Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001534.1 Hibiscus syriacus cultivar Beakdansim tig00003010_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: 71290
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:754 original size:21 final size:21
Alignment explanation
Indices: 687--754 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
677 TATGAATCGG
* *
687 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAACGGTGGCAGGGGA
* * * * *
708 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGCAGGGGA
*
730 CTCTTGAACGGTGGTAGGGGA
1 CTCTTGAACGGTGGCAGGGGA
751 CTCT
1 CTCT
755 CGAGGATGAT
Statistics
Matches: 33, Mismatches: 13, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.19, C:0.21, G:0.35, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGCAGGGGA
Found at i:775 original size:41 final size:43
Alignment explanation
Indices: 687--775 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
677 TATGAATCGG
* *
687 CTCTTGAATGGTGGGAGGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGACCTCTTCAACGATGACAGGGGC
* * * *
730 CTCTTGAACGGTGGTAGGGGA-CTC-TCGAGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACCTCTTCAACGATGACAGGGGC
771 CTCTT
1 CTCTT
776 CACGATAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
41 18 0.45
42 3 0.08
43 19 0.47
ACGTcount: A:0.19, C:0.20, G:0.36, T:0.25
Consensus pattern (43 bp):
CTCTTGAACGGTGGGAGGGGACCTCTTCAACGATGACAGGGGC
Found at i:1204 original size:91 final size:90
Alignment explanation
Indices: 1024--1210 Score: 279
Period size: 91 Copynumber: 2.0 Consensus size: 90
1014 ATATTTCAAA
*
1024 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
* *
1089 GCATAATTGGCAGCAACCGAATAAATTT
63 GCATAATTGGAAGCAACCAAATAAATTT
1117 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
1181 CAGT-ATTGGAAGCAACCAAATAAATTT
64 CA-TAATTGGAAGCAACCAAATAAATTT
1208 ACT
1 ACT
1211 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
91 39 0.44
92 1 0.01
93 21 0.24
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
TAATTGGAAGCAACCAAATAAATTT
Found at i:1412 original size:63 final size:63
Alignment explanation
Indices: 1353--1494 Score: 151
Period size: 63 Copynumber: 2.3 Consensus size: 63
1343 CTTAGAGCGG
* * *
1353 TAACCTCAC-CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 TAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * *** *
1416 TGATCTCCTCACGCAAGGCATTGACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 TAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
** *
1479 CGATCTCCTCACGCAA
1 TAACCTCCTCACGCAA
1495 GGCATTGACC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 1 0.01
63 68 0.99
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20
Consensus pattern (63 bp):
TAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:1495 original size:63 final size:63
Alignment explanation
Indices: 1376--1506 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
1366 TAAAGTAGAC
*
1376 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACTGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1439 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1502 ACCTC
1 ACCTC
1507 ATCACGTAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:2998 original size:19 final size:20
Alignment explanation
Indices: 2949--3010 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
2939 TTTTGGTTGA
*
2949 AATGAAAATCGCAACGAGAT
1 AATGACAATCGCAACGAGAT
* *
2969 AATGAGAATCGCAACGCGA-
1 AATGACAATCGCAACGAGAT
*
2988 AATGACTATCGCAACGAGAT
1 AATGACAATCGCAACGAGAT
3008 AAT
1 AAT
3011 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (20 bp):
AATGACAATCGCAACGAGAT
Found at i:3057 original size:19 final size:19
Alignment explanation
Indices: 3035--3079 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3025 AAAATTGCAA
*
3035 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* * *
3054 TGCGCTTTTTATTTCGTGT
1 TGCGATTTTGATTTCGCGT
3073 TGCGATT
1 TGCGATT
3080 CTCTCGTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:3659 original size:20 final size:20
Alignment explanation
Indices: 3634--3686 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3624 GCGCTATGTA
*
3634 AATCGCGTTGCGAAAGTTAG
1 AATCGCGTTGCGAAAGTCAG
3654 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
3674 TATCTCGTTGCGA
1 AATCGCGTTGCGA
3687 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:3720 original size:20 final size:20
Alignment explanation
Indices: 3695--3748 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3685 GATTTTGTAT
3695 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
3715 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
3735 TATCGCATTGCGAT
1 TATCGCATTGCGAT
3749 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:3733 original size:61 final size:61
Alignment explanation
Indices: 3635--3751 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
3625 CGCTATGTAA
* * * * *
3635 ATCGCGTTGCGAAAGTTAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
3696 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
3752 TCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:3767 original size:61 final size:61
Alignment explanation
Indices: 3630--3769 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 61
3620 AATGGCGCTA
* * * * *
3630 TGTAA-ATCGCGTTGCGAAAGTTAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
3690 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
3751 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
3770 TTATTTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
60 5 0.08
61 59 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:3859 original size:21 final size:21
Alignment explanation
Indices: 3819--3859 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3809 ACTGTAGACC
**
3819 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
3840 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
3860 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:4816 original size:2 final size:2
Alignment explanation
Indices: 4809--4885 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
4799 GCTTCTCAAT
4809 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
4851 TA 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 TA T
4886 TATTCTGCCA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6395 original size:6 final size:6
Alignment explanation
Indices: 6384--6410 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6374 GTCGTTTGTT
6384 GGTGCA GGTGCA GGTGCA GGTGCA GGT
1 GGTGCA GGTGCA GGTGCA GGTGCA GGT
6411 ACATGTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.19
Consensus pattern (6 bp):
GGTGCA
Found at i:6418 original size:18 final size:18
Alignment explanation
Indices: 6384--6418 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6374 GTCGTTTGTT
*
6384 GGTGCAGGTGCAGGTGCA
1 GGTGCAGGTACAGGTGCA
*
6402 GGTGCAGGTACATGTGC
1 GGTGCAGGTACAGGTGC
6419 TCCACCATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.17, G:0.46, T:0.20
Consensus pattern (18 bp):
GGTGCAGGTACAGGTGCA
Found at i:6854 original size:30 final size:30
Alignment explanation
Indices: 6818--6881 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
6808 TTATGATTTA
6818 AATGTTGCCAATAATAGTCTGGATCTGAAG
1 AATGTTGCCAATAATAGTCTGGATCTGAAG
6848 AATGTTGCCAATAATAGTCTGGATCTGAAG
1 AATGTTGCCAATAATAGTCTGGATCTGAAG
6878 AATG
1 AATG
6882 CAGCCACTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (30 bp):
AATGTTGCCAATAATAGTCTGGATCTGAAG
Found at i:11231 original size:5 final size:5
Alignment explanation
Indices: 11221--11246 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11211 TGACTTAGAA
11221 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
11247 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:16464 original size:60 final size:60
Alignment explanation
Indices: 16396--16538 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
16386 CTTTAAAATG
* * *
16396 TTTCAATTTCATCCCTAAACTATCA-CTATCATTCTAAATTAGTC-CTTAAA-ATTTTGAGCA
1 TTTCAATTTCATCCC-AAACTATCACCT-TCATTCCAAATTAGTCTC-CAAACATTTTGAACA
** *
16456 TTTCAATTTCATCCCCAAACTAAGACCTTCATTCCAAATTAGTCTCCAAACTTTTTGAACA
1 TTTCAATTTCAT-CCCAAACTATCACCTTCATTCCAAATTAGTCTCCAAACATTTTGAACA
* *
16517 TTCCAATTTTATCCCAAACTAT
1 TTTCAATTTCATCCCAAACTAT
16539 ATGTATATAC
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
60 46 0.66
61 24 0.34
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (60 bp):
TTTCAATTTCATCCCAAACTATCACCTTCATTCCAAATTAGTCTCCAAACATTTTGAACA
Found at i:22472 original size:26 final size:28
Alignment explanation
Indices: 22442--22503 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
22432 GAAAATTTTA
22442 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
22468 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
22499 AGCTC
1 AGCTC
22504 AGCAATACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:29802 original size:24 final size:25
Alignment explanation
Indices: 29766--29825 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
29756 TCAATCGAAA
** *
29766 ATATTATGAATAAGATAAAAT-TTT
1 ATATTATTTATAACATAAAATATTT
*
29790 ATATTATTTATAACCTAAAATATTT
1 ATATTATTTATAACATAAAATATTT
29815 -TATT-TTTATAA
1 ATATTATTTATAA
29826 TATTTTTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 7 0.23
24 21 0.68
25 3 0.10
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
ATATTATTTATAACATAAAATATTT
Found at i:30974 original size:16 final size:16
Alignment explanation
Indices: 30951--30986 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
30941 TTTCTTGTCA
*
30951 ATTT-TATTATTTATT
1 ATTTATATTATATATT
30966 ATTTATATTATATATT
1 ATTTATATTATATATT
30982 ATTTA
1 ATTTA
30987 CGTTACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTATATTATATATT
Found at i:31036 original size:24 final size:24
Alignment explanation
Indices: 31005--31067 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
30995 ATAGCTTAAT
31005 ATATTATTTATTATTCATTGTATA
1 ATATTATTTATTATTCATTGTATA
31029 ATATTATTTATTATTCATTGTATA
1 ATATTATTTATTATTCATTGTATA
31053 ATATTATTTATTATT
1 ATATTATTTATTATT
31068 ACAAATTAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (24 bp):
ATATTATTTATTATTCATTGTATA
Found at i:31949 original size:20 final size:19
Alignment explanation
Indices: 31899--31952 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
31889 TCATTGATTG
*
31899 TTGTTGAT-ATGGAAATGA
1 TTGTTGATGATGAAAATGA
31917 TTG-TGAATGGATGAAAATGA
1 TTGTTG-AT-GATGAAAATGA
31937 TGTGTTGATGATGAAA
1 T-TGTTGATGATGAAA
31953 TTATGCTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
20 17 0.57
21 4 0.13
22 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (19 bp):
TTGTTGATGATGAAAATGA
Found at i:33444 original size:23 final size:23
Alignment explanation
Indices: 33415--33458 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
33405 AAGACAAAAG
33415 AAAACGTGTCATGA-AGGCAGAGA
1 AAAACGTGTCAT-ATAGGCAGAGA
33438 AAAACGTGTCATATAGGCAGA
1 AAAACGTGTCATATAGGCAGA
33459 CTTATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (23 bp):
AAAACGTGTCATATAGGCAGAGA
Found at i:34810 original size:17 final size:17
Alignment explanation
Indices: 34790--34855 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
34780 ATACAATATT
34790 GTAAAAGATATAGTACA
1 GTAAAAGATATAGTACA
* *
34807 GTAAATGATACAGTACA
1 GTAAAAGATATAGTACA
* *
34824 ATAAAAGAAATAGTACAA
1 GTAAAAGATATAGTAC-A
34842 G-AAAAGATATAGTA
1 GTAAAAGATATAGTA
34856 TGAAAAAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 39 0.98
18 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (17 bp):
GTAAAAGATATAGTACA
Found at i:37706 original size:84 final size:84
Alignment explanation
Indices: 37618--38508 Score: 797
Period size: 84 Copynumber: 10.7 Consensus size: 84
37608 CTTAATGTAA
* * * *
37618 TCGAACTCGGAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATAATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*
37683 GCCTTGGAGCTGAGCTTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
37702 TCGAACTCAAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *** *
37766 ATCCTCAAAGTTGAGCGTAG
66 -GCCTTGGAGCTGAGCGTAG
* * * *
37786 TCGAACTCGAGGGTC--T--TTGGCAGATAGCTCTTCTCGTA-TTAAGCTATGCTACAAATGATG
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG-ACTTAAGCTATGCTGCAAATGATG
*
37846 TGCCTTGGAGCTGAGTGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * * * * * *
37866 TCAAACTCGAAGGTCTTTTAG-TGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * * *
37930 TGCCATCGAAGCTGAGTGTAA
65 TGCC-TTGGAGCTGAGCGTAG
* * * * *
37951 TCGAACTTGAGGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGC
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*
38012 GCCTTGGAGCTGAGCGTAA
66 GCCTTGGAGCTGAGCGTAG
* * * *
38031 TCGAACTCCAAGGTCTTTGGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*
38096 GCCTTGGAGCTGAACGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
38115 TCGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*
38180 GCCTTGGAGCTGAGCATAG
66 GCCTTGGAGCTGAGCGTAG
* ** * * *
38199 TCAAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
38264 ACCTTGGAGCTGAACGTAG
66 GCCTTGGAGCTGAGCGTAG
** * * * * * * *
38283 TCGAACTCGAATATCTTTTGTTGGCAAATATCCCTTCTTG-CTTTGAGCTATGTTGTAAATGATG
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC-TTAAGCTATGCTGCAAATGATG
* * * * *
38347 TGCCCTCGAAGTTGAGTGTAA
65 TG-CCTTGGAGCTGAGCGTAG
** * * *
38368 TCGAACTCGGGGGAC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
38429 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * **
38448 TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTTGTCTTGAGCTATATTGCAAATG
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
38509 TTGTCTTAAA
Statistics
Matches: 638, Mismatches: 148, Indels: 42
0.77 0.18 0.05
Matches are distributed among these distances:
80 81 0.13
81 107 0.17
82 3 0.00
83 39 0.06
84 361 0.57
85 47 0.07
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:37965 original size:165 final size:164
Alignment explanation
Indices: 37638--38467 Score: 774
Period size: 165 Copynumber: 5.0 Consensus size: 164
37628 AGGTCTTCGG
* * * *
37638 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATAATGTGCCTTGGAGCTGAGCTTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * * * * *
37703 CGAACTCAAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTA
66 CAAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT-
* * *
37767 TCCTCAAAGTTGAGCGTAGTCGAACTCGAGGGTCT
130 GCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCT
* * *
37802 TTGGCAGATAGCTCTTCTCGTA-TTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGTGTAG
1 TTGGCAGATAGCCCTTCTCG-ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * *
37866 TCAAACTCGAAGGTCTTTTAGTGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGT
65 TCAAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * *
37931 GCCATCGAAGCTGAGTGTAATCGAACTTGAGGGTCT
130 GCC-TCGAAGCTGAGCGTAGTCGAACTCGAGGGTCT
* * * *
37967 TTGGTAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAAT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * ** * * *
38032 CGAACTCCAAGGTCTTTGGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
66 CAAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * * * *
38097 CCTTGGAGCTGAACGTAGTCGAACTCGAAGGTATTTT
131 CCTCGAAGCTGAGCGTAGTCGAACTCG-AGG--GTCT
* * * * * *
38134 GTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAG
1 -TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * * *
38199 TCAAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
65 TCAAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * * ***
38264 ACCTTGGAGCTGAACGTAGTCGAACTCGAATATCTTTT
130 GCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTC---T
* * * * * * * * * *
38302 GTTGGCAAATATCCCTTCTTG-CTTTGAGCTATGTTGTAAATGATGTGCCCTCGAAGTTGAGTGT
1 -TTGGCAGATAGCCCTTCTCGAC-TTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGT
* * ** * * * * *
38366 AATCGAACTCGGGGGAC-TTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGAT
63 AGTCAAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
* * *
38427 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
128 GTGCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCT
38464 TTGG
1 TTGG
38468 TTAGCAAATA
Statistics
Matches: 566, Mismatches: 87, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
161 4 0.01
162 1 0.00
164 90 0.16
165 256 0.45
166 1 0.00
167 4 0.01
168 187 0.33
169 23 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (164 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CAAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
CCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCT
Found at i:57335 original size:16 final size:15
Alignment explanation
Indices: 57304--57364 Score: 86
Period size: 15 Copynumber: 4.0 Consensus size: 15
57294 CGTAGGACTC
*
57304 CTACATCCCGAAGGA
1 CTACATCCCAAAGGA
57319 CTACATCCCAAAAGGA
1 CTACATCCC-AAAGGA
57335 CTACATCCCAAAGGA
1 CTACATCCCAAAGGA
* *
57350 CTACGTCCCGAAGGA
1 CTACATCCCAAAGGA
57365 TTATTATACC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
15 28 0.67
16 14 0.33
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.13
Consensus pattern (15 bp):
CTACATCCCAAAGGA
Found at i:57546 original size:12 final size:12
Alignment explanation
Indices: 57512--57546 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
57502 TATCATGTTC
**
57512 TCATATCACAGG
1 TCATATCACATA
57524 TCATATCACATA
1 TCATATCACATA
57536 TCATATCACAT
1 TCATATCACAT
57547 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:57945 original size:64 final size:64
Alignment explanation
Indices: 57857--58077 Score: 223
Period size: 64 Copynumber: 3.5 Consensus size: 64
57847 TAATGAAGGT
* * * * **
57857 ATGCATCGATTCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGT-TTCATTATTAATGGG
* ** **
57921 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTAATGGG
* ** * **
57985 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATG-TTTCATTATTAATGGG
**
58048 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
58078 ACACCTTCAA
Statistics
Matches: 135, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 4 0.03
64 125 0.93
65 6 0.04
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTAATGGG
Found at i:64247 original size:15 final size:15
Alignment explanation
Indices: 64227--64259 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
64217 CGTAGGACTC
64227 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
64242 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
64257 CTA
1 CTA
64260 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:64438 original size:12 final size:12
Alignment explanation
Indices: 64402--64438 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
64392 TATATCATGT
64402 TATCATATCACA
1 TATCATATCACA
**
64414 GGTCATATCACA
1 TATCATATCACA
64426 TATCATATCACA
1 TATCATATCACA
64438 T
1 T
64439 GAACATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.32
Consensus pattern (12 bp):
TATCATATCACA
Found at i:64856 original size:64 final size:62
Alignment explanation
Indices: 64748--64867 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 62
64738 TAATGAAGGT
* *
64748 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGTTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGT-TT-TTATTGTTGGG
* * **
64812 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTTTTTATT
64868 TTAAAAGAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
62 5 0.10
63 2 0.04
64 43 0.86
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (62 bp):
ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTTTTTATTGTTGGG
Found at i:64881 original size:64 final size:64
Alignment explanation
Indices: 64748--64892 Score: 161
Period size: 64 Copynumber: 2.3 Consensus size: 64
64738 TAATGAAGGT
* * **
64748 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGTTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTATTATTATTGTTAAG
* * **
64812 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT-TT-TTATT-TTAAAA
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTATTATTATTGTT--AA
64874 G
64 G
*
64875 AGTGCATTGATGCACTAC
1 A-TGCATCGATGCACTAC
64893 CAATGAATCG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
61 2 0.03
62 5 0.07
63 4 0.06
64 58 0.84
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTATTATTATTGTTAAG
Found at i:68081 original size:31 final size:30
Alignment explanation
Indices: 68014--68081 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
68004 TAATATTTGA
* * *
68014 TCACTTTTATTTTTATTTAATTAAGTTTTG
1 TCACTTTTATTTTTATTTAATTAAATGTGG
*
68044 TCCACTTTTGTTTTTATTTAATTATAATGTGG
1 T-CACTTTTATTTTTATTTAATTA-AATGTGG
68076 TCACTT
1 TCACTT
68082 AGGGTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 26 0.81
32 5 0.16
ACGTcount: A:0.22, C:0.10, G:0.09, T:0.59
Consensus pattern (30 bp):
TCACTTTTATTTTTATTTAATTAAATGTGG
Found at i:68201 original size:38 final size:39
Alignment explanation
Indices: 68150--68240 Score: 139
Period size: 38 Copynumber: 2.4 Consensus size: 39
68140 AATTAAAAAT
68150 GTAAACTACACAAATGATCACTAATGTT-AAAAAAAAGG
1 GTAAACTACACAAATGATCACTAATGTTCAAAAAAAAGG
* * * *
68188 GTAAACTATACAAATGATCATTAATGTTCAACAAAAGGG
1 GTAAACTACACAAATGATCACTAATGTTCAAAAAAAAGG
68227 GTAAACTACACAAA
1 GTAAACTACACAAA
68241 AATAAGTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 26 0.55
39 21 0.45
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (39 bp):
GTAAACTACACAAATGATCACTAATGTTCAAAAAAAAGG
Done.