Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007168.1 Hibiscus syriacus cultivar Beakdansim tig00018798_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: 78637
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:5893 original size:41 final size:41
Alignment explanation
Indices: 5836--6192 Score: 288
Period size: 41 Copynumber: 8.7 Consensus size: 41
5826 TTTTTTGAAT
* * *
5836 AAACGCCGCAAAAGACTCTTACTTTAGTGGTATTTGTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGTATTTTTATAC
** * * *
5877 AAACGCCGCTAAAGACTATTACTTTAGAGGTGTTTGTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGTATTTTTATAC
* * * * **
5918 AAATGCCACTAAAGACTCGTACTATAGCGGCGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGTATTTTTATAC
* * *
5959 ATACGCCGATATAA-ACTCGTACTTTAGTGGCATTTTTTTTATAC
1 AAACGCCGCTA-AAGACTCGTACTTTAGTGG---TATTTTTATAC
* **
6003 AAACGCCGCTAAAGACTCGTACTTTCGTGGTA-TTTTACGC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGTATTTTTATAC
* * * * * *
6043 AAACGACGTTATATACTCGAACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGTATTTTTATAC
* * * *
6084 AAA-GACCGTTATAGACTCGTATTTTAGTGGCATTTTTATAC
1 AAACG-CCGCTAAAGACTCGTACTTTAGTGGTATTTTTATAC
* * * * * ***
6125 AAACGTCACTATAGATTGGTACTTTAGTGACGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGTATTTTTATAC
* *
6166 AAACACCGCTAAAGACTCGAACTTTAG
1 AAACGCCGCTAAAGACTCGTACTTTAG
6193 GAAATGCATG
Statistics
Matches: 254, Mismatches: 54, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
40 32 0.13
41 184 0.72
42 3 0.01
43 2 0.01
44 33 0.13
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTCGTACTTTAGTGGTATTTTTATAC
Found at i:6061 original size:40 final size:40
Alignment explanation
Indices: 5968--6119 Score: 128
Period size: 40 Copynumber: 3.7 Consensus size: 40
5958 CATACGCCGA
* * *
5968 TATAAACTCGTACTTTAGTGGCATTTTTTTTATACAAACG-CCGC
1 TATAGACTCGTACTTTAGTGGCA----TTTTACACAAA-GACCGT
* * * *
6012 TAAAGACTCGTACTTTCGTGGTATTTTACGCAAACGA-CGT
1 TATAGACTCGTACTTTAGTGGCATTTTACACAAA-GACCGT
* * *
6052 TATATACTCGAACTTTAGTGGCATTTTTATACAAAGACCGT
1 TATAGACTCGTACTTTAGTGGCA-TTTTACACAAAGACCGT
*
6093 TATAGACTCGTATTTTAGTGGCATTTT
1 TATAGACTCGTACTTTAGTGGCATTTT
6120 TATACAAACG
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
40 37 0.42
41 32 0.36
44 19 0.22
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (40 bp):
TATAGACTCGTACTTTAGTGGCATTTTACACAAAGACCGT
Found at i:12713 original size:14 final size:14
Alignment explanation
Indices: 12690--12727 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
12680 TCTGTCTATA
12690 TGCAGAGATTT-TT
1 TGCAGAGATTTATT
*
12703 TCGCAGGGATTTATT
1 T-GCAGAGATTTATT
12718 TGCAGAGATT
1 TGCAGAGATT
12728 ACTTCCCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 1 0.05
14 17 0.81
15 3 0.14
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (14 bp):
TGCAGAGATTTATT
Found at i:13760 original size:3 final size:3
Alignment explanation
Indices: 13752--13795 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
13742 GGGATAAAAA
*
13752 TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT ATACT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT TAT T
13796 TACATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.81
4 4 0.11
5 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:15090 original size:30 final size:30
Alignment explanation
Indices: 15050--15108 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
15040 TTGAGTTTAT
15050 GTTTTGCTATTTAGGTCCTCTAAGTTTCTA
1 GTTTTGCTATTTAGGTCCTCTAAGTTTCTA
* * *
15080 GTTTTTCTATTTAGGTCTTTTAAGTTTCT
1 GTTTTGCTATTTAGGTCCTCTAAGTTTCT
15109 GTAATTACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.14, G:0.15, T:0.56
Consensus pattern (30 bp):
GTTTTGCTATTTAGGTCCTCTAAGTTTCTA
Found at i:15120 original size:30 final size:30
Alignment explanation
Indices: 15056--15120 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
15046 TTATGTTTTG
* *
15056 CTATTTAGGTCCTCTAAGTTTCTAGTTTTT
1 CTATTTAGGTCCTCTAAGTTTCTAGTATTA
* *
15086 CTATTTAGGTCTTTTAAGTTTCT-GTAATTA
1 CTATTTAGGTCCTCTAAGTTTCTAGT-ATTA
15116 CTATT
1 CTATT
15121 ATGGGACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (30 bp):
CTATTTAGGTCCTCTAAGTTTCTAGTATTA
Found at i:19171 original size:167 final size:167
Alignment explanation
Indices: 18895--19227 Score: 648
Period size: 167 Copynumber: 2.0 Consensus size: 167
18885 TGTTAGTACT
*
18895 CTTTCACCTTGCACGGCACTGGGAAATTTGGAACTTGGCATGGATATTGCCGTGACGGAGGAACT
1 CTTTCACCTTGCACGGCACTGAGAAATTTGGAACTTGGCATGGATATTGCCGTGACGGAGGAACT
*
18960 TGAACTGACTACTACAGTGAGCTATCTTTGTTAGACCTGTATTGTAAGTGTGGTTGTCTAGATAT
66 TGAACTGACTACTACAGTGAGCAATCTTTGTTAGACCTGTATTGTAAGTGTGGTTGTCTAGATAT
19025 GGTCAGGAAACTTATTGACTAGATGCCGAGTAAAAAA
131 GGTCAGGAAACTTATTGACTAGATGCCGAGTAAAAAA
19062 CTTTCACCTTGCACGGCACTGAGAAATTTGGAACTTGGCATGGATATTGCCGTGACGGAGGAACT
1 CTTTCACCTTGCACGGCACTGAGAAATTTGGAACTTGGCATGGATATTGCCGTGACGGAGGAACT
19127 TGAACTGACTACTACAGTGAGCAATCTTTGTTAGACCTGTATTGTAAGTGTGGTTGTCTAGATAT
66 TGAACTGACTACTACAGTGAGCAATCTTTGTTAGACCTGTATTGTAAGTGTGGTTGTCTAGATAT
19192 GGTCAGGAAACTTATTGACTAGATGCCGAGTAAAAA
131 GGTCAGGAAACTTATTGACTAGATGCCGAGTAAAAA
19228 TGTTAATTGT
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 164 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (167 bp):
CTTTCACCTTGCACGGCACTGAGAAATTTGGAACTTGGCATGGATATTGCCGTGACGGAGGAACT
TGAACTGACTACTACAGTGAGCAATCTTTGTTAGACCTGTATTGTAAGTGTGGTTGTCTAGATAT
GGTCAGGAAACTTATTGACTAGATGCCGAