Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004011.1 Hibiscus syriacus cultivar Beakdansim tig00008748_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: 243343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:141826 original size:123 final size:123
Alignment explanation
Indices: 141598--142217 Score: 685
Period size: 123 Copynumber: 5.0 Consensus size: 123
141588 ATAGCGGCAT
* * *
141598 TTTAGCGGCGTTTTTAGA-ACAAACGCCGATAAATACTCGTAATTTAGTGGCGTTTTTATACAAA
1 TTTAGTGGCGTTTTTAGACA-AAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTATACAAA
* * * *
141662 CGCCGCTAAAGACTATACTTTAGTGGCGTTTTTACACAAACGCCGCTACAGACT-GTAC
65 CGCCGCTAAAGAATATACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGTAC
** * * *
141720 TTTAGCAGCGTTTTTAGACAAAATGCCGCTAAATACTTGTACTTTAGTGGTGTTTTTAATACAAA
1 TTTAGTGGCGTTTTTAGACAAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTT-ATACAAA
* * *
141785 CACCGCTAAAGAATATACTTTAGCGGCGCTTTTATACAAACGCCGCTATATACTCGTAC
65 CGCCGCTAAAGAATATACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGTAC
* * * *
141844 TTTAGTGGCATTTTTATACAAAA-GCCGCTAAATACTTGTACTTTAGTGGCATTTTTAATACAAA
1 TTTAGTGGCGTTTTTAGACAAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTT-ATACAAA
* * * * *
141908 CGCCGCTAAAGAATGTATTTTAGCGGTGTTTTTATATAAACGCCGCTATATACTCGTAC
65 CGCCGCTAAAGAATATACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGTAC
* * * * *
141967 TTTAGTGGCGTTTTTA-ATACAGACGCCGCTATAGACTCGTATTTTAGTGGCGTTTTTATACAAA
1 TTTAGTGGCGTTTTTAGACA-AAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTATACAAA
* * * * *
142031 TGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCGTAC
65 CGCCGCTAAAGAAT-ATACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGTAC
* * * * * ***
142091 TTTAGTGGCGTTTTTATAC-AAACGCCGTTATAGACTCGTATTTTAGTGGTACTTTTATACAAAC
1 TTTAGTGGCGTTTTTAGACAAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTATACAAAC
* ** ** * *
142155 GCCGCTATAGACCCATGA-TTTAGCGGTTTTTTTTATACAAACGTCGCTATAGACTCGTGC
66 GCCGCTAAAGA-ATAT-ACTTTAGCGG-CGTTTTTATACAAACGCCGCTATAGACTCGTAC
142215 TTT
1 TTT
142218 GGAGTCGTTA
Statistics
Matches: 432, Mismatches: 56, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
122 51 0.12
123 240 0.56
124 140 0.32
125 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (123 bp):
TTTAGTGGCGTTTTTAGACAAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTATACAAAC
GCCGCTAAAGAATATACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGTAC
Found at i:145692 original size:43 final size:43
Alignment explanation
Indices: 145629--146070 Score: 458
Period size: 43 Copynumber: 10.2 Consensus size: 43
145619 ATGGTAATTA
** * * *
145629 GCGGCGTTTGTATAAAAAAATGTCGTTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATATGACCTTTT
*
145672 GTGGCGTTTGTATCCAAAAATGCCGCTATAGATATGA-CTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATATGACCTTTT
* * *
145714 GCAGCGTTTGTATCCAAAAATACCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATATGACCTTTT
* * * * *
145757 GCGGCATTTGTATCCAAAAAACGCTGTTATAGATATGAACTTTT
1 GCGGCGTTTGTATCC-AAAAATGCCGCTATAGATATGACCTTTT
* * *
145801 GCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGATCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATATGACCTTTT
* * *
145844 GCTGCTTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATATGACCTTTT
* * * *
145887 GCGACATTTGTATCCAAAAAATGCTGCTATAGATATGAACTTTT
1 GCGGCGTTTGTATCC-AAAAATGCCGCTATAGATATGACCTTTT
* * * *
145931 GCGGCGTTTGTATCTAAAAACGCAGCTATAGATATGATCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATATGACCTTTT
** * *** * *
145974 GCTACTTTTGTGAAATAAAAATGCCGCTATAGATCTCAACCTTTT
1 GCGGCGTTTGT-ATCCAAAAATGCCGCTATAGATAT-GACCTTTT
* * *
146019 GCGGCGTTTGT-TTCAAAAAAGCCGCTATAGA-ACTTGACTTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATA--TGACCTTTT
146062 GCGGCGTTT
1 GCGGCGTTT
146071 TTATTTCACA
Statistics
Matches: 331, Mismatches: 61, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
42 38 0.11
43 187 0.56
44 92 0.28
45 14 0.04
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAATGCCGCTATAGATATGACCTTTT
Found at i:145830 original size:87 final size:86
Alignment explanation
Indices: 145629--146070 Score: 460
Period size: 87 Copynumber: 5.1 Consensus size: 86
145619 ATGGTAATTA
** * * * *
145629 GCGGCGTTTGTATAAAAAAATGTCGTTATAGATCTGACCTTTTGTGGCGTTTGTATCCAAAAATG
1 GCGGCGTTTGTATCTAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACG
145694 CCGCTATAGATATG-ACTTTT
66 CCGCTATAGATATGAACTTTT
* * * *
145714 GCAGCGTTTGTATCCAAAAATACCGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAAAC
1 GCGGCGTTTGTATCTAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCC-AAAAAC
* *
145779 GCTGTTATAGATATGAACTTTT
65 GCCGCTATAGATATGAACTTTT
* * * * * *
145801 GCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGATCTTTTGCTGCTTTTGTATCCAAAAATG
1 GCGGCGTTTGTATCTAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACG
* *
145866 CCGCTATAGATCTGACCTTTT
66 CCGCTATAGATATGAACTTTT
* * * * * * *
145887 GCGACATTTGTATCCAAAAAATGCTGCTATAGATATGAACTTTTGCGGCGTTTGTATCTAAAAAC
1 GCGGCGTTTGTAT-CTAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAAC
* *
145952 GCAGCTATAGATATGATCTTTT
65 GCCGCTATAGATATGAACTTTT
** * ** * *
145974 GCTACTTTTGTGAAATAAAAATGCCGCTATAGATCTCAACCTTTTGCGGCGTTTGT-TTCAAAAA
1 GCGGCGTTTGT-ATCTAAAAATGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTATCCAAAAA
*
146038 AGCCGCTATAGA-ACTTG-ACTTTTT
64 CGCCGCTATAGATA--TGAAC-TTTT
146062 GCGGCGTTT
1 GCGGCGTTT
146071 TTATTTCACA
Statistics
Matches: 295, Mismatches: 54, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
85 50 0.17
86 53 0.18
87 162 0.55
88 30 0.10
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (86 bp):
GCGGCGTTTGTATCTAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACG
CCGCTATAGATATGAACTTTT
Found at i:145895 original size:130 final size:129
Alignment explanation
Indices: 145655--146090 Score: 574
Period size: 130 Copynumber: 3.3 Consensus size: 129
145645 AAAATGTCGT
* * * * * *
145655 TATAGATCTGACCTTTTGTGGCGTTTGTATCCAAAAATGCCGCTATAGATATGA-CTTTTGCAGC
1 TATAGATATGAACTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGATCTTTTGCTGC
* * *
145719 GTTTGTATCCAAAAATACCGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAAACGCTGT
66 TTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAAA-GCTGC
145784 TATAGATATGAACTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGATCTTTTGCTGC
1 TATAGATATGAACTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGATCTTTTGCTGC
*
145849 TTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTTGCGACATTTGTATCCAAAAAATGCTGC
66 TTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAAA-GCTGC
* *
145914 TATAGATATGAACTTTTGCGGCGTTTGTATCTAAAAACGCAGCTATAGATATGATCTTTTGCTAC
1 TATAGATATGAACTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGATCTTTTGCTGC
*** * * * *
145979 TTTTGTGAAATAAAAATGCCGCTATAGATCTCAACCTTTTGCGGCGTTTGT-TTCAAAAAAGCCG
66 TTTTGT-ATCCAAAAATGCCGCTATAGATCT-GACCTTTTGCGGCATTTGTATCCAAAAAAGCTG
146043 C
129 C
* * *
146044 TATAGA-ACTTG-ACTTTTTGCGGCGTTTTTATTTCACAAACGCCGCTA
1 TATAGATA--TGAAC-TTTTGCGGCGTTTGTATCT-AAAAACGCCGCTA
146091 ACATTAGCGA
Statistics
Matches: 275, Mismatches: 25, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
129 50 0.18
130 150 0.55
131 48 0.17
132 27 0.10
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (129 bp):
TATAGATATGAACTTTTGCGGCGTTTGTATCTAAAAACGCCGCTATAGATATGATCTTTTGCTGC
TTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAAAGCTGC
Found at i:146637 original size:39 final size:39
Alignment explanation
Indices: 146550--146644 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
146540 GCATAAGGAT
* * * *
146550 CTGCGGTAAAGACTTACCCTGAGCACAAAGCATATGAGC
1 CTGCGGTAAGGACTTACCATGAGCACAAAGCAGAGGAGC
* *
146589 CTACGGTAAGGACTTACCATGAGCACAAAGTAGAGGAGC
1 CTGCGGTAAGGACTTACCATGAGCACAAAGCAGAGGAGC
*
146628 CTGCGGTAAGGTCTTAC
1 CTGCGGTAAGGACTTAC
146645 AAGTCATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (39 bp):
CTGCGGTAAGGACTTACCATGAGCACAAAGCAGAGGAGC
Found at i:151405 original size:21 final size:21
Alignment explanation
Indices: 151363--151405 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
151353 CCCTACCCTT
**
151363 AACTTAAAACACTAAATTATA
1 AACTTAAAACACTAAACCATA
* *
151384 AACTTTAAACCCTAAACCATA
1 AACTTAAAACACTAAACCATA
151405 A
1 A
151406 CTCTATTACC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (21 bp):
AACTTAAAACACTAAACCATA
Found at i:153123 original size:35 final size:35
Alignment explanation
Indices: 153076--153151 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
153066 AAAACAGTCC
* * *
153076 TCAATTTTATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
**
153111 TCAATTTCATTCTAAACCTTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
153146 TCAATT
1 TCAATT
153152 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:153701 original size:130 final size:130
Alignment explanation
Indices: 153548--153795 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
153538 TATTTATATA
** * **
153548 ATCAATTTGGTGTTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
153613 TTAGCACATAATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATAATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
153678 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
153743 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATAATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
153796 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATAATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:153826 original size:130 final size:129
Alignment explanation
Indices: 153562--153826 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
153552 ATTTGGTGTT
* ** *
153562 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATAATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATAATCA
* *** * * **** *
153627 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
153692 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATAATCA
* * * *
153757 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
153821 -A
128 CA
153822 AAATT
1 AAATT
153827 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATAATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:154286 original size:16 final size:18
Alignment explanation
Indices: 154265--154298 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
154255 ATTTCTTATT
154265 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
154281 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
154299 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:163189 original size:60 final size:60
Alignment explanation
Indices: 163111--163319 Score: 224
Period size: 60 Copynumber: 3.5 Consensus size: 60
163101 TGGTTTCGGT
*
163111 TCTAAATCCTTCTTTGGCTTTAATTCCTCCTCATA-TAACATATCCTTACTTAGCAT-CAGC
1 TCTACATCCTTCTTTGGCTTTAATTCCTCCTCATAGT-ACATATCCTTACTTAGCATCCA-C
* * * * * * *
163171 TCTGCATCCTTATTTGGCTTTAATTTCTCTTCATAGTACATATCCTTCCTTGGCTTCCAC
1 TCTACATCCTTCTTTGGCTTTAATTCCTCCTCATAGTACATATCCTTACTTAGCATCCAC
* * * * *
163231 TCTACATCCTTCTTTGGCTTTAGTTCCTCCTCATAGTACATATCATTCCTTCGCTTCCAC
1 TCTACATCCTTCTTTGGCTTTAATTCCTCCTCATAGTACATATCCTTACTTAGCATCCAC
* ** * *
163291 TCTAAATCCTTAGTCGGCTTTAAATCCTC
1 TCTACATCCTTCTTTGGCTTTAATTCCTC
163320 AATATTTATC
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
60 123 0.98
61 3 0.02
ACGTcount: A:0.20, C:0.30, G:0.09, T:0.42
Consensus pattern (60 bp):
TCTACATCCTTCTTTGGCTTTAATTCCTCCTCATAGTACATATCCTTACTTAGCATCCAC
Found at i:170909 original size:19 final size:18
Alignment explanation
Indices: 170879--170923 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
170869 AATGACAATA
170879 AATATCTTTGAT-ATCTGT
1 AATATCTTTGATGAT-TGT
170897 AATATCGTTTGATGATTGT
1 AATATC-TTTGATGATTGT
170916 ATATATCT
1 A-ATATCT
170924 CACTACAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.25
19 11 0.46
20 7 0.29
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (18 bp):
AATATCTTTGATGATTGT
Found at i:174558 original size:17 final size:17
Alignment explanation
Indices: 174521--174559 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
174511 TTAATATAGG
*
174521 ATGATTAATTATCTTGG
1 ATGATTAATTATCTTGC
* *
174538 ATGATTAATTATTTTTC
1 ATGATTAATTATCTTGC
174555 ATGAT
1 ATGAT
174560 CAGATTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (17 bp):
ATGATTAATTATCTTGC
Found at i:183066 original size:2 final size:2
Alignment explanation
Indices: 183059--183093 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
183049 TTCCATCCCC
183059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
183094 ATTATAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:190406 original size:15 final size:16
Alignment explanation
Indices: 190380--190409 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
190370 AATAGTATCG
190380 TTGTTAATGCAATTGC
1 TTGTTAATGCAATTGC
190396 TTGTTAA-GCAATTG
1 TTGTTAATGCAATTG
190410 ATTTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (16 bp):
TTGTTAATGCAATTGC
Found at i:190478 original size:95 final size:95
Alignment explanation
Indices: 190315--190514 Score: 355
Period size: 95 Copynumber: 2.1 Consensus size: 95
190305 GTTGTGATTT
* * *
190315 ATTTTGTTTTAGATTTTTGTTCTCTTTCATTCATGTTAAATAATCTCATAATACTAATAGTATCG
1 ATTTTCTTTTAGATCTTTGTTCACTTTCATTCATGTTAAATAATCTCATAATACTAATAGTATCG
190380 TTGTTAATGCAATTGCTTGTTAAGCAATTG
66 TTGTTAATGCAATTGCTTGTTAAGCAATTG
* *
190410 ATTTTCTTTTAGATCTTTGTTCACTTTCATTCATGTTAAATAATCTCATATTACTAATAGTATTG
1 ATTTTCTTTTAGATCTTTGTTCACTTTCATTCATGTTAAATAATCTCATAATACTAATAGTATCG
190475 TTGTTAATGCAATTGCTTGTTAAGCAATTG
66 TTGTTAATGCAATTGCTTGTTAAGCAATTG
190505 ATTTTCTTTT
1 ATTTTCTTTT
190515 GATAATAGTG
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (95 bp):
ATTTTCTTTTAGATCTTTGTTCACTTTCATTCATGTTAAATAATCTCATAATACTAATAGTATCG
TTGTTAATGCAATTGCTTGTTAAGCAATTG
Found at i:190489 original size:15 final size:15
Alignment explanation
Indices: 190471--190504 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
190461 TACTAATAGT
190471 ATTG-TTGTTAATGCA
1 ATTGCTTGTTAA-GCA
190486 ATTGCTTGTTAAGCA
1 ATTGCTTGTTAAGCA
190501 ATTG
1 ATTG
190505 ATTTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (15 bp):
ATTGCTTGTTAAGCA
Found at i:190496 original size:49 final size:49
Alignment explanation
Indices: 190348--190497 Score: 132
Period size: 49 Copynumber: 3.1 Consensus size: 49
190338 CTTTCATTCA
* *
190348 TGTTAAATAATCTCATAATACTAATAGTATCGTTGTTAATGCAATTGCT
1 TGTTAAATAATCTCATATTACTAATAGTATTGTTGTTAATGCAATTGCT
** * * ** * * *
190397 TGTTAAGCAAT-TGAT-TTTCTTTTAG-ATCT-TTGTTCACTTTC-ATT-CA
1 TGTTAAATAATCTCATATTACTAATAGTAT-TGTTGTT-A-ATGCAATTGCT
190443 TGTTAAATAATCTCATATTACTAATAGTATTGTTGTTAATGCAATTGCT
1 TGTTAAATAATCTCATATTACTAATAGTATTGTTGTTAATGCAATTGCT
190492 TGTTAA
1 TGTTAA
190498 GCAATTGATT
Statistics
Matches: 72, Mismatches: 20, Indels: 18
0.65 0.18 0.16
Matches are distributed among these distances:
46 17 0.24
47 15 0.21
48 17 0.24
49 23 0.32
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (49 bp):
TGTTAAATAATCTCATATTACTAATAGTATTGTTGTTAATGCAATTGCT
Found at i:194525 original size:20 final size:21
Alignment explanation
Indices: 194500--194539 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
194490 CTTTGTATAG
194500 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
194520 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
194540 CTCAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:200545 original size:16 final size:16
Alignment explanation
Indices: 200524--200561 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
200514 GTAGTGCATC
200524 GATGCACATGTTAAAG
1 GATGCACATGTTAAAG
200540 GATGCACATGTTAAAG
1 GATGCACATGTTAAAG
200556 GATGCA
1 GATGCA
200562 TCGATACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (16 bp):
GATGCACATGTTAAAG
Found at i:202150 original size:21 final size:21
Alignment explanation
Indices: 202126--202185 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
202116 GTCGAGGGAT
202126 TATCAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
*
202147 TATCAGTGGTCATTCGGGAC-
1 TATCAGTGGTCCTTCGGGACA
202167 -AT-AGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
202186 AATATTCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.42
19 2 0.06
21 19 0.53
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (21 bp):
TATCAGTGGTCCTTCGGGACA
Found at i:207300 original size:42 final size:41
Alignment explanation
Indices: 207254--207340 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
207244 AGGCTATCAA
* * *
207254 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
1 TAAGTCTTTCGAGCAAGATG-ATAAATCCTTCGGGCCATCTG
* *
207296 TAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTT
1 TAAGTCTTTCGAGCAAGATGATAAATCCTTCGGGCCATCTG
207337 TAAG
1 TAAG
207341 ACCTTCGGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 21 0.52
42 19 0.47
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
TAAGTCTTTCGAGCAAGATGATAAATCCTTCGGGCCATCTG
Found at i:207561 original size:249 final size:249
Alignment explanation
Indices: 207116--207895 Score: 1098
Period size: 249 Copynumber: 3.1 Consensus size: 249
207106 TAAGTTGTTT
* * * *
207116 TGAAAACGAGAAAGCGATTACCATAGCTTCTCATTTAATCTTTT-ATGAAAATGAAATTTTTGAA
1 TGAAAACGAGAAAGCAATTACCAAAGTTTCTCATTTAATGTTTTCA-GAAAATGAAATTTTTGAA
* *
207180 AAGTAAGAAAGCGATAACCAAAGTTTCTTACCAGTAAACTATTTCCAAAATTTGTAAGTCCTTC-
65 AAGTAAGAAAGCGATTACCAAAGTTTCTTACCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
* * * * *
207244 AGGCTATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAG
130 A-GCCATCAGTAAGTTTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTGAG
* **
207309 CAAGATGATAAGTCCTTCGGGCCATCTTTAAGACCTTCGGGTAGGATGTTTTCACA
194 CAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACA
* * * *
207365 TGAAAATGAGAAAGTAATTACCAAATTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
1 TGAAAACGAGAAAGCAATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
* *
207430 AGTAAGAAAGCGATTTCCAAAGTTTCTTACCAGTAAATTATTTCCGAAATTTGTAAGTCCTTCGA
66 AGTAAGAAAGCGATTACCAAAGTTTCTTACCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCGA
* ** *
207495 GCCATCAGTAAGTTTTTCAAGCATGATGCTTAAATAATTTGGGTCATCTATAAGTCTTTTGAGCA
131 GCCATCAGTAAGTTTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTGAGCA
* *
207560 AGATGATAAATCATTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACA
196 AGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACA
* * * *
207614 TGAAAATGGGAAAGCAATTACCAAAGTTTCTCATTTAATGTTTCCAGAAATTGAAATTTTTGAAA
1 TGAAAACGAGAAAGCAATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
* *
207679 AGTAATAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCTAAAATTTGCAAGTCCTTC
66 AGTAAGAAAGCGATTACCAAAGTTTCTTA-CCAGTAAATTATTTCC-AAAATTTGTAAGTCCTTC
* * *
207744 GAGCCATCGGTAAATCTTTT-GAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTTGA
129 GAGCCATCAGTAAGT-TTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTGA
* * * ** * *
207808 GCAAGATGATAAGTCATTTGGGTCATCCGTAAGAAATTTGGGTAGAATGTTTTCACA
193 GCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACA
**
207865 TGAAAACGAGAAAGTGATTACCAAAGTTTCT
1 TGAAAACGAGAAAGCAATTACCAAAGTTTCT
207896 TAACTAGTAA
Statistics
Matches: 470, Mismatches: 56, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
249 305 0.65
250 18 0.04
251 143 0.30
252 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (249 bp):
TGAAAACGAGAAAGCAATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
AGTAAGAAAGCGATTACCAAAGTTTCTTACCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCGA
GCCATCAGTAAGTTTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTGAGCA
AGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACA
Found at i:207785 original size:42 final size:42
Alignment explanation
Indices: 207738--207817 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
207728 AATTTGCAAG
* *
207738 TCCTTCGAGCCATCGGTAAATCTTTTGAGCATGATGATTAAA
1 TCCTTCGAGCCATCGATAAATCTTTTGAGCAAGATGATTAAA
* * * *
207780 TCCTTCGGGTCATCTATAAGTCTTTTGAGCAAGATGAT
1 TCCTTCGAGCCATCGATAAATCTTTTGAGCAAGATGAT
207818 AAGTCATTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (42 bp):
TCCTTCGAGCCATCGATAAATCTTTTGAGCAAGATGATTAAA
Found at i:207973 original size:189 final size:189
Alignment explanation
Indices: 207685--208209 Score: 655
Period size: 189 Copynumber: 2.8 Consensus size: 189
207675 GAAAAGTAAT
* * *
207685 AAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCTAAAATTTGCAAGTCCTTC-GAGCC
1 AAAGTGATTACCAAAGTTTCTTAACCAGTAAATTATTTCC-AAAATTTGTAAGTCCTTCTG-GCC
* ** * *
207749 ATCG-GTAAATCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTTGAGCAAG
64 AT-GAGTAAGTCTTTAAAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAG
* * *
207813 ATGATAAGTCATTT-GGGTCATCCGTAAGAAATTTGGGTAGAATGTTTTCACATGAAAACGAG
128 ATGATAAGTC-TTTCGGGTAATCCGTAAGAAATTCGAGTAGAATGTTTTCACATGAAAACGAG
* * *
207875 AAAGTGATTACCAAAGTTTCTTAACTAGTAAATTATATCCAAAATTTGTAAGTCCTTCTGGTCAT
1 AAAGTGATTACCAAAGTTTCTTAACCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCTGGCCAT
* * * *
207940 GAGTAAGTCTTTAAAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCTTTCAAGCAATATA
66 GAGTAAGTCTTTAAAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG
** * *
208005 ATAAGTCTTTCGGGTAATCCGTAAGACCTTCGAGTAGGATGTTTTCACATGAAAATGAG
131 ATAAGTCTTTCGGGTAATCCGTAAGAAATTCGAGTAGAATGTTTTCACATGAAAACGAG
* *
208064 AAAGTGATTACCAAAGTTTCTT-ACCAGTAAATTATTTCAAAAAATTTGTAAGTCATT-TGGGCC
1 AAAGTGATTACCAAAGTTTCTTAACCAGTAAATTATTTC-CAAAATTTGTAAGTCCTTCT-GGCC
* * * * * * * *
208127 ATTAGTGAGTCTTTCAAGCATGATGATTAAATTCTTTGGGCCATATGTAAGTCTTTCGAGTAAGA
64 ATGAGTAAGTCTTTAAAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* *
208192 TGATAAGTCCTTCTGGTA
129 TGATAAGTCTTTCGGGTA
208210 GGATGCTTTC
Statistics
Matches: 289, Mismatches: 41, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
188 19 0.07
189 233 0.81
190 37 0.13
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (189 bp):
AAAGTGATTACCAAAGTTTCTTAACCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCTGGCCAT
GAGTAAGTCTTTAAAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG
ATAAGTCTTTCGGGTAATCCGTAAGAAATTCGAGTAGAATGTTTTCACATGAAAACGAG
Found at i:208253 original size:169 final size:169
Alignment explanation
Indices: 208038--208373 Score: 449
Period size: 169 Copynumber: 2.0 Consensus size: 169
208028 AGACCTTCGA
* * *
208038 GTAGGATGTTTTCACATGAAAATGAGAAAGTGATTACCAAAGTTTCTTA-CCAGTAAATTATTTC
1 GTAGGATGCTTTCACATGAAAATGAGAAAGCGAATACCAAAGTTTCTTACCCAGTAAATTATTTC
* * * * * * *
208102 AAAAAATTTGTAAGTCATTTGGGCCATTAGTGAGTCTTTCAAGCATGATGATTAAATTCTTTGGG
66 -AAAAATTTATAAGTCATTTGGGCCATCAGTAAGTCTTTCAAGAATGATGATTAAATCCTTCGAG
*
208167 CCATATGTAAGTCTTTCGAGTAAGATGATAAGTCCTTCTG
130 CCATATGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCTG
* *
208207 GTAGGATGCTTTCACTTGAAAATGAGAAAGCGAATACCAGAGTTTCTTACCCAGTAAATTATTTC
1 GTAGGATGCTTTCACATGAAAATGAGAAAGCGAATACCAAAGTTTCTTACCCAGTAAATTATTTC
* * * ** * *
208272 CAAAATTTATAAGTCCTTTGGGTCATCAGTAAGTCTTTTGAGAATGATTATTAAATCCTTCGAGT
66 AAAAATTTATAAGTCATTTGGGCCATCAGTAAGTCTTTCAAGAATGATGATTAAATCCTTCGAGC
* * *
208337 CATCTGTCAGTCTTTCGAGCAAGATGATAAGTGCTTC
131 CATATGTAAGTCTTTCGAGCAAGATGATAAGTCCTTC
208374 GGGCCATCCG
Statistics
Matches: 143, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
169 128 0.90
170 15 0.10
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (169 bp):
GTAGGATGCTTTCACATGAAAATGAGAAAGCGAATACCAAAGTTTCTTACCCAGTAAATTATTTC
AAAAATTTATAAGTCATTTGGGCCATCAGTAAGTCTTTCAAGAATGATGATTAAATCCTTCGAGC
CATATGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCTG
Found at i:208572 original size:62 final size:62
Alignment explanation
Indices: 208422--208819 Score: 432
Period size: 61 Copynumber: 6.5 Consensus size: 62
208412 TTTGTTATTC
* *
208422 TTGACTTCCTTGTGAAGAGAAATCAACCTTTGTTATTTCTGACT--CCAGTAGAGTCAATCT
1 TTGACTTTCTTGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAGTAGAGTCAATCT
* * * * * **
208482 TTAACTTCCTTGTGAAGAGAAGTGAACCTTTATTATTCCTGACTCCCCAGTAGAGTCAATGA
1 TTGACTTTCTTGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAGTAGAGTCAATCT
* *
208544 TTGACTTTCTTGTGAAGATAAGTCAACCTTTGTTATTTCTGACTCCCCAGTAGAGTCAATAT
1 TTGACTTTCTTGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAGTAGAGTCAATCT
* * * * * *
208606 TTGAC-TTCTTAATGAAGAGAAGCCAACTTTTGTTATTT-TGACTCCTCAGTAGAGTTATTCT
1 TTGACTTTCTT-GTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAGTAGAGTCAATCT
* * * * * * *
208667 TTGACTTTCTTGTGAAAAGAAATTAACCTTTATTATTCCTGAC-GCCCAGTAGAGTCAATCC
1 TTGACTTTCTTGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAGTAGAGTCAATCT
* * * * * *
208728 TTGACTTTCTCGTGAAAAGAAGTCAACTTTTGTTATTTCTGACTCCTC-GTAGAGTTAATTT
1 TTGACTTTCTTGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAGTAGAGTCAATCT
* *
208789 TTGACTTCCTCGTGAAGATG-AGTCAATCCTT
1 TTGACTTTCTTGTGAAGA-GAAGTCAA-CCTT
208820 GACTTCCTCG
Statistics
Matches: 280, Mismatches: 50, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
60 39 0.14
61 130 0.46
62 111 0.40
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (62 bp):
TTGACTTTCTTGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAGTAGAGTCAATCT
Found at i:208878 original size:90 final size:90
Alignment explanation
Indices: 208718--208894 Score: 243
Period size: 90 Copynumber: 2.0 Consensus size: 90
208708 ACGCCCAGTA
* * **
208718 GAGTCAATCCTTGACTTTCTCGTGAAAAGAAGTCAACTTTTGTTATTTCTGACTCCTCGTAGAGT
1 GAGTCAATCCTTGACTTCCTCGTGAAAAGAAGTCAACTTTTATTATCCCTGACTCCTCGTAGAGT
*
208783 TAATTTTTGACTTCCTCGTGAAGAT
66 TAATTTTTGACTTCCTCATGAAGAT
* *
208808 GAGTCAATCCTTGACTTCCTCGTGAATAGAAGTCAA-TATTTATTATCCCTGATTCC-CAGTAGA
1 GAGTCAATCCTTGACTTCCTCGTGAAAAGAAGTCAACT-TTTATTATCCCTGACTCCTC-GTAGA
208871 -TTCAATTTTTGACTTCCTCATGAA
64 GTT-AATTTTTGACTTCCTCATGAA
208895 AAGAAATCTA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
89 4 0.05
90 73 0.95
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (90 bp):
GAGTCAATCCTTGACTTCCTCGTGAAAAGAAGTCAACTTTTATTATCCCTGACTCCTCGTAGAGT
TAATTTTTGACTTCCTCATGAAGAT
Found at i:209166 original size:55 final size:55
Alignment explanation
Indices: 209104--209237 Score: 178
Period size: 55 Copynumber: 2.4 Consensus size: 55
209094 GGTCTTCATG
* * *
209104 CCCTGAAAGAAGAGTGGAGAAGACCCGTCTTCAAAAGATTTCTCGAGTATTATCT
1 CCCTGAAAGAAGAGTGGAGTAGACCAGTCTTCAAAAGATTTCTCAAGTATTATCT
* * * * * *
209159 CCTTGAAAGAAGAGTGGAGTATACCAGTTTTCCAAAGATTTCTCAATTCTTATCT
1 CCCTGAAAGAAGAGTGGAGTAGACCAGTCTTCAAAAGATTTCTCAAGTATTATCT
*
209214 CCCTGAAAGAAGACTGGAGTAGAC
1 CCCTGAAAGAAGAGTGGAGTAGAC
209238 TCATTTTCCA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (55 bp):
CCCTGAAAGAAGAGTGGAGTAGACCAGTCTTCAAAAGATTTCTCAAGTATTATCT
Found at i:209302 original size:82 final size:81
Alignment explanation
Indices: 209201--209385 Score: 237
Period size: 82 Copynumber: 2.3 Consensus size: 81
209191 CAAAGATTTC
* * * * *
209201 TCAATTCTTATCTCCCTGAAAGAAGACTGGAGTAG-ACTCATTTTCCAAAATTGATCTGACTACC
1 TCAAGTCTGATCTCCCTGAAAGAAGACTGGAGCAGAAC-CATCTTCAAAAATTGATCTGACTACC
*
209265 AGAAAAAGAGGAACATA
65 AGAAAAAGAGGAACAAA
* * *
209282 TCAAGTCTGATCTCCACTGAAAGAAGAGTGGAGCAGAACCGTCTTCAAAAATTGATCTGACTACT
1 TCAAGTCTGATCTCC-CTGAAAGAAGACTGGAGCAGAACCATCTTCAAAAATTGATCTGACTACC
209347 AGAAAAAGAGGAACAAA
65 AGAAAAAGAGGAACAAA
* *
209364 TAAAGTCCGATCTACCCTGAAA
1 TCAAGTCTGATCT-CCCTGAAA
209386 TAGTAGTGGA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
81 13 0.14
82 73 0.81
83 4 0.04
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (81 bp):
TCAAGTCTGATCTCCCTGAAAGAAGACTGGAGCAGAACCATCTTCAAAAATTGATCTGACTACCA
GAAAAAGAGGAACAAA
Found at i:209529 original size:3 final size:3
Alignment explanation
Indices: 209521--209549 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
209511 TTTATTCATA
209521 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
209550 AATAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:211435 original size:17 final size:16
Alignment explanation
Indices: 211406--211447 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
211396 CAAACACATC
211406 AATT-TTTTATCTTTTAA
1 AATTATTTTATC--TTAA
211423 AATTATTTT-TCTTAA
1 AATTATTTTATCTTAA
211438 AATTATTTTA
1 AATTATTTTA
211448 AAAGGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTATTTTATCTTAA
Found at i:212290 original size:36 final size:36
Alignment explanation
Indices: 212241--212329 Score: 151
Period size: 36 Copynumber: 2.4 Consensus size: 36
212231 TATCTGGCCT
* *
212241 ATGGAAAAAATGCACTTAGGAAAGTGAATTTGAAGGA
1 ATGG-AAAAATGCACTTAGGAAAGTGAATATAAAGGA
212278 ATGGAAAAATGCACTTAGGAAAGTGAATATAAAGGA
1 ATGGAAAAATGCACTTAGGAAAGTGAATATAAAGGA
212314 ATGGAAAAATGCACTT
1 ATGGAAAAATGCACTT
212330 GCATAAGGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 46 0.92
37 4 0.08
ACGTcount: A:0.47, C:0.07, G:0.25, T:0.21
Consensus pattern (36 bp):
ATGGAAAAATGCACTTAGGAAAGTGAATATAAAGGA
Found at i:221560 original size:168 final size:167
Alignment explanation
Indices: 221343--221678 Score: 622
Period size: 168 Copynumber: 2.0 Consensus size: 167
221333 CCTGTTTCAA
221343 TTTTCTCTCTGGTATCTATCATACGTATTGCAATAGCTATCTGATATAGTCATTATCTAAGAACT
1 TTTTCTCTCTGGTATCTATCATACGTATTGCAATAGCTATCTGATATAGTCATTATCTAAGAACT
221408 TCTATGGAATTTATTTGTTGTGTAACTTATGTATTTTATCC-GTGTATGCGTCAATGGGTATTGG
66 TCTATGGAATTTATTTGTTGTGTAACTTATGTATTTTATCCGGTGTATGCGTCAATGGGTATTGG
221472 ATCTCTTTG-TCATTGATTTAGGTGCTAGGCTTTACT
131 ATCTCTTTGTTCATTGATTTAGGTGCTAGGCTTTACT
221508 TTTTCTCTCTGGTATCTATCATTGACGTATATGCAATAGCTATCTGATATAGTCATTATCTAAGA
1 TTTTCTCTCTGGTATCTATCA-T-ACGTAT-TGCAATAGCTATCTGATATAGTCATTATCTAAGA
221573 ACTTCTATGGAATTTATTTGTTGTGTAACTTATGTATTTTATCCGTGTGTATGCGTCAATGGGTA
63 ACTTCTATGGAATTTATTTGTTGTGTAACTTATGTATTTTATCCG-GTGTATGCGTCAATGGGTA
221638 TTGGATCTCTTTGTTCATTGATTTAGGTGCTAGGCTTTACT
127 TTGGATCTCTTTGTTCATTGATTTAGGTGCTAGGCTTTACT
221679 AAAATCATCT
Statistics
Matches: 165, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
165 21 0.13
166 1 0.01
167 6 0.04
168 78 0.47
170 32 0.19
171 27 0.16
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (167 bp):
TTTTCTCTCTGGTATCTATCATACGTATTGCAATAGCTATCTGATATAGTCATTATCTAAGAACT
TCTATGGAATTTATTTGTTGTGTAACTTATGTATTTTATCCGGTGTATGCGTCAATGGGTATTGG
ATCTCTTTGTTCATTGATTTAGGTGCTAGGCTTTACT
Found at i:223429 original size:20 final size:20
Alignment explanation
Indices: 223393--223430 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
223383 ATCCTATTCC
**
223393 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
223413 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
223431 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:224092 original size:2 final size:2
Alignment explanation
Indices: 224080--224111 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
224070 TTGTATGAAT
224080 TA TA T- 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 T
224112 TAGAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:224724 original size:14 final size:14
Alignment explanation
Indices: 224705--224736 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
224695 CGTTCGTGAA
224705 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
224719 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
224733 CGTT
1 CGTT
224737 TATGTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:224753 original size:24 final size:24
Alignment explanation
Indices: 224706--224756 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
224696 GTTCGTGAAC
* *
224706 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
224730 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
224754 GTT
1 GTT
224757 TAACCCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:225849 original size:16 final size:16
Alignment explanation
Indices: 225827--225883 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
225817 GGCCTCCAAT
225827 GTTTATGTTTGTGTTC
1 GTTTATGTTTGTGTTC
* *
225843 ATTTATGTTCGTGTTC
1 GTTTATGTTTGTGTTC
225859 GTTTATGTTTGTGTTC
1 GTTTATGTTTGTGTTC
225875 GTTTATGTT
1 GTTTATGTT
225884 CGTTTATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.09, C:0.07, G:0.23, T:0.61
Consensus pattern (16 bp):
GTTTATGTTTGTGTTC
Found at i:226295 original size:19 final size:19
Alignment explanation
Indices: 226271--226311 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
226261 GGTTGTGTTG
226271 GCTCAGCCTTCACCCCTCT
1 GCTCAGCCTTCACCCCTCT
226290 GCTCAGCCTTCACCCCTCT
1 GCTCAGCCTTCACCCCTCT
226309 GCT
1 GCT
226312 TACCTATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.51, G:0.12, T:0.27
Consensus pattern (19 bp):
GCTCAGCCTTCACCCCTCT
Found at i:230015 original size:25 final size:28
Alignment explanation
Indices: 229964--230015 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 28
229954 TCATGAATAG
**
229964 TTTAAAATTTAATATATTATTTTTAATT
1 TTTAAAATTTAATATATTATTAATAATT
229992 TTTAAAATTT-A-A-ATTATTAATAAT
1 TTTAAAATTTAATATATTATTAATAAT
230016 ATTAATGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 1 0.05
28 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTAAAATTTAATATATTATTAATAATT
Found at i:235581 original size:7 final size:7
Alignment explanation
Indices: 235569--235594 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
235559 TATGAGTAAT
235569 ATATTAA
1 ATATTAA
235576 ATATTAA
1 ATATTAA
235583 ATATTAA
1 ATATTAA
235590 ATATT
1 ATATT
235595 TTTAGTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATTAA
Done.