Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006482.1 Hibiscus syriacus cultivar Beakdansim tig00015730_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: 91703
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:126 original size:37 final size:36
Alignment explanation
Indices: 69--353 Score: 272
Period size: 37 Copynumber: 8.1 Consensus size: 36
59 CAAAGATTGG
* *
69 TGTTTCAAGAGAAA-TCGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGGGAAACT-GTCTCAAGAGAGACAAAA-TT
106 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
143 AGTTCCGAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* ** *
179 TGTTTCAAGGAAAACAAAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT
208 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
244 TGTTTTAAGGAAAACTGTCTCAAGAGACAAAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
280 TGTTTCAA--GAAACTGTCTC-A-AGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
312 TGTTTTAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
349 TGTTT
1 TGTTT
354 TGAGTAAATT
Statistics
Matches: 203, Mismatches: 30, Indels: 30
0.77 0.11 0.11
Matches are distributed among these distances:
28 1 0.00
29 19 0.09
30 1 0.00
31 1 0.00
32 19 0.09
33 3 0.01
34 20 0.10
35 2 0.01
36 66 0.33
37 70 0.34
38 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:232 original size:102 final size:101
Alignment explanation
Indices: 104--288 Score: 282
Period size: 102 Copynumber: 1.8 Consensus size: 101
94 GAGATAAAAC
* *
104 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCGA-GAGAAACTGTCTCAAGG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAGGA-AAACTGTCTCAAGA
* *
168 GAGACAAAATTTGTTTCAAGGAAAACAAATTCAAAGAT
64 GACAAAAAATTTGTTTCAAGGAAAACAAATTCAAAGAT
* **
206 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGAAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAGGAAAACTGTCTCAAGAGA
271 CAAAAAATTTGTTTCAAG
66 CAAAAAATTTGTTTCAAG
289 AAACTGTCTC
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 37 0.49
102 38 0.51
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (101 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAGGAAAACTGTCTCAAGAGA
CAAAAAATTTGTTTCAAGGAAAACAAATTCAAAGAT
Found at i:275 original size:34 final size:35
Alignment explanation
Indices: 219--372 Score: 188
Period size: 36 Copynumber: 4.4 Consensus size: 35
209 GTTTCAAGGG
219 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGA
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAA-GA
* * *
255 AAACTGTCTCAAGAGACAAAAAATTTGTTTCAAG-
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
289 AAACTGTCTC-A-AGAGACAAAATTTGTTTTAAGA
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
* * *
322 GAAATTGTCTCAAGAGAGACAAAACTTTGTTTTGAGT
1 -AAACTGTCTCAAGAGAGACAAAA-TTTGTTTTAAGA
*
359 AAATTAGTCTCAAG
1 AAACT-GTCTCAAG
373 CGAAACGACA
Statistics
Matches: 103, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
32 18 0.17
33 1 0.01
34 19 0.18
35 2 0.02
36 45 0.44
37 18 0.17
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (35 bp):
AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
Found at i:316 original size:68 final size:72
Alignment explanation
Indices: 206--353 Score: 216
Period size: 68 Copynumber: 2.1 Consensus size: 72
196 ATTCAAAGAT
206 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAG-GAAAACTGTCTCAAGAG
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAG-AAACTGTCTCAAGAG
270 ACA-AAAAA
64 ACACAAAAA
* *
278 TTTGTTTCAA-GAAACTGTCTC-A-AGAGACAAAATTTGTTTTAAGAGAAATTGTCTCAAGAGAG
1 TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAC
*
340 ACAAAAC
66 ACAAAAA
347 TTTGTTT
1 TTTGTTT
354 TGAGTAAATT
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
68 37 0.52
69 13 0.18
70 11 0.15
72 10 0.14
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (72 bp):
TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAC
ACAAAAA
Found at i:923 original size:41 final size:41
Alignment explanation
Indices: 852--931 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
842 AATCGTGTGT
*
852 GTGGGCACGATATCCACCATCGGAGTTGAAATCGTGGATCC
1 GTGGGCACGATATCCACCATCGGAGTTGAAATCATGGATCC
* *
893 GTGGGTACGATATCCTCC-TCGTGGAG-TGAAATCATGGAT
1 GTGGGCACGATATCCACCATC--GGAGTTGAAATCATGGAT
932 GACCCCTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 2 0.06
41 28 0.82
42 4 0.12
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (41 bp):
GTGGGCACGATATCCACCATCGGAGTTGAAATCATGGATCC
Found at i:6355 original size:35 final size:36
Alignment explanation
Indices: 6306--6408 Score: 127
Period size: 35 Copynumber: 2.8 Consensus size: 36
6296 TGGATCTTAT
* *
6306 TTTTAGGAGTTTGAATCAAAGTAAAACTCTAT-CAAA
1 TTTTA-GAATTTGAATCATAGTAAAACTCTATCCAAA
* *
6342 TTTTAGAATTTGAATCATAGTAAAACTCTATCCTAT
1 TTTTAGAATTTGAATCATAGTAAAACTCTATCCAAA
* *
6378 TTTTAAAAATTTGAATCCTAGTAAAACTCTA
1 TTTT-AGAATTTGAATCATAGTAAAACTCTA
6409 ACGTTATGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 24 0.41
36 11 0.19
37 24 0.41
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (36 bp):
TTTTAGAATTTGAATCATAGTAAAACTCTATCCAAA
Found at i:6400 original size:37 final size:35
Alignment explanation
Indices: 6315--6408 Score: 125
Period size: 37 Copynumber: 2.6 Consensus size: 35
6305 TTTTTAGGAG
* *
6315 TTTGAATCAAAGTAAAACTCTATCAAATTTTAGAA
1 TTTGAATCATAGTAAAACTCTATCAAATTTTAAAA
* *
6350 TTTGAATCATAGTAAAACTCTATCCTATTTTTAAAAA
1 TTTGAATCATAGTAAAACTCTAT-CAAATTTT-AAAA
*
6387 TTTGAATCCTAGTAAAACTCTA
1 TTTGAATCATAGTAAAACTCTA
6409 ACGTTATGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
35 22 0.42
36 6 0.12
37 24 0.46
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (35 bp):
TTTGAATCATAGTAAAACTCTATCAAATTTTAAAA
Found at i:13310 original size:3 final size:3
Alignment explanation
Indices: 13302--13328 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13292 ATAAAATTAA
13302 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
13329 CAACTAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:17177 original size:20 final size:20
Alignment explanation
Indices: 17154--17215 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
17144 ATTGAACAAG
17154 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
* **
17174 TTCTTCTTC-TT-TGGGACTAG
1 TTCTTC-TCATTAT-GAACTTC
17194 TTCTTCTCATTATGAAC-TC
1 TTCTTCTCATTATGAACTTC
17213 TTC
1 TTC
17216 CACTTCTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
19 6 0.19
20 23 0.72
21 3 0.09
ACGTcount: A:0.16, C:0.24, G:0.10, T:0.50
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTTC
Found at i:17226 original size:39 final size:39
Alignment explanation
Indices: 17152--17258 Score: 187
Period size: 39 Copynumber: 2.7 Consensus size: 39
17142 ATATTGAACA
**
17152 AGTTCTTCTCATTATGAACTTCTTCTTCTTCTTTGGGACT
1 AGTTCTTCTCATTATGAAC-TCTTCCACTTCTTTGGGACT
17192 AGTTCTTCTCATTATGAACTCTTCCACTTCTTTGGGACT
1 AGTTCTTCTCATTATGAACTCTTCCACTTCTTTGGGACT
17231 AGTTCTTCTCATTATGAACTCTTCCACT
1 AGTTCTTCTCATTATGAACTCTTCCACT
17259 AGGAATGACA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
39 46 0.71
40 19 0.29
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.46
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTCTTCCACTTCTTTGGGACT
Found at i:17567 original size:123 final size:122
Alignment explanation
Indices: 17437--17769 Score: 501
Period size: 122 Copynumber: 2.7 Consensus size: 122
17427 GAAATAAGGC
*
17437 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-CCTTCAGATGAGTTTTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCCTTC-TCAGATGAGTTTTTCTCATTA
* * * *
17501 TGAAATCTATCTGGAAATGTTGATGTTGATATATCTCCTTCTGTGATAGAGTCGAGCAA
64 TGAACTCTATCTGGCAATGTTGATGCTGATATATCTCATTCTGTGATAGAGTCGAGCAA
*
17560 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTTTCCTTCTCAGATGA-TTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCCTTCTCAGATGAGTTT-TTCTCATTAT
* *
17624 GAACTCTATCTGGCAATATT-AGTGCTGATTTATCTCATTCTGTGATAGAGTCGAGCAA
65 GAACTCTATCTGGCAATGTTGA-TGCTGATATATCTCATTCTGTGATAGAGTCGAGCAA
* * *
17682 AAGGTTGAACAATTTCTTCTCATTATGAACTTTTTCTTTCTTCTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAAC-TTTTCTTCCTTCTCAGATGAGTTTTTCTCATTAT
17747 GAACTCTATCTGGCAATGTTGAT
65 GAACTCTATCTGGCAATGTTGAT
17770 CCATCGAGTG
Statistics
Matches: 191, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
121 4 0.02
122 103 0.54
123 81 0.42
124 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCCTTCTCAGATGAGTTTTTCTCATTATG
AACTCTATCTGGCAATGTTGATGCTGATATATCTCATTCTGTGATAGAGTCGAGCAA
Found at i:18285 original size:21 final size:22
Alignment explanation
Indices: 18261--18301 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
18251 AGATGTTTAT
18261 AAAAGAATAAA-TT-GAATTTCG
1 AAAAG-ATAAACTTAGAATTTCG
18282 AAAAGATAAACTTAGAATTT
1 AAAAGATAAACTTAGAATTT
18302 ATTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.54, C:0.05, G:0.12, T:0.29
Consensus pattern (22 bp):
AAAAGATAAACTTAGAATTTCG
Found at i:18683 original size:20 final size:18
Alignment explanation
Indices: 18654--18716 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 18
18644 CTCTTTTTAT
*
18654 TTTTTATTTTCTTTTCTTTC
1 TTTTTCTTTT-TTTTC-TTC
18674 TTTTTCTTTTTTTCTCCTTC
1 TTTTTCTTTTTTT-T-CTTC
18694 TTTTTTCTTCTTTTTTCTTC
1 -TTTTTCTT-TTTTTTCTTC
18714 TTT
1 TTT
18717 AAGCATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 6 0.16
20 17 0.45
21 10 0.26
22 5 0.13
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTTTTTCTTC
Found at i:18709 original size:10 final size:10
Alignment explanation
Indices: 18665--18716 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
18655 TTTTATTTTC
18665 TTTTCTT-TCT
1 TTTTCTTCT-T
18675 TTTTCTT-TT
1 TTTTCTTCTT
18684 TTTCTCCTTCTT
1 TTT-T-CTTCTT
18696 TTTTCTTCTT
1 TTTTCTTCTT
18706 TTTTCTTCTT
1 TTTTCTTCTT
18716 T
1 T
18717 AAGCATAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
9 4 0.10
10 26 0.67
11 4 0.10
12 5 0.13
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:24544 original size:28 final size:28
Alignment explanation
Indices: 24511--24564 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
24501 CATGACGTTC
24511 TATCTTTTCTTCCATTCTCTTACTTGTT
1 TATCTTTTCTTCCATTCTCTTACTTGTT
24539 TATCTTTTCTTCCATTCTCTTACTTG
1 TATCTTTTCTTCCATTCTCTTACTTG
24565 CTTTCCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.11, C:0.26, G:0.04, T:0.59
Consensus pattern (28 bp):
TATCTTTTCTTCCATTCTCTTACTTGTT
Found at i:27570 original size:16 final size:17
Alignment explanation
Indices: 27551--27582 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27541 CTATAATCCT
27551 TAATTCACATA-ATTTC
1 TAATTCACATACATTTC
27567 TAATTCACATACATTT
1 TAATTCACATACATTT
27583 ATTCAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTCACATACATTTC
Found at i:33791 original size:14 final size:16
Alignment explanation
Indices: 33753--33792 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
33743 AAATTGACCT
33753 AAAATCATTATGATGA
1 AAAATCATTATGATGA
33769 ACAAA-CATT-T-ATGA
1 A-AAATCATTATGATGA
33783 AAAATCATTA
1 AAAATCATTA
33793 AAACTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.14
14 9 0.43
15 1 0.05
16 5 0.24
17 3 0.14
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (16 bp):
AAAATCATTATGATGA
Found at i:37686 original size:19 final size:19
Alignment explanation
Indices: 37655--37705 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
37645 GACCAAAACC
37655 AAAATGAAA-ATAAATAAAT
1 AAAAT-AAATATAAATAAAT
37674 AAAATAAATATAAATAAAT
1 AAAATAAATATAAATAAAT
* *
37693 TATA-AAATATAAA
1 AAAATAAATATAAA
37706 ATATATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATAAATATAAATAAAT
Found at i:37860 original size:37 final size:37
Alignment explanation
Indices: 37777--37948 Score: 190
Period size: 37 Copynumber: 4.6 Consensus size: 37
37767 AAAGATTATA
* * *
37777 TATATTATATACATTTTTAAAAAAATGTTTTCTAAAAC
1 TATATTATATA-GTTTTCAAAAAAATGTTTTCAAAAAC
*
37815 TATA-TATATA-TATTCAAAAAATATGTTTTCAAAAAC
1 TATATTATATAGTTTTCAAAAAA-ATGTTTTCAAAAAC
* **
37851 TATATTATATATGTTTTCACAAAACCGTTTT-AAAAAC
1 TATATTATATA-GTTTTCAAAAAAATGTTTTCAAAAAC
*
37888 TATA-TATTATACGTTTTCAAAAATATGTTTTCAAAAAC
1 TATATTA-TATA-GTTTTCAAAAAAATGTTTTCAAAAAC
37926 TATATTATATACGTTTTCAAAAA
1 TATATTATATA-GTTTTCAAAAA
37949 CTATATATTA
Statistics
Matches: 115, Mismatches: 12, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
35 9 0.08
36 19 0.17
37 41 0.36
38 35 0.30
39 11 0.10
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (37 bp):
TATATTATATAGTTTTCAAAAAAATGTTTTCAAAAAC
Found at i:37941 original size:24 final size:24
Alignment explanation
Indices: 37914--37973 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
37904 TCAAAAATAT
37914 GTTTTCAAAAACTATAT-TATATAC
1 GTTTTCAAAAACTATATAT-TATAC
*
37938 GTTTTCAAAAACTATATATTATAT
1 GTTTTCAAAAACTATATATTATAC
37962 GTTTTCAAAAAC
1 GTTTTCAAAAAC
37974 ATGTTTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 33 0.97
25 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (24 bp):
GTTTTCAAAAACTATATATTATAC
Found at i:37943 original size:99 final size:97
Alignment explanation
Indices: 37839--38045 Score: 269
Period size: 99 Copynumber: 2.1 Consensus size: 97
37829 CAAAAAATAT
37839 GTTTTCAAAAACTATAT-TATATATGTTTTCACAAAAC-CGTTTTAAAAACTATA-TATTATACG
1 GTTTTCAAAAACTATATAT-TATATGTTTTCA-AAAACACGTTTTAAAAACTATATTA-TATACG
*
37901 TTTTCAAAAA-TATGTTTTCAAAAACTATATTATATAC
63 TTTTCAAAAACT-TGTTTTCAAAAACTAT-GTAT-TAC
* * *
37938 GTTTTCAAAAACTATATATTATATGTTTTCAAAAACATGTTTTCAAAACTATATTATATATGTTT
1 GTTTTCAAAAACTATATATTATATGTTTTCAAAAACACGTTTTAAAAACTATATTATATACGTTT
* * *
38003 TCAAAAACTTTTTTTTAAAAACTATGTATTAT
66 TCAAAAACTTGTTTTCAAAAACTATGTATTAC
38035 GTTTTCAAAAA
1 GTTTTCAAAAA
38046 TGTATTTCCA
Statistics
Matches: 97, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
97 13 0.13
98 8 0.08
99 72 0.74
100 4 0.04
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (97 bp):
GTTTTCAAAAACTATATATTATATGTTTTCAAAAACACGTTTTAAAAACTATATTATATACGTTT
TCAAAAACTTGTTTTCAAAAACTATGTATTAC
Found at i:37960 original size:62 final size:61
Alignment explanation
Indices: 37876--38011 Score: 229
Period size: 62 Copynumber: 2.2 Consensus size: 61
37866 TTCACAAAAC
*
37876 CGTTTT-AAAAACTATATATTATACGTTTTCAAAAATATGTTTTCAAAAACTATATTATATA
1 CGTTTTCAAAAACTATATATTATACGTTTTCAAAAACATGTTTTC-AAAACTATATTATATA
*
37937 CGTTTTCAAAAACTATATATTATATGTTTTCAAAAACATGTTTTCAAAACTATATTATATA
1 CGTTTTCAAAAACTATATATTATACGTTTTCAAAAACATGTTTTCAAAACTATATTATATA
*
37998 TGTTTTCAAAAACT
1 CGTTTTCAAAAACT
38012 TTTTTTTAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
61 35 0.49
62 36 0.51
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (61 bp):
CGTTTTCAAAAACTATATATTATACGTTTTCAAAAACATGTTTTCAAAACTATATTATATA
Found at i:37991 original size:37 final size:38
Alignment explanation
Indices: 37938--38067 Score: 155
Period size: 37 Copynumber: 3.5 Consensus size: 38
37928 TATTATATAC
37938 GTTTTCAAAAACTATATATTATATGTTTTCAAAAACAT
1 GTTTTCAAAAACTATATATTATATGTTTTCAAAAACAT
*
37976 GTTTTC-AAAACTATAT-TATATATGTTTTCAAAAACTT
1 GTTTTCAAAAACTATATAT-TATATGTTTTCAAAAACAT
* * *
38013 TTTTTTAAAAACTATGTA-T-TATGTTTTC-AAAA-AT
1 GTTTTCAAAAACTATATATTATATGTTTTCAAAAACAT
38047 GTATTTCCAAAAACTATATAT
1 GT-TTT-CAAAAACTATATAT
38068 ATTGTATATT
Statistics
Matches: 78, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
34 2 0.03
35 7 0.09
36 21 0.27
37 33 0.42
38 15 0.19
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (38 bp):
GTTTTCAAAAACTATATATTATATGTTTTCAAAAACAT
Found at i:38059 original size:36 final size:35
Alignment explanation
Indices: 37938--38069 Score: 151
Period size: 36 Copynumber: 3.6 Consensus size: 35
37928 TATTATATAC
37938 GTTTTCAAAAACTATATATTATATGTTTTCAAAAACAT
1 GTTTTCAAAAACTATATA-TATATGTTTTC-AAAA-AT
37976 GTTTTC-AAAACTATATTATATATGTTTTCAAAAACTT
1 GTTTTCAAAAACTATA-TATATATGTTTTCAAAAA--T
* * *
38013 TTTTTTAAAAACTATGTAT-TATGTTTTCAAAAAT
1 GTTTTCAAAAACTATATATATATGTTTTCAAAAAT
38047 GTATTTCCAAAAACTATATATAT
1 GT-TTT-CAAAAACTATATATAT
38070 TGTATATTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
34 2 0.02
35 4 0.05
36 30 0.37
37 29 0.36
38 16 0.20
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (35 bp):
GTTTTCAAAAACTATATATATATGTTTTCAAAAAT
Found at i:39392 original size:200 final size:200
Alignment explanation
Indices: 38779--39558 Score: 778
Period size: 201 Copynumber: 3.9 Consensus size: 200
38769 AAATTGGCTT
* * * * * * * **
38779 ATTGTTG-TCAAATCGTAGTCAACCTTGGTCTTCTTATTGGCTTAAAGACTTTGATTTTAAATTC
1 ATTGTTGCT-AAATCGTAGCCAACATAGGTCTTCTTCTTGACTTAAAGACCTCG-TTCAAAATTC
* * * * * *
38843 AACCGAAAAGTAGTTCCTCGCTGCTACCATACAATTGATACACCCCTCGAACTAAATGGAATCGA
64 AACCAAAAAGTAGTTCCTCACTGCTACCATGCAGTTGATACA-CCCTCGAGCTGAATGGAATCGA
** * * * ** * * * * **
38908 ACTTGAAAGTTTTTGTTGACATACAACTTTTCTCGACTTAAGCTATGTTGTAAATTAGACTGGGA
128 ACTCAAAAGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTAGGTTGGGA
*
38973 -GATATTTC
193 TG-TAGTTC
* * *
38981 CTTGTTGCTATATTGTAGCCAACATAGGTCTTCTTCTTGACTTAAAGACCTCGATTCAAAATTCA
1 ATTGTTGCTAAATCGTAGCCAACATAGGTCTTCTTCTTGACTTAAAGACCTCG-TTCAAAATTCA
* * * * * * * * * *
39046 ACCAAAAAGTAGTTCCTCGCAGCTACCTTGCGGTTAATGCGCCCTCGAGCTTAACGGAATCAAAC
65 ACCAAAAAGTAGTTCCTCACTGCTACCATGCAGTTGATACACCCTCGAGCTGAATGGAATCGAAC
* * * * * *
39111 TCGAAAGTTTTCGTTGACAGATAGTCCTTCTTGCCTTGAGCTATGCTATAAATTAGGTTGAGATA
130 TCAAAAGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTAGGTTGGGATG
*
39176 TAGATC
195 TAGTTC
* * * *
39182 ATTGTTGCTAAATCGTAGCCAATATAGGTCTTCTTCTTGACTAAAAGACCTCAGTTTAAACTTCA
1 ATTGTTGCTAAATCGTAGCCAACATAGGTCTTCTTCTTGACTTAAAGACCTC-GTTCAAAATTCA
** ** * *
39247 ACTGAAAAGTAGTTCCTCACTGCTATTATGCAGTTGATA-ACCCTTGAGCTGAATGTAATCGAAC
65 ACCAAAAAGTAGTTCCTCACTGCTACCATGCAGTTGATACACCCTCGAGCTGAATGGAATCGAAC
* * * *
39311 TTAAAAGTTTTTATTGATAGATAGCCCTTCTTGCCTTGAGCTATGCTATAAATTAGGTTGGGATG
130 TCAAAAGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTAGGTTGGGATG
39376 TAGTTC
195 TAGTTC
* *
39382 ATTGTTGCTAAATCGTAGCCAACATAGGTATTCTTCTTCACTTAAAGACCTCGGTTCAAAATTCA
1 ATTGTTGCTAAATCGTAGCCAACATAGGTCTTCTTCTTGACTTAAAGACCTC-GTTCAAAATTCA
* * * * * *
39447 A-CAAGAAAGTAGTTCCT-AGTTGCTACCATGCAGCTGATACGCCCTCAAGTTGAATGAAATCGA
65 ACCAA-AAAGTAGTTCCTCA-CTGCTACCATGCAGTTGATACACCCTCGAGCTGAATGGAATCGA
** *
39510 ACTCAAAAGTTTTTGTTGATTGATAGCCCTTCTCGTCTTGAGCTATGCT
128 ACTCAAAAGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCT
39559 GTGAATGGTT
Statistics
Matches: 473, Mismatches: 99, Indels: 13
0.81 0.17 0.02
Matches are distributed among these distances:
199 2 0.00
200 168 0.36
201 218 0.46
202 84 0.18
203 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (200 bp):
ATTGTTGCTAAATCGTAGCCAACATAGGTCTTCTTCTTGACTTAAAGACCTCGTTCAAAATTCAA
CCAAAAAGTAGTTCCTCACTGCTACCATGCAGTTGATACACCCTCGAGCTGAATGGAATCGAACT
CAAAAGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTAGGTTGGGATGT
AGTTC
Found at i:45360 original size:5 final size:5
Alignment explanation
Indices: 45350--45403 Score: 56
Period size: 5 Copynumber: 10.0 Consensus size: 5
45340 AATTATCTAC
45350 AAAAT AAAAT AAGAAT AAAAAT AAAAT AAAAAT AAAAT AAAGGA- AAAAT
1 AAAAT AAAAT AA-AAT -AAAAT AAAAT -AAAAT AAAAT AAA--AT AAAAT
45399 AAAAT
1 AAAAT
45404 TGTTATTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 1 0.02
5 25 0.58
6 14 0.33
7 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:45368 original size:11 final size:11
Alignment explanation
Indices: 45350--45390 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
45340 AATTATCTAC
45350 AAAAT-AAAAT
1 AAAATAAAAAT
45360 AAGAATAAAAAT
1 AA-AATAAAAAT
45372 AAAATAAAAAT
1 AAAATAAAAAT
45383 AAAATAAA
1 AAAATAAA
45391 GGAAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 2 0.07
11 20 0.69
12 7 0.24
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:45370 original size:17 final size:16
Alignment explanation
Indices: 45350--45403 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
45340 AATTATCTAC
*
45350 AAAATAAAATAAGAAT
1 AAAATAAAATAAAAAT
45366 AAAAATAAAATAAAAAT
1 -AAAATAAAATAAAAAT
**
45383 AAAATAAAGGAAAAAT
1 AAAATAAAATAAAAAT
45399 AAAAT
1 AAAAT
45404 TGTTATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 19 0.56
17 15 0.44
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:60436 original size:13 final size:14
Alignment explanation
Indices: 60411--60449 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
60401 ATTGTCCTAA
60411 AAAGATAAAAAAAT
1 AAAGATAAAAAAAT
*
60425 AAAGTTAAAAAAAT
1 AAAGATAAAAAAAT
60439 AAA-ATAAAAAA
1 AAAGATAAAAAA
60450 CAAAGAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAGATAAAAAAAT
Found at i:60496 original size:16 final size:17
Alignment explanation
Indices: 60471--60504 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
60461 TATTAAGATC
60471 AAAATAAAGTAAATAAA
1 AAAATAAAGTAAATAAA
60488 AAAAT-AAGTAAATAAA
1 AAAATAAAGTAAATAAA
60504 A
1 A
60505 GGAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAATAAAGTAAATAAA
Found at i:61211 original size:17 final size:18
Alignment explanation
Indices: 61174--61211 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
61164 TTATTTCGAA
*
61174 TGCTTTGCTTGCCTTGTT
1 TGCTTTGCTTGCCTTGAT
*
61192 TGCTTTG-TTGGCTTGAT
1 TGCTTTGCTTGCCTTGAT
61209 TGC
1 TGC
61212 CCCCCGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.03, C:0.18, G:0.26, T:0.53
Consensus pattern (18 bp):
TGCTTTGCTTGCCTTGAT
Found at i:61656 original size:2 final size:2
Alignment explanation
Indices: 61649--61675 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61639 AATAAATAAA
61649 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 A
61676 AAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61824 original size:24 final size:24
Alignment explanation
Indices: 61792--61848 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
61782 AAAAAATCGT
* *
61792 TTTTTAAAAACTATA-TGTATATG
1 TTTTCAAAAACTATATTATATATG
61815 TTTTCAAAAACTATATTATATATG
1 TTTTCAAAAACTATATTATATATG
61839 TTTTCAAAAA
1 TTTTCAAAAA
61849 ACCGTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (24 bp):
TTTTCAAAAACTATATTATATATG
Found at i:61833 original size:62 final size:61
Alignment explanation
Indices: 61764--61885 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 61
61754 TCAAAGATTA
* *
61764 TATATTATAT-TCGATTTCAAAAAATCGTTTTTTAAAAACTATAT-GTATATGTTTTCAAAAAC
1 TATATTATATAT-GATTTCAAAAAACCG--TTTTAAAAACTATATAGTATACGTTTTCAAAAAC
* * *
61826 TATATTATATATGTTTTCAAAAAACCGTTTTAACAACTATATATTATACGTTTTCAAAAA
1 TATATTATATATGATTTCAAAAAACCGTTTTAAAAACTATATAGTATACGTTTTCAAAAA
61886 TATGTTTTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 14 0.26
61 15 0.28
62 23 0.43
63 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.43
Consensus pattern (61 bp):
TATATTATATATGATTTCAAAAAACCGTTTTAAAAACTATATAGTATACGTTTTCAAAAAC
Found at i:61856 original size:38 final size:38
Alignment explanation
Indices: 61814--61980 Score: 175
Period size: 37 Copynumber: 4.5 Consensus size: 38
61804 ATATGTATAT
61814 GTTTTCAAAAACTATATTATATATGTTTTCAAAAAACC
1 GTTTTCAAAAACTATATTATATATGTTTTCAAAAAACC
* * *
61852 GTTTT-AACAACTATA-TATTATACGTTTTCAAAAATA-T
1 GTTTTCAAAAACTATATTA-TATATGTTTTCAAAAA-ACC
*
61889 GTTTTCAAAAATTATATTATATATGTTTTC-AAAAACC
1 GTTTTCAAAAACTATATTATATATGTTTTCAAAAAACC
** ***
61926 GTTTTTTTAAAACTATA-TAT-TATGTTTTCAAAAATGT
1 G-TTTTCAAAAACTATATTATATATGTTTTCAAAAAACC
*
61963 ATTTTCAAAAACTATATT
1 GTTTTCAAAAACTATATT
61981 GTATCTTAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
36 25 0.24
37 42 0.40
38 36 0.34
39 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.44
Consensus pattern (38 bp):
GTTTTCAAAAACTATATTATATATGTTTTCAAAAAACC
Found at i:61896 original size:75 final size:72
Alignment explanation
Indices: 61810--61980 Score: 254
Period size: 74 Copynumber: 2.3 Consensus size: 72
61800 AACTATATGT
61810 ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAAACCG-TTTTAACAACTATATATTATA
1 ATATGTTTTCAAAAACTATATTATATATGTTTTC-AAAAACCGTTTTTAA-AACTATATATTAT-
61874 CGTTTTCAAAA
63 -GTTTTCAAAA
*
61885 ATATGTTTTCAAAAATTATATTATATATGTTTTCAAAAACCGTTTTTTTAAAACTATATATTATG
1 ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCG--TTTTTAAAACTATATATTATG
61950 TTTTCAAAA
64 TTTTCAAAA
* *
61959 ATGTATTTTCAAAAACTATATT
1 ATATGTTTTCAAAAACTATATT
61981 GTATCTTAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
74 37 0.42
75 33 0.37
76 13 0.15
77 6 0.07
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.44
Consensus pattern (72 bp):
ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCGTTTTTAAAACTATATATTATGTT
TTCAAAA
Found at i:61905 original size:36 final size:36
Alignment explanation
Indices: 61810--61980 Score: 125
Period size: 38 Copynumber: 4.6 Consensus size: 36
61800 AACTATATGT
*
61810 ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAA
1 ATATGTTTTCAAAAATTATA-T-TATATGTTTTCAAAA
* * *
61848 A-ACCGTTTT-AACAACTATATATTATACGTTTTCAAAA
1 ATA-TGTTTTCAA-AAAT-TATATTATATGTTTTCAAAA
61885 ATATGTTTTCAAAAATTATATTATATATGTTTTCAAAA
1 ATATGTTTTCAAAAATTATA-T-TATATGTTTTCAAAA
** ** *
61923 A-CCGTTTTTTTAAAACTATA-TATTATGTTTTCAAAA
1 ATATG-TTTTCAAAAATTATATTA-TATGTTTTCAAAA
* * *
61959 ATGTATTTTCAAAAACTATATT
1 ATATGTTTTCAAAAATTATATT
61981 GTATCTTAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
35 2 0.02
36 31 0.30
37 29 0.28
38 39 0.37
39 4 0.04
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.44
Consensus pattern (36 bp):
ATATGTTTTCAAAAATTATATTATATGTTTTCAAAA
Found at i:65942 original size:3 final size:3
Alignment explanation
Indices: 65928--65978 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
65918 TAAAAAACAT
* *
65928 TAA TAA -AA TAA TAA TAA AAA CAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
65973 TAA TAA
1 TAA TAA
65979 ACATATATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:65959 original size:22 final size:23
Alignment explanation
Indices: 65907--65978 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 23
65897 TGGACCTAAA
65907 AATAA-AATAAATAAAAAACATTAAT
1 AATAATAAT-AAT-AAAAACA-TAAT
65932 AA-AATAATAATAAAAACA-AAT
1 AATAATAATAATAAAAACATAAT
*
65953 AATAATAATAAT-AATA-ATAAT
1 AATAATAATAATAAAAACATAAT
65974 AATAA
1 AATAA
65979 ACATATATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
20 1 0.02
21 16 0.37
22 9 0.21
23 7 0.16
24 5 0.12
25 5 0.12
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (23 bp):
AATAATAATAATAAAAACATAAT
Found at i:66005 original size:9 final size:8
Alignment explanation
Indices: 65905--66001 Score: 50
Period size: 9 Copynumber: 10.8 Consensus size: 8
65895 ATTGGACCTA
*
65905 AAAATAAA
1 AAAATAAT
*
65913 ATAAATAAA
1 A-AAATAAT
65922 AAACATTAAT
1 AAA-A-TAAT
65932 AAAATAAT
1 AAAATAAT
* *
65940 AATAAAAACA
1 AA-AATAA-T
65950 AATAATAAT
1 AA-AATAAT
65959 AATAATAAT
1 AA-AATAAT
65968 AATAATAAT
1 AA-AATAAT
65977 AAACATATAT
1 AAA-ATA-AT
*
65987 AATATATAT
1 AAAATA-AT
65996 AAAATA
1 AAAATA
66002 TATATTTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
8 10 0.13
9 48 0.64
10 17 0.23
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAATAAT
Found at i:66039 original size:36 final size:36
Alignment explanation
Indices: 65999--66320 Score: 218
Period size: 36 Copynumber: 8.8 Consensus size: 36
65989 TATATATAAA
65999 ATATATATTTTCAAAAATGTTTTAAAACTATATATT
1 ATATATATTTTCAAAAATGTTTTAAAACTATATATT
*
66035 ATATA-AGTTTTC-AAAATGATTTCAAAACTATATATT
1 ATATATA-TTTTCAAAAATG-TTTTAAAACTATATATT
*
66071 ATATA-AGTTTT-TAAAATGTTTTCAAAACCTATATATT
1 ATATATA-TTTTCAAAAATGTTTT-AAAA-CTATATATT
* * *
66108 ATATATATTTTCAAAAA--TTATATATATTATATATAT
1 ATATATATTTTCAAAAATGTTTTA-AAACTATATAT-T
* * ** *
66144 ATATATATATTCAAAAATCATTTGCAAACTATATAAT
1 ATATATATTTTCAAAAAT-GTTTTAAAACTATATATT
* *
66181 ATATATATTTTCAAAAATCATTTTCAAAGCTATATA--
1 ATATATATTTTCAAAAAT-GTTTT-AAAACTATATATT
* * *
66217 ATATATATTTTTAAAAATCAATTTTTTAAAC-AGTATATT
1 ATATATATTTTCAAAAAT---GTTTTAAAACTA-TATATT
* * *
66256 ATATGT-TTTTCAAAAATTGTTTTCTAAACAAT-TA-T
1 ATATATATTTTCAAAAA-TGTTTT-AAAACTATATATT
*
66291 ATATTATATTTTTCAAAAATATTTTCAAAA
1 ATA-TATA-TTTTCAAAAATGTTTT-AAAA
66321 ATTATACTAT
Statistics
Matches: 234, Mismatches: 28, Indels: 47
0.76 0.09 0.15
Matches are distributed among these distances:
35 22 0.09
36 95 0.41
37 63 0.27
38 46 0.20
39 8 0.03
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATATATTTTCAAAAATGTTTTAAAACTATATATT
Found at i:66129 original size:19 final size:19
Alignment explanation
Indices: 66105--66161 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
66095 AAACCTATAT
66105 ATTATATATATTTTCAAAA
1 ATTATATATATTTTCAAAA
* * *
66124 ATTATATATATTAT-ATAT
1 ATTATATATATTTTCAAAA
*
66142 A-TATATATATATTCAAAA
1 ATTATATATATTTTCAAAA
66160 AT
1 AT
66162 CATTTGCAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 10 0.34
18 6 0.21
19 13 0.45
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTATATATATTTTCAAAA
Found at i:66233 original size:73 final size:71
Alignment explanation
Indices: 65993--66319 Score: 249
Period size: 73 Copynumber: 4.5 Consensus size: 71
65983 ATATAATATA
* * * *
65993 TATAAAATATATATTTTCAAAAATGTTTTAAAACTATATATTATATA-AGTTTTC-AAAATGA-T
1 TATATAATATATATTTTCAAAAATATTTTCAAACTATATATTATATATA-TTTTCAAAAATCATT
66055 TTCAAAAC
65 TTC-AAAC
* * * *
66063 TATATATTATATAAGTTTT-TAAAATGTTTTCAAAACCTATATATTATATATATTTTCAAAAATT
1 TATATAATATAT-A-TTTTCAAAAATATTTTC-AAA-CTATATATTATATATATTTTCAAAAATC
* *
66127 ATATAT-ATTA-
62 AT-TTTCA-AAC
* * *
66137 TATATATATATATATATTCAAAAATCATTTGCAAACTATATAATATATATATTTTCAAAAATCAT
1 TATATA-ATATATATTTTCAAAAAT-ATTTTCAAACTATATATTATATATATTTTCAAAAATCAT
66202 TTTCAAAGC
64 TTTCAAA-C
* * * *
66211 TATATAATATATATTTTTAAAAATCAATTTTTTAAAC-AGTATATTATATGT-TTTTCAAAAATT
1 TATATAATATATATTTTCAAAAAT--A-TTTTCAAACTA-TATATTATATATATTTTCAAAAATC
*
66274 GTTTTCTAAAC
62 ATTTTC-AAAC
*
66285 AAT-TATATATTATATTTTTCAAAAATATTTTCAAA
1 TATATA-ATA-TATA-TTTTCAAAAATATTTTCAAA
66320 AATTATACTA
Statistics
Matches: 207, Mismatches: 28, Indels: 41
0.75 0.10 0.15
Matches are distributed among these distances:
70 10 0.05
71 11 0.05
72 10 0.05
73 76 0.37
74 54 0.26
75 34 0.16
76 12 0.06
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (71 bp):
TATATAATATATATTTTCAAAAATATTTTCAAACTATATATTATATATATTTTCAAAAATCATTT
TCAAAC
Found at i:66332 original size:38 final size:38
Alignment explanation
Indices: 66133--66334 Score: 138
Period size: 38 Copynumber: 5.3 Consensus size: 38
66123 AATTATATAT
* *
66133 ATTATATATATATATATATATTCAAAAATCATTTGC--AA
1 ATTATATATAT-TATAT-TTTTCAAAAATCATTTTCAAAA
*
66171 ACTATATA-ATATATATATTTTCAAAAATCATTTTC-AAA
1 ATTATATATAT-TATAT-TTTTCAAAAATCATTTTCAAAA
** * *
66209 GCTATATA-ATATATATTTTT-AAAAATCAATTTTTTAAAC
1 ATTATATATAT-TATATTTTTCAAAAATC-A-TTTTCAAAA
* * **
66248 AGTATAT-TA-TATGTTTTTCAAAAATTGTTTTCTAAACA
1 ATTATATATATTATATTTTTCAAAAATCATTTTC-AAA-A
66286 A-T-TATATATTATATTTTTCAAAAAT-ATTTTCAAAA
1 ATTATATATATTATATTTTTCAAAAATCATTTTCAAAA
66321 ATTATACTATATTA
1 ATTATA-TATATTA
66335 ATATATATAT
Statistics
Matches: 136, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
35 2 0.01
36 18 0.13
37 51 0.38
38 57 0.42
39 8 0.06
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (38 bp):
ATTATATATATTATATTTTTCAAAAATCATTTTCAAAA
Found at i:66361 original size:5 final size:5
Alignment explanation
Indices: 66351--66377 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
66341 ATATATATAT
66351 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
66378 TCCAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:67069 original size:85 final size:85
Alignment explanation
Indices: 66932--67110 Score: 243
Period size: 85 Copynumber: 2.1 Consensus size: 85
66922 TACCATGCGG
*
66932 TTGATATGTCATCAAGCTGAATGAAATCGAACTCGATAGTTTTTGTTAACAGATAACCCTTCTCA
1 TTGATATGTCATCAAGCTGAATGAAATCGAACTCGATAGTTTTGGTTAACAGATAACCCTTCTCA
*
66997 CCTTGAGATATGTTGTAAAT
66 CCTTGAGATATGCTGTAAAT
* ** * * *
67017 TTGATATGTCTTTGAGCTGAATGTAATCGATCTCGA-AGGTTTTGGTTGACAGATAACCCTTCTC
1 TTGATATGTCATCAAGCTGAATGAAATCGAACTCGATA-GTTTTGGTTAACAGATAACCCTTCTC
* *
67081 GCCTTGAGTTATGCTGTAAAT
65 ACCTTGAGATATGCTGTAAAT
*
67102 TTTATATGT
1 TTGATATGT
67111 AATCGAACTT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 1 0.01
85 81 0.99
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (85 bp):
TTGATATGTCATCAAGCTGAATGAAATCGAACTCGATAGTTTTGGTTAACAGATAACCCTTCTCA
CCTTGAGATATGCTGTAAAT
Found at i:67125 original size:70 final size:70
Alignment explanation
Indices: 67037--67180 Score: 216
Period size: 70 Copynumber: 2.1 Consensus size: 70
67027 TTTGAGCTGA
* *
67037 ATGTAATCGATCTCGAAGGTTTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
1 ATGTAATCGAACTCGAAGGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
67102 TTTAT
66 TTTAT
* * * * *
67107 ATGTAATCGAACTTGAAGGTTTTCGTTGGCAGATAACCCTTTTTGGCTTGAGTTATGCTGTAAAT
1 ATGTAATCGAACTCGAAGGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
*
67172 TTTTT
66 TTTAT
67177 ATGT
1 ATGT
67181 CCTTGAGCTG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41
Consensus pattern (70 bp):
ATGTAATCGAACTCGAAGGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
TTTAT
Found at i:67228 original size:85 final size:84
Alignment explanation
Indices: 67107--67400 Score: 376
Period size: 85 Copynumber: 3.5 Consensus size: 84
67097 TAAATTTTAT
* * * * *
67107 ATGTAATCGAACTTGAAGGTTTTCGTTGGCAGATAACCCTTTTTGGCTTGAGTTATGCTGTAAAT
1 ATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAACCCTTTTT-CCTTGAGTTATGCTGTAAAT
**
67172 TTTTTATGTCCTTGAGCTGA
65 TTGATATGTCCTTGAGCTGA
* * **
67192 ATGTAATCGAACTCGAAGTTTTTGGTTGACAAATAACCATTCTTTCCTTGAGTTATATTGTAAAT
1 ATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAACCCTT-TTTCCTTGAGTTATGCTGTAAAT
*
67257 TTGATATGTCCTTGAGCTAA
65 TTGATATGTCCTTGAGCTGA
** *
67277 ATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAACCCTTCTCACCTTGAGTTATGCTATAAAT
1 ATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAACCCTT-TTTCCTTGAGTTATGCTGTAAAT
*
67342 TTGATATGTCCTTGAGTTGA
65 TTGATATGTCCTTGAGCTGA
* * *
67362 ATGTAATCAAACTCGAATG-TTT-GTTGACAGATAACCCTT
1 ATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAACCCTT
67401 CTCACCTTGA
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
83 16 0.09
84 3 0.02
85 162 0.88
86 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (84 bp):
ATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAACCCTTTTTCCTTGAGTTATGCTGTAAATT
TGATATGTCCTTGAGCTGA
Found at i:72725 original size:18 final size:18
Alignment explanation
Indices: 72699--72782 Score: 125
Period size: 18 Copynumber: 4.7 Consensus size: 18
72689 TTTTATGAAA
*
72699 ACATCGAATGCATTTGCT
1 ACATCGAATGCATTTGAT
*
72717 ACATTGAATGCATTTGAT
1 ACATCGAATGCATTTGAT
72735 ACATCGAATGCATTTGAT
1 ACATCGAATGCATTTGAT
*
72753 GCATCGAATGCATTTGAT
1 ACATCGAATGCATTTGAT
*
72771 GCATCG-ATGCAT
1 ACATCGAATGCAT
72783 CAATGCACCA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
17 6 0.10
18 56 0.90
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (18 bp):
ACATCGAATGCATTTGAT
Found at i:72801 original size:19 final size:19
Alignment explanation
Indices: 72777--72847 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
72767 TGATGCATCG
*
72777 ATGCATCAATGCACCAGTC
1 ATGCATCGATGCACCAGTC
72796 ATGCATCGATGCACCAGTC
1 ATGCATCGATGCACCAGTC
72815 ATGCATCGATGCACCAGTC
1 ATGCATCGATGCACCAGTC
72834 ATGCATCGATGCAC
1 ATGCATCGATGCAC
72848 TCTGGCTATT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACCAGTC
Found at i:73454 original size:16 final size:16
Alignment explanation
Indices: 73435--73472 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
73425 AATCCTTAGT
*
73435 GTGGATAGCTAAGGTA
1 GTGGACAGCTAAGGTA
73451 GTGGACAGCTAAGGTA
1 GTGGACAGCTAAGGTA
73467 GTGGAC
1 GTGGAC
73473 GTAGAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.39, T:0.21
Consensus pattern (16 bp):
GTGGACAGCTAAGGTA
Found at i:79596 original size:65 final size:64
Alignment explanation
Indices: 79479--79686 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
79469 TTTCAAAGTG
* * * *
79479 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATT-G-AACATCGAATGCAT
1 ATGCATCGATGCACCACT-CATGCATCGATGCACTCA-GG-CT-ATTTAGAAACATCGAATGCAT
79541 TTC
62 TTC
79544 ATGCATCGATGCACACACT-ATGCATCGATGCACTCAGAG-T-TTTAAGAAAACATCGAATGCAT
1 ATGCATCGATGCAC-CACTCATGCATCGATGCACTCAG-GCTATTT-AG-AAACATCGAATGCAT
*
79606 TTG
62 TTC
* * * *
79609 ATGCATCGATGCACCAGTCATGCATCGATGCATTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACCACTCATGCATCGATGCACTCAGGCTATTTAGAAACATCGAATGCATTTC
79673 ATGCATCGATGCAC
1 ATGCATCGATGCAC
79687 TAAGGGTCCA
Statistics
Matches: 124, Mismatches: 9, Indels: 21
0.81 0.06 0.14
Matches are distributed among these distances:
61 2 0.02
63 2 0.02
64 50 0.40
65 64 0.52
66 6 0.05
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACCACTCATGCATCGATGCACTCAGGCTATTTAGAAACATCGAATGCATTTC
Found at i:87923 original size:29 final size:28
Alignment explanation
Indices: 87855--87970 Score: 80
Period size: 29 Copynumber: 4.1 Consensus size: 28
87845 AAAAAAAGTG
* * *
87855 TATTTATA-ATATTATAAAATATTTTTAAT
1 TATTTATATAT-TTTTAAAATA-TATTATT
*
87884 T-TTTATTTATTTTTAAAATCATATTATT
1 TATTTATATATTTTTAAAAT-ATATTATT
**
87912 TATTTATATATTTGAAAAAATATTAATTATT
1 TATTTATATATTT-TTAAAATA-T-ATTATT
87943 TATTTGA-AT-TTTTTAAAAT-TATTATT
1 TATTT-ATATATTTTTAAAATATATTATT
87969 TA
1 TA
87971 GTTTTAAAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
26 8 0.11
27 1 0.01
28 19 0.27
29 20 0.28
30 9 0.13
31 13 0.18
32 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTTATATATTTTTAAAATATATTATT
Found at i:88127 original size:21 final size:20
Alignment explanation
Indices: 88070--88131 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 20
88060 AATAATTTAA
88070 AAATA-ATATTATTT-TAAAT
1 AAATATATATT-TTTATAAAT
88089 AAATATTAATATGATTTTATAAATT
1 AAATA-T-ATAT--TTTTATAAA-T
88114 AAATATATATTTTTATAA
1 AAATATATATTTTTATAA
88132 TAATTTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
19 5 0.14
21 8 0.22
22 4 0.11
23 7 0.19
24 6 0.17
25 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATATATATTTTTATAAAT
Found at i:89139 original size:18 final size:19
Alignment explanation
Indices: 89111--89148 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
89101 GGTTTCAATT
89111 GCAAGGGGAAAGCAATTGC
1 GCAAGGGGAAAGCAATTGC
*
89130 GCAA-GGGAAATCAATTGC
1 GCAAGGGGAAAGCAATTGC
89148 G
1 G
89149 TGGGTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.16, G:0.34, T:0.13
Consensus pattern (19 bp):
GCAAGGGGAAAGCAATTGC
Found at i:89299 original size:15 final size:15
Alignment explanation
Indices: 89267--89299 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
89257 CCAATAGGAA
89267 TTAGGTTTTTGATAT
1 TTAGGTTTTTGATAT
89282 TTAGGATTTTTGAT-T
1 TTAGG-TTTTTGATAT
89297 TTA
1 TTA
89300 TGAATTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (15 bp):
TTAGGTTTTTGATAT
Found at i:91218 original size:26 final size:24
Alignment explanation
Indices: 91177--91224 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
91167 AATTAAAAAA
91177 GTAAAAAATATATAAAAATTAATT
1 GTAAAAAATATATAAAAATTAATT
*
91201 GTAAAAATATATTTTAAAAATTAA
1 GTAAAAA-ATA-TATAAAAATTAA
91225 AATTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
GTAAAAAATATATAAAAATTAATT
Found at i:91231 original size:26 final size:24
Alignment explanation
Indices: 91153--91232 Score: 63
Period size: 26 Copynumber: 3.1 Consensus size: 24
91143 AAAATAAAAT
*
91153 AAAATATATAATTAAATTAAAAAAGTAA
1 AAAATATATAA--AAATT--AAAATTAA
*
91181 AAAATATATAAAAATT-AATTGTAA
1 AAAATATATAAAAATTAAAAT-TAA
*
91205 AAATATATTTTAAAAATTAAAATTAA
1 AAA-ATA-TATAAAAATTAAAATTAA
91231 AA
1 AA
91233 TAAAATTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
23 2 0.05
24 6 0.14
25 3 0.07
26 19 0.43
27 3 0.07
28 11 0.25
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (24 bp):
AAAATATATAAAAATTAAAATTAA
Done.