Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001109.1 Hibiscus syriacus cultivar Beakdansim tig00002191_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: 50839
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:2119 original size:21 final size:21
Alignment explanation
Indices: 2094--2142 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
2084 AAATTTTTCC
2094 AAAAACCCCTTTTAACTTTAA
1 AAAAACCCCTTTTAACTTTAA
* *
2115 AAAAA-CCTTTTTAACTTTCA
1 AAAAACCCCTTTTAACTTTAA
*
2135 TAAAACCC
1 AAAAACCC
2143 TAACCCCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAACCCCTTTTAACTTTAA
Found at i:3371 original size:2 final size:2
Alignment explanation
Indices: 3364--3396 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3354 CATTTAAGTC
3364 AT AT AT AT AT AT AT AT AT AT ACT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A
3397 CACAAACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.93
3 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3420 original size:12 final size:12
Alignment explanation
Indices: 3364--3420 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
3354 CATTTAAGTC
*
3364 ATATATATATAT
1 ATATATATACAT
*
3376 ATATATATACTT
1 ATATATATACAT
*
3388 ATATATATACAC
1 ATATATATACAT
*
3400 AAACT-TATACAT
1 ATA-TATATACAT
*
3412 CTATATATA
1 ATATATATA
3421 TTTTAAAACT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 1 0.03
12 33 0.94
13 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATATACAT
Found at i:3747 original size:29 final size:32
Alignment explanation
Indices: 3695--3760 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 32
3685 TCAATGTATG
*
3695 TATAATGTTTTTAAATTTATTTTTTTAATAAA
1 TATAATGTTTTTAAATTTATTTTTTTAAAAAA
*
3727 TATAAT-TTTTT-TATTT-TTTTTTTAAAAAA
1 TATAATGTTTTTAAATTTATTTTTTTAAAAAA
*
3756 AATAA
1 TATAA
3761 ATTTGATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.52
30 4 0.13
31 5 0.16
32 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
TATAATGTTTTTAAATTTATTTTTTTAAAAAA
Found at i:4853 original size:122 final size:123
Alignment explanation
Indices: 4577--4917 Score: 381
Period size: 122 Copynumber: 2.8 Consensus size: 123
4567 AATTTAGAAC
* *
4577 GAAAACTATAATATCTAATTATTTCCAAT-GAGAATAAATGACCTTTCATGCCTTAAAGTAGTCA
1 GAAAACTAT-ATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGTAATCA
* * * * **
4641 --TTTACTCTGATCGAAATGAAGAGATATCCCCCTTTGTCTTAAAATTAATATTGATTCGAGT
65 TTTTTACTCCGACCGAAATGAAGAGATAT----CTTCGTCTTAAAATTAATATTGATTCAAAA
* * * * *
4702 GAAAA-TGAAATGTCTAATGATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAGCAATCA
1 GAAAACT-ATATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGTAATCA
* *
4766 TTTTTAC-CCGACCGAAATGATATA-CTAT-TTCGTCTTAAAATTCAATATTGATTCAAAA
65 TTTTTACTCCGACCGAAATGA-AGAGATATCTTCGTCTTAAAATT-AATATTGATTCAAAA
*
4824 GAAAACTATATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTTAAGTAATCAT
1 GAAAACTATATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGTAATCAT
* * *
4889 TTATTACTCCAACTGAAATGAAAAGATAT
66 TT-TTACTCCGACCGAAATGAAGAGATAT
4918 TACTATTTTC
Statistics
Matches: 181, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
121 13 0.07
122 71 0.39
123 7 0.04
124 32 0.18
125 37 0.20
126 14 0.08
127 7 0.04
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (123 bp):
GAAAACTATATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGTAATCAT
TTTTACTCCGACCGAAATGAAGAGATATCTTCGTCTTAAAATTAATATTGATTCAAAA
Found at i:6704 original size:392 final size:393
Alignment explanation
Indices: 5930--6715 Score: 1375
Period size: 392 Copynumber: 2.0 Consensus size: 393
5920 ATCAAGCCAA
* *
5930 AACCTCCTAATCACTCAGATCTATACCTCCAGGCCTAGATCTAGGGCTAGAACTACCTAAAGAGG
1 AACCTCCTAATCACTCAGATCTACACCTCCAGGCCTAGATCTAGGGCTAAAACTACCTAAAGAGG
*
5995 CTCTAAACAACCCAAAAGAAGACCCTGACCTTTTGGTACTCACACTCCAGCCGCCGTAAAGACGA
66 CTCTAAACAACCCAAAAGAAGACCCTGACCTTTTGGTACTCACACTCCAGCCGCCGCAAAGACGA
* * *
6060 ACCGACCGTATGGTTTGACTATCCCCTGATAACTAGATCTGCTCCATTCCCTTGTTTATTGTTTC
131 ACCAACCGTATCGTTTGACTATCCCCAGATAACTAGATCTGCTCCATTCCCTTGTTTATTGTTTC
*
6125 ATTCAAAGCTTTTTATTTCTTTTTTATTTATTTTGAAACTGAAAAAAATACCAAAAAATATACAT
196 ATTCAAAGCTTTTTATTTCCTTTTTATTTATTTTGAAACTGAAAAAAATACCAAAAAATATACAT
*
6190 TCGAATGTTTCCGTTTTCATTTTTTGCATGTATTGCTTTTTAGGAAAAAAACCCGAAAGGGGAGA
261 TCGAATGTTTCCGATTT-ATTTTTTGCATGTATTGCTTTTTAGGAAAAAAACCCGAAAGGGGAGA
6255 AACCTCTATCCTTACAATATTCTCGGGTTTTATAACCCTCGTTTACAGATCTTTTTTT-TTT-TT
325 AACCTCTATCCTTACAATATTCTCGGGTTTTATAACCCTCGTTTACAGATCTTTTTTTATTTATT
6318 TTTT
390 TTTT
6322 AACCTCCTAATCACTCAGATCTACACCTCCAGGCCTAGATCTAGGGCTAAAACTACCTAAA-AGG
1 AACCTCCTAATCACTCAGATCTACACCTCCAGGCCTAGATCTAGGGCTAAAACTACCTAAAGA-G
*
6386 GCTCTAAACAACCCAAAAGAAGACCTTGACCTTTTGGTACTCACACTCCAGCCGCCGCAAAGACG
65 GCTCTAAACAACCCAAAAGAAGACCCTGACCTTTTGGTACTCACACTCCAGCCGCCGCAAAGACG
* *
6451 AACTAACCGTATCGTTTGACTATCCCCAGGTAACTAGATCTGCTCCATTCCCTTGTTTATTGTTT
130 AACCAACCGTATCGTTTGACTATCCCCAGATAACTAGATCTGCTCCATTCCCTTGTTTATTGTTT
*
6516 CATTCAAAGCTTTTTATTTCCTTTTTATTTGTTTTGAAACTGAAAAAAATACCAAAAAATATACA
195 CATTCAAAGCTTTTTATTTCCTTTTTATTTATTTTGAAACTGAAAAAAATACCAAAAAATATACA
*
6581 TTCGAATGTTTCC-ATTT-TTTTTTGCTTGTATTGCTTTTTAGGAAAAAAACCCGAAAGGGGAGA
260 TTCGAATGTTTCCGATTTATTTTTTGCATGTATTGCTTTTTAGGAAAAAAACCCGAAAGGGGAGA
6644 AACCTCTATCCTTACAATATTCTCGGGTTTTATAACCCTCGTTTACAGATCTCTTTTTTTTATTT
325 AACCTCTATCCTTACAATATTCTCGGGTTTTATAACCCTCGTTTACAGA--TC-TTTTTTTATTT
6709 ATTTTTT
387 ATTTTTT
6716 TGTTTGAAAC
Statistics
Matches: 375, Mismatches: 13, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
389 94 0.25
391 6 0.02
392 266 0.71
393 3 0.01
394 6 0.02
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (393 bp):
AACCTCCTAATCACTCAGATCTACACCTCCAGGCCTAGATCTAGGGCTAAAACTACCTAAAGAGG
CTCTAAACAACCCAAAAGAAGACCCTGACCTTTTGGTACTCACACTCCAGCCGCCGCAAAGACGA
ACCAACCGTATCGTTTGACTATCCCCAGATAACTAGATCTGCTCCATTCCCTTGTTTATTGTTTC
ATTCAAAGCTTTTTATTTCCTTTTTATTTATTTTGAAACTGAAAAAAATACCAAAAAATATACAT
TCGAATGTTTCCGATTTATTTTTTGCATGTATTGCTTTTTAGGAAAAAAACCCGAAAGGGGAGAA
ACCTCTATCCTTACAATATTCTCGGGTTTTATAACCCTCGTTTACAGATCTTTTTTTATTTATTT
TTT
Found at i:7111 original size:15 final size:15
Alignment explanation
Indices: 7084--7130 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
7074 AATGGCCTGC
7084 AACATTTAA-AATAAT
1 AACA-TTAATAATAAT
*
7099 TACATTAATAATAAT
1 AACATTAATAATAAT
* *
7114 AACAATAATAGTAAT
1 AACATTAATAATAAT
