Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003109.1 Hibiscus syriacus cultivar Beakdansim tig00006498_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: 50558
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:4885 original size:66 final size:67
Alignment explanation
Indices: 4794--4953 Score: 171
Period size: 67 Copynumber: 2.4 Consensus size: 67
4784 TGAGATCAAT
* * * * * *
4794 TTTGTTTCAAGTGAAATAAATTCAAA-ATTTGA-GCTTCAAGAGAAATTGTCTCAAGCAAGACAA
1 TTTGTTTCGAGAGAAACAAACTCAAAGATTT-ATGCTTCAAGAGAAACTGTCTCAAACAAGACAA
4857 AAC
65 AAC
* * * ** *
4860 TTTGTTTCGAGAGAAACAAACTCAAAGGTTTATGTTTCAATAGAAACTGTCTCAAATGAGACTAA
1 TTTGTTTCGAGAGAAACAAACTCAAAGATTTATGCTTCAAGAGAAACTGTCTCAAACAAGACAAA
4925 AC
66 AC
* *
4927 TTTATTTCGAGAGAAACAATCTCAAAG
1 TTTGTTTCGAGAGAAACAAACTCAAAG
4954 GTGACAAACA
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
66 23 0.29
67 55 0.71
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (67 bp):
TTTGTTTCGAGAGAAACAAACTCAAAGATTTATGCTTCAAGAGAAACTGTCTCAAACAAGACAAA
AC
Found at i:4911 original size:67 final size:67
Alignment explanation
Indices: 4828--4955 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 67
4818 AAATTTGAGC
* * *
4828 TTCAAGAGAAATTGTCTCAAGCAAGACAAAACTTTGTTTCGAGAGAAACAAACTCAAAGGTTTAT
1 TTCAAGAGAAACTGTCTCAAACAAGACAAAACTTTATTTCGAGAGAAACAAACTCAAAGGTTTAT
4893 GT
66 GT
* ** * *
4895 TTCAATAGAAACTGTCTCAAATGAGACTAAACTTTATTTCGAGAGAAACAATCTCAAAGGT
1 TTCAAGAGAAACTGTCTCAAACAAGACAAAACTTTATTTCGAGAGAAACAAACTCAAAGGT
4956 GACAAACAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAACAAGACAAAACTTTATTTCGAGAGAAACAAACTCAAAGGTTTAT
GT
Found at i:17116 original size:19 final size:21
Alignment explanation
Indices: 17092--17131 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17082 TGTGATAATG
17092 AATCAAA-TATG-AAAGAAAA
1 AATCAAAGTATGCAAAGAAAA
*
17111 AATCAAAGTGTGCAAAGAAAA
1 AATCAAAGTATGCAAAGAAAA
17132 CTTTTGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.62, C:0.07, G:0.15, T:0.15
Consensus pattern (21 bp):
AATCAAAGTATGCAAAGAAAA
Found at i:31192 original size:26 final size:26
Alignment explanation
Indices: 31163--31215 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
31153 CGTTAAATTT
31163 CATTTTATTTATGGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
*
31189 CATTTTATTTATGGCATCCTTTTATG
1 CATTTTATTTATGGCATCCTTTCATG
31215 C
1 C
31216 CAATAATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (26 bp):
CATTTTATTTATGGCATCCTTTCATG
Found at i:31256 original size:34 final size:34
Alignment explanation
Indices: 31207--31508 Score: 118
Period size: 34 Copynumber: 7.9 Consensus size: 34
31197 TTATGGCATC
* *
31207 CTTTTATGCCAATAATTCACACATATGCATTATT
1 CTTTTATACCAATAATGCACACATATGCATTATT
* *
31241 CTTTTATACCGATAATGCACCCATATGCATTTCATCTAT
1 CTTTTATACCAATAATGCACACATATGCA-TT-A--T-T
* *
31280 GGCGTCATTTCATGCCAATAATGCACCCATATGCATTATT
1 --C-T--TTT-ATACCAATAATGCACACATATGCATTATT
* * *
31320 CTTTTATGCTAATAATGCACCCATATGCATTTCAGCTAT
1 CTTTTATACCAATAATGCACACATATGCA-TT-A--T-T
* * *
31359 GGCATCCTTTCATGCCAATAATGCACCCATATGCAATATT
1 --C-T--TTT-ATACCAATAATGCACACATATGCATTATT
* * *
31399 CTTTTATGCCGATAATGCACTCATATGCATTTCAGCTACGACAT
1 CTTTTATACCAATAATGCACACATATGCA-TT-A--T------T
* * *
31443 CCTTTCATGCCAATAATGCACCCATATGCATTATT
1 -CTTTTATACCAATAATGCACACATATGCATTATT
* * *
31478 CTTTTATGCCGATAATGCACCCATATGCATT
1 CTTTTATACCAATAATGCACACATATGCATT
31509 TCAACTATGG
Statistics
Matches: 218, Mismatches: 17, Indels: 66
0.72 0.06 0.22
Matches are distributed among these distances:
34 99 0.45
35 12 0.06
36 3 0.01
37 2 0.01
38 5 0.02
39 2 0.01
40 2 0.01
41 5 0.02
42 2 0.01
43 3 0.01
44 12 0.06
45 71 0.33
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (34 bp):
CTTTTATACCAATAATGCACACATATGCATTATT
Found at i:31281 original size:79 final size:79
Alignment explanation
Indices: 31198--31640 Score: 715
Period size: 79 Copynumber: 5.6 Consensus size: 79
31188 GCATTTTATT
* * * *
31198 TATGGCATCCTTTTATGCCAATAATTCACACATATGCATTATTCTTTTATACCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
*
31263 ATATGCATTTCATC
66 ATATGCATTTCAGC
* * **
31277 TATGGCGTCATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTAATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
31342 ATATGCATTTCAGC
66 ATATGCATTTCAGC
* *
31356 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCAATATTCTTTTATGCCGATAATGCACTC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
31421 ATATGCATTTCAGC
66 ATATGCATTTCAGC
* *
31435 TACGACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
*
31500 ATATGCATTTCAAC
66 ATATGCATTTCAGC
* * *
31514 TATGGCATCCTTTCATGTCAATAATGCACTCATATGCATTATACTTTTATGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
31579 ATATGCATTTCAGC
66 ATATGCATTTCAGC
* *
31593 TATGGCATCCTTTCATGCCAATAATGCACCCGTATGCATTATTTTTTT
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTT
31641 TATTCATTCG
Statistics
Matches: 333, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 333 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.36
Consensus pattern (79 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
ATATGCATTTCAGC
Found at i:31459 original size:45 final size:43
Alignment explanation
Indices: 31399--31632 Score: 189
Period size: 45 Copynumber: 5.7 Consensus size: 43
31389 ATGCAATATT
* * *
31399 CTTTTATGCCGATAATGCACTCATATGCATTTCAGCTACGACATC
1 CTTTCATGCCAATAATGCACCCATATGCATTTCA-CTA-GACATC
31444 CTTTCATGCCAATAATGCACCCATATGCA-TT-A-T-----T-
1 CTTTCATGCCAATAATGCACCCATATGCATTTCACTAGACATC
* * *
31478 CTTTTATGCCGATAATGCACCCATATGCATTTCAACTATGGCATC
1 CTTTCATGCCAATAATGCACCCATATGCATTTC-ACTA-GACATC
* *
31523 CTTTCATGTCAATAATGCACTCATATGCA-TT-A-T--AC-T-
1 CTTTCATGCCAATAATGCACCCATATGCATTTCACTAGACATC
* *
31559 -TTT-ATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATC
1 CTTTCATGCCAATAATGCACCCATATGCATTTCA-CTA-GACATC
*
31602 CTTTCATGCCAATAATGCACCCGTATGCATT
1 CTTTCATGCCAATAATGCACCCATATGCATT
31633 ATTTTTTTTA
Statistics
Matches: 151, Mismatches: 16, Indels: 44
0.72 0.08 0.21
Matches are distributed among these distances:
34 48 0.32
35 8 0.05
36 1 0.01
37 2 0.01
38 3 0.02
41 3 0.02
42 2 0.01
43 1 0.01
44 8 0.05
45 75 0.50
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (43 bp):
