Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001230.1 Hibiscus syriacus cultivar Beakdansim tig00002423_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: 104821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1239 original size:21 final size:22
Alignment explanation
Indices: 1187--1240 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
1177 CATAATTATT
*
1187 TAAAAA-ATTAAATAAAAATAC
1 TAAAAACATTTAATAAAAATAC
*
1208 TAAAAACATTTAAT-AAAATTC
1 TAAAAACATTTAATAAAAATAC
1229 TAAAAACATTTA
1 TAAAAACATTTA
1241 GGTTGAACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAACATTTAATAAAAATAC
Found at i:8487 original size:6 final size:6
Alignment explanation
Indices: 8450--8484 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
8440 TTAAAAAGTC
*
8450 TGTAAA TGTAAA TGTAAA TGTAAA TGTAAT TGTAA
1 TGTAAA TGTAAA TGTAAA TGTAAA TGTAAA TGTAA
8485 TTGAACTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (6 bp):
TGTAAA
Found at i:24679 original size:24 final size:24
Alignment explanation
Indices: 24634--24685 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
24624 GAACGAAGAG
*
24634 GTCTACGAATTGGAGAGCGGCTCC
1 GTCTACGAATTGGAGAGCGGCTAC
*
24658 GTCTACGAATTGGTGGAG-GGCTAC
1 GTCTACGAATTGG-AGAGCGGCTAC
24682 GTCT
1 GTCT
24686 CCGATTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.19, C:0.21, G:0.35, T:0.25
Consensus pattern (24 bp):
GTCTACGAATTGGAGAGCGGCTAC
Found at i:25775 original size:3 final size:3
Alignment explanation
Indices: 25767--25817 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
25757 AAAGTGCCTC
25767 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25815 AAT
1 AAT
25818 GATATCAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28061 original size:21 final size:21
Alignment explanation
Indices: 28037--28076 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28027 AATTACAAGT
28037 TTAAAATGTTTATT-TTTTAAA
1 TTAAAATGTTT-TTATTTTAAA
*
28058 TTAAATTGTTTTTATTTTA
1 TTAAAATGTTTTTATTTTA
28077 TTTTTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TTAAAATGTTTTTATTTTAAA
Found at i:29797 original size:59 final size:60
Alignment explanation
Indices: 29726--29847 Score: 187
Period size: 59 Copynumber: 2.0 Consensus size: 60
29716 GCAATTGAAG
*
29726 TAAACTAGAACAATGAGCATAAATTGAGTTCCTTCTGTC-T-CTCTGT-TAGTCTGTCATCC
1 TAAACTAGAACAATGAGCATAAATTG-GTTCCTTCTATCGTCCTCTGTCT-GTCTGTCATCC
29785 TAAACTAGAACAATGAGCATAAATTGGTTCCTTCTATCTGTCCTCTGTCTGTCTGTCATCC
1 TAAACTAGAACAATGAGCATAAATTGGTTCCTTCTATC-GTCCTCTGTCTGTCTGTCATCC
29846 TA
1 TA
29848 CTCCTGTCTG
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
58 11 0.19
59 26 0.45
60 1 0.02
61 19 0.33
62 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (60 bp):
TAAACTAGAACAATGAGCATAAATTGGTTCCTTCTATCGTCCTCTGTCTGTCTGTCATCC
Found at i:34240 original size:21 final size:20
Alignment explanation
Indices: 34206--34261 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
34196 TTAAGCCAGT
* *
34206 TACATTTTCTCATAAACTTA
1 TACATTGTCTCATAAACATA
*
34226 TACGTTGTACTCAT-AACATA
1 TACATTGT-CTCATAAACATA
34246 TACATTGTCTCATAAA
1 TACATTGTCTCATAAA
34262 ATAAAATCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.17
20 20 0.67
21 5 0.17
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (20 bp):
TACATTGTCTCATAAACATA
Found at i:36460 original size:127 final size:126
Alignment explanation
Indices: 36323--36579 Score: 435
Period size: 127 Copynumber: 2.0 Consensus size: 126
36313 AAAAATACTA
*
36323 TTTT-AAATAAAAATAATAATATATAGAATTGACATCGTAAAATTGAAATATAAAGATTAAATTT
1 TTTTAAAATAAAAATAATAATATATAGAATTGAAATCGTAAAATTGAAATATAAAGATTAAATTT
* * *
36387 TAAAATTAAAATTGTACAGATATTAGTGGCATGTTATAAATTTTCTATTGGTCTCTCGGTAT
66 TAAAATTAAAATTGTACAAATATTAGTGGCATGTTATAAATTTTCTATTGGTATCTCAGT-T
*
36449 TTTTAAAATAAAAATAATAATATATAGAATTGAAATCGTAAATTTGAAATATAAAGATTAAATTT
1 TTTTAAAATAAAAATAATAATATATAGAATTGAAATCGTAAAATTGAAATATAAAGATTAAATTT
* *
36514 TAAAATTAAAATTGTACAAATGTTAGTGGCATGTTATAATTTTTCTATTGGTATCTCAGTT
66 TAAAATTAAAATTGTACAAATATTAGTGGCATGTTATAAATTTTCTATTGGTATCTCAGTT
36575 TTTTA
1 TTTTA
36580 TGACTTTATC
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
126 10 0.08
127 113 0.92
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.40
Consensus pattern (126 bp):
TTTTAAAATAAAAATAATAATATATAGAATTGAAATCGTAAAATTGAAATATAAAGATTAAATTT
TAAAATTAAAATTGTACAAATATTAGTGGCATGTTATAAATTTTCTATTGGTATCTCAGTT
Found at i:40058 original size:18 final size:18
Alignment explanation
Indices: 40035--40070 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40025 TTAATGATTG
40035 ATGTTGTTGAGGTCCTAT
1 ATGTTGTTGAGGTCCTAT
40053 ATGTTGTTGAGGTCCTAT
1 ATGTTGTTGAGGTCCTAT
40071 CTTTTTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.44
Consensus pattern (18 bp):
ATGTTGTTGAGGTCCTAT
Found at i:48820 original size:17 final size:16
Alignment explanation
Indices: 48800--48841 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
48790 GAAAATAATT
48800 AATATTATTATTTTTAA
1 AATATTATTATTTTT-A
*
48817 AATATTGA-AATTTTTA
1 AATATT-ATTATTTTTA
48833 AATATTATT
1 AATATTATT
48842 TGTCAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 1 0.05
16 7 0.33
17 12 0.57
18 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
AATATTATTATTTTTA
Found at i:48820 original size:24 final size:26
Alignment explanation
Indices: 48767--48818 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
48757 ATAAATAAGT
48767 ATAATAAATAATATTATTTATTAGAAA
1 ATAATAAATAATATTATTTATTA-AAA
* *
48794 ATAATTAATATTATTATTT-TTAAAA
1 ATAATAAATAATATTATTTATTAAAA
48819 TATTGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 3 0.13
27 17 0.74
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATAATAAATAATATTATTTATTAAAA
Found at i:48922 original size:83 final size:83
Alignment explanation
Indices: 48813--49017 Score: 367
Period size: 83 Copynumber: 2.5 Consensus size: 83
48803 ATTATTATTT
48813 TTAAAATATTGAAATTTTTAAATATTATTTGTCAATATTACTGTTAAAATTTTATAAATAAAAAT
1 TTAAAATA-T-AAATTTTTAAATATTATTTGTCAATATTACTGTTAAAATTTTATAAATAAAAAT
48878 ATTAAGACTACTATATTCTA
64 ATTAAGACTACTATATTCTA
*
48898 TTAAAATATAAATTTTTAAATATTATTTGTCAATATTATTGTTAAAATTTTATAAATAAAAATAT
1 TTAAAATATAAATTTTTAAATATTATTTGTCAATATTACTGTTAAAATTTTATAAATAAAAATAT
48963 TAAGACTACTATATTCTA
66 TAAGACTACTATATTCTA
*
48981 TTAAAATATAAATTTTTAAATATTA-TTGTTAATATTA
1 TTAAAATATAAATTTTTAAATATTATTTGTCAATATTA
49018 TATTAATTAC
Statistics
Matches: 118, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
82 11 0.09
83 98 0.83
84 1 0.01
85 8 0.07
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (83 bp):
TTAAAATATAAATTTTTAAATATTATTTGTCAATATTACTGTTAAAATTTTATAAATAAAAATAT
TAAGACTACTATATTCTA
Found at i:49004 original size:41 final size:41
Alignment explanation
Indices: 48874--49005 Score: 126
Period size: 41 Copynumber: 3.2 Consensus size: 41
48864 TTATAAATAA
48874 AAATATTAAGACTACTATATTCTATTAAAATATAAATTTTT
1 AAATATTAAGACTACTATATTCTATTAAAATATAAATTTTT
**** * * * **
48915 AAATATTATTTGT-CAATATTATTGTTAAAATTTTATAAA--TAA
1 AAATATTAAGACTACTATATT-CTATTAAAA---TATAAATTTTT
48957 AAATATTAAGACTACTATATTCTATTAAAATATAAATTTTT
1 AAATATTAAGACTACTATATTCTATTAAAATATAAATTTTT
48998 AAATATTA
1 AAATATTA
49006 TTGTTAATAT
Statistics
Matches: 66, Mismatches: 18, Indels: 14
0.67 0.18 0.14
Matches are distributed among these distances:
39 6 0.09
40 6 0.09
41 25 0.38
42 17 0.26
43 6 0.09
44 6 0.09
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (41 bp):
AAATATTAAGACTACTATATTCTATTAAAATATAAATTTTT
Found at i:49270 original size:29 final size:31
Alignment explanation
Indices: 49215--49283 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 31
49205 TATATTATTA
*
49215 ATAATATTAAAATTATTATAAAACTAAAAAT
1 ATAATATTAAAATAATTATAAAACTAAAAAT
* *
49246 ATATTATTAAAATAATT-T-ATACTAAAAAT
1 ATAATATTAAAATAATTATAAAACTAAAAAT
49275 ATAATATTA
1 ATAATATTA
49284 TATTAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
30 1 0.03
31 15 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (31 bp):
ATAATATTAAAATAATTATAAAACTAAAAAT
Found at i:53183 original size:120 final size:120
Alignment explanation
Indices: 52844--55747 Score: 4728
Period size: 120 Copynumber: 24.2 Consensus size: 120
52834 CAAATTGACT
* * * *
52844 AAAACTTAGCAAAAGGAAACCATTCCTTAAATTTATTTCTCTGACTTAATCGTTTACAAAGATGT
1 AAAACTTAGC-AAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGT
52909 GGCC-AACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
65 GGCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* ** * *
52964 AAAACTTAGCAAATGAAATCATTTCTTAAATTTATTT-CCCGACTTAATTGTTTAGAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* *
53028 GCCTAACTCTATCTATAGGCCGATTCTATGACTTCCAACAT-AACTAAAATTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACT-AAACTAGGA
*
53083 AAAACTTAGCGAAA-GAAGCCATTTCTTAAATTTATTTCCCCGACTTAATTGTTTACAAAGATGT
1 AAAACTTAGC-AAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGT
* * * *
53147 GACCTAACTCTATTTATAGGTCGGTTCTATGACTTCCAACATAAATTAAACTAGGA
65 GGCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* *
53203 AAAACTTAGCAAAGGAAGTCATTTCTTAAATTTATTTCCCCGACTTAATCTTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* ** *
53268 GCATAACTCTATCTATAGGTTGCTTCTATGACTTCCAACATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
53323 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* * * *
53388 GCATAACTCTATCTATAGGCCGGTTCTATGACTTCCAGCATAAACGAAACTATGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* * *
53443 AAAACTTAGCAAAGGAAGTCATTTCTTAAATTTATTTTCTCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* *
53508 GCCTAACTCTATCTATAGGTCGGTTCTATGACTTCCAACATAAATTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
*
53563 AAAACTTAGCAAAGGAAGTCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* ** *
53628 GCATAACTCTATCTATAGGTTGCTTCTATGACTTCCAACATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
*
53683 AAAACTTAGCAAAGGAAACCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* * *
53748 GCATAACTCTATCTATAGGTCGGTTCTATGACTTCCAGCATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* *
53803 AAAACTTAGCAAAGGAAACCATTTCTTAAATTTATTTCCCCGACTTAATCATTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
53868 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACAT-AACTTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAAC-TAAACTAGGA
**
53923 AAAACTTAGCAAAGGAAGTAATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* ** *
53988 GCATAACTCTATCTATAGGTTGCTTCTATGACTTCCAACATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
*
54043 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTGTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* ** * *
54108 GCATAACTCTATCTATAGGTTGGTTCTATGACTTCTAGCATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
*
54163 AAAACTTAGCAAAGGAAACCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
*
54228 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACGT-AACTTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAAC-TAAACTAGGA
54283 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* *
54348 GCATAACTCCATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* *
54403 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTTCCCGACTTAATTGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
54468 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACAT-AACTTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAAC-TAAACTAGGA
** *
54523 AAAACTTAGCAAAGGAAGTAATTTCTTAAATTTATTTCCCCGACTTAATCATTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* ** * *
54588 GCATAACTCTATCTATAGGTTGCTTCTATGACTTCCAACATAAACTAAACTATGAA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTA-GGA
*
54644 AAAACTTAGCAAAGGAAGCCCTTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* *
54709 GCATAACTCTATCTATAGGCTGGTTCTATGACTTCCAACATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
*
54764 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATTGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
*
54829 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACGT-AACTTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAAC-TAAACTAGGA
** *
54884 AAAACTTAGCAAAGGAAGTAATTTCTTAAATTTATTTTCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* *
54949 GCATAACTCTATCTATAGGCTGGTTCTATGACTTCCAACATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* * * *
55004 AAAACTTAGCAAAAGAAGTCATTTCTTAAATTTATTTCCTCGACTTAATTGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* * *
55069 GCCTAACTTTATCTATAGGTCGGTTCTATGACTTCCAACATAAACTAAAGTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
*
55124 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATTGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
*
55189 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAAGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
*
55244 AAAACTTAGCAAAGG-AGTCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
*
55308 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAATTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* *
55363 AAAACTTAGCAAAGGAAGTCATTTCTTAAATTTATTTCCCCGACTTATTCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* * *
55428 GCATAATTCTATCTATAGGTCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* * *
55483 AAAGCTTAGTAAAGGAAGTCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
*
55548 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAATTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
*
55603 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCAACTTAATCGTTTACAAAGATGTG
1 AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
* * *
55668 ACCTAACTCTATCTGTAGGCCAGTTCTATGACTTCCAACATAAACTAAACTAGGA
66 GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
* * *
55723 AACACTTAGTAAAGGAAGCTATTTC
1 AAAACTTAGCAAAGGAAGCCATTTC
55748 CACTAAATCG
Statistics
Matches: 2606, Mismatches: 162, Indels: 32
0.93 0.06 0.01
Matches are distributed among these distances:
118 30 0.01
119 229 0.09
120 2219 0.85
121 128 0.05
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (120 bp):
AAAACTTAGCAAAGGAAGCCATTTCTTAAATTTATTTCCCCGACTTAATCGTTTACAAAGATGTG
GCCTAACTCTATCTATAGGCCGGTTCTATGACTTCCAACATAAACTAAACTAGGA
Found at i:61751 original size:14 final size:14
Alignment explanation
Indices: 61732--61781 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
61722 TGAACGATCA
61732 GTTATGTTCGTTCG
1 GTTATGTTCGTTCG
61746 GTTATGTTCG-T--
1 GTTATGTTCGTTCG
61757 -TTATGTTCGTTCG
1 GTTATGTTCGTTCG
61770 GTTATGTTCGTT
1 GTTATGTTCGTT
61782 TATGTTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 9 0.28
11 1 0.03
13 1 0.03
14 21 0.66
ACGTcount: A:0.08, C:0.12, G:0.26, T:0.54
Consensus pattern (14 bp):
GTTATGTTCGTTCG
Found at i:61760 original size:10 final size:10
Alignment explanation
Indices: 61741--61788 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
61731 AGTTATGTTC
*
61741 GTTCGGTTAT
1 GTTCGTTTAT
61751 GTTCGTTTAT
1 GTTCGTTTAT
61761 GTTCGTTCGGTTAT
1 GTTCG-T---TTAT
61775 GTTCGTTTAT
1 GTTCGTTTAT
61785 GTTC
1 GTTC
61789 ATTCATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.54
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:61801 original size:24 final size:24
Alignment explanation