7129 AA
1 AA
7131 TAATAATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (15 bp):
AACATTAATAATAAT
Found at i:7112 original size:3 final size:3
Alignment explanation
Indices: 7104--7137 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
7094 ATAATTACAT
* *
7104 TAA TAA TAA TAA CAA TAA TAG TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
7138 TGTAACACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:7761 original size:26 final size:25
Alignment explanation
Indices: 7690--7872 Score: 103
Period size: 26 Copynumber: 7.8 Consensus size: 25
7680 ATACATTTAA
*
7690 ATTATGGCATCCTTTCATGC--CTT
1 ATTATGGCATCCTTTCATGCATTTT
* *
7713 A--AT-GCATCCTTCCATTCCA-TTT
1 ATTATGGCATCCTTTCA-TGCATTTT
7735 AGTTATGGCATCCTTTCATGCATTTT
1 A-TTATGGCATCCTTTCATGCATTTT
* **
7761 AGTTATGGTATCCTTTCAT--ACCTT
1 A-TTATGGCATCCTTTCATGCATTTT
* *
7785 A--AT-GCATCGTTTCATTCATTTT
1 ATTATGGCATCCTTTCATGCATTTT
* *
7807 AATTATGGTATCCTTTCATGC--CTT
1 -ATTATGGCATCCTTTCATGCATTTT
*
7831 A--AT-GCATCCTTTCATGGATTTT
1 ATTATGGCATCCTTTCATGCATTTT
7853 AATTATGG-ATCCTTTCATGC
1 -ATTATGGCATCCTTTCATGC
7873 CTTAATGCCT
Statistics
Matches: 121, Mismatches: 20, Indels: 36
0.68 0.11 0.20
Matches are distributed among these distances:
20 32 0.26
21 8 0.07
22 8 0.07
23 4 0.03
24 6 0.05
25 20 0.17
26 43 0.36
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (25 bp):
ATTATGGCATCCTTTCATGCATTTT
Found at i:7788 original size:72 final size:72
Alignment explanation
Indices: 7691--7827 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
7681 TACATTTAAA
* *
7691 TTATGGCATCCTTTCATGCCTTAATGCATCCTTCCATTCCA-TTTAGTTATGGCATCCTTTCATG
1 TTATGGCATCCTTTCATACCTTAATGCATCCTTCCATT-CATTTTAATTATGGCATCCTTTCATG
7755 CATTTTAG
65 CATTTTAG
* * * *
7763 TTATGGTATCCTTTCATACCTTAATGCATCGTTTCATTCATTTTAATTATGGTATCCTTTCATGC
1 TTATGGCATCCTTTCATACCTTAATGCATCCTTCCATTCATTTTAATTATGGCATCCTTTCATGC
7828 CTTAATGCAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 2 0.03
72 56 0.97
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (72 bp):
TTATGGCATCCTTTCATACCTTAATGCATCCTTCCATTCATTTTAATTATGGCATCCTTTCATGC
ATTTTAG
Found at i:7792 original size:46 final size:46
Alignment explanation
Indices: 7742--7955 Score: 279
Period size: 46 Copynumber: 4.6 Consensus size: 46
7732 TTTAGTTATG
* *
7742 GCATCCTTTCATGCATTTTAGTTATGGTATCCTTTCATACCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGTATCCTTTCATGCCTTAAT
* *
7788 GCATCGTTTCATTCATTTTAATTATGGTATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGTATCCTTTCATGCCTTAAT
*
7834 GCATCCTTTCATGGATTTTAATTATGG-ATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGTATCCTTTCATGCCTTAAT
* * *
7879 GCCTTTCATGCCTTTCATGCA-TTTAGTTGTGGTATCCTTTCATGTCTTAAT
1 G-----CAT-CCTTTCATGCATTTTAATTATGGTATCCTTTCATGCCTTAAT
*
7930 GCATCATTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
7956 CTCTAAAACT
Statistics
Matches: 146, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
45 29 0.20
46 77 0.53
50 12 0.08
51 28 0.19
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAATTATGGTATCCTTTCATGCCTTAAT
Found at i:7889 original size:9 final size:9
Alignment explanation
Indices: 7863--7898 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
7853 AATTATGGAT
7863 CCTTTCATG
1 CCTTTCATG
*
7872 CC-TTAATG
1 CCTTTCATG
7880 CCTTTCATG
1 CCTTTCATG
7889 CCTTTCATG
1 CCTTTCATG
7898 C
1 C
7899 ATTTAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.14, C:0.33, G:0.11, T:0.42
Consensus pattern (9 bp):
CCTTTCATG
Found at i:7933 original size:96 final size:92
Alignment explanation
Indices: 7742--7955 Score: 279
Period size: 96 Copynumber: 2.3 Consensus size: 92
7732 TTTAGTTATG
* * *
7742 GCATCCTTTCATGCATTTTAGTTATGGTATCCTTTCATACCTTAATGCATCGTTTCATTCATTTT
1 GCATCCTTTCATGCATTTTAATTATGGTATCCTTTCATACCTTAATGCATCCTTTCATGCATTTT
7807 AATTATGGTATCCTTTCATGCCTTAAT
66 AATTATGGTATCCTTTCATGCCTTAAT
* *
7834 GCATCCTTTCATGGATTTTAATTATGG-ATCCTTTCATGCCTTAATGCCTTTCATGCCTTTCATG
1 GCATCCTTTCATGCATTTTAATTATGGTATCCTTTCATACCTTAATG-----CAT-CCTTTCATG
* * *
7898 CA-TTTAGTTGTGGTATCCTTTCATGTCTTAAT
60 CATTTTAATTATGGTATCCTTTCATGCCTTAAT
*
7930 GCATCATTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
7956 CTCTAAAACT
Statistics
Matches: 106, Mismatches: 10, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
91 18 0.17
92 25 0.24
96 54 0.51
97 9 0.08
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (92 bp):
GCATCCTTTCATGCATTTTAATTATGGTATCCTTTCATACCTTAATGCATCCTTTCATGCATTTT
AATTATGGTATCCTTTCATGCCTTAAT
Found at i:9809 original size:135 final size:135
Alignment explanation
Indices: 9567--9887 Score: 385
Period size: 135 Copynumber: 2.4 Consensus size: 135
9557 TTTAGGGTAG
* * * * * * * *
9567 ATCAGATCTAGAAACGTCGATTCATTCCACTGTTCTTCATGGAAGATTGAATCGAGGTAGACTTG
1 ATCAGATCTGGAGACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCAAAGAAGACTTG
* ** * * * *
9632 TTCGACTGCTACTCAGGGAAGATAAAGTTTGGAAACAAAGGGGATTTGTTCCGCTGTTTCGTCAG
66 TTCCACTAATACTCAGGGAAGATAAAGTATAGAAACAAAGGGGATCTGTTCCACTGTTTCGTCAG
9697 GGAAA
131 GGAAA
*
9702 ATCAGATCTGGAGACGTTGATTCATTCCATTGTTCTTTAGGGAAGATTGAATCAAAGAAGACTTG
1 ATCAGATCTGGAGACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCAAAGAAGACTTG
* * * *
9767 TTCCACTAATACTCTGGGAAGATCAAA-TATAGAAAGATAGGGGATCTGTTCCACTGTTTCTTCA
66 TTCCACTAATACTCAGGGAAGAT-AAAGTATAGAAACAAAGGGGATCTGTTCCACTGTTTCGTCA
*
9831 GGGAGA
130 GGGAAA
* * * * *
9837 ATCAAATCTGGAGATGTTGATTTATTCCACTGTTC-CTCGGGAAGATTGAAT
1 ATCAGATCTGGAGACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAAT
9888 TGAGTTTGAT
Statistics
Matches: 158, Mismatches: 27, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
134 14 0.09
135 141 0.89
136 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (135 bp):
ATCAGATCTGGAGACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCAAAGAAGACTTG
TTCCACTAATACTCAGGGAAGATAAAGTATAGAAACAAAGGGGATCTGTTCCACTGTTTCGTCAG
GGAAA
Found at i:11140 original size:29 final size:29
Alignment explanation
Indices: 11099--11169 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
11089 CCCCCTTTAT
11099 ATTTATTCTATTTTTTTTC-TTTCCTTTTCTC
1 ATTT-TTC-ATTTTTTTTCTTTTCCTTTT-TC
* *
11130 TTTTTTCA-TTTTTTTCTTTTTCTTTTTC
1 ATTTTTCATTTTTTTTCTTTTCCTTTTTC
11158 ATTTTTCATTTT
1 ATTTTTCATTTT
11170 CTTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 17 0.49
29 12 0.34
30 3 0.09
31 3 0.09
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (29 bp):
ATTTTTCATTTTTTTTCTTTTCCTTTTTC
Found at i:11141 original size:7 final size:7
Alignment explanation
Indices: 11140--11185 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 7
11130 TTTTTTCATT
11140 TTTTTC-
1 TTTTTCA
11146 TTTTTC-
1 TTTTTCA
11152 TTTTTCA
1 TTTTTCA
11159 TTTTTCA
1 TTTTTCA
11166 TTTTCTTCA
1 -TTT-TTCA
11175 -TTTTCA
1 TTTTTCA
11181 TTTTT
1 TTTTT
11186 TTAATTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 16 0.44
7 13 0.36
8 3 0.08
9 4 0.11
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:11162 original size:28 final size:27
Alignment explanation
Indices: 11110--11185 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
11100 TTTATTCTAT
* *
11110 TTTTTTTCTTTCCTTTTCTCTTTTTTCA
1 TTTTTTTCTTTTCTTTT-TCATTTTTCA
11138 TTTTTTTCTTTTTCTTTTTCATTTTTCA
1 TTTTTTTC-TTTTCTTTTTCATTTTTCA
*
11166 TTTTCTTCATTTTCATTTTT
1 TTTTTTTC-TTTTC-TTTTT
11186 TTAATTTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 29 0.69
29 13 0.31
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTTTTCTTTTCTTTTTCATTTTTCA
Found at i:11192 original size:15 final size:15
Alignment explanation
Indices: 11132--11194 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
11122 CTTTTCTCTT
**
11132 TTTTCATTTTTTTCT
1 TTTTCATTTTTTTAA
* *
11147 TTTTC--TTTTTCAT
1 TTTTCATTTTTTTAA
* *
11160 TTTTCATTTTCTTCA
1 TTTTCATTTTTTTAA
11175 TTTTCATTTTTTTAA
1 TTTTCATTTTTTTAA
11190 TTTTC
1 TTTTC
11195 TTTCTTAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 11 0.29
15 27 0.71
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCATTTTTTTAA
Found at i:22367 original size:131 final size:131
Alignment explanation
Indices: 22019--22376 Score: 434
Period size: 131 Copynumber: 2.7 Consensus size: 131
22009 AATGATTTTA
* * *
22019 AATATCTAAGTATTT-TCAATTGAGAATAAATGACCTCTCATGCCCTAAAGCAGTCATTTATTAC
1 AATATCTAATTATTTCT-AATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTAC
* * **
22083 TCCGA-TCGAAATGAAGATATATCT-CTATTTCTTCTTAAAATTCAATATTGACTCGAGTGAAAA
65 TCCGACT-GAAATGAAAATATAT-TACTATTTCGTCTTAAAATTCAATATTGACTCGAAAGAAAA
**
22146 TGAT
128 CCAT
* * * **
22150 AATGTCTAATGATTTCCAATCGAGAATAAATGACAACTCATGCCTTAAAGCAGTCATTTATTACT
1 AATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACT
* * * * * * *
22215 CCGACCGAAATTATAAGATATTATTATTTCGTCTTTAAATTCAATATTGATTCGAAAGAAAACCA
66 CCGACTGAAATGAAAATATATTACTATTTCGTCTTAAAATTCAATATTGACTCGAAAGAAAACCA
22280 T
131 T
* *
22281 AATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTTAAGCAATCATTTATTACT
1 AATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACT
* *
22346 CCAACTAAAATGAAAATATATTACTAATTTC
66 CCGACTGAAATGAAAATATATTACT-ATTTC
22377 AATAGTGATT
Statistics
Matches: 188, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
130 1 0.01
131 182 0.97
132 5 0.03
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (131 bp):
AATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACT
CCGACTGAAATGAAAATATATTACTATTTCGTCTTAAAATTCAATATTGACTCGAAAGAAAACCA
T
Found at i:25549 original size:18 final size:18
Alignment explanation
Indices: 25519--25562 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
25509 CATTAGATTA
*
25519 TTTATTT-ATTATTTTCT
1 TTTATTTAATTATTATCT
25536 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATCT
25554 TTTATTTAA
1 TTTATTTAA
25563 AAAAAACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:25651 original size:16 final size:16
Alignment explanation
Indices: 25605--25655 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
25595 CTACTATTAT
**
25605 TTATTATTTTATTAAA
1 TTATTATTTTATTTTA
*
25621 TT-TCTCTTTTA-TTTA
1 TTAT-TATTTTATTTTA
25636 TTATTATTTTATTTTA
1 TTATTATTTTATTTTA
25652 TTAT
1 TTAT
25656 ACCTTTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTATTTTATTTTA
Found at i:25881 original size:32 final size:33
Alignment explanation
Indices: 25844--25938 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 33
25834 ATTTTCTAAA
25844 ATTTAATATTTTCTTCATTTATTTTATTTTTCT
1 ATTTAATATTTTCTTCATTTATTTTATTTTTCT
* * *
25877 -TTTAACATTTT-TT-ATATAACTTTT-TTTTTTT
1 ATTTAATATTTTCTTCAT-TTA-TTTTATTTTTCT
25908 AATTTAATATTTTCTTC-TTTGA-TTTATTTTT
1 -ATTTAATATTTTCTTCATTT-ATTTTATTTTT
25939 TAATCGAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
30 2 0.04
31 10 0.20
32 17 0.35
33 16 0.33
34 4 0.08
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.69
Consensus pattern (33 bp):
ATTTAATATTTTCTTCATTTATTTTATTTTTCT
Found at i:25938 original size:33 final size:33
Alignment explanation
Indices: 25843--25939 Score: 85
Period size: 33 Copynumber: 3.0 Consensus size: 33
25833 TATTTTCTAA
* *
25843 AATTTAATATTTTCTTCATTTATTTTATTTTTCT
1 AATTTAATATTTTCTTC-TTTACTTTATTTTTTT
* * * *
25877 --TTTAACATTTT-TTATATAACTTTTTTTTTTT
1 AATTTAATATTTTCTTCT-TTACTTTATTTTTTT
25908 AATTTAATATTTTCTTCTTTGA-TTTATTTTTT
1 AATTTAATATTTTCTTCTTT-ACTTTATTTTTT
25940 AATCGAATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
30 1 0.02
31 13 0.27
32 10 0.21
33 20 0.42
34 4 0.08
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.69
Consensus pattern (33 bp):
AATTTAATATTTTCTTCTTTACTTTATTTTTTT
Found at i:26022 original size:12 final size:12
Alignment explanation
Indices: 26005--26038 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
25995 GAATCGAATC
26005 TTTAAATTTTAA
1 TTTAAATTTTAA
26017 TTTAAATTTTAA
1 TTTAAATTTTAA
26029 TTTAAATTTT
1 TTTAAATTTT
26039 CGCAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:28231 original size:24 final size:24
Alignment explanation
Indices: 28204--28275 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
28194 AAACGGAGAT
* * *
28204 ATCATAAATCAAAACAGAATTTAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
28228 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
28252 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
28276 GTAATGTATC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:28275 original size:12 final size:12
Alignment explanation
Indices: 28216--28275 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
28206 CATAAATCAA
*
28216 AACAGAATTTAG
1 AACAGAATTCAG
*
28228 ATCAG-ATATCAG
1 AACAGAAT-TCAG
*
28240 AACAGAATCCAG
1 AACAGAATTCAG
* *
28252 ATCAGAAATCAG
1 AACAGAATTCAG
28264 AACAGAATTCAG
1 AACAGAATTCAG
28276 GTAATGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:32903 original size:12 final size:12
Alignment explanation
Indices: 32876--32945 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
32866 ACAGAGATAT
* *
32876 CAGAAATCAAAA
1 CAGAATTCAGAA
*
32888 CAGAATTCAGAT
1 CAGAATTCAGAA
32900 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
32912 CAGAATCCAGAT
1 CAGAATTCAGAA
*
32924 CAGAAATCAGAA
1 CAGAATTCAGAA
32936 CAGAATTCAG
1 CAGAATTCAG
32946 GTAATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:32908 original size:24 final size:24
Alignment explanation
Indices: 32874--32945 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
32864 AAACAGAGAT
*
32874 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
32898 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
32922 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
32946 GTAATGTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:32956 original size:24 final size:24
Alignment explanation
Indices: 32874--32964 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
32864 AAACAGAGAT
* *
32874 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
*
32898 ATCAGATATCAGAACAGAATCCAG
1 ATCAGATATCAGAACAGAATTCAG
*
32922 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* *
32946 GTAATG-TATCAGAACAGAA
1 ATCA-GATATCAGAACAGAA
32965 CTCAAGTCGG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATTCAG
Found at i:32978 original size:48 final size:48
Alignment explanation
Indices: 32874--32978 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
32864 AAACAGAGAT
* *
32874 ATCAGAAATCAAAACAGAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
* *
32922 ATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAACTCAAG
1 ATCAGAAATCAAAACAGAATTCAGATAA-GATATCAGAACAGAA-TCAAG
*
32971 -TCGGAAAT
1 ATCAGAAAT
32979 TAGATAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 45 0.90
49 5 0.10
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
Found at i:35455 original size:15 final size:15
Alignment explanation
Indices: 35435--35469 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
35425 AACGCCTGTC
35435 AACGGTCAACGAGTA
1 AACGGTCAACGAGTA
*
35450 AACGGTCAACGAGTC
1 AACGGTCAACGAGTA
35465 AACGG
1 AACGG
35470 GTCGGGTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.23, G:0.29, T:0.11
Consensus pattern (15 bp):
AACGGTCAACGAGTA
Found at i:35485 original size:18 final size:18
Alignment explanation
Indices: 35462--35499 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35452 CGGTCAACGA
35462 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
**
35480 GTCAACTTGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
35498 GT
1 GT
35500 TATGACCGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.21, G:0.45, T:0.24
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGG
Found at i:41593 original size:28 final size:29
Alignment explanation
Indices: 41544--41598 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
41534 GGCTTATTGT
*
41544 ATATATTATTATAGTATAGTTTTTGAAAAC
1 ATATATTATAATAGTATAG-TTTTGAAAAC
*
41574 ATATA-TATAATA-TATGGTTTTGAAA
1 ATATATTATAATAGTATAGTTTTGAAA
41599 GTATTTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 4 0.17
29 6 0.26
30 5 0.22
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (29 bp):
ATATATTATAATAGTATAGTTTTGAAAAC
Found at i:42764 original size:19 final size:18
Alignment explanation
Indices: 42740--42783 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
42730 CATTAAATTA
*
42740 TTTATTTAATTATTTTCTT
1 TTTATTTAATTATTATC-T
*
42759 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
42777 TTTATTT
1 TTTATTT
42784 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:43015 original size:16 final size:15
Alignment explanation
Indices: 42990--43019 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42980 TTAACACTTC
42990 TTTTTTTTTATTTTG
1 TTTTTTTTTATTTTG
43005 TTTTATTTTTATTTT
1 TTTT-TTTTTATTTT
43020 CCCACTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTATTTTG
Found at i:43050 original size:41 final size:38
Alignment explanation
Indices: 42984--43061 Score: 129
Period size: 41 Copynumber: 2.0 Consensus size: 38
42974 TAAAATTTAA
42984 CACTTCTTTTTTTTTATTTTGTTTTATTTTTATTTTCC
1 CACTTCTTTTTTTTTATTTTGTTTTATTTTTATTTTCC
43022 CACTTCTTTCTTTATTTTATTTTGTTTTATTTTTATTTTC
1 CACTTC-TT-TTT-TTTTATTTTGTTTTATTTTTATTTTC
43062 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
38 6 0.16
39 2 0.05
40 3 0.08
41 26 0.70
ACGTcount: A:0.12, C:0.13, G:0.03, T:0.73
Consensus pattern (38 bp):
CACTTCTTTTTTTTTATTTTGTTTTATTTTTATTTTCC
Found at i:43090 original size:16 final size:15
Alignment explanation
Indices: 43032--43091 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 15
43022 CACTTCTTTC
43032 TTTATTTTATT-TTGT
1 TTTATTTTATTATT-T
43047 TTTA-TTT-TTATTT
1 TTTATTTTATTATTT
* **
43060 TCTATTTTAAAATTT
1 TTTATTTTATTATTT
43075 TTATATTTTATTATTT
1 TT-TATTTTATTATTT
43091 T
1 T
43092 CTTTTCTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
13 6 0.17
14 8 0.23
15 9 0.26
16 12 0.34
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTATTTTATTATTT
Found at i:43113 original size:30 final size:31
Alignment explanation
Indices: 43054--43113 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
43044 TGTTTTATTT
*
43054 TTATTTTCTATTTTAAAATTTTTATATTTTA
1 TTATTTTCTATTTTAAAATTTTAATATTTTA
*
43085 TTATTTTCT-TTTCTGAAA-TTTAATATTTT
1 TTATTTTCTATTT-TAAAATTTTAATATTTT
43114 CTTCATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (31 bp):
TTATTTTCTATTTTAAAATTTTAATATTTTA
Found at i:43159 original size:14 final size:15
Alignment explanation
Indices: 43126--43163 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
43116 TCATTTATTT
*
43126 TATTTTTTATTTTAA
1 TATTTTTTATTATAA
*
43141 CATTTTTTA-TATAA
1 TATTTTTTATTATAA
43155 TATTTTTTA
1 TATTTTTTA
43164 AAATTTAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTATTATAA
Found at i:44834 original size:27 final size:27
Alignment explanation
Indices: 44796--44850 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
44786 ATAAATTTCA
44796 CCTTAAGTGTAAAATGA-CCAAAATAC
1 CCTTAAGTGTAAAATGACCCAAAATAC
*
44822 CCTTGAAGTGTAAAATGACCCAAAGTAC
1 CCTT-AAGTGTAAAATGACCCAAAATAC
44850 C
1 C
44851 TCCAAGCCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.15
27 13 0.50
28 9 0.35
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (27 bp):
CCTTAAGTGTAAAATGACCCAAAATAC
Done.