CTTTCATGCCAATAATGCACCCATATGCATTTCACTAGACATC
Found at i:32098 original size:22 final size:19
Alignment explanation
Indices: 32049--32119 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 19
32039 TGACTCCATA
* *
32049 GTATCGATACCCCTACCATG
1 GTATCGATA-CTCTACTATG
32069 GTATCGATACTACTATACTATG
1 GTATCGATACT-C--TACTATG
*
32091 GTACCGATACTCTACTATG
1 GTATCGATACTCTACTATG
32110 GTATCGATAC
1 GTATCGATAC
32120 CATTTTTGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 17 0.39
20 10 0.23
21 1 0.02
22 16 0.36
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (19 bp):
GTATCGATACTCTACTATG
Found at i:32170 original size:20 final size:21
Alignment explanation
Indices: 32145--32195 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
32135 CTTTGAAATT
*
32145 GTATCGATACCTTCCC-TTCG
1 GTATCGATACCTACCCTTTCG
32165 GTATCGATA-CTACCCTTTCG
1 GTATCGATACCTACCCTTTCG
*
32185 GCATCGATACC
1 GTATCGATACC
32196 GATTGAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 21 0.78
21 1 0.04
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (21 bp):
GTATCGATACCTACCCTTTCG
Found at i:33908 original size:25 final size:25
Alignment explanation
Indices: 33870--33919 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
33860 AGAAGATCAA
33870 TAATCATTTCATAACTTTTAAAAAT
1 TAATCATTTCATAACTTTTAAAAAT
*
33895 TAATCATTTTATAACTTTTAAAAAT
1 TAATCATTTCATAACTTTTAAAAAT
33920 ATATTCGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATCATTTCATAACTTTTAAAAAT
Found at i:35415 original size:2 final size:2
Alignment explanation
Indices: 35408--35448 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
35398 TGACCACTCA
*
35408 AT AT AT AT AT AT AT AT AT AT AT GT AT -T AT AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35447 AT
1 AT
35449 TCTTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:36652 original size:19 final size:19
Alignment explanation
Indices: 36625--36677 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
36615 CAATGTTTTT
*
36625 GTGATAAATTATATTTGTA
1 GTGATAAATTATATTTATA
* * *
36644 GTTATAAATTTTAGTTATA
1 GTGATAAATTATATTTATA
*
36663 GTGATAAAATATATT
1 GTGATAAATTATATT
36678 GTTAGAATTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (19 bp):
GTGATAAATTATATTTATA
Found at i:38011 original size:22 final size:22
Alignment explanation
Indices: 37974--38041 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
37964 TTAAATATAT
*
37974 TTTTAGTTATCATAACCAATTA
1 TTTTAGTTATCATAACAAATTA
37996 TTTTAGTTAT-ATTAACAAATTCTA
1 TTTTAGTTATCA-TAACAAA-T-TA
*
38020 TTTT-G-TAGCATCAACAAATTA
1 TTTTAGTTATCAT-AACAAATTA
38041 T
1 T
38042 CATAAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
21 4 0.10
22 20 0.51
23 9 0.23
24 6 0.15
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (22 bp):
TTTTAGTTATCATAACAAATTA
Found at i:38177 original size:44 final size:42
Alignment explanation
Indices: 38084--38183 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 42
38074 GATTTAGTCA
*
38084 AAATAAAAATTATGTAAAATTTATTTAGTCAAAATATTTTAT
1 AAATAAAAATTATGTAAAATTTATTTAGTCAAAATAATTTAT
38126 CAAAATAAAAATTATG-ACAAATTTATTTAGTTACAATAATAATTTAT
1 --AAATAAAAATTATGTA-AAATTTATTTAG-T-CAA-AATAATTTAT
*
38173 -AATAAATATTA
1 AAATAAAAATTA
38184 ATTTATCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
43 1 0.02
44 36 0.72
45 1 0.02
46 3 0.06
47 9 0.18
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (42 bp):
AAATAAAAATTATGTAAAATTTATTTAGTCAAAATAATTTAT
Found at i:38379 original size:197 final size:197
Alignment explanation
Indices: 38032--38851 Score: 908
Period size: 197 Copynumber: 4.2 Consensus size: 197
38022 TTGTAGCATC
* * * * *
38032 AACAAATTATCATAAATTTATTTAGTCACAATTAAAAAAATAGATTTAGTCAAAAT-AAAAATTA
1 AACAAATTATCACAAATTTATTTATTCACAA-TAACATATTAGATTTAGTCAAAATAAAAAATTA
* * * * * *
38096 TGTAAAATTTATTTAGTCAAAATATTTTATCAAAATAAAAATTATGACAAATTTATTTAGTTACA
65 TGTCAAATTTATTTAGTCACAATATTTTCTCAAAATAAAAATTATGAAAAATTTATTTAATCACA
* * *
38161 AT-AATAATTTATAATAAATATTAATTTATCAGTATAAAAAATTATGAAAAATAATATTCTTTCA
130 ATAAAT-ATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATATTCTTTCA
38225 T-AT
194 TAAT
* * * * *
38228 AATAAATTATCACAAATTTATTTATTCTCAATAACATGTTAGATTTAGTCAAGATAAGAAATTAT
1 AACAAATTATCACAAATTTATTTATTCACAATAACATATTAGATTTAGTCAAAATAAAAAATTAT
* * * * * *
38293 GTCAAATTGT-TTTAATCACAGTATTTTCTTAAAATATAAAATGATAAAAAAATTATTTAATCAC
66 GTCAAATT-TATTTAGTCACAATATTTTCTCAAAATA-AAAATTATGAAAAATTTATTTAATCAC
* * *
38357 AATAAATATTTATAACAAATATTAATTTCTCAATATAAAAATTTATAAAAAAACAATATT-TTTC
129 AATAAATATTTATAACAAATATTAATTTCTCAATATAAAAAATTAT-GAAAAATAATATTCTTTC
38421 ATAAT
193 ATAAT
* * * * *
38426 AATAAATTATAACATATTTATTTAGTCACAATAACAT-TATA-TTTTA-TCAAAATAAAAAAATT
1 AACAAATTATCACAAATTTATTTATTCACAATAACATAT-TAGATTTAGTCAAAAT-AAAAAATT
* * * * * *
38488 ATGTCAAATTTATTTTGTCACAATATTTTCTTAAAATAATAATTTTTGAAAATTTTATTTAATTA
64 ATGTCAAATTTATTTAGTCACAATATTTTCTCAAAATAA-AAATTATGAAAAATTTATTTAATCA
* * * *
38553 TAATAACA-ATTCATAACAAATATTAATTTCTCAATATAAAAAAATATGACAAATAATATTCTTT
128 CAATAA-ATATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATATTCTTT
38617 CATAAT
192 CATAAT
* * * *
38623 AACAAATTGT-AGCAAATTTATTTAGTT-ACAATAACACATTAAATTTAATCAAAATAAAAAGAT
1 AACAAATTATCA-CAAATTTATTTA-TTCACAATAACATATTAGATTTAGTCAAAATAAAAA-AT
* * * * *
38686 TATATTAAATTTATTTCGTCACAATATTTTCTCAAAATAAAAGTT-TGACAAATTTATTTAATCA
63 TATGTCAAATTTATTTAGTCACAATATTTTCTCAAAATAAAAATTATGAAAAATTTATTTAATCA
* * * *
38750 TAATAAAAATTTATAAAAAATATTAATTTCTCAATATAAAAAAATTATGAAAAATAATATTATTT
128 CAATAAATATTTATAACAAATATTAATTTCTCAATAT-AAAAAATTATGAAAAATAATATTCTTT
*
38815 CACAAT
192 CATAAT
* *
38821 AACAAATTGTGACAAATTTATTTATTCACAA
1 AACAAATTATCACAAATTTATTTATTCACAA
38852 AAAAATATAA
Statistics
Matches: 530, Mismatches: 72, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
195 19 0.04
196 83 0.16
197 260 0.49
198 122 0.23
199 46 0.09
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (197 bp):
AACAAATTATCACAAATTTATTTATTCACAATAACATATTAGATTTAGTCAAAATAAAAAATTAT
GTCAAATTTATTTAGTCACAATATTTTCTCAAAATAAAAATTATGAAAAATTTATTTAATCACAA
TAAATATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAAAAATAATATTCTTTCATA
AT
Found at i:38640 original size:99 final size:97
Alignment explanation
Indices: 38509--38844 Score: 249
Period size: 99 Copynumber: 3.4 Consensus size: 97
38499 ATTTTGTCAC
* * * * *
38509 AATATTTTCTTAAAATAATAATTTTTGA-AAATTTTATTTAATTATAATAACAATTCATAACAAA
1 AATATTTT-TCAAAATAACAAATTGTGACAAA-TTTATTTAATTATAATAACAATTAATAACAAA
38573 TATTAATTTCTCAATATAAAAAAATATGACAAAT
64 TATTAATTTCTCAATATAAAAAAATATGACAAAT
* * *
38607 AATATTCTTTCATAATAACAAATTGT-AGCAAATTTATTTAGTTACAATAACACATTAAATTTAA
1 AATATT-TTTCAAAATAACAAATTGTGA-CAAATTTATTTAATTATAATAACA-ATT-AA--TAA
** ** *** * *
38671 TCAAAATAAAAAGAT-T--ATATTAAATTTATTTCGTCACAAT
60 -C-AAATATTAATTTCTCAATA-TAAAAAAATAT-GACA-AAT
* * * * * *
38711 -AT-TTTCTCAAAATAA-AAGTT-TGACAAATTTATTTAATCATAATAAAAATTTATAAAAAATA
1 AATATTTTTCAAAATAACAAATTGTGACAAATTTATTTAATTATAATAACAATTAATAACAAATA
*
38772 TTAATTTCTCAATATAAAAAAATTATGAAAAAT
66 TTAATTTCTCAATATAAAAAAA-TATGACAAAT
*
38805 AATATTATTTCACAATAACAAATTGTGACAAATTTATTTA
1 AATATT-TTTCAAAATAACAAATTGTGACAAATTTATTTA
38845 TTCACAAAAA
Statistics
Matches: 177, Mismatches: 39, Indels: 43
0.68 0.15 0.17
Matches are distributed among these distances:
93 8 0.05
94 4 0.02
95 12 0.07
96 7 0.04
97 11 0.06
98 43 0.24
99 44 0.25
100 6 0.03
101 12 0.07
102 12 0.07
103 7 0.04
104 11 0.06
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (97 bp):
AATATTTTTCAAAATAACAAATTGTGACAAATTTATTTAATTATAATAACAATTAATAACAAATA
TTAATTTCTCAATATAAAAAAATATGACAAAT
Found at i:39183 original size:21 final size:22
Alignment explanation
Indices: 39152--39192 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39142 TGTACTTCTC
39152 GTGACGAAATAGTTAATTGATT
1 GTGACGAAATAGTTAATTGATT
* *
39174 GTGAC-AAATATTTTATTGA
1 GTGACGAAATAGTTAATTGA
39193 GATAGGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (22 bp):
GTGACGAAATAGTTAATTGATT
Found at i:39886 original size:22 final size:21
Alignment explanation
Indices: 39859--39910 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
39849 TTATAAGGTA
39859 GTATCGATACCTTGTCAATGGG
1 GTATCGATACCTT-TCAATGGG
**
39881 GTATCGATA-CTTTTTATGGG
1 GTATCGATACCTTTCAATGGG
39901 GTATCGATAC
1 GTATCGATAC
39911 TCGAGACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 15 0.56
21 3 0.11
22 9 0.33
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (21 bp):
GTATCGATACCTTTCAATGGG
Found at i:42448 original size:17 final size:16
Alignment explanation
Indices: 42423--42454 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42413 ATCATTATCA
42423 TAAAAATATTAATTAT
1 TAAAAATATTAATTAT
42439 TAAAATATATTAATTA
1 TAAAA-ATATTAATTA
42455 ATATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAAATATTAATTAT
Found at i:42815 original size:20 final size:21
Alignment explanation
Indices: 42771--42822 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
42761 TATTGACATA
*
42771 AATAATA-TTTAATAGATTAT
1 AATAATATTTTAATAGATAAT
*
42791 TATAATATTTTAATA-ATAAT
1 AATAATATTTTAATAGATAAT
42811 AATAATAGTTTT
1 AATAATA-TTTT
42823 GTATTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
AATAATATTTTAATAGATAAT
Found at i:42845 original size:18 final size:18
Alignment explanation
