ATCTT ATCTT A-TTT ATTTC ATTTGT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T
*
47401 TTTTT AATTGTTT ATTTT ATTTT ATTT
1 ATTTT -A-T-TTT ATTTT ATTTT ATTT
47428 ACTTTCATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
4 9 0.16
5 39 0.68
6 4 0.07
7 2 0.04
8 3 0.05
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:47443 original size:38 final size:38
Alignment explanation
Indices: 47364--47443 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
47354 TTTTATTTTA
* * **
47364 TTTTATTTTTTTATCTTATCTTATTTATTTCATTTGTT
1 TTTTAATTGTTTATCTTATCTTATTTATTTCATTTACT
* *
47402 TTTTAATTGTTTATTTTATTTTATTTACTTTCA-TTACT
1 TTTTAATTGTTTATCTTATCTTATTTA-TTTCATTTACT
47440 TTTT
1 TTTT
47444 TCCTTCAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 30 0.86
39 5 0.14
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (38 bp):
TTTTAATTGTTTATCTTATCTTATTTATTTCATTTACT
Found at i:48519 original size:17 final size:19
Alignment explanation
Indices: 48475--48534 Score: 93
Period size: 19 Copynumber: 3.1 Consensus size: 19
48465 ACCCCTGTTA
48475 AATTATATTTTAAAAAAAT
1 AATTATATTTTAAAAAAAT
48494 AATTATATTTTAAAAAAAT
1 AATTATATTTTAAAAAAAT
* *
48513 AATTATTTTTTTATAAAAAT
1 AATTA-TATTTTAAAAAAAT
48533 AA
1 AA
48535 ATTTAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 24 0.63
20 14 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTATATTTTAAAAAAAT
Found at i:49165 original size:2 final size:2
Alignment explanation
Indices: 49158--49190 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49148 GCGGTCTGTC
49158 TA 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 TA T
49191 GCAAACACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58483 original size:19 final size:19
Alignment explanation
Indices: 58440--58485 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
58430 TATTTAATAT
*
58440 TATTATAATATAATTTTAA
1 TATTATATTATAATTTTAA
*
58459 TA--ATATTATATTTTTAA
1 TATTATATTATAATTTTAA
58476 TATTATATTA
1 TATTATATTA
58486 ATATGTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATATTATAATTTTAA
Found at i:58488 original size:11 final size:10
Alignment explanation
Indices: 58360--58494 Score: 56
Period size: 11 Copynumber: 13.8 Consensus size: 10
58350 ACTCAAAAAT
*
58360 ATATTATTTT
1 ATATTATTTA
58370 AT-TTATTTA
1 ATATTATTTA
58379 ATATTAATTTA
1 ATATT-ATTTA
58390 ATA-T-TTTA
1 ATATTATTTA
* *
58398 GTATCATTTTA
1 ATATTA-TTTA
** *
58409 ATAAAAAATT-
1 AT-ATTATTTA
58419 A-ATTA-TTA
1 ATATTATTTA
*
58427 A-AATATTTA
1 ATATTATTTA
58436 ATATTATTATA
1 ATATTATT-TA
*
58447 ATATAATTTTA
1 ATATTA-TTTA
*
58458 ATAATA-TT-
1 ATATTATTTA
58466 ATATT-TTTA
1 ATATTATTTA
58475 ATATTATATTA
1 ATATTAT-TTA
58486 ATATGTATT
1 ATAT-TATT
58495 CAGATATATT
Statistics
Matches: 94, Mismatches: 15, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
7 2 0.02
8 18 0.19
9 19 0.20
10 12 0.13
11 36 0.38
12 7 0.07
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (10 bp):
ATATTATTTA
Found at i:58870 original size:29 final size:30
Alignment explanation
Indices: 58817--58897 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
58807 TTCAGGAAAT
* * *
58817 GTAATTTATTTTACGTAAAATAATTAT-AG
1 GTAATTCATTTTACGTAAAACAATTATCAC
* *
58846 GTTATTCATTTTACGTAAAACAATTTTCAC
1 GTAATTCATTTTACGTAAAACAATTATCAC
58876 GTAATTCATTTTACGTAAAACA
1 GTAATTCATTTTACGTAAAACA
58898 TTTTTGATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
29 23 0.51
30 22 0.49
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAACAATTATCAC
Found at i:58885 original size:30 final size:29
Alignment explanation
Indices: 58817--58902 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 29
58807 TTCAGGAAAT
* * * *
58817 GTAATTTATTTTACGTAAAATAATTATAG
1 GTAATTCATTTTACGTAAAACAATTTTAC
*
58846 GTTATTCATTTTACGTAAAACAATTTTCAC
1 GTAATTCATTTTACGTAAAACAATTTT-AC
*
58876 GTAATTCATTTTACGTAAAACATTTTT
1 GTAATTCATTTTACGTAAAACAATTTT
58903 GATGAAAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 23 0.47
30 26 0.53
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.45
Consensus pattern (29 bp):
GTAATTCATTTTACGTAAAACAATTTTAC
Found at i:58899 original size:14 final size:14
Alignment explanation
Indices: 58852--58901 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
58842 ATAGGTTATT
58852 CATTTTACGTAAAA
1 CATTTTACGTAAAA
**
58866 CAATTTTCACGTAATT
1 C-ATTTT-ACGTAAAA
58882 CATTTTACGTAAAA
1 CATTTTACGTAAAA
58896 CATTTT
1 CATTTT
58902 TGATGAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 13 0.43
15 10 0.33
16 7 0.23
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (14 bp):
CATTTTACGTAAAA
Found at i:67493 original size:28 final size:28
Alignment explanation
Indices: 67455--67576 Score: 208
Period size: 28 Copynumber: 4.4 Consensus size: 28
67445 GATGACTGCG
67455 AACAATAAGTAAAACTTGTTGTTTCTAC
1 AACAATAAGTAAAACTTGTTGTTTCTAC
67483 AACAATAAGTAAAACTTGTTGTTTCTAC
1 AACAATAAGTAAAACTTGTTGTTTCTAC
* *
67511 AACAGTAAGTAAAACTTGTTGTTTCTAT
1 AACAATAAGTAAAACTTGTTGTTTCTAC
*
67539 AACAGTAAGTAAAACTTGTTGTTTCTAC
1 AACAATAAGTAAAACTTGTTGTTTCTAC
*
67567 AACAAGAAGT
1 AACAATAAGT
67577 TTTTTTCATC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 89 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (28 bp):
AACAATAAGTAAAACTTGTTGTTTCTAC
Found at i:69166 original size:3 final size:3
Alignment explanation
Indices: 69158--69182 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
69148 TTTAATCTGC
69158 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
69183 AATGCCAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:69679 original size:11 final size:12
Alignment explanation
Indices: 69663--69693 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
69653 ATAGAAAAAT
69663 ACCTAACTC-TC
1 ACCTAACTCTTC
69674 ACCTAACTCTTC
1 ACCTAACTCTTC
69686 ACCTAACT
1 ACCTAACT
69694 AAATTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:74950 original size:26 final size:24
Alignment explanation
Indices: 74920--74976 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
74910 GTATTTTTAA
*
74920 TTTTAAATATTAAAGATAATTATATT
1 TTTTAAAT-TTAAA-ATAATAATATT
* *
74946 TTTTATATTTCAAATAATAATATT
1 TTTTAAATTTAAAATAATAATATT
74970 TATTTAA
1 T-TTTAA
74977 GTTTGAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 11 0.42
25 8 0.31
26 7 0.27
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTAAATTTAAAATAATAATATT
Done.