Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001615.1 Hibiscus syriacus cultivar Beakdansim tig00003207_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: 88191
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:959 original size:52 final size:51
Alignment explanation
Indices: 878--995 Score: 175
Period size: 52 Copynumber: 2.3 Consensus size: 51
868 ACCCCCTTGG
* *
878 GGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-CAAAACTGTTTA
1 GGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGG-GCCAAAAC-ATTTA
*
930 GGGGGATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGCCAAAACATTTA
1 GGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGGCCAAAACATTTA
981 GGGGGAATCGGTTCC
1 GGGGG-ATCGGTTCC
996 TCCTATGGGG
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
51 10 0.16
52 51 0.84
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (51 bp):
GGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGGCCAAAACATTTA
Found at i:1472 original size:6 final size:6
Alignment explanation
Indices: 1461--1498 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1451 AACACGTATT
1461 ACCACG ACCACG ACCCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG A-CCACG ACCACG ACCACG ACCACG ACC
1499 CGAGACGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.32
6 15 0.48
7 6 0.19
ACGTcount: A:0.29, C:0.55, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1480 original size:13 final size:13
Alignment explanation
Indices: 1462--1489 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1452 ACACGTATTA
1462 CCACGACCACGAC
1 CCACGACCACGAC
1475 CCACGACCACGAC
1 CCACGACCACGAC
1488 CC
1 CC
1490 GACCCGACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.57, G:0.14, T:0.00
Consensus pattern (13 bp):
CCACGACCACGAC
Found at i:2739 original size:21 final size:21
Alignment explanation
Indices: 2713--2784 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
2703 GTTTCCAGAT
2713 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
2734 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
2755 TCGCAATGCTAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
2776 TCGCAATGC
1 TCGCAATGC
2785 AATATGTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:2823 original size:21 final size:22
Alignment explanation
Indices: 2797--2894 Score: 70
Period size: 20 Copynumber: 4.7 Consensus size: 22
2787 TATGTAAATT
2797 GCATTGCGATAGTCGACTA-TC
1 GCATTGCGATAGTCGACTAGTC
* *
2818 GCATTGCGAT--T-TACATATTC
1 GCATTGCGATAGTCGAC-TAGTC
*
2838 GCATTGCGATATTTC-A--AGTTC
1 GCATTGCGATA-GTCGACTAG-TC
*
2859 GCGTTGCGATAGTCGA--AGTC
1 GCATTGCGATAGTCGACTAGTC
2879 GCATTGCGATAGTCGA
1 GCATTGCGATAGTCGA
2895 AGTTCGCGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 32 0.50
21 25 0.39
23 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (22 bp):
GCATTGCGATAGTCGACTAGTC
Found at i:2906 original size:21 final size:21
Alignment explanation
Indices: 2797--2908 Score: 101
Period size: 21 Copynumber: 5.4 Consensus size: 21
2787 TATGTAAATT
*
2797 GCATTGCGATAGTCG-ACTATC
1 GCATTGCGATAGTCGAAGT-TC
*
2818 GCATTGCGAT-TTAC-ATA-TTC
1 GCATTGCGATAGT-CGA-AGTTC
*
2838 GCATTGCGATATTTC-AAGTTC
1 GCATTGCGATA-GTCGAAGTTC
*
2859 GCGTTGCGATAGTCGAAG-TC
1 GCATTGCGATAGTCGAAGTTC
2879 GCATTGCGATAGTCGAAGTTC
1 GCATTGCGATAGTCGAAGTTC
*
2900 GCGTTGCGA
1 GCATTGCGA
2909 ATCTGAAACG
Statistics
Matches: 78, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
20 35 0.45
21 40 0.51
22 3 0.04
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (21 bp):
GCATTGCGATAGTCGAAGTTC
Found at i:5424 original size:24 final size:27
Alignment explanation
Indices: 5392--5445 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 27
5382 ATGCAGCTTT
*
5392 AACATTAAATTT-ATTTA-A-AATTAA
1 AACACTAAATTTAATTTACAGAATTAA
5416 AACACTAAATTTGAATTTACAGAATTAA
1 AACACTAAATTT-AATTTACAGAATTAA
5444 AA
1 AA
5446 ACAATGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 11 0.44
26 5 0.20
27 1 0.04
28 8 0.32
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (27 bp):
AACACTAAATTTAATTTACAGAATTAA
Found at i:19734 original size:81 final size:83
Alignment explanation
Indices: 19598--19836 Score: 286
Period size: 84 Copynumber: 2.9 Consensus size: 83
19588 TTTTCCCCTT
* ** * * * * * *
19598 ATATATATAACCTTATGTAAACATAAAAAAACCCTACTACGTT-CATTATACATTTATATATGTA
1 ATATATATAGCCCAATGTTAACATAAAAAAAACCTAATGCTTTCCATTATACATTTATATATATA
19662 ACCTAATGTTATTAGTC-
66 ACCTAATGTTATTAGTCA
* * * *
19679 A-ATATATAGGCCATTGTTCACATAAAAAAAACCTAATGCTTTCCATTATACATTTATATATATT
1 ATATATATAGCCCAATGTTAACATAAAAAAAACCTAATGCTTTCCATTATACATTTATATATATA
19743 ACCTAATGTTATTAGTCA
66 ACCTAATGTTATTAGTCA
* * * * *
19761 ATATATATAGCCCAATGTTAAAATAAAAAGGAGCCTAATGCTTTCCAGTATATATTTATATATAT
1 ATATATATAGCCCAATGTTAACATAAAAA-AAACCTAATGCTTTCCATTATACATTTATATATAT
19826 AACCTAATGTT
65 AACCTAATGTT
19837 CCATAAATGT
Statistics
Matches: 132, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
80 30 0.23
81 37 0.28
82 1 0.01
83 23 0.17
84 41 0.31
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (83 bp):
ATATATATAGCCCAATGTTAACATAAAAAAAACCTAATGCTTTCCATTATACATTTATATATATA
ACCTAATGTTATTAGTCA
Found at i:22375 original size:2 final size:2
Alignment explanation
Indices: 22370--22398 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22360 ATTTAATCCG
22370 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 T
22399 GATTTTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22753 original size:64 final size:64
Alignment explanation
Indices: 22622--22755 Score: 200
Period size: 65 Copynumber: 2.1 Consensus size: 64
22612 TAATCACATC
* *
22622 TATAAGATGTGTCTTGTGCATAAATTTAAAAAAAGTTTATATATATAGTTAATAAAAGAAATTTA
1 TATAAGATGTGTCTTGTGCATAAATTTAAAAAAAGTTTATATACATA-TTAATAAAAAAAATTTA
*
22687 TATAAGATGTGTCTTGTGCATAAATTT-TAAAAAGTTTATATACAT-TTAATAAAAAAAAAGTTT
1 TATAAGATGTGTCTTGTGCATAAATTTAAAAAAAGTTTATATACATATTAAT-AAAAAAAA-TTT
22750 A
64 A
22751 TATAA
1 TATAA
22756 AACTATTATA
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
62 5 0.08
63 7 0.11
64 25 0.39
65 27 0.42
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (64 bp):
TATAAGATGTGTCTTGTGCATAAATTTAAAAAAAGTTTATATACATATTAATAAAAAAAATTTA
Found at i:24407 original size:16 final size:16
Alignment explanation
Indices: 24381--24437 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
24371 AGAAAACTTG
*
24381 TTGCTCGTTAAGCTCA
1 TTGCTCATTAAGCTCA
*
24397 TTGCTTATTAAGCTCA
1 TTGCTCATTAAGCTCA
* *
24413 TTACTCGTTAAGCTCA
1 TTGCTCATTAAGCTCA
*
24429 ATGCTCATT
1 TTGCTCATT
24438 GCCGCCTCGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (16 bp):
TTGCTCATTAAGCTCA
Found at i:30334 original size:19 final size:19
Alignment explanation
Indices: 30302--30339 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30292 ACCCGACTCG
30302 AAATAATATATTTATTAAA
1 AAATAATATATTTATTAAA
* *
30321 AAATATTATTTTTATTAAA
1 AAATAATATATTTATTAAA
30340 TAAAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATAATATATTTATTAAA
Found at i:32051 original size:18 final size:18
Alignment explanation
Indices: 32030--32088 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
32020 CTCATCAGCC
32030 TCATCTTCATCCTCAGAA
1 TCATCTTCATCCTCAGAA
* *
32048 TCATC-TGAGTCATCAGAA
1 TCATCTTCA-TCCTCAGAA
* *
32066 CCA-CTTTCATCCTCTGAA
1 TCATC-TTCATCCTCAGAA
32084 TCATC
1 TCATC
32089 ATCGTCGTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.32
Consensus pattern (18 bp):
TCATCTTCATCCTCAGAA
Found at i:36083 original size:64 final size:62
Alignment explanation
Indices: 35931--36091 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 62
35921 AATTGTTCAG
* * * *
35931 TGTGTATCGATGCACAGGAAATGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATT
1 TGTGCATCGATGCACAGG-AATGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
* * * * * **
35994 GGTACATCGATGCATAAGGAGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATT
1 TGTGCATCGATGCA-CAGGAATGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATT
* *
36058 TGTGCATCGATGCACGGGTACTGCATCGATGCAC
1 TGTGCATCGATGCACAGG-AATGCATCGATGCAC
36092 ATGCTAAAGA
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
63 27 0.34
64 52 0.66
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (62 bp):
TGTGCATCGATGCACAGGAATGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
Found at i:36125 original size:20 final size:20
Alignment explanation
Indices: 36060--36136 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
36050 AGGTGATTTG
* * *
36060 TGCATCGATGCACGGGT-AC
1 TGCATCGATGCACTGTTGAA
*
36079 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--TGAA
36103 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
36123 TGCATCGATGCACT
1 TGCATCGATGCACT
36137 TCAAGAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.27
20 18 0.38
22 1 0.02
23 2 0.04
24 14 0.29
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (20 bp):
TGCATCGATGCACTGTTGAA
Found at i:36982 original size:8 final size:8
Alignment explanation
Indices: 36971--37002 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
36961 TAAATGATGA
36971 CATGTATG
1 CATGTATG
36979 CATGTATG
1 CATGTATG
*
36987 TATGTATG
1 CATGTATG
36995 CATGTATG
1 CATGTATG
37003 TAATGGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (8 bp):
CATGTATG
Found at i:36993 original size:16 final size:16
Alignment explanation
Indices: 36972--37004 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
36962 AAATGATGAC
36972 ATGTATGCATGTATGT
1 ATGTATGCATGTATGT
36988 ATGTATGCATGTATGT
1 ATGTATGCATGTATGT
37004 A
1 A
37005 ATGGTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (16 bp):
ATGTATGCATGTATGT
Found at i:37291 original size:30 final size:30
Alignment explanation
Indices: 37257--37359 Score: 197
Period size: 30 Copynumber: 3.4 Consensus size: 30
37247 GGTTCTTCGG
*
37257 GACCTCTAGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
37287 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
37317 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
37347 GACCTCTGGATAG
1 GACCTCTGGATAG
37360 GTCATTCACA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:40830 original size:64 final size:63
Alignment explanation
Indices: 40762--40918 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 63
40752 TTCAGTTTGT
* * *
40762 ATCGATGCACAGAAAGTGCATCGATGCACCTATTAAAAATGGAAACATCGAATGTAATTGGTGC
1 ATCGATGCACAGAAAGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGGTAATTGGTGC
* * * * *
40826 ATCGATGCATA-AGGAGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGC
1 ATCGATGCACAGA-AAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGTAATTGGTGC
* ** *
40890 ATCGATGCACGGGTACTGCATCGATGCAC
1 ATCGATGCACAGAAAGTGCATCGATGCAC
40919 ATGCTAAAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
63 2 0.03
64 71 0.92
65 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (63 bp):
ATCGATGCACAGAAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGTAATTGGTGC
Found at i:40952 original size:20 final size:20
Alignment explanation
Indices: 40887--40960 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
40877 AGGTGATTTG
* * *
40887 TGCATCGATGCACGGGT-AC
1 TGCATCGATGCACTGTTGAA
*
40906 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--TGAA
40930 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
40950 TGCATCGATGC
1 TGCATCGATGC
40961 GCTTCAAGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 13 0.29
20 15 0.33
22 1 0.02
23 2 0.04
24 14 0.31
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (20 bp):
TGCATCGATGCACTGTTGAA
Found at i:41803 original size:4 final size:4
Alignment explanation
Indices: 41794--41818 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41784 AAATGATGAC
41794 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
41819 ATGGTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:42105 original size:30 final size:30
Alignment explanation
Indices: 42071--42203 Score: 221
Period size: 30 Copynumber: 4.4 Consensus size: 30
42061 GGTTTTTCGG
* *
42071 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
42101 GACCTCTGGATAATTACCGAGGATCATTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
42131 GACCTCTGAATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
42161 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
42191 GACCTCTGGATAG
1 GACCTCTGGATAG
42204 GTCATTCGAA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 95 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:44809 original size:25 final size:27
Alignment explanation
Indices: 44781--44832 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
44771 TTTAGATAAT
44781 TAATGTAAAAAATA-AT-ATTTATTTA
1 TAATGTAAAAAATACATGATTTATTTA
* *
44806 TAATTTAAATAATACATGATTTATTTA
1 TAATGTAAAAAATACATGATTTATTTA
44833 CTCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 2 0.09
27 9 0.39
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (27 bp):
TAATGTAAAAAATACATGATTTATTTA
Found at i:44877 original size:12 final size:12
Alignment explanation
Indices: 44860--44899 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
44850 TTTATCTTTT
44860 AAATTTTATAAA
1 AAATTTTATAAA
*
44872 AAATTTTATATAT
1 AAATTTTATA-AA
44885 AAATTTTATTAAA
1 AAATTTTA-TAAA
44898 AA
1 AA
44900 GTATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.42
13 12 0.50
14 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATTTTATAAA
Found at i:44890 original size:13 final size:12
Alignment explanation
Indices: 44859--44893 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
44849 ATTTATCTTT
44859 TAAATTTTATAA
1 TAAATTTTATAA
*
44871 AAAATTTTATATA
1 TAAATTTTATA-A
44884 TAAATTTTAT
1 TAAATTTTAT
44894 TAAAAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAAATTTTATAA
Found at i:44906 original size:25 final size:25
Alignment explanation
Indices: 44859--44906 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44849 ATTTATCTTT
* *
44859 TAAATTTTATAAAAAATTTTATATA
1 TAAATTTTATAAAAAAGTATATATA
*
44884 TAAATTTTATTAAAAAGTATATA
1 TAAATTTTATAAAAAAGTATATA
44907 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TAAATTTTATAAAAAAGTATATATA
Found at i:45154 original size:18 final size:19
Alignment explanation
Indices: 45119--45155 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
45109 CACGGAATGT
45119 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
45139 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
45156 GGATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:45322 original size:21 final size:21
Alignment explanation
Indices: 45298--45337 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45288 TTTTAAAGTG
* *
45298 AAATTCTAAATATTTAAATAA
1 AAATTATAAATATATAAATAA
*
45319 AAATTATATATATATAAAT
1 AAATTATAAATATATAAAT
45338 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTATAAATATATAAATAA
Found at i:47859 original size:2 final size:2
Alignment explanation
Indices: 47852--47878 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47842 TTTACATTCT
47852 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 T
47879 TATGACCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50670 original size:20 final size:19
Alignment explanation
Indices: 50645--50741 Score: 108
Period size: 18 Copynumber: 5.1 Consensus size: 19
50635 CTAGACTATT
50645 AGGAAAAGAATCAAAAGCAA
1 AGGAAAA-AATCAAAAGCAA
**
50665 AGG-AAAAATTGAAAGCAA
1 AGGAAAAAATCAAAAGCAA
*
50683 AGGAAAAGAATCAAAATCAA
1 AGGAAAA-AATCAAAAGCAA
*
50703 AGG-AAAAATTAAAAGCAA
1 AGGAAAAAATCAAAAGCAA
*
50721 AGGAAAATAATCAAAATCAA
1 AGGAAAA-AATCAAAAGCAA
50741 A
1 A
50742 AGCAAAGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
18 26 0.41
19 12 0.19
20 26 0.41
ACGTcount: A:0.65, C:0.08, G:0.16, T:0.10
Consensus pattern (19 bp):
AGGAAAAAATCAAAAGCAA
Found at i:50696 original size:38 final size:38
Alignment explanation
Indices: 50645--50741 Score: 167
Period size: 38 Copynumber: 2.6 Consensus size: 38
50635 CTAGACTATT
* *
50645 AGGAAAAGAATCAAAAGCAAAGGAAAAATTGAAAGCAA
1 AGGAAAAGAATCAAAATCAAAGGAAAAATTAAAAGCAA
50683 AGGAAAAGAATCAAAATCAAAGGAAAAATTAAAAGCAA
1 AGGAAAAGAATCAAAATCAAAGGAAAAATTAAAAGCAA
*
50721 AGGAAAATAATCAAAATCAAA
1 AGGAAAAGAATCAAAATCAAA
50742 AGCAAAGTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.65, C:0.08, G:0.16, T:0.10
Consensus pattern (38 bp):
AGGAAAAGAATCAAAATCAAAGGAAAAATTAAAAGCAA
Found at i:51663 original size:20 final size:21
Alignment explanation
Indices: 51638--51683 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
51628 ATTGTTTTTG
51638 TATTTTT-AAATTAAATTCAT
1 TATTTTTCAAATTAAATTCAT
* *
51658 TATTTTTCATATTAAATTTAT
1 TATTTTTCAAATTAAATTCAT
51679 TATTT
1 TATTT
51684 AATAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTCAAATTAAATTCAT
Found at i:51663 original size:27 final size:26
Alignment explanation
Indices: 51633--51719 Score: 69
Period size: 27 Copynumber: 3.5 Consensus size: 26
51623 AATTTATTGT
51633 TTTTGTATTTTTAAATTAAATTCATTA
1 TTTT-TATTTTTAAATTAAATTCATTA
*
51660 TTTTTCA----T--ATTAAATTTATTA
1 TTTTT-ATTTTTAAATTAAATTCATTA
* *
51681 TTTAATAATTTTAAATTAAATTCATTA
1 TTT-TTATTTTTAAATTAAATTCATTA
*
51708 TTTTTATATTTA
1 TTTTTATTTTTA
51720 TATTTCTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 17
0.67 0.09 0.25
Matches are distributed among these distances:
21 16 0.35
22 1 0.02
23 1 0.02
25 1 0.02
26 7 0.15
27 20 0.43
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (26 bp):
TTTTTATTTTTAAATTAAATTCATTA
Found at i:52952 original size:23 final size:25
Alignment explanation
Indices: 52901--52954 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 25
52891 TAACTATATT
52901 TATTTTA-AAATATATTATATATAA
1 TATTTTATAAATATATTATATATAA
52925 -A--TTATAAAT-TATTAT-TATAA
1 TATTTTATAAATATATTATATATAA
52945 TATTTTATAA
1 TATTTTATAA
52955 TATCAGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
20 5 0.19
21 10 0.38
22 4 0.15
23 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTTATAAATATATTATATATAA
Found at i:53245 original size:14 final size:14
Alignment explanation
Indices: 53220--53258 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
53210 CGTTTAAATT
*
53220 ATAAATGAACACAA
1 ATAAACGAACACAA
*
53234 ATGAACGAACACAA
1 ATAAACGAACACAA
53248 ATAAACGAACA
1 ATAAACGAACA
53259 TAAACTAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.62, C:0.18, G:0.10, T:0.10
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:53584 original size:40 final size:39
Alignment explanation
Indices: 53524--53636 Score: 156
Period size: 40 Copynumber: 2.8 Consensus size: 39
53514 AAATTATCGA
*
53524 ATGTTCATTCATTTAAATAAAAAGATATATAATTTTATTC
1 ATGTTCATTCATTTAAATAAAAA-ACATATAATTTTATTC
* * *
53564 ATGTCCATTTATTTAAATAAACAAACATATAATTTTATTT
1 ATGTTCATTCATTTAAATAAA-AAACATATAATTTTATTC
53604 ATGTTCATTCATTTAAATAAAATAACATA-AATT
1 ATGTTCATTCATTTAAATAAAA-AACATATAATT
53637 AATTTATCGT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
39 5 0.08
40 58 0.89
41 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (39 bp):
ATGTTCATTCATTTAAATAAAAAACATATAATTTTATTC
Found at i:68650 original size:2 final size:2
Alignment explanation
Indices: 68645--68677 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
68635 ACACCTATGC
*
68645 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
68678 CAAATGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73760 original size:18 final size:19
Alignment explanation
Indices: 73727--73762 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
73717 TAAAGGTAAA
*
73727 TAAATTATTCATTTTATTT
1 TAAATTATTAATTTTATTT
73746 TAAATT-TTAATTTTATT
1 TAAATTATTAATTTTATT
73763 AATATTTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TAAATTATTAATTTTATTT
Found at i:73795 original size:20 final size:18
Alignment explanation
Indices: 73748--73798 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
73738 TTTTATTTTA
73748 AATTTTAATTTTATTAAT
1 AATTTTAATTTTATTAAT
*
73766 -ATTTCGAATTGCTTATTAAT
1 AATTT-TAATT--TTATTAAT
73786 AATTTTAATTTTA
1 AATTTTAATTTTA
73799 ATTTTGTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 4 0.15
18 7 0.26
20 12 0.44
21 4 0.15
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (18 bp):
AATTTTAATTTTATTAAT
Found at i:74745 original size:58 final size:56
Alignment explanation
Indices: 74658--74798 Score: 219
Period size: 58 Copynumber: 2.5 Consensus size: 56
74648 ATTATTTTTC
* *
74658 AATTAATCATGTTCAATAAATAACTTATTTTAACTTTTAATGATTATAATTAATTT
1 AATTAATCATGTTCAATAAATAAATTATTTTAACTTGTAATGATTATAATTAATTT
* * *
74714 TATTAATCATGTTCAATGCCAATAAATTATTTTAACTTGTAATTATTATAATTAATTT
1 AATTAATCATGTTCAAT--AAATAAATTATTTTAACTTGTAATGATTATAATTAATTT
74772 AATTAATCATGTTCAATAAATAAATTA
1 AATTAATCATGTTCAATAAATAAATTA
74799 CTTAATAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
56 25 0.33
58 51 0.67
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (56 bp):
AATTAATCATGTTCAATAAATAAATTATTTTAACTTGTAATGATTATAATTAATTT
Found at i:76904 original size:2 final size:2
Alignment explanation
Indices: 76892--76922 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
76882 ATTTTATAAC
76892 AT AT GAT 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
76923 TCAAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76955 original size:21 final size:21
Alignment explanation
Indices: 76930--76994 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
76920 TATTCAAATT
76930 TTTTTAATAATAATTTTAGTA
1 TTTTTAATAATAATTTTAGTA
76951 TTTTTAAT-ATAAATATTTA--A
1 TTTTTAATAAT-AAT-TTTAGTA
*
76971 TTTTT-A-AATAA-TTTAGTT
1 TTTTTAATAATAATTTTAGTA
76989 TTTTTA
1 TTTTTA
76995 GTATTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
16 4 0.11
18 7 0.19
19 3 0.08
20 8 0.22
21 11 0.30
22 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTTAATAATAATTTTAGTA
Found at i:77029 original size:46 final size:47
Alignment explanation
Indices: 76943--77031 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 47
76933 TTAATAATAA
*
76943 TTTTAGTATTTTTAATATAAATATTTAATTTTTAAATAATTTAGTTT
1 TTTTAGTATTTTTAATATAAATATTTAATATTTAAATAATTTAGTTT
* ** * *
76990 TTTTAGTATTTTTTATAT-TTTTTTTAATATTTGAATAATTTA
1 TTTTAGTATTTTTAATATAAATATTTAATATTTAAATAATTTA
77032 TATTTATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 19 0.53
47 17 0.47
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (47 bp):
TTTTAGTATTTTTAATATAAATATTTAATATTTAAATAATTTAGTTT
Found at i:77180 original size:21 final size:21
Alignment explanation
Indices: 77154--77216 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
77144 CATCAGTCGC
* *
77154 ATTGGACAACCACGTCAACAT
1 ATTGGACTACCACGCCAACAT
77175 ATTGGACTACCACGCCAACAT
1 ATTGGACTACCACGCCAACAT
*
77196 ATTGGACTACCACGCTAACAT
1 ATTGGACTACCACGCCAACAT
77217 TGTAACAGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.21
Consensus pattern (21 bp):
ATTGGACTACCACGCCAACAT
Found at i:77980 original size:2 final size:2
Alignment explanation
Indices: 77975--78069 Score: 61
Period size: 2 Copynumber: 53.5 Consensus size: 2
77965 TTAATATAAA
*
77975 AT AT AT A- AA AT AT -T AT AT AT AT AT AT AT AT AT A- AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
78012 AT AT A- AA AT AT AT AA AT AT -T AT AT AT AT A- AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
78049 A- AA AT AT -T AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
78070 ATCAGGGCGG
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
1 12 0.16
2 62 0.84
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:78035 original size:33 final size:34
Alignment explanation
Indices: 77977--78069 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 34
77967 AATATAAAAT
*
77977 ATATAAAATATTATATATATATATATATATAATTA
1 ATATAAAATATTATAAATAT-TATATATATAATTA
78012 ATATAAAATA-TATAAATATTATATATATAATTA
1 ATATAAAATATTATAAATATTATATATATAATTA
*
78045 ATATAAAATATTATACATA-TATATA
1 ATATAAAATATTATAAATATTATATA
78070 ATCAGGGCGG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 30 0.55
34 15 0.27
35 10 0.18
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
ATATAAAATATTATAAATATTATATATATAATTA
Found at i:78049 original size:44 final size:44
Alignment explanation
Indices: 77958--78040 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
77948 GGGTTTGTAT
77958 TATATAATTAATATAAAATATATAAAATATTATATATATATATA
1 TATATAATTAATATAAAATATATAAAATATTATATATATATATA
78002 TATATAATTAATATAAAATATAT-AAATATTATATATATA
1 TATATAATTAATATAAAATATATAAAATATTATATATATA
78041 ATTAATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
43 16 0.41
44 23 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (44 bp):
TATATAATTAATATAAAATATATAAAATATTATATATATATATA
Found at i:84226 original size:241 final size:240
Alignment explanation
Indices: 83804--84292 Score: 960
Period size: 241 Copynumber: 2.0 Consensus size: 240
83794 AGTACACAAA
83804 GCTCAATAACATGCAAGGGGAGGGGAGGGGAGATGCAGAGGCTTAACCCTGCTCCACAAAAAGTT
1 GCTCAATAACATGCAAGGGGAGGGGAGGGGAGATGCAGAGGCTTAACCCTGCTCCACAAAAAGTT
*
83869 GTTTTTATGAACTGAAAGTTGAAAACTAGAACTCCGTGTCACGATCAAGAAGCCACACCAATGTA
66 GTTTTTATGAACTGAAAGTTGAAAACTAGAACTCCGTGTCACAATCAAGAAGCCACACCAATGTA
83934 TCATATCTTAACATGCTATATTTATCACATCTTTATGTGAGAACTTGAATAAATAACTAACTATA
131 TCATATCTTAACATGCTATATTTATCACATCTTTATGTGAGAACTTGAATAAATAACTAACTATA
83999 TGTGCAAAGTACTAGCATTTACAGTCTCAACCTTGTTATCACATT
196 TGTGCAAAGTACTAGCATTTACAGTCTCAACCTTGTTATCACATT
84044 GCTCAATAACATGCAAGGGGAGGGGAGGGGAGATGCAGGAGGCTTAACCCTGCTCCACAAAAAGT
1 GCTCAATAACATGCAAGGGGAGGGGAGGGGAGATGCA-GAGGCTTAACCCTGCTCCACAAAAAGT
84109 TGTTTTTATGAACTGAAAGTTGAAAACTAGAACTCCGTGTCACAATCAAGAAGCCACACCAATGT
65 TGTTTTTATGAACTGAAAGTTGAAAACTAGAACTCCGTGTCACAATCAAGAAGCCACACCAATGT
84174 ATCATATCTTAACATGCTATATTTATCACATCTTTATGTGAGAACTTGAATAAATAACTAACTAT
130 ATCATATCTTAACATGCTATATTTATCACATCTTTATGTGAGAACTTGAATAAATAACTAACTAT
84239 ATGTGCAAAGTACTAGCATTTACAGTCTCAACCTTGTTATCACATT
195 ATGTGCAAAGTACTAGCATTTACAGTCTCAACCTTGTTATCACATT
84285 GCTCAATA
1 GCTCAATA
84293 CATAACTGAT
Statistics
Matches: 247, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
240 37 0.15
241 210 0.85
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (240 bp):
GCTCAATAACATGCAAGGGGAGGGGAGGGGAGATGCAGAGGCTTAACCCTGCTCCACAAAAAGTT
GTTTTTATGAACTGAAAGTTGAAAACTAGAACTCCGTGTCACAATCAAGAAGCCACACCAATGTA
TCATATCTTAACATGCTATATTTATCACATCTTTATGTGAGAACTTGAATAAATAACTAACTATA
TGTGCAAAGTACTAGCATTTACAGTCTCAACCTTGTTATCACATT
Found at i:85428 original size:26 final size:27
Alignment explanation
Indices: 85396--85464 Score: 131
Period size: 26 Copynumber: 2.6 Consensus size: 27
85386 TTAGACATCT
85396 AAAACTGTTGTTAGAGTTCTTAT-AAA
1 AAAACTGTTGTTAGAGTTCTTATAAAA
85422 AAAACTGTTGTTAGAGTTCTTATAAAA
1 AAAACTGTTGTTAGAGTTCTTATAAAA
85449 AAAACTGTTGTTAGAG
1 AAAACTGTTGTTAGAG
85465 AAAATATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 23 0.55
27 19 0.45
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (27 bp):
AAAACTGTTGTTAGAGTTCTTATAAAA
Done.