Indices: 42808--42870 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
42798 TTTTAATAAT
42808 AATAATAATAGTTTTGTATTA
1 AATAAT-ATA-TTTT-TATTA
42829 AATAATATATTTTTATTA
1 AATAATATATTTTTATTA
* ** * *
42847 TATTTTATATTTATAATA
1 AATAATATATTTTTATTA
42865 AATAAT
1 AATAAT
42871 TAAAAATATA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
18 21 0.62
19 4 0.12
20 3 0.09
21 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
AATAATATATTTTTATTA
Found at i:44001 original size:19 final size:19
Alignment explanation
Indices: 43974--44026 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
43964 CAATGTTTTT
*
43974 GTGATAAATTATATTTGTA
1 GTGATAAATTATATTTATA
* * *
43993 GTTATAAATTTTAGTTATA
1 GTGATAAATTATATTTATA
*
44012 GTGATAAAATATATT
1 GTGATAAATTATATT
44027 GTTAGAATTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (19 bp):
GTGATAAATTATATTTATA
Found at i:49245 original size:58 final size:58
Alignment explanation
Indices: 49123--49452 Score: 305
Period size: 58 Copynumber: 5.7 Consensus size: 58
49113 AATATAAAGG
* * ** **
49123 AAATAAATTACTGAATTTATTTCATCGTT-AGAATTTTGTGTAGA-TCTAACTTTGTAAGGG
1 AAATAAATTATTGAATTTATTTC--C-TTGAGAATCTTGAAT-GATTCTAACTTTGTAAGAA
* *
49183 AAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTCAGGA
1 AAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGAA
* *
49241 AAATAAA-TAGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAAATTTATAAGAA
1 AAATAAATTA-TTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGAA
* * * * * * *
49299 AAATAAATTGTTGAATTTATTTTCTTGAGAATCATGACTGATTATATCTTT-TAAAAA
1 AAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGAA
* * * * *
49356 GAAATAAATTATTAAATTT-TTTTCTTGAGAATCTTAAATGATTCT-ATTTTGTTAA-ATG
1 -AAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTG-TAAGA-A
* * * *
49414 AAATAAATTTTTAAATTTATTTTCTCGAGAATCTTGAAT
1 AAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAAT
49453 AAAGAATTAA
Statistics
Matches: 231, Mismatches: 30, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
56 3 0.01
57 51 0.22
58 154 0.67
59 1 0.00
60 22 0.10
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (58 bp):
AAATAAATTATTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGAA
Found at i:49531 original size:99 final size:100
Alignment explanation
Indices: 49353--49536 Score: 237
Period size: 99 Copynumber: 1.9 Consensus size: 100
49343 TATCTTTTAA
* * *
49353 AAAGAAATAAATTATTAAATTTTTTTCTTGAGAATCTTAAATGATTCTATTTTGTTAAATGAAAT
1 AAAGAAATAAATTATTAAATTTATTTCTTGAGAATCTTAAATGATTCTATTTTGTAAAAGGAAAT
***
49418 AAATTTTTAAATTTATTTTCTCGAGAATCTTGAAT
66 AAATCGCTAAATTTATTTTCTCGAGAATCTTGAAT
* * * * *
49453 AAAGAATTAAATTGTTGAATTTATTTCTT-AGAATCTTTAATGATTCTATCTTT-TAAAAGGAAT
1 AAAGAAATAAATTATTAAATTTATTTCTTGAGAATCTTAAATGATTCTAT-TTTGTAAAAGGAAA
*
49516 TAAATCGCTAGATTTATTTTC
65 TAAATCGCTAAATTTATTTTC
49537 CTGGTTTGTA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
99 43 0.61
100 28 0.39
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (100 bp):
AAAGAAATAAATTATTAAATTTATTTCTTGAGAATCTTAAATGATTCTATTTTGTAAAAGGAAAT
AAATCGCTAAATTTATTTTCTCGAGAATCTTGAAT
Done.