Indices: 61733--61788 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
61723 GAACGATCAG
61733 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
61757 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
61781 TTATGTTC
1 TTATGTTC
61789 ATTCATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.09, C:0.12, G:0.23, T:0.55
Consensus pattern (24 bp):
TTATGTTCGTTCGGTTATGTTCGT
Found at i:62834 original size:10 final size:10
Alignment explanation
Indices: 62819--62893 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
62809 GGGTCTCCAA
62819 CGTTTATGTT
1 CGTTTATGTT
62829 CGTTTATGTT
1 CGTTTATGTT
62839 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
62850 ATGTTCGTGTT
1 -CGTTTATGTT
62861 CGTTTATGTT
1 CGTTTATGTT
62871 CG----TGTT
1 CGTTTATGTT
62877 CGTTTATGTT
1 CGTTTATGTT
62887 CGTTTAT
1 CGTTTAT
62894 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:62850 original size:16 final size:16
Alignment explanation
Indices: 62825--62889 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
62815 CCAACGTTTA
62825 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
62841 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
62857 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
62873 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
62889 T
1 T
62890 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:62980 original size:16 final size:16
Alignment explanation
Indices: 62959--62989 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
62949 AAAAAAAATT
62959 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
62975 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
62990 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:70093 original size:29 final size:30
Alignment explanation
Indices: 70033--70121 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 30
70023 TGATTAATTT
* *
70033 TAATGATAA-AAATTAAT-ACTATTTTATTA
1 TAAT-ATAATAAATTAATAATTATTTTATAA
*
70062 TAATA-GATCAAATTAATAATTATTTT-TAA
1 TAATATAAT-AAATTAATAATTATTTTATAA
*
70091 TAATATAATAAATTTAATAATTATTATATAA
1 TAATATAATAAA-TTAATAATTATTTTATAA
70122 AATTTTTTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
27 1 0.02
28 1 0.02
29 22 0.45
30 22 0.45
31 3 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
TAATATAATAAATTAATAATTATTTTATAA
Found at i:75954 original size:17 final size:18
Alignment explanation
Indices: 75932--75966 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
75922 CAATAATATT
75932 ATATAAT-TAAAATAAAA
1 ATATAATATAAAATAAAA
*
75949 ATATAATATAATATAAAA
1 ATATAATATAAAATAAAA
75967 CTAGCATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATATAATATAAAATAAAA
Found at i:78462 original size:26 final size:27
Alignment explanation
Indices: 78410--78464 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
78400 TTAAAAGACA
*
78410 ATAATTTTTTAAAAATATATGAAATTT
1 ATAATTTTTTAAAAATATATAAAATTT
*
78437 ATAA-TTTTTAAAATTATA-AAATATTT
1 ATAATTTTTTAAAAATATATAAA-ATTT
78463 AT
1 AT
78465 TATTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 19 0.76
27 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAATTTTTTAAAAATATATAAAATTT
Found at i:85231 original size:12 final size:12
Alignment explanation
Indices: 85214--85241 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
85204 GTTGAGGAAG
85214 GCAGTAACGGAT
1 GCAGTAACGGAT
85226 GCAGTAACGGAT
1 GCAGTAACGGAT
85238 GCAG
1 GCAG
85242 AACACATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (12 bp):
GCAGTAACGGAT
Found at i:104223 original size:2 final size:2
Alignment explanation
Indices: 104212--104242 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
104202 CCCAACCCTC
104212 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104243 TCAATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.