Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000582.1 Hibiscus syriacus cultivar Beakdansim tig00001137_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: 52774
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:2499 original size:19 final size:19
Alignment explanation
Indices: 2477--2520 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2467 CGACTATTAC
*
2477 GATGAGTTATAACTAGGAT
1 GATGACTTATAACTAGGAT
2496 GATGACTTATAACTAGGAT
1 GATGACTTATAACTAGGAT
2515 GATGAC
1 GATGAC
2521 AAGGACTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (19 bp):
GATGACTTATAACTAGGAT
Found at i:3975 original size:27 final size:25
Alignment explanation
Indices: 3910--3984 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 25
3900 TTTTTATTTT
*
3910 TTTTAT-TAATT-ATATATATAATA
1 TTTTATATAATTAATATATAAAATA
* **
3933 TTTTATAAAACAAATATATAAAATA
1 TTTTATATAATTAATATATAAAATA
*
3958 TTATATATATAATTAATATAAAAAATA
1 TT-T-TATATAATTAATATATAAAATA
3985 AAAAAGTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 13 0.32
26 1 0.03
27 18 0.45
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTATATAATTAATATATAAAATA
Found at i:3995 original size:35 final size:39
Alignment explanation
Indices: 3918--4005 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 39
3908 TTTTTTATTA
**
3918 ATTATATATATAATATTTTATAAAACAAATATATAAAAT
1 ATTATATATATAATATAATATAAAACAAATATATAAAAT
3957 ATTATATATATAAT-TAATAT-AAA-AAATA-A-AAAAGT
1 ATTATATATATAATATAATATAAAACAAATATATAAAA-T
3992 ATTATATATATAAT
1 ATTATATATATAAT
4006 CGGGGCGGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 4 0.09
35 16 0.35
36 5 0.11
37 3 0.07
38 4 0.09
39 14 0.30
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (39 bp):
ATTATATATATAATATAATATAAAACAAATATATAAAAT
Found at i:7040 original size:22 final size:24
Alignment explanation
Indices: 7013--7078 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 24
7003 AACGATCAAA
7013 AAAACGTGTCA-AAAGACAGAAG-
1 AAAACGTGTCATAAAGACAGAAGT
*
7035 AAAACGTGTCATAAAGGCA-AAGT
1 AAAACGTGTCATAAAGACAGAAGT
* *
7058 AAAACGTCTCATACAGACAGA
1 AAAACGTGTCATAAAGACAGA
7079 CTTATTGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.38
23 22 0.59
24 1 0.03
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.14
Consensus pattern (24 bp):
AAAACGTGTCATAAAGACAGAAGT
Found at i:12855 original size:302 final size:300
Alignment explanation
Indices: 12311--12858 Score: 868
Period size: 302 Copynumber: 1.8 Consensus size: 300
12301 GCTTGAGGTG
* **
12311 TTAATTGTGCATGAATCCATATGTTGCGACACTTGTTAGGGTATTTTTTAATATATATATTGATG
1 TTAATTGTGCATGAATCCATATATTGCGACACTTGTTAGGGTATTTTAAAATATATATATTGATG
* *
12376 ATATATTTTAGTACAGTTTAGGTTAAGATATATAAATAATCATTCAATTATATTAAAATAATATT
66 ATATATTTTAGTACAATTTAGGTTAAGATATATAAATAATCATTAAATTATATTAAAATAATATT
* * * * * *
12441 TTTTATTATTAAAATTTAAAAATTATAAAATGATTATTAAAATTATTAAATTGTTATAGAATATT
131 TATTATCACTAAAATTTAAAAATTACAAAATGATTATTAAAATTATTAAATTGCTATAAAATATT
*
12506 CCTCGCATATTATAAAATAATAATAAATTCAAAGATAATTCTTAATAATTTTAAATTTAACAAAT
196 CCTCGCATATTATAAAATAATAATAAATTCAAAAATAATTCTTAATAATTTTAAATTTAACAAAT
12571 ATTTTATAACAATTAAATAAATTTAGAAAAAGATATATTT
261 ATTTTATAACAATTAAATAAATTTAGAAAAAGATATATTT
* *
12611 TTAATTGTGCAT-ATATCGATATATTGCGACACTTTTTAGGGTATTTTAAAATATATATATATTG
1 TTAATTGTGCATGA-ATCCATATATTGCGACACTTGTTAGGGTATTTT-AAA-ATATATATATTG
*
12675 ATGATATATTTTAGTACAATTTAGGTTGAA-ATATATAAATAATTATTAAATTATATTAAAATAA
63 ATGATATATTTTAGTACAATTTAGGTT-AAGATATATAAATAATCATTAAATTATATTAAAATAA
*
12739 TATTTATTATCACTAAAATTTAAAAATTACAAAATGATTATTAAATTTATTAAATTGCTATAAAA
127 TATTTATTATCACTAAAATTTAAAAATTACAAAATGATTATTAAAATTATTAAATTGCTATAAAA
* *
12804 TATTCCTCGCATATTATAAAATAATAATAAATTTTAAAAAT-ATTTTTAATAATTT
192 TATTCCTCGCATATTATAAAATAATAATAAA-TTCAAAAATAATTCTTAATAATTT
12859 AATCAATTTT
Statistics
Matches: 225, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
299 1 0.00
300 42 0.19
301 1 0.00
302 172 0.76
303 9 0.04
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (300 bp):
TTAATTGTGCATGAATCCATATATTGCGACACTTGTTAGGGTATTTTAAAATATATATATTGATG
ATATATTTTAGTACAATTTAGGTTAAGATATATAAATAATCATTAAATTATATTAAAATAATATT
TATTATCACTAAAATTTAAAAATTACAAAATGATTATTAAAATTATTAAATTGCTATAAAATATT
CCTCGCATATTATAAAATAATAATAAATTCAAAAATAATTCTTAATAATTTTAAATTTAACAAAT
ATTTTATAACAATTAAATAAATTTAGAAAAAGATATATTT
Found at i:13561 original size:27 final size:29
Alignment explanation
Indices: 13521--13576 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
13511 TGTCTTCCAG
*
13521 ATTTTGTATTATTATA-TTTTTTATTGGA
1 ATTTTGTAATATTATATTTTTTTATTGGA
13549 ATTTT-TAATATTATATTTTTTTATTGGA
1 ATTTTGTAATATTATATTTTTTTATTGGA
13577 TAAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (29 bp):
ATTTTGTAATATTATATTTTTTTATTGGA
Found at i:16097 original size:84 final size:82
Alignment explanation
Indices: 15907--16488 Score: 674
Period size: 84 Copynumber: 7.1 Consensus size: 82
15897 ACCTGCCACC
* * * * *
15907 AAGACCTTCTAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCTAG
* *
15972 AAGAGCTATCTG--CCA
66 AAGGGTTATCTGTACCA
* * * * * * * *
15987 AAGAACCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCT
1 AAG-ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTACAGCATAACTTAAGTCT
*
16051 AGAAGGGTTATCTGTTAGCA
64 AGAAGGGTTATCTG-TACCA
* * * * *
16071 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCTAG
*
16136 AAGGGCTATCTG--CCA
66 AAGGGTTATCTGTACCA
* * * * * * *
16151 AAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCTA
16216 GAAGGGTTATCTGTCACCA
65 GAAGGGTTATCTGT-ACCA
* *
16235 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCTAG
*
16300 AAGGGTTATCTGCCAACCA
66 AAGGGTTATCTG--TACCA
* * *
16319 AAGACCTTCGAGTTCGACTACGCTCAGCCCCAAGGCACATCATTTACAGCATAACTCAAGGCTAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCTAG
16384 AAGGGTTATCTGTCACCCA
66 AAGGGTTATCTGT-A-CCA
* * * *
16403 AAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCTAG
*
16468 AAGGGCTATCTG--CCA
66 AAGGGTTATCTGTACCA
16483 AAGACC
1 AAGACC
16489 CCCGGGTTCG
Statistics
Matches: 424, Mismatches: 64, Indels: 28
0.82 0.12 0.05
Matches are distributed among these distances:
80 59 0.14
81 78 0.18
83 85 0.20
84 202 0.48
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (82 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCTAG
AAGGGTTATCTGTACCA
Found at i:16149 original size:164 final size:164
Alignment explanation
Indices: 15863--16563 Score: 911
Period size: 164 Copynumber: 4.3 Consensus size: 164
15853 TTTGCAAACG
* * * * * * * *
15863 ATCATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTACCTGCCACC-AAGACCTTCTAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
* *
15927 CGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAA
** *
15992 CCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
131 CCTCGAGTTCGACTACACTCAGCTTCAAGGGCAT
* * * *
16026 AACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
* *
16091 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAA
** *
16156 CCTCGAGTTCGACTACGTTCAGCTTCGAGGGCAT
131 CCTCGAGTTCGACTACACTCAGCTTCAAGGGCAT
16190 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
* * * * * * *
16255 CGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGTTATCTGCCAACCAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA--AG
* ** *
16320 AGACCTTCGAGTTCGACTACGCTCAGCCCCAA-GGCAC
129 A-ACC-TCGAGTTCGACTACACTCAGCTTCAAGGGCAT
16357 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCCAAAGACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA-CCAAAGACCTTCGAGTTCGACT
* *
16422 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGA
65 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * * * * * *
16487 CCCCCGGGTTCGATTACACTCAACTTCGAGGTCAT
130 ACCTCGAGTTCGACTACACTCAGCTTCAAGGGCAT
* * * * * *
16522 ATTATTTACAACATAGCTCAAGGCAAGAAGGGCTATTTGTCA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
16564 ATAAAATTGT
Statistics
Matches: 467, Mismatches: 64, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
163 34 0.07
164 241 0.52
165 41 0.09
166 4 0.01
167 48 0.10
168 99 0.21
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAA
CCTCGAGTTCGACTACACTCAGCTTCAAGGGCAT
Found at i:16516 original size:332 final size:327
Alignment explanation
Indices: 15863--16563 Score: 972
Period size: 332 Copynumber: 2.1 Consensus size: 327
15853 TTTGCAAACG
* * * * * *
15863 ATCATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTACCTGCCACCAAGACCTTCTAGTTCGACTAC
1 ATCATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCACCAAGACCTTCGAGTTCGACTAC
* * * * *
15928 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAAC
66 GCTCAGCTCCAAGGCACATCATTTACAGCACAACTTAAGTCGAGAAGAGCTATCTGCCAAAAAAC
* ** *
15993 CTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGG
131 CTTAAGTTCGACTACACTCAGCCCCAAGGGCACAACATTTACAGCATAACTCAAGGCTAGAAGGG
* * *
16058 TTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAAT
196 TTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAAT
* * ** *
16123 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGGGC
261 AGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAACTTCGAGGGC
16188 AT
326 AT
* * *
16190 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
1 ATCATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCACC-AAGACCTTCGAGTTCGACTA
* * * *
16255 CGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGTTATCTGCCAACCAA
65 CGCTCAGCTCCAAGGCACATCATTTACAGCACAACTTAAGTCGAGAAGAGCTATCTGCCAA--AA
* * *
16320 AGACCTTCGAGTTCGACTACGCTCAGCCCCAA-GGCACATCATTTACAGCATAACTCAAGGCTAG
128 A-ACCTT-AAGTTCGACTACACTCAGCCCCAAGGGCACAACATTTACAGCATAACTCAAGGCTAG
*
16384 AAGGGTTATCTGTCACCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTG
191 AAGGGTTATCTGTCA-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* * *
16449 CAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGGGTTCGATTACACTCAACTTC
255 CAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAACTTC
*
16514 GAGGTCAT
320 GAGGGCAT
* * *
16522 ATTATTTACAACATAGCTCAAGGCAAGAAGGGCTATTTGTCA
1 ATCATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCA
16564 ATAAAATTGT
Statistics
Matches: 325, Mismatches: 43, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
327 37 0.11
328 72 0.22
330 2 0.01
331 49 0.15
332 165 0.51
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (327 bp):
ATCATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCACCAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTACAGCACAACTTAAGTCGAGAAGAGCTATCTGCCAAAAAAC
CTTAAGTTCGACTACACTCAGCCCCAAGGGCACAACATTTACAGCATAACTCAAGGCTAGAAGGG
TTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAAT
AGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAACTTCGAGGGC
AT
Found at i:17162 original size:39 final size:35
Alignment explanation
Indices: 17108--17294 Score: 153
Period size: 39 Copynumber: 5.0 Consensus size: 35
17098 TATACATATA
* *
17108 TATATATTATATAGTTTGCAAACGATCTTTGAAAATAC
1 TATATAATATATAGTTTGAAAAC-ATCTTTG-AAA-AC
* *
17146 GTATATAATATATAGTTTTTAAAACATTTTTGAAAAC
1 -TATATAATATATAG-TTTGAAAACATCTTTGAAAAC
* * *
17183 TATATAATATATAGTTTAAAAAAAACGTTTTAGAAAA-
1 TATATAATATATAGTTTGAAAACATC--TTT-GAAAAC
* *
17220 TATAGATAATATATAGTTTTTAAAATCATTTTTGAAAAC
1 TAT--ATAATATATAG-TTTGAAAA-CATCTTTGAAAAC
17259 TTATATAATATATAGTTTTGAAAACAT-TTTGAAAAC
1 -TATATAATATATAG-TTTGAAAACATCTTTGAAAAC
17295 ATTTATATGT
Statistics
Matches: 125, Mismatches: 13, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
35 8 0.06
36 23 0.18
37 11 0.09
38 32 0.26
39 33 0.26
40 17 0.14
41 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.41
Consensus pattern (35 bp):
TATATAATATATAGTTTGAAAACATCTTTGAAAAC
Found at i:17290 original size:11 final size:11
Alignment explanation
Indices: 17274--17298 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17264 TAATATATAG
17274 TTTTGAAAACA
1 TTTTGAAAACA
17285 TTTTGAAAACA
1 TTTTGAAAACA
17296 TTT
1 TTT
17299 ATATGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:17376 original size:25 final size:26
Alignment explanation
Indices: 17327--17376 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
17317 AAAAAAAAAC
*
17327 ATTTTTGAAAATATATATAATATATA
1 ATTTTTGAAAATATATATAAAATATA
* *
17353 ATTTTT-AAAATATTTTTAAAATAT
1 ATTTTTGAAAATATATATAAAATAT
17377 GTATATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTTTGAAAATATATATAAAATATA
Found at i:17423 original size:38 final size:38
Alignment explanation
Indices: 17135--17419 Score: 244
Period size: 38 Copynumber: 7.4 Consensus size: 38
17125 GCAAACGATC
*
17135 TTTGAAAATACGTATATAATATATAGTTTTTAAAACAT-T
1 TTTGAAAATA--TATATAATATATAGTTTTTAAAAAATAT
* ** **
17174 TTTGAAAA-CTATATAATATATAGTTTAAAAAAAACGT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAAATAT
* *
17211 TTTAGAAAATATAGATAATATATAGTTTTTAAAATCAT-T
1 TTT-GAAAATATATATAATATATAGTTTTTAAAA-AATAT
* *
17250 TTTGAAAACT-TATATAATATATAG-TTTT-GAAAACAT
1 TTTGAAAA-TATATATAATATATAGTTTTTAAAAAATAT
* ** *
17286 TTTGAAAACATTTATATGTTATATAGTTTTTAAAAAAAAACATT
1 TTTG-AAA-ATATATATAATATATAGTTTTT---AAAAAATA-T
*
17330 TTTGAAAATATATATAATATATAATTTTT--AAAATAT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAAATAT
* * *
17366 TTTTAAAATATGTATATTATATAGTTTTTAAAAAATAT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAAATAT
*
17404 TTTGAAAATTTATATA
1 TTTGAAAATATATATA
17420 TTATGTGCTT
Statistics
Matches: 199, Mismatches: 30, Indels: 35
0.75 0.11 0.13
Matches are distributed among these distances:
35 1 0.01
36 55 0.28
37 17 0.09
38 56 0.28
39 37 0.19
40 1 0.01
42 18 0.09
43 9 0.05
44 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (38 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAAAATAT
Found at i:17857 original size:26 final size:26
Alignment explanation
Indices: 17788--17859 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
17778 TCTTATATAT
**
17788 ATATATTT-TATTTATTTCTTTATTTTT
1 ATATATTTATA-TTATTT-TTTATTTAC
*
17815 ATATATTT-TATGATTTTTTA-TTAC
1 ATATATTTATATTATTTTTTATTTAC
17839 ATATATTCTATATTATTTTTT
1 ATATATT-TATATTATTTTTT
17860 TTAATTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 9 0.23
25 5 0.13
26 15 0.38
27 10 0.26
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (26 bp):
ATATATTTATATTATTTTTTATTTAC
Found at i:23016 original size:84 final size:82
Alignment explanation
Indices: 22798--23472 Score: 628
Period size: 84 Copynumber: 8.2 Consensus size: 82
22788 TGCATCTTAG
* * * *
22798 CTCAAGGCCAGAAGGGCTACCTGCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTG-TACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * *
22862 ACATCATTTGCAGTATAG
65 ACATCATTTACAGCATAA
* * * * * * * * *
22880 CTTAAGTCGAGAAGAGCTATCTG--CCAAAGAACCTT-AAGTTCGATTACACTCAGCTTCAAGGG
1 CTCAAGGCTAGAAGGGTTATCTGTACCAAAG-ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GG
* *
22942 CATAACATTTACAGCATAA
64 CACATCATTTACAGCATAA
* *
22961 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTG-TACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * *
23026 ACATCATTTGCAGAATAG
65 ACATCATTTACAGCATAA
* * * * * * * *
23044 CTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGGGC
1 CTCAAGGCTAGAAGGGTTATCTGTACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGC
*
23107 ATATCATTTACAGCATAA
65 ACATCATTTACAGCATAA
23125 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGT-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * *
23190 ATATCATTTGCAGCACAA
65 ACATCATTTACAGCATAA
* * * * *
23208 CTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCCCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTG--TACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
23273 CACATCATTTACAACATAA
64 CACATCATTTACAGCATAA
* * *
23292 CTCAAGGCTAGAAGGGTTATATGTCACCCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCTAAGG
1 CTCAAGGCTAGAAGGGTTATCTGT-A-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
** *
23357 CACATCATTTGTAGCATAG
64 CACATCATTTACAGCATAA
* * * * ** * * * * * *
23376 CTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCCCCGGGTTCGATTACACTCAACTTCGAGGTC
1 CTCAAGGCTAGAAGGGTTATCTGTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG-C
* * *
23439 ATATCATTTACAACATAG
65 ACATCATTTACAGCATAA
*
23457 CTCAAGGCAAGAAGGG
1 CTCAAGGCTAGAAGGG
23473 CTATTTGTCA
Statistics
Matches: 481, Mismatches: 96, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
79 2 0.00
80 78 0.16
81 106 0.22
82 18 0.04
83 84 0.17
84 193 0.40
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (82 bp):
CTCAAGGCTAGAAGGGTTATCTGTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
CATCATTTACAGCATAA
Found at i:23068 original size:164 final size:164
Alignment explanation
Indices: 22798--23482 Score: 897
Period size: 164 Copynumber: 4.2 Consensus size: 164
22788 TGCATCTTAG
* * * *
22798 CTCAAGGCCAGAAGGGCTACCTGCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * ** *
22862 ACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAACCTTAAGTTCGATTAC
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAACCTCGAGTTCGACTAC
* *
22927 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATATCATTTACAACATAA
* * *
22961 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* *
23026 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAACCTCGAGTTCGACTAC
** * *
23091 GTTCAGCTTCGAGGGCATATCATTTACAGCATAA
131 ACTCAGCTTCAAGGGCATATCATTTACAACATAA
23125 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * * * *
23190 ATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGA
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA--AGA-ACC-TCGAGTTCGA
* ** *
23255 CTACGCTCAGCCCCAA-GGCACATCATTTACAACATAA
127 CTACACTCAGCTTCAAGGGCATATCATTTACAACATAA
* * *
23292 CTCAAGGCTAGAAGGGTTATATGTCACCCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCTAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTCA-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * * * *
23357 CACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGGGTTCGATTA
65 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAACCTCGAGTTCGACTA
* * * *
23422 CACTCAACTTCGAGGTCATATCATTTACAACATAG
130 CACTCAGCTTCAAGGGCATATCATTTACAACATAA
* * *
23457 CTCAAGGCAAGAAGGGCTATTTGTCA
1 CTCAAGGCTAGAAGGGTTATCTGTCA
23483 ATAAAATTGT
Statistics
Matches: 454, Mismatches: 61, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
163 22 0.05
164 242 0.53
165 43 0.09
166 4 0.01
167 46 0.10
168 97 0.21
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (164 bp):
CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAACCTCGAGTTCGACTAC
ACTCAGCTTCAAGGGCATATCATTTACAACATAA
Found at i:23435 original size:332 final size:327
Alignment explanation
Indices: 22798--23482 Score: 949
Period size: 332 Copynumber: 2.1 Consensus size: 327
22788 TGCATCTTAG
* * *
22798 CTCAAGGCCAGAAGGGCTACCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
1 CTCAAGGCAAGAAGGGCTATCTGTCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
* * * * *
22863 CATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAACCTTAAGTTCGATTACA
66 CATCATTTGCAGCACAACTTAAGTCGAGAAGAGCTATCTGCCAAAAAACCTTAAGTTCGACTACA
** * * * * *
22928 CTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAG
131 CTCAGCCCCAAGGGCACAACATTTACAACATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAG
*
22993 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAG
196 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAG
* ** * *
23058 GGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGGGCATATCATTTACAGCAT
261 GGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAACTTCGAGGGCATATCATTTACAACAT
23123 AA
326 AA
* *
23125 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCAAGAAGGGCTATCTGTCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * * *
23190 ATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGA
65 ACATCATTTGCAGCACAACTTAAGTCGAGAAGAGCTATCTGCCAA--AAA-ACCTT-AAGTTCGA
* *
23255 CTACGCTCAGCCCCAA-GGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATATGTCAC
126 CTACACTCAGCCCCAAGGGCACAACATTTACAACATAACTCAAGGCTAGAAGGGTTATATGTCA-
* * * *
23319 CCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGTAGCATAGCTTAAGTC
190 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTC
* * *
23384 GAGAAGGGCTATCTGCCAAAGACCCCCGGGTTCGATTACACTCAACTTCGAGGTCATATCATTTA
255 GAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAACTTCGAGGGCATATCATTTA
*
23449 CAACATAG
320 CAACATAA
*
23457 CTCAAGGCAAGAAGGGCTATTTGTCA
1 CTCAAGGCAAGAAGGGCTATCTGTCA
23483 ATAAAATTGT
Statistics
Matches: 311, Mismatches: 41, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
327 24 0.08
328 74 0.24
330 2 0.01
331 47 0.15
332 164 0.53
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (327 bp):
CTCAAGGCAAGAAGGGCTATCTGTCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
CATCATTTGCAGCACAACTTAAGTCGAGAAGAGCTATCTGCCAAAAAACCTTAAGTTCGACTACA
CTCAGCCCCAAGGGCACAACATTTACAACATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAG
GGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAACTTCGAGGGCATATCATTTACAACAT
AA
Found at i:24081 original size:40 final size:36
Alignment explanation
Indices: 24025--24205 Score: 125
Period size: 38 Copynumber: 4.7 Consensus size: 36
24015 TTTATACATA
* *
24025 TATATATATTATATAGTTTGCAAACGATCTTTGAAAATAC
1 TATATA-AATATATAGTTTGAAAAC-ATCTTTG-AAA-AC
* *
24065 GTATATAAATATATAGTTTTTAAAACATTTTTGAAAAC
1 -TATATAAATATATAG-TTTGAAAACATCTTTGAAAAC
* * *
24103 TATAT-AATATATAGTTTAAAAAAAACGTTTTAGAAAA-
1 TATATAAATATATAGTTTGAAAACATC--TTT-GAAAAC
* * *
24140 TATAGATAATATATAGTTTTTAAAATCATTTTTGAAAAC
1 TATATA-AATATATAG-TTTGAAAA-CATCTTTGAAAAC
24179 T-TATATAATATATAGTTTTGAAAACAT
1 TATATA-AATATATAG-TTTGAAAACAT
24206 TTATATGTTA
Statistics
Matches: 116, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
35 8 0.07
36 9 0.08
37 15 0.13
38 33 0.28
39 16 0.14
40 21 0.18
41 14 0.12
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (36 bp):
TATATAAATATATAGTTTGAAAACATCTTTGAAAAC
Found at i:24128 original size:38 final size:37
Alignment explanation
Indices: 24066--24317 Score: 140
Period size: 38 Copynumber: 7.0 Consensus size: 37
24056 TGAAAATACG
**
24066 TATATAAATATATAGTTT-TTAAAACATTTTTGAAAAC
1 TATAT-AATATATAGTTTAAAAAAACATTTTTGAAAAC
* *
24103 TATATAATATATAGTTTAAAAAAAACGTTTTAGAAAA-
1 TATATAATATATAGTTT-AAAAAAACATTTTTGAAAAC
** *
24140 TATAGATAATATATAGTTTTTAAAATCATTTTTGAAAAC
1 TAT--ATAATATATAGTTTAAAAAAACATTTTTGAAAAC
**
24179 TTATATAATATATAGTTT-TGAAAACA--TTT----A-
1 -TATATAATATATAGTTTAAAAAAACATTTTTGAAAAC
* *
24209 TATGT--TATATAGTTTTAAAAAAACATTTTTGAAAATA
1 TATATAATATATAG-TTTAAAAAAACATTTTTGAAAA-C
* ** *
24246 TATATAATATATAATTT-TTAAAATATTTTT-AAAA-
1 TATATAATATATAGTTTAAAAAAACATTTTTGAAAAC
* **
24280 TACGTATATTATATAGTTTTTAAAAA-ATATTTTGAAAA
1 TA--TATAATATATAGTTTAAAAAAACAT-TTTTGAAAA
24318 TTTATATATT
Statistics
Matches: 170, Mismatches: 22, Indels: 45
0.72 0.09 0.19
Matches are distributed among these distances:
27 7 0.04
28 3 0.02
29 10 0.06
31 4 0.02
34 2 0.01
35 4 0.02
36 31 0.18
37 37 0.22
38 49 0.29
39 20 0.12
40 3 0.02
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTAAAAAAACATTTTTGAAAAC
Found at i:24203 original size:25 final size:26
Alignment explanation
Indices: 24169--24229 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
24159 TTAAAATCAT
24169 TTTTGAAAAC-TTATATAATATATAG
1 TTTTGAAAACATTATATAATATATAG
**
24194 TTTTGAAAACATTTATATGTTATATAG
1 TTTTGAAAACA-TTATATAATATATAG
*
24221 TTTTAAAAA
1 TTTTGAAAA
24230 AACATTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 10 0.32
27 21 0.68
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTTGAAAACATTATATAATATATAG
Found at i:24218 original size:104 final size:102
Alignment explanation
Indices: 24110--24304 Score: 284
Period size: 104 Copynumber: 1.9 Consensus size: 102
24100 AACTATATAA
* * *
24110 TATATAGTTTAAAAAAAACGTTTTAGAAAATATAGATAATATATAGTTTTTAAAATCATTTTTGA
1 TATATAGTTTAAAAAAAACATTTTAGAAAATATAGATAATATATAATTTTTAAAAT-ATTTTTAA
*
24175 AA-ACTTATATAATATATAGTTTTGAAAACATTTATATGT
65 AATACGTATAT--TATATAGTTTTGAAAACATTTATATGT
* * *
24214 TATATAGTTTTAAAAAAACATTTTTGAAAATATATATAATATATAATTTTTAAAATATTTTTAAA
1 TATATAGTTTAAAAAAAACATTTTAGAAAATATAGATAATATATAATTTTTAAAATATTTTTAAA
*
24279 ATACGTATATTATATAGTTTTTAAAA
66 ATACGTATATTATATAGTTTTGAAAA
24305 AATATTTTGA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
102 15 0.18
103 9 0.11
104 58 0.71
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (102 bp):
TATATAGTTTAAAAAAAACATTTTAGAAAATATAGATAATATATAATTTTTAAAATATTTTTAAA
ATACGTATATTATATAGTTTTGAAAACATTTATATGT
Found at i:24252 original size:66 final size:65
Alignment explanation
Indices: 24149--24273 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 65
24139 ATATAGATAA
* * *
24149 TATATAGTTTTTAAAATCATTTTTGAAAACTTATATAATATATAGTTTTGAAAACATTTATATGT
1 TATATAGTTTTAAAAAACATTTTTGAAAACTTATATAATATATAATTTTGAAAACATTTATATGT
* *
24214 TATATAGTTTTAAAAAAACATTTTTGAAAA-TATATATAATATATAATTTTTAAAATATTT
1 TATATAGTTTT-AAAAAACATTTTTGAAAACT-TATATAATATATAATTTTGAAAACATTT
24274 TTAAAATACG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 12 0.23
66 41 0.77
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (65 bp):
TATATAGTTTTAAAAAACATTTTTGAAAACTTATATAATATATAATTTTGAAAACATTTATATGT
Found at i:24318 original size:38 final size:38
Alignment explanation
Indices: 24208--24329 Score: 131
Period size: 36 Copynumber: 3.2 Consensus size: 38
24198 GAAAACATTT
* * * *
24208 ATATGTTATATAGTTTTAAAAAAACATTTTTGAAAATAT
1 ATATATTATATAGTTTTTAAAAAATA-TTTTGAAAATAC
* * *
24247 ATATAATATATAATTTTT--AAAATATTTTTAAAATAC
1 ATATATTATATAGTTTTTAAAAAATATTTTGAAAATAC
* **
24283 GTATATTATATAGTTTTTAAAAAATATTTTGAAAATTT
1 ATATATTATATAGTTTTTAAAAAATATTTTGAAAATAC
24321 ATATATTAT
1 ATATATTAT
24330 GTGCTTTTGT
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
36 25 0.37
37 5 0.07
38 23 0.34
39 14 0.21
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (38 bp):
ATATATTATATAGTTTTTAAAAAATATTTTGAAAATAC
Found at i:24324 original size:36 final size:37
Alignment explanation
Indices: 24194--24324 Score: 124
Period size: 36 Copynumber: 3.5 Consensus size: 37
24184 TAATATATAG
* * *
24194 TTTTGAAAACATTTATATGTTATATAGTTTTAAAAAAACA
1 TTTTGAAAATA-TTATA--TTATATAGTTTTTAAAAAATA
* *
24234 TTTTTGAAAATATATATAATATATAATTTTT--AAAATA
1 -TTTTGAAAATAT-TATATTATATAGTTTTTAAAAAATA
* *
24271 TTTTTAAAATACGTATATTATATAGTTTTTAAAAAATA
1 TTTTGAAAATA-TTATATTATATAGTTTTTAAAAAATA
24309 TTTTGAAAAT-TTATAT
1 TTTTGAAAATATTATAT
24325 ATTATGTGCT
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
36 30 0.40
37 5 0.07
38 15 0.20
39 10 0.13
40 1 0.01
41 14 0.19
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTTGAAAATATTATATTATATAGTTTTTAAAAAATA
Found at i:25601 original size:2 final size:2
Alignment explanation
Indices: 25594--25630 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25584 ATACTACTCT
25594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25631 TTATTTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27746 original size:15 final size:15
Alignment explanation
Indices: 27726--27771 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
27716 CCCTGCACAA
*
27726 AAATAAATGAGAAAT
1 AAATAAATGAAAAAT
*
27741 AAATAAATTAAAAAT
1 AAATAAATGAAAAAT
27756 AAA-AAAT-AAATAAT
1 AAATAAATGAAA-AAT
27770 AA
1 AA
27772 TAATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 3 0.11
14 9 0.32
15 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (15 bp):
AAATAAATGAAAAAT
Found at i:27851 original size:38 final size:36
Alignment explanation
Indices: 27791--28037 Score: 223
Period size: 38 Copynumber: 6.7 Consensus size: 36
27781 ATATATAAAC
* *
27791 GTTTTCAAAAAC-ATATAATATATAAATTTTTAAAAT
1 GTTTT-AAAAACTATATATTATATAAATTTTAAAAAT
* *
27827 GTTTTAAAAAAACTATATATTATATATATTTTCAAAAT
1 GTTTT--AAAAACTATATATTATATAAATTTTAAAAAT
* * * *
27865 GATTTTTAAAAATTATATATTATATAAATGTTTTCATAAC
1 G--TTTTAAAAACTATATATTATATAAA--TTTTAAAAAT
* * * *
27905 GTTTTCAAAAGTATATATTATATATATTTTAAAAAC
1 GTTTTAAAAACTATATATTATATAAATTTTAAAAAT
27941 GTTTTCAAAAACTATATATTATAT-AATTTTCAAAAAT
1 GTTTT-AAAAACTATATATTATATAAATTTT-AAAAAT
* * * *
27978 ATTTTAAAAACTATATAATATACATATTTTCAAAAAAT
1 GTTTTAAAAACTATATATTATATAAATTTT--AAAAAT
28016 GTTTT--AAACTATATATTATATA
1 GTTTTAAAAACTATATATTATATA
28038 TGTATTTTCA
Statistics
Matches: 176, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
36 54 0.31
37 36 0.20
38 73 0.41
40 13 0.07
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (36 bp):
GTTTTAAAAACTATATATTATATAAATTTTAAAAAT
Found at i:28044 original size:38 final size:36
Alignment explanation
Indices: 27835--28077 Score: 213
Period size: 36 Copynumber: 6.5 Consensus size: 36
27825 ATGTTTTAAA
*
27835 AAAACTATATATTATATATATTTTCAAAATGATTTTT
1 AAAACTATATATTATATATATTTTCAAAA-AATTTTT
* * * ** *
27872 AAAAATTATATATTATATAAATGTTTTCATAACGTTTTC
1 -AAAACTATATATTATAT--ATATTTTCAAAAAATTTTT
* * *
27911 AAAAGTATATATTATATATATTTT-AAAAACGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAAA-ATTTT-T
*
27948 AAAACTATATATTATATA-ATTTTCAAAAATATTTTA
1 AAAACTATATATTATATATATTTTCAAAAA-ATTTTT
* *
27984 AAAACTATATAATATACATATTTTCAAAAAATGTTTT
1 AAAACTATATATTATATATATTTTCAAAAAAT-TTTT
* *
28021 -AAACTATATATTATATATGTATTTTCAAAAACAATTTG
1 AAAACTATATATTATATA--TATTTTCAAAAA-ATTTTT
* *
28059 CAAACTATATAATATATAT
1 AAAACTATATATTATATAT
28078 GTGTATATAT
Statistics
Matches: 172, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
35 3 0.02
36 50 0.29
37 41 0.24
38 47 0.27
39 21 0.12
40 10 0.06
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
AAAACTATATATTATATATATTTTCAAAAAATTTTT
Found at i:28064 original size:111 final size:110
Alignment explanation
Indices: 27835--28077 Score: 273
Period size: 111 Copynumber: 2.2 Consensus size: 110
27825 ATGTTTTAAA
* *
27835 AAAACTATATATTATATATATTTTCAAAATGATTTTTAAAAATTATATATTATATAAATGTTTTC
1 AAAACTATATATTATATATATTTTCAAAATGATTTTTAAAAACTATATA-TATATAAATATTTTC
* * * *
27900 ATAACGTTTTCAAAAGTATATATTATATATATTTTAAAAACGTTTTC
65 AAAACGTTTT-AAAACTATATATTATATATATTTTAAAAACATTTGC
*
27947 AAAAACTATATATTATATA-ATTTTCAAAA--ATATTTTAAAAACTATATA-ATATACATATTTT
1 -AAAACTATATATTATATATATTTTCAAAATGAT-TTTTAAAAACTATATATATATAAATATTTT
*
28008 CAAAAAATGTTTT-AAACTATATATTATATATGTATTTTCAAAAACAATTTGC
64 C--AAAACGTTTTAAAACTATATATTATATA--TATTTT-AAAAAC-ATTTGC
*
28060 -AAACTATATAATATATAT
1 AAAACTATATATTATATAT
28078 GTGTATATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 17
0.81 0.06 0.12
Matches are distributed among these distances:
109 28 0.25
110 2 0.02
111 45 0.40
112 16 0.14
113 22 0.19
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (110 bp):
AAAACTATATATTATATATATTTTCAAAATGATTTTTAAAAACTATATATATATAAATATTTTCA
AAACGTTTTAAAACTATATATTATATATATTTTAAAAACATTTGC
Found at i:36918 original size:14 final size:14
Alignment explanation
Indices: 36892--36925 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
36882 TTGAGAGTAA
36892 AAATTTGTTTGTTG
1 AAATTTGTTTGTTG
36906 AAGATTT-TTTGTTG
1 AA-ATTTGTTTGTTG
36920 AAATTT
1 AAATTT
36926 CCTTAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 11 0.58
15 4 0.21
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (14 bp):
AAATTTGTTTGTTG
Found at i:37100 original size:27 final size:26
Alignment explanation
Indices: 37052--37102 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
37042 AATAATAATA
*
37052 ATTTTTATAATTGTATTAAATAATTT
1 ATTTTTATAATTGTATGAAATAATTT
37078 ATTTTTA-AATTGTAGTGAGAATAAT
1 ATTTTTATAATTGTA-TGA-AATAAT
37103 GAGGCATTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (26 bp):
ATTTTTATAATTGTATGAAATAATTT
Found at i:38839 original size:17 final size:18
Alignment explanation
Indices: 38809--38850 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
38799 TCTATCCATT
* *
38809 AAAATATTATATTTTTAA
1 AAAATATTAAATTTTCAA
38827 AAAAT-TTAAATTTTCAA
1 AAAATATTAAATTTTCAA
38844 AAAATAT
1 AAAATAT
38851 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATATTAAATTTTCAA
Found at i:41923 original size:24 final size:24
Alignment explanation
Indices: 41891--41944 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
41881 CTTATTGTCT
41891 GAAAATTAAAGAAAGATTAAGTTA
1 GAAAATTAAAGAAAGATTAAGTTA
41915 GAAAATTAAAGAAAGATTAAGTTA
1 GAAAATTAAAGAAAGATTAAGTTA
41939 GAAAAT
1 GAAAAT
41945 CATCGAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (24 bp):
GAAAATTAAAGAAAGATTAAGTTA
Found at i:47603 original size:229 final size:227
Alignment explanation
Indices: 47198--47646 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 227
47188 GTAAATTATC
* * *
47198 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
47263 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
47328 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
47393 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
47426 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
47491 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* * *
47556 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
47621 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
47647 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 40 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:47735 original size:20 final size:19
Alignment explanation
Indices: 47712--47757 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
47702 CGATATACCA
47712 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
47732 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
47752 GGTAAA
1 GGTAAA
47758 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:47925 original size:17 final size:19
Alignment explanation
Indices: 47886--47928 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
47876 AGGTAAAAAT
47886 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
47906 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
47923 ATGATA
1 ATGATA
47929 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:50274 original size:33 final size:33
Alignment explanation
Indices: 50232--50297 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
50222 AAATAGATGG
*
50232 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
50265 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
50298 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:52090 original size:19 final size:19
Alignment explanation
Indices: 52066--52113 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
52056 AATGTCGAGT
52066 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
52085 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
52104 -ATTTTTGTAT
1 TAATTTTGTAT
52114 GTGAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:52562 original size:193 final size:195
Alignment explanation
Indices: 52230--52774 Score: 920
Period size: 193 Copynumber: 2.8 Consensus size: 195
52220 CAATATGGCC
* *
52230 AACAGGGTGCACCCATAAAGTG-CGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG--A
*
52294 ACCAAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAG
63 ACCCAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAG
*
52359 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTT-CAGAATGAAT
128 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
52422 GGAA
193 -GAA
52426 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCCAAAATCATCGAAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCCAAAATCATCGAAC
52490 CCAAAGTATAATGTAATA-GTAATTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAA
65 CCAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAA
*
52554 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATT
130 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAATG
52619 AA
194 AA
*
52621 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
52686 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 C-AAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAG
52751 AATATGTCTAAATAATGTGTCGAC
128 AATATGTCTAAATAATGTGTCGAC
Statistics
Matches: 333, Mismatches: 6, Indels: 17
0.94 0.02 0.05
Matches are distributed among these distances:
193 89 0.27
194 20 0.06
195 72 0.22
196 72 0.22
197 16 0.05
198 30 0.09
199 34 0.10
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (195 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAAT
ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGAA
Done.