Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008728.1 Hibiscus syriacus cultivar Beakdansim tig00111795_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: 149072
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:68 original size:22 final size:19
Alignment explanation
Indices: 23--68 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 19
13 ATATATATAT
23 ATAATATATACTATAAAAA
1 ATAATATATACTATAAAAA
42 A-AATATATACATATAATAAA
1 ATAATATATAC-TATAA-AAA
62 ATTAATA
1 A-TAATA
69 AAAGTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.39
19 6 0.26
20 4 0.17
22 4 0.17
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATATATACTATAAAAA
Found at i:70 original size:31 final size:34
Alignment explanation
Indices: 7--71 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
1 AATAAG
* *
7 AAATATATATATATATATAATATATACTATAAAAA
1 AAATATATACATATATATAAAATATAC-ATAAAAA
42 AAATATATACATATA-ATAAAAT-TA-ATAAAA
1 AAATATATACATATATATAAAATATACATAAAA
72 GTAATATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.21
33 2 0.07
34 6 0.21
35 14 0.50
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (34 bp):
AAATATATACATATATATAAAATATACATAAAAA
Found at i:537 original size:34 final size:35
Alignment explanation
Indices: 455--555 Score: 143
Period size: 34 Copynumber: 2.9 Consensus size: 35
445 ATAGTAGAAC
455 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCT-A-AAAAT
* *
492 T-TCATCATATTTTTAGGAGTTTGAATCCT-GAAAT
1 TCT-ATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
526 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
556 GTAGGACGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
34 30 0.52
35 1 0.02
36 1 0.02
37 26 0.45
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:1415 original size:105 final size:105
Alignment explanation
Indices: 1095--2126 Score: 1608
Period size: 105 Copynumber: 10.0 Consensus size: 105
1085 CATTGTTCCA
* * * ** * * *
1095 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * *
1160 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1201 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA--T-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1260 AGCGGTCCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1301 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1366 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** * *
1406 AGTCAAATATCCTTCGTTGCAAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1471 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1511 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1575 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1615 AGTCCAATATCCTTCGTTGTGAA-TTGAAATTGGCTCTGAAATTGAGAAGTT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1678 AGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1717 AGTCC-ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1781 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1821 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1886 AGCGGTCCCTTCGTCGTGAAGTTGAACTT-CGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1925 AGTCC-ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1989 AGCGGTCCCTTCGTCGTGAAGTTG-ACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
2028 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
2092 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
2127 CCTCGAGTGC
Statistics
Matches: 873, Mismatches: 38, Indels: 32
0.93 0.04 0.03
Matches are distributed among these distances:
99 19 0.02
100 64 0.07
101 18 0.02
102 71 0.08
103 196 0.22
104 186 0.21
105 263 0.30
106 56 0.06
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1728 original size:310 final size:313
Alignment explanation
Indices: 1095--2126 Score: 1595
Period size: 310 Copynumber: 3.3 Consensus size: 313
1085 CATTGTTCCA
* * * ** * *
1095 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAC
* * *
1160 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCG-AGTCCAATATCCTTCGTTGTGAA
64 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTCGTTGTGAA
** *
1224 GTTGAAATTGAATCTG-AA-TGA-A-AT-TTGTTGACAAGCAGCGGTCCCTTTCGTCGTGAAGTT
128 GTTGAAATTGGCTCTGAAATTGAGAGTTGTTGTTGACAAGCAGCGGTCCC-TTCGTCGTGAAGTT
* *
1284 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGA
192 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
*
1349 AGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
257 AGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** * * *
1406 AGTCAAATATCCTTCGTTGCAAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTC-CATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAACC
*
1471 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGT
65 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGT
1536 TGAAATTGGCTCTGAAATTGAGAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
130 TGAAATTGGCTCTGAAATTGAGAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
1601 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA-TTGAAATTGGCTCTGAAATTGAGAAGT
195 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
*
1665 T-TTGTTGACAAGCAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
260 TGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
1717 AGTCCATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCA
1 AGTCCATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAACCA
* *
1782 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
66 GCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
*
1847 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAG-AGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
* *
1912 CTT-CGTTGTCTGAAGTCC-ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
195 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
*
1975 TGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTG-ACTTGCGTTGTCTGG
260 TGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2028 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AGTTGTTGTTGACAACC
1 AGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAACC
* *
2092 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
2127 CCTCGAGTGC
Statistics
Matches: 668, Mismatches: 41, Indels: 24
0.91 0.06 0.03
Matches are distributed among these distances:
309 17 0.03
310 263 0.39
311 207 0.31
312 78 0.12
313 27 0.04
314 55 0.08
315 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (313 bp):
AGTCCATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAACCA
GCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAAATTGAGAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
GTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1873 original size:415 final size:418
Alignment explanation
Indices: 1094--2126 Score: 1631
Period size: 415 Copynumber: 2.5 Consensus size: 418
1084 GCATTGTTCC
* * * ** * *
1094 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* * * * * *
1159 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAATATCCTTCGTTGTGAA
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
1224 GTTGAAATTGAATCTG-AA-TGA-AA--TTTGTTGACAAGCAGCGGTCCCTTTCGTCGTGAAGTT
130 GTTGAAATTGGCTCTGAAATTGAGAAGTTTTGTTGACAAGCAGCGGTCCC-TTCGTCGTGAAGTT
* * * *
1284 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGA
194 GAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
*
1349 AGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCAAAT
259 AGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCAAAT
* * *
1414 ATCCTTCGTTGCAAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCC
324 ATCCTTCATTGCAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCC
1479 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
389 CTTCGTCGTGAAGTTGAACTT-CGTTGTCTG
1510 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AGTTGTTGTTGACAAG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1574 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA-
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
1638 TTGAAATTGGCTCTGAAATTGAGAAGTTTTGTTGACAAGCAGCGGT-CCTTCGTCGTGAAGTTGA
131 TTGAAATTGGCTCTGAAATTGAGAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
1702 ACTTGCGTTGTCTGAAGTCC-ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
196 ACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
* * *
1766 TTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATAT
261 TTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCAAATAT
** *
1831 CCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCT
326 CCTTCATTGCAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCT
1896 TCGTCGTGAAGTTGAACTTCGTTGTCTG
391 TCGTCGTGAAGTTGAACTTCGTTGTCTG
* *
1924 AAGTCC-ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1988 CAGCGGTCCCTTCGTCGTGAAGTTG-ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* * *
2052 TTGAAATTGGCTCTGAAATTGAG-AGTTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
131 TTGAAATTGGCTCTGAAATTGAGAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
*
2116 AACTTGTGTTG
195 AACTTGCGTTG
2127 CCTCGAGTGC
Statistics
Matches: 573, Mismatches: 35, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
413 95 0.17
414 165 0.29
415 213 0.37
416 79 0.14
417 2 0.00
418 19 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (418 bp):
AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAAATTGAGAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
TTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCAAATAT
CCTTCATTGCAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTCGTTGTCTG
Found at i:2844 original size:68 final size:65
Alignment explanation
Indices: 2754--2911 Score: 208
Period size: 68 Copynumber: 2.4 Consensus size: 65
2744 AAGATATCTG
* * ** *
2754 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAG-G
2819 TT
64 TT
* * *
2821 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGT
2886 T
65 T
*
2887 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
2912 ATAGACGAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 32 0.40
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:2927 original size:65 final size:67
Alignment explanation
Indices: 2755--3145 Score: 214
Period size: 65 Copynumber: 5.7 Consensus size: 67
2745 AGATATCTGT
* * * * ** *
2755 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
2820 TTG
65 TTG
* * *
2823 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
2887 T-
66 TG
* * * * *
2888 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT--GTCTCAAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AG
*
2950 AGACAAAAATT-
62 AG------TTTG
* * * * ** * * * * * *
2961 AGTTCCAAAAG-AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
3024 T-
66 TG
* * * *
3025 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT--GTCTCAAGATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-A
*
3088 GACGAAATT-
61 GA-G--TTTG
*
3097 TG-TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
3146 CTGTCTCAAG
Statistics
Matches: 251, Mismatches: 48, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
64 11 0.04
65 76 0.30
66 11 0.04
67 24 0.10
68 34 0.14
71 49 0.20
72 36 0.14
73 10 0.04
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:2938 original size:36 final size:35
Alignment explanation
Indices: 2887--3165 Score: 254
Period size: 36 Copynumber: 8.0 Consensus size: 35
2877 TTCAAAGGTT
* *
2887 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
2923 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * * * *
2959 TTAGTTCCAAAAG-AACTGTCTCAAGGGAGACGGAAT
1 TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
2995 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
3024 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
3059 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
3095 TT-TGTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGT-TTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
3130 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
3166 CTCTTCTAGT
Statistics
Matches: 201, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 4 0.02
35 37 0.18
36 125 0.62
37 11 0.05
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2985 original size:137 final size:136
Alignment explanation
Indices: 2826--3146 Score: 421
Period size: 137 Copynumber: 2.4 Consensus size: 136
2816 GATTTTGTGT
* * * * * *
2826 TTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGT
1 TTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGT
* *
2891 TTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
66 TTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGAC-
2955 AAAATTAG
129 AAAATTAG
** * * * *
2963 TTCCAAAAG-AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTG
1 TT-CAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTG
* * *
3027 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACG
65 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACA
*
3092 AAATTTG
130 AAATTAG
* *
3099 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 TTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
3147 TGTCTCAAGA
Statistics
Matches: 158, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
135 5 0.03
136 46 0.29
137 102 0.65
138 5 0.03
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (136 bp):
TTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGT
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAA
AATTAG
Found at i:3028 original size:101 final size:101
Alignment explanation
Indices: 2923--3109 Score: 270
Period size: 101 Copynumber: 1.9 Consensus size: 101
2913 TAGACGAAAA
*
2923 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTAGTTCCAAAAG-AACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTA-TTCCAAAAGAAACTGTCTCAAGAGA
*
2987 GACGGAATTTGTTTCAA-AGAAAACATATTCAAATATT
65 GACGAAATTTG-TTCAAGAGAAAACATATTCAAATATT
* * * ** *
3024 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTATTCCAAAAGAAACTGTCTCAAGAGAG
3089 ACGAAATTTGTTCAAGAGAAA
66 ACGAAATTTGTTCAAGAGAAA
3110 CTGTCTCAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
100 11 0.14
101 65 0.86
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (101 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTATTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTCAAGAGAAAACATATTCAAATATT
Found at i:3144 original size:71 final size:72
Alignment explanation
Indices: 3023--3161 Score: 244
Period size: 71 Copynumber: 1.9 Consensus size: 72
3013 ATTCAAATAT
* *
3023 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
3088 GACGAAA
66 GACGAAA
*
3095 TTTG-TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
3159 GAC
66 GAC
3162 AAAACTCTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 60 0.94
72 4 0.06
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (72 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
GACGAAA
Found at i:3187 original size:71 final size:71
Alignment explanation
Indices: 3028--3197 Score: 234
Period size: 71 Copynumber: 2.4 Consensus size: 71
3018 AATATTTTGT
* *
3028 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACGA
** *
3093 AATTTG
66 AAACTC
*
3099 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACGA
3163 AAACTC
66 AAACTC
* * * *
3169 TTCTAGTGAAAACGGTCTCAAGCGAGACA
1 TTCAAGAG-AAACTGTCTCAAGAGAGACA
3198 TCTGTTTTAA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
70 10 0.11
71 78 0.89
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (71 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACGA
AAACTC
Found at i:4083 original size:22 final size:22
Alignment explanation
Indices: 4057--4105 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
4047 TTGTGTTTGG
* *
4057 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
4079 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
4101 TCAAA
1 TCAAA
4106 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:4112 original size:22 final size:22
Alignment explanation
Indices: 4069--4112 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4059 AAAGGTTTGG
* * *
4069 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
4091 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
4113 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:4840 original size:20 final size:20
Alignment explanation
Indices: 4815--4852 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4805 ATTATTATTA
4815 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
4835 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
4853 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:4884 original size:16 final size:18
Alignment explanation
Indices: 4863--4897 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
4853 TTTACTCATT
4863 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
4879 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
4897 T
1 T
4898 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:5514 original size:34 final size:36
Alignment explanation
Indices: 5469--5568 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 36
5459 TCGTCCTACT
5469 AGGATTCAAACTCCTAAAAATAGGATAGAA-TT-TC
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
* * *
5503 ATGATTCAAACTCCTAAAAATATGAT-GAAATTTTGTT
1 AGGATTCAAACTCCTAAAAATAGGATAG-AA-TTTGTC
5540 AGGATTCAAACTCCTAAAAATAGGATAGA
1 AGGATTCAAACTCCTAAAAATAGGATAGA
5569 GTTCTACTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
33 1 0.02
34 26 0.46
36 2 0.04
37 26 0.46
38 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (36 bp):
AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
Found at i:6117 original size:20 final size:20
Alignment explanation
Indices: 6092--6129 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6082 TTTATTATTA
6092 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
6112 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
6130 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:6268 original size:2 final size:2
Alignment explanation
Indices: 6261--6296 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6251 ATTTTATCTC
6261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6297 TAGGATCGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7243 original size:37 final size:37
Alignment explanation
Indices: 7202--7279 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
7192 ATGAAATATC
*
7202 TTAAATTACAAAAAATATTTATAATTATAGTTGTAAA
1 TTAAATTACAAAAAATATTTATAATCATAGTTGTAAA
7239 TTAAATTACAAAAAATATTTATAATCATAGTTGTAAA
1 TTAAATTACAAAAAATATTTATAATCATAGTTGTAAA
7276 TTAA
1 TTAA
7280 GCATATAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (37 bp):
TTAAATTACAAAAAATATTTATAATCATAGTTGTAAA
Found at i:9853 original size:7 final size:7
Alignment explanation
Indices: 9841--9887 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
9831 TATAATCACA
9841 TTTAGGT
1 TTTAGGT
*
9848 TTTAGGA
1 TTTAGGT
9855 TTTAGGGT
1 TTTA-GGT
9863 TTATA-GT
1 TT-TAGGT
*
9870 TTTAGGG
1 TTTAGGT
9877 TTTAGGT
1 TTTAGGT
9884 TTTA
1 TTTA
9888 TAGTTTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 2 0.06
7 25 0.76
8 4 0.12
9 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (7 bp):
TTTAGGT
Found at i:9871 original size:22 final size:22
Alignment explanation
Indices: 9846--9908 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
9836 TCACATTTAG
9846 GTTTTAGGATTTAGGGTTTATA
1 GTTTTAGGATTTAGGGTTTATA
* *
9868 GTTTTAGGGTTTAGGTTTTATA
1 GTTTTAGGATTTAGGGTTTATA
* *
9890 G-TTTATGATTTAGAGTTTA
1 GTTTTAGGATTTAGGGTTTA
9909 GGGTTTATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.52
Consensus pattern (22 bp):
GTTTTAGGATTTAGGGTTTATA
Found at i:11592 original size:19 final size:20
Alignment explanation
Indices: 11564--11606 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
11554 TTTAAAATTC
*
11564 ATAAAATTTA-AAATTTTAT
1 ATAAAATTTATAAATTTTAA
* *
11583 ATAAATTTTATGAATTTTAA
1 ATAAAATTTATAAATTTTAA
11603 ATAA
1 ATAA
11607 GTTTGACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATAAAATTTATAAATTTTAA
Found at i:15035 original size:25 final size:25
Alignment explanation
Indices: 15001--15048 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
14991 CACTTACCCC
*
15001 AAGCACCATCTCGTTGTGGTATCCT
1 AAGCACCATCCCGTTGTGGTATCCT
15026 AAGCACCATCCCGTTGTGGTATC
1 AAGCACCATCCCGTTGTGGTATC
15049 TGGCCACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (25 bp):
AAGCACCATCCCGTTGTGGTATCCT
Found at i:17596 original size:21 final size:21
Alignment explanation
Indices: 17570--17677 Score: 84
Period size: 21 Copynumber: 5.2 Consensus size: 21
17560 CTGCATTTCG
17570 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
17591 CGTTGCGAT--TTTTCA-TTT
1 CGTTGCGATAGTCTACAGTGT
17609 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * *
17632 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
17650 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
17673 CGTTG
1 CGTTG
17678 TGATTTTGCA
Statistics
Matches: 65, Mismatches: 12, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
18 4 0.06
19 8 0.12
20 18 0.28
21 23 0.35
22 8 0.12
23 4 0.06
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:17608 original size:41 final size:41
Alignment explanation
Indices: 17563--17684 Score: 226
Period size: 41 Copynumber: 3.0 Consensus size: 41
17553 ATTCGCGCTG
*
17563 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
17604 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
*
17645 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGTGATTTT
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTT
17685 GCACTTCCTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 79 1.00
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.41
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
Found at i:17616 original size:20 final size:20
Alignment explanation
Indices: 17591--17660 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
17581 TCTACAGTGT
*
17591 CGTTGCGATTTTTCATTTCG
1 CGTTGCGATTTTACATTTCG
* *
17611 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTACATTTCG
*
17631 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTACATTTCG
17652 CGTTGCGAT
1 CGTTGCGAT
17661 AGTCTACAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 11 0.28
22 4 0.10
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTACATTTCG
Found at i:17890 original size:41 final size:41
Alignment explanation
Indices: 17833--18096 Score: 435
Period size: 41 Copynumber: 6.4 Consensus size: 41
17823 CATTTTTAAA
*
17833 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
17874 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
17915 ACTATCGCAACGCGAAATGGAAAACCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
17956 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
17997 ACTATCGCAACACGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* *
18038 ACTATCGCAACGCGAAATGGAAAA-CTGCAACG-CGATTTTCA-
1 ACTATCGCAACGCGAAATGGAAAATC-GCAACGAC-ACTGT-AG
18079 ACTATCGCAACGCGAAAT
1 ACTATCGCAACGCGAAAT
18097 ACAGTGCGAA
Statistics
Matches: 213, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
40 2 0.01
41 210 0.99
42 1 0.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.15
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:29395 original size:12 final size:12
Alignment explanation
Indices: 29374--29424 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
29364 TTTATTTAAC
*
29374 GTTCGCGAACAT
1 GTTCGTGAACAT
29386 GTTCGTGAACAT
1 GTTCGTGAACAT
* *
29398 ATTCGTTTAA-AT
1 GTTCG-TGAACAT
29410 GTTCGTGAACAT
1 GTTCGTGAACAT
29422 GTT
1 GTT
29425 TGTTTAGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 3 0.09
12 26 0.81
13 3 0.09
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (12 bp):
GTTCGTGAACAT
Found at i:29429 original size:24 final size:24
Alignment explanation
Indices: 29384--29430 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29374 GTTCGCGAAC
29384 ATGTTCGTGAACATATTCGTTTAA
1 ATGTTCGTGAACATATTCGTTTAA
* *
29408 ATGTTCGTGAACATGTTTGTTTA
1 ATGTTCGTGAACATATTCGTTTA
29431 GGGTTCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (24 bp):
ATGTTCGTGAACATATTCGTTTAA
Found at i:31110 original size:2 final size:2
Alignment explanation
Indices: 31098--31141 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
31088 CACTTTAATT
*
31098 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31140 TA
1 TA
31142 ACTTTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:32205 original size:17 final size:17
Alignment explanation
Indices: 32185--32217 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
32175 TACAAATAAA
32185 ATTTCATAG-TGAATACG
1 ATTTCA-AGATGAATACG
32202 ATTTCAAGATGAATAC
1 ATTTCAAGATGAATAC
32218 CATCAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (17 bp):
ATTTCAAGATGAATACG
Found at i:36250 original size:9 final size:9
Alignment explanation
Indices: 36228--36261 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
36218 ATCTATTCCT
36228 TTTATTTTGC
1 TTTATTTT-C
*
36238 TTTATTTTT
1 TTTATTTTC
36247 TTTATTTTC
1 TTTATTTTC
36256 TTTATT
1 TTTATT
36262 ATATTCGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTATTTTC
Found at i:41173 original size:52 final size:50
Alignment explanation
Indices: 41071--41209 Score: 205
Period size: 52 Copynumber: 2.8 Consensus size: 50
41061 TCGCTTAAGA
* * *
41071 TGAAAACCCGAAAGGGCGTCCTAAGTTG---GAAAAA-AAACGTTTAGGG
1 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAGAAACGTTTAGGG
41117 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAACAAGAAAGCGTTTAGGG
1 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAA-AAGAAA-CGTTTAGGG
41169 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAGAAA
1 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAGAAA
41210 AAATAGAAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
46 26 0.31
49 3 0.04
50 2 0.02
51 9 0.11
52 44 0.52
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (50 bp):
TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAGAAACGTTTAGGG
Found at i:41218 original size:19 final size:19
Alignment explanation
Indices: 41191--41239 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
41181 AGGGCGCCCT
* *
41191 AAATTGAAAAAAAAAGAAA
1 AAATAGAAAAAAAAACAAA
*
41210 AAATAGAAAAACAAACAAA
1 AAATAGAAAAAAAAACAAA
*
41229 AGAAGAGAAAA
1 A-AATAGAAAA
41240 TAAGGTGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.78, C:0.04, G:0.12, T:0.06
Consensus pattern (19 bp):
AAATAGAAAAAAAAACAAA
Found at i:42170 original size:105 final size:105
Alignment explanation
Indices: 41988--42543 Score: 891
Period size: 105 Copynumber: 5.4 Consensus size: 105
41978 AGGTTTTACC
*
41988 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
42053 GCGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
* *
42093 CAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
42158 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
42198 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
42263 ACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
*
42296 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
42357 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAATTT
* *
42398 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
42463 ACGAAGGGACCGCTAGTTGTCAACAAACAATTTCCCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAATTT
*
42504 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
42544 GAAACAACAC
Statistics
Matches: 422, Mismatches: 17, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
94 82 0.19
95 2 0.00
97 1 0.00
98 7 0.02
102 7 0.02
103 1 0.00
104 2 0.00
105 187 0.44
106 133 0.32
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
Found at i:42269 original size:43 final size:43
Alignment explanation
Indices: 42208--42363 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
42198 CAGAGCCAAT
*
42208 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
* *** ** * * * *
42251 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CACAAG
42302 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
*
42345 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
42364 GACCGCTGGT
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 38 0.45
44 3 0.04
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 3 0.04
51 20 0.24
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
Found at i:42472 original size:200 final size:199
Alignment explanation
Indices: 41988--42501 Score: 812
Period size: 200 Copynumber: 2.5 Consensus size: 199
41978 AGGTTTTACC
*
41988 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
42053 GCGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTTAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAA-AAA-A-----CAATTTC----CCAATTTCAACTTCACAACG
* *
42118 AAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
120 AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
42183 AACATTTCTCAATTT
185 AACATTTCCCAATTT
42198 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
42263 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
66 ACGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
*
42328 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
131 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCC
42393 AATTT
195 AATTT
* *
42398 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
42463 ACGAAGGGACCGCTAGTTGTCAACAAACAATTTCCCAAT
66 ACGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCCAAT
42502 CTCGGAGCCA
Statistics
Matches: 291, Mismatches: 12, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
199 84 0.29
200 111 0.38
203 7 0.02
208 1 0.00
209 2 0.01
210 86 0.30
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (199 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCA
ATTT
Found at i:42551 original size:106 final size:106
Alignment explanation
Indices: 42297--42555 Score: 437
Period size: 106 Copynumber: 2.4 Consensus size: 106
42287 AAACAATTTC
42297 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
* * *
42362 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
66 GGGACCGCTAGTTGTCAACAAACAATTTCCCAATCTCAGAG
* **
42403 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
*
42468 GGGACCGCTAGTTGTCAACAAACAATTTCCCAATCTCGGAG
66 GGGACCGCTAGTTGTCAACAAACAATTTCCCAATCTCAGAG
* *
42509 CCAATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAACACAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAA
42556 TTTGCTCGAG
Statistics
Matches: 141, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 141 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.22
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
GGGACCGCTAGTTGTCAACAAACAATTTCCCAATCTCAGAG
Found at i:54446 original size:2 final size:2
Alignment explanation
Indices: 54439--54501 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
54429 AAGATCTTTG
54439 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54480 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
54502 GAATATTACT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55715 original size:103 final size:103
Alignment explanation
Indices: 55490--55707 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
55480 GTCGAGGGTC
55490 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
55555 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
55593 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
55658 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
55696 TATGTGGTCCTT
1 TATGTGGTCCTT
55708 ATGGACATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:55791 original size:23 final size:23
Alignment explanation
Indices: 55723--55783 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
55713 CATTATTATA
*
55723 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
55746 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
55769 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
55784 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:60543 original size:2 final size:2
Alignment explanation
Indices: 60538--60562 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60528 TATATATATA
60538 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
60563 ATGGGAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:65309 original size:60 final size:60
Alignment explanation
Indices: 65179--65314 Score: 143
Period size: 60 Copynumber: 2.2 Consensus size: 60
65169 GTATAGTTTG
* * * *
65179 GGATGAAATTAGAATGTTCAAAAAGTTTAGGGGCCAATTTAGAATGAAGGTCATAGTTTA
1 GGATGAAATTAAAATGTTCAAAAAGTTTAGGGACCAATTTAAAATGAAGGTCATAATTTA
* * *
65239 GGAATAAAATTAAAATGTTC-AAAA-TTTCGAGGACTAATTTAAAATG-AGAGTCATAATTTA
1 GG-ATGAAATTAAAATGTTCAAAAAGTTTAG-GGACCAATTTAAAATGAAG-GTCATAATTTA
*
65299 GAGATGAAATTGAAAT
1 G-GATGAAATTAAAAT
65315 ATCTAAAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
59 6 0.10
60 41 0.65
61 16 0.25
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (60 bp):
GGATGAAATTAAAATGTTCAAAAAGTTTAGGGACCAATTTAAAATGAAGGTCATAATTTA
Found at i:69691 original size:23 final size:23
Alignment explanation
Indices: 69661--69709 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
69651 AAGATGAGGT
69661 CGTCGGCGCACTTTAGCAACCAC
1 CGTCGGCGCACTTTAGCAACCAC
69684 CGTCGGCGCACTTTAGCAACCAC
1 CGTCGGCGCACTTTAGCAACCAC
69707 CGT
1 CGT
69710 GAGTCATGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.39, G:0.22, T:0.18
Consensus pattern (23 bp):
CGTCGGCGCACTTTAGCAACCAC
Found at i:69879 original size:25 final size:25
Alignment explanation
Indices: 69845--69893 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
69835 TTTACTATGA
*
69845 TAATCATATCTTAATTAAACGAAAG
1 TAATAATATCTTAATTAAACGAAAG
*
69870 TAATAATATCTTAATTAAATGAAA
1 TAATAATATCTTAATTAAACGAAA
69894 ATAAAAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (25 bp):
TAATAATATCTTAATTAAACGAAAG
Found at i:72132 original size:194 final size:194
Alignment explanation
Indices: 71760--72148 Score: 638
Period size: 195 Copynumber: 2.0 Consensus size: 194
71750 TCCCCAACTC
71760 CCATCCCATGTTGCTTTGGATGTGATTTTTTATTTTTCCTTTTCCCTAAAAGGAGAGCCATTGCC
1 CCATCCCATGTTGCTTTGGATGTGATTTTTTATTTTTCCTTTTCCCTAAAAGGAGAGCCATTGCC
*
71825 AACCATGACCCAACTCTTACTTTCTTGTAATAATAATTTTTAATGAATTTTTGGTCTAATTGCTT
66 AACCATGACCCAACTCTTACTTTCTTGTAATAATAATTTTTAACGAATTTTTGGTCTAATT-CTT
71890 CTTTAGTCCATTTATGATGATAAGATTAGAGATTTAATTCATCTAATTTTGATTTGATTATAATT
130 CTTTAGTCCATTTATGATGATAAGATTAGAGATTTAATTCATCTAATTTTGATTTGATTATAATT
* * * *
71955 CCATCCCATGTTGCTTTGGATGT-ATTTTTTTTTTTTTCCTTTTTCCTAGAAGGAGATCCATTGC
1 CCATCCCATGTTGCTTTGGATGTGA-TTTTTTATTTTTCCTTTTCCCTAAAAGGAGAGCCATTGC
* * * *
72019 CAACCATGGCCCAACTCTTACTTTCTTGTAATAATGATTTTTAACGATTTTTTGGTTTAATT-TT
65 CAACCATGACCCAACTCTTACTTTCTTGTAATAATAATTTTTAACGAATTTTTGGTCTAATTCTT
* *
72083 GCTTTAGTCCCTTTATGATGATAAGATTAGAGATTTAATTCATCTAATTTTGATTTTATTATAAT
130 -CTTTAGTCCATTTATGATGATAAGATTAGAGATTTAATTCATCTAATTTTGATTTGATTATAAT
72148 T
194 T
72149 TAGATATTAT
Statistics
Matches: 181, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
193 2 0.01
194 64 0.35
195 115 0.64
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (194 bp):
CCATCCCATGTTGCTTTGGATGTGATTTTTTATTTTTCCTTTTCCCTAAAAGGAGAGCCATTGCC
AACCATGACCCAACTCTTACTTTCTTGTAATAATAATTTTTAACGAATTTTTGGTCTAATTCTTC
TTTAGTCCATTTATGATGATAAGATTAGAGATTTAATTCATCTAATTTTGATTTGATTATAATT
Found at i:73020 original size:2 final size:2
Alignment explanation
Indices: 73013--73045 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
73003 AATTTACCCA
73013 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 A
73046 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82239 original size:165 final size:165
Alignment explanation
Indices: 81944--82267 Score: 416
Period size: 165 Copynumber: 2.0 Consensus size: 165
81934 ATCTATTGGA
* * * *
81944 ATTTGTTGTGGCATCTGAGAACTTTCTATTCCCATTTTTGATTTCTTAGGATGTTTTGTTGCAGA
1 ATTTGTTGTGGCATCTGAGAACTTTCTATTCCCATTTTTGATTTCTTAAGATGCTCTGTTGCAAA
* * * * * * * * ** *
82009 ATACATCTTTGGTTCGAGCTCTTTGGTTTGTAATTCTTGATGCTGCTCAACTTGGAAATGGACAT
66 AGACATCTTCGGTTCCAGCTCTTCGCTCTGTAATTCTCGAGGCTGCTCAACTTCAAAACGGACAT
*
82074 TCTGCATTTCCTCTGAAAGAGACCAGACTATAGGC
131 TCTGCATTTCCTCCGAAAGAGACCAGACTATAGGC
* * *
82109 ATTTGTTGTGGCATTTGAGAACTTTCTATTGCCATTTTTGATTTCTTAAGCTGCTCTGTTGCAAA
1 ATTTGTTGTGGCATCTGAGAACTTTCTATTCCCATTTTTGATTTCTTAAGATGCTCTGTTGCAAA
* *
82174 AGACATCTTCGGTTCCAGCTCTTCGACTCT-TAATTCTCGAGGTTGCTTAACTTCAAAACGGACA
66 AGACATCTTCGGTTCCAGCTCTTCG-CTCTGTAATTCTCGAGGCTGCTCAACTTCAAAACGGACA
* * *
82238 TTTTGCATTTCCTCCGAGAGAGACCGGACT
130 TTCTGCATTTCCTCCGAAAGAGACCAGACT
82268 GCAGTTTCCG
Statistics
Matches: 134, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
165 132 0.99
166 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (165 bp):
ATTTGTTGTGGCATCTGAGAACTTTCTATTCCCATTTTTGATTTCTTAAGATGCTCTGTTGCAAA
AGACATCTTCGGTTCCAGCTCTTCGCTCTGTAATTCTCGAGGCTGCTCAACTTCAAAACGGACAT
TCTGCATTTCCTCCGAAAGAGACCAGACTATAGGC
Found at i:84417 original size:34 final size:34
Alignment explanation
Indices: 84363--84429 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
84353 AACATGTTCG
* *
84363 CGAAAGCTAAACAAATATATTTACAAATGATAAA
1 CGAAAGCTAAACAAACATATTCACAAATGATAAA
* * *
84397 CGAATGCTAAACGAACATATTCGCAAATGATAA
1 CGAAAGCTAAACAAACATATTCACAAATGATAA
84430 TTGAATATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (34 bp):
CGAAAGCTAAACAAACATATTCACAAATGATAAA
Found at i:84447 original size:34 final size:34
Alignment explanation
Indices: 84369--84466 Score: 88
Period size: 34 Copynumber: 2.9 Consensus size: 34
84359 TTCGCGAAAG
* * * *
84369 CTAAACAAATATATTTACAAATGATAAACGAATG
1 CTAAACGAACATATTCACAAATGATAAACGAATA
* **
84403 CTAAACGAACATATTCGCAAATGATAATTGAATA
1 CTAAACGAACATATTCACAAATGATAAACGAATA
* * * * *
84437 TTAAATGAACATGTTCACAAACGTTAAACG
1 CTAAACGAACATATTCACAAATGATAAACG
84467 CTAAATGAAT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (34 bp):
CTAAACGAACATATTCACAAATGATAAACGAATA
Found at i:84490 original size:28 final size:30
Alignment explanation
Indices: 84438--84494 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
84428 AATTGAATAT
84438 TAAATGAACATGTTCACAAACGTTAAACGC
1 TAAATGAACATGTTCACAAACGTTAAACGC
* *
84468 TAAATG-A-ATGTTCATAAATGTTAAACG
1 TAAATGAACATGTTCACAAACGTTAAACG
84495 AACATGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 1 0.04
30 6 0.24
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (30 bp):
TAAATGAACATGTTCACAAACGTTAAACGC
Found at i:84594 original size:26 final size:23
Alignment explanation
Indices: 84561--84608 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
84551 CGAACAAGAT
*
84561 ACTAAAAAATTAAACGAACATGAAC
1 ACTAAAAAAATAAAC-AA-ATGAAC
84586 ACTATAAAAAATAAACAAATGAA
1 ACTA-AAAAAATAAACAAATGAA
84609 TACGAACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 6 0.29
26 10 0.48
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.17
Consensus pattern (23 bp):
ACTAAAAAAATAAACAAATGAAC
Found at i:101171 original size:21 final size:21
Alignment explanation
Indices: 101145--101194 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
101135 GTGCATGGAC
101145 GGTATTGGGAACTTGTTTTAG
1 GGTATTGGGAACTTGTTTTAG
101166 GGTATTGGGAACTTGTTTTAG
1 GGTATTGGGAACTTGTTTTAG
101187 GGTATTGG
1 GGTATTGG
101195 AAAGCAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.04, G:0.36, T:0.42
Consensus pattern (21 bp):
GGTATTGGGAACTTGTTTTAG
Found at i:101552 original size:60 final size:60
Alignment explanation
Indices: 101503--101625 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 60
101493 GTCTTCCGAT
* *
101503 TATAGGGTATT-TCTTTATTAAGT-CTTTCGACTATTAAAAGTTACAAAATGATCCTCCAAC
1 TATAGAGTATTAT-TTTATTAAGTCCCTT-GACTATTAAAAGTTACAAAATGATCCTCCAAC
* * * * *
101563 TATAGAGTGTTATTTTGTTGAGTCCCTTGACTATTAAAAGTTACAAAATGATCATCCTAC
1 TATAGAGTATTATTTTATTAAGTCCCTTGACTATTAAAAGTTACAAAATGATCCTCCAAC
101623 TAT
1 TAT
101626 TCATTATGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 50 0.93
61 4 0.07
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (60 bp):
TATAGAGTATTATTTTATTAAGTCCCTTGACTATTAAAAGTTACAAAATGATCCTCCAAC
Found at i:103067 original size:71 final size:71
Alignment explanation
Indices: 102986--103125 Score: 271
Period size: 71 Copynumber: 2.0 Consensus size: 71
102976 TATTATCAAA
*
102986 CTATAATTAATTGATTCCGAGTGTAGGTTACCGATATGTTAACAATAGAGAAAGACAAAATATTG
1 CTATAATTAATTGATTCCGAGTGTAGGTTACCGATATGTTAACAATAAAGAAAGACAAAATATTG
103051 GGACAC
66 GGACAC
103057 CTATAATTAATTGATTCCGAGTGTAGGTTACCGATATGTTAACAATAAAGAAAGACAAAATATTG
1 CTATAATTAATTGATTCCGAGTGTAGGTTACCGATATGTTAACAATAAAGAAAGACAAAATATTG
103122 GGAC
66 GGAC
103126 GTTTAAATCC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (71 bp):
CTATAATTAATTGATTCCGAGTGTAGGTTACCGATATGTTAACAATAAAGAAAGACAAAATATTG
GGACAC
Found at i:108500 original size:41 final size:42
Alignment explanation
Indices: 108412--108516 Score: 158
Period size: 41 Copynumber: 2.5 Consensus size: 42
108402 ACGCGATAGT
* *
108412 CGAAGTTCGCGTTGCGATTCATTCCAAATTCATTGCGAGAGG
1 CGAAGTTCGCATTGCGATTCATTCCAAATTCATTGCGACAGG
* *
108454 CGAAGTTTGCATTGCGATTCATTCC-AATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAAATTCATTGCGACAGG
*
108495 TGAAGTTCGCATTGCGATTCAT
1 CGAAGTTCGCATTGCGATTCAT
108517 ACTTCGCCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 34 0.60
42 23 0.40
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (42 bp):
CGAAGTTCGCATTGCGATTCATTCCAAATTCATTGCGACAGG
Found at i:109349 original size:6 final size:6
Alignment explanation
Indices: 109333--109361 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
109323 TCCCGTCTCG
109333 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
109362 ACGTGTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:109483 original size:42 final size:42
Alignment explanation
Indices: 109436--109568 Score: 230
Period size: 42 Copynumber: 3.2 Consensus size: 42
109426 AATATTTGGA
*
109436 CTATCGCAACGAATTTGGAATGAATCACAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
109478 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
109520 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
109562 CTATCGC
1 CTATCGC
109569 GTTGTGAATC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:109546 original size:21 final size:20
Alignment explanation
Indices: 109429--109549 Score: 68
Period size: 21 Copynumber: 5.8 Consensus size: 20
109419 CAAATGCAAT
*
109429 ATTTGGACT-ATCGCAACGA
1 ATTTGGAATAATCGCAACGA
*
109448 ATTTGGAATGAATCACAACGCGA
1 ATTTGGAAT-AATCGCAA--CGA
* * **
109471 ACTTCGCCT-ATCGCAACGA
1 ATTTGGAATAATCGCAACGA
109490 ATTTGGAATGAATCGCAACGCGA
1 ATTTGGAAT-AATCGCAA--CGA
* * **
109513 ACTTCGCCT-ATCGCAACGA
1 ATTTGGAATAATCGCAACGA
109532 ATTTGGAATAAATCGCAA
1 ATTTGGAAT-AATCGCAA
109550 TGCGAACTTC
Statistics
Matches: 73, Mismatches: 19, Indels: 18
0.66 0.17 0.16
Matches are distributed among these distances:
19 24 0.33
21 33 0.45
23 16 0.22
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
ATTTGGAATAATCGCAACGA
Found at i:109567 original size:21 final size:20
Alignment explanation
Indices: 109467--109568 Score: 64
Period size: 21 Copynumber: 4.9 Consensus size: 20
109457 GAATCACAAC
*
109467 GCGAACTTCGCCTATCGCAA
1 GCGAACTTCGACTATCGCAA
* * *
109487 -CGAATTTGGAATGAATCGCAA
1 GCGAACTTCGACT--ATCGCAA
*
109508 CGCGAACTTCGCCTATCGCAA
1 -GCGAACTTCGACTATCGCAA
* * *
109529 -CGAATTTGGAATAAATCGCAA
1 GCGAACTTCGACT--ATCGCAA
109550 TGCGAACTTCGACTATCGC
1 -GCGAACTTCGACTATCGC
109569 GTTGTGAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 15
0.66 0.17 0.17
Matches are distributed among these distances:
19 16 0.27
21 26 0.44
23 17 0.29
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (20 bp):
GCGAACTTCGACTATCGCAA
Found at i:118419 original size:13 final size:12
Alignment explanation
Indices: 118389--118435 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
118379 CTCTTTTCGA
*
118389 TTTTTTCTTTAT
1 TTTTTTCTTTTT
*
118401 GTTTTTCTTTTT
1 TTTTTTCTTTTT
118413 TTCTTTTCTTTTCT
1 TT-TTTTCTTTT-T
118427 TTTTTTCTT
1 TTTTTTCTT
118436 GCATGTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.37
13 16 0.53
14 3 0.10
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:118424 original size:18 final size:20
Alignment explanation
Indices: 118389--118435 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
118379 CTCTTTTCGA
*
118389 TTTTTTCTTTATGTTTTTCT
1 TTTTTTCTTTATGCTTTTCT
118409 TTTTTTCTTT-T-CTTTTCT
1 TTTTTTCTTTATGCTTTTCT
118427 TTTTTTCTT
1 TTTTTTCTT
118436 GCATGTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 15 0.58
19 1 0.04
20 10 0.38
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTTCTTTATGCTTTTCT
Found at i:118485 original size:24 final size:25
Alignment explanation
Indices: 118438--118490 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 25
118428 TTTTTCTTGC
118438 ATGTTATCTCCTTTGTGACTTGTAG
1 ATGTTATCTCCTTTGTGACTTGTAG
118463 ATGTTATCTCCTTT-TGACTTGTAG
1 ATGTTATCTCCTTTGTGACTTGTAG
118487 ATGT
1 ATGT
118491 GAGTGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (25 bp):
ATGTTATCTCCTTTGTGACTTGTAG
Found at i:130692 original size:16 final size:16
Alignment explanation
Indices: 130668--130701 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
130658 TATCGCCGAC
*
130668 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
130684 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
130700 CG
1 CG
130702 TGAATAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:136215 original size:16 final size:17
Alignment explanation
Indices: 136188--136222 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
136178 TATCGCCGAC
136188 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
136205 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
136221 CG
1 CG
136223 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:138335 original size:21 final size:20
Alignment explanation
Indices: 138302--138342 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
138292 TTATTTTATT
138302 TATTTTTTAATTAAAAATAA
1 TATTTTTTAATTAAAAATAA
*
138322 TATTTTTATTATTAAAAATAA
1 TATTTTT-TAATTAAAAATAA
138343 AAAATAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTTTTAATTAAAAATAA
Found at i:138716 original size:60 final size:59
Alignment explanation
Indices: 138652--138765 Score: 129
Period size: 60 Copynumber: 1.9 Consensus size: 59
138642 ACTATGGTTA
* * * **
138652 TCATTATGAATTACTTCTCAAACTTTTGAATGTTTCAATTTCATTCCCAAACTATGACCT
1 TCATTATAAATTACTCCCCAAACTTTTGAACATTTCAATTTCA-TCCCAAACTATGACCT
* ** * *
138712 TCATTCTAAATTGGTCCCCAAATTTTTGAACATTTTAATTTCATCCCAAACTAT
1 TCATTATAAATTACTCCCCAAACTTTTGAACATTTCAATTTCATCCCAAACTAT
138766 ACATATATAC
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
59 11 0.25
60 33 0.75
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (59 bp):
TCATTATAAATTACTCCCCAAACTTTTGAACATTTCAATTTCATCCCAAACTATGACCT
Found at i:141745 original size:14 final size:13
Alignment explanation
Indices: 141726--141756 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
141716 TAAATTGAAT
141726 AAATATGAAATTAC
1 AAATATGAAATT-C
141740 AAATATGAAATTC
1 AAATATGAAATTC
141753 AAAT
1 AAAT
141757 CAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (13 bp):
AAATATGAAATTC
Found at i:141842 original size:11 final size:11
Alignment explanation
Indices: 141826--141876 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
141816 AAATTAAAAA
141826 AATAATAATAT
1 AATAATAATAT
141837 AATAATTATATAT
1 AATAA-TA-ATAT
*
141850 ATATAAAAACTAT
1 A-ATAATAA-TAT
141863 -ATAATAATAT
1 AATAATAATAT
141873 AATA
1 AATA
141877 TATATAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
10 3 0.09
11 14 0.42
12 3 0.09
13 9 0.27
14 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
AATAATAATAT
Found at i:141877 original size:26 final size:28
Alignment explanation
Indices: 141833--141906 Score: 102
Period size: 26 Copynumber: 2.8 Consensus size: 28
141823 AAAAATAATA
141833 ATATAATAATTATATATATATAAAAACT
1 ATATAATAATTATATATATATAAAAACT
*
141861 ATATAATAA-TATA-ATATATATAAACT
1 ATATAATAATTATATATATATAAAAACT
*
141887 ATATAAT--TTATATTTATATA
1 ATATAATAATTATATATATATA
141907 TTATATATAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.10
26 25 0.60
27 4 0.10
28 9 0.21
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATAATAATTATATATATATAAAAACT
Found at i:142176 original size:13 final size:13
Alignment explanation
Indices: 142158--142182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
142148 TTTTTATTTT
142158 TATATTATTTAAA
1 TATATTATTTAAA
142171 TATATTATTTAA
1 TATATTATTTAA
142183 TTACTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTATTTAAA
Found at i:142254 original size:14 final size:15
Alignment explanation
Indices: 142237--142268 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
142227 ATAATAAATA
142237 ATTAT-AAATATATT
1 ATTATAAAATATATT
142251 ATTATAAAATATATT
1 ATTATAAAATATATT
142266 ATT
1 ATT
142269 TTTAGCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:142294 original size:58 final size:57
Alignment explanation
Indices: 142195--142315 Score: 172
Period size: 58 Copynumber: 2.1 Consensus size: 57
142185 ACTAAAAATC
* *
142195 ATTAT-AAATATATTATTTTAACCGTTTAAAATATAATAAATAATTATAAATATATT
1 ATTATAAAATATATTATTTTAACAGTTTAAAATATAAAAAATAATTATAAATATATT
* * * *
142251 ATTATAAAATATATTATTTTTAGCATTTTAAAATGTAAAAAATATTTATAAATATATT
1 ATTATAAAATATATTA-TTTTAACAGTTTAAAATATAAAAAATAATTATAAATATATT
142309 ATTATAA
1 ATTATAA
142316 TTTATAAAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 5 0.09
57 10 0.18
58 42 0.74
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (57 bp):
ATTATAAAATATATTATTTTAACAGTTTAAAATATAAAAAATAATTATAAATATATT
Found at i:142318 original size:21 final size:21
Alignment explanation
Indices: 142294--142355 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
142284 TGTAAAAAAT
142294 ATTTATAAATATATTATTATA
1 ATTTATAAATATATTATTATA
*
142315 ATTTATAAAGTATATTATT-TT
1 ATTTATAAA-TATATTATTATA
* *
142336 ATTTTTAAA-ATATTAATATA
1 ATTTATAAATATATTATTATA
142356 TTTTGATCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 7 0.20
20 1 0.03
21 18 0.51
22 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTATAAATATATTATTATA
Found at i:143903 original size:31 final size:31
Alignment explanation
Indices: 143861--143927 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
143851 AATACGGTGG
* * *
143861 AGTGACCATTTTGTTATAAATTAATAATATT
1 AGTGACCATTTTATTACAAATAAATAATATT
*
143892 AGTGACTATTTTATTACAAATAAATAATATT
1 AGTGACCATTTTATTACAAATAAATAATATT
143923 AGTGA
1 AGTGA
143928 TTTAATTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTGACCATTTTATTACAAATAAATAATATT
Found at i:144902 original size:39 final size:39
Alignment explanation
Indices: 144859--144950 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 39
144849 TTTAAAAAAC
*
144859 AATTTAGAATGTTAAT-CTA-AAATAGTTTAAGAAATTAAG
1 AATTTAGAATGTTAATGATAGAAA-A-TTTAAGAAATTAAG
* *
144898 AATTTAGAAAGAT-ATGATAGTAAAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGATAG-AAAATTTAAGAAATTAAG
144937 AATTTAGAATGTTA
1 AATTTAGAATGTTA
144951 GAGTGAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
38 2 0.05
39 38 0.86
40 1 0.02
41 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.35
Consensus pattern (39 bp):
AATTTAGAATGTTAATGATAGAAAATTTAAGAAATTAAG
Found at i:145963 original size:16 final size:15
Alignment explanation
Indices: 145943--145985 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
145933 TATTTTTTTC
145943 AAATAATTATAATAA
1 AAATAATTATAATAA
*
145958 ACAATAAGTATAATAA
1 A-AATAATTATAATAA
*
145974 AAAAAATTATAA
1 AAATAATTATAA
145986 CGAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATAATTATAATAA
Found at i:147979 original size:2 final size:2
Alignment explanation
Indices: 147972--147999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
147962 TATCGTCCAC
147972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
148000 GTATTAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:148544 original size:16 final size:16
Alignment explanation
Indices: 148500--148546 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
148490 AGCTAAAACT
148500 GCATGGTGTTTTGCTA
1 GCATGGTGTTTTGCTA
** *
148516 GTCA-CCTGCTTTGCTA
1 G-CATGGTGTTTTGCTA
148532 GCATGGTGTTTTGCT
1 GCATGGTGTTTTGCT
148547 CCTGTATTGC
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.11, C:0.19, G:0.28, T:0.43
Consensus pattern (16 bp):
GCATGGTGTTTTGCTA
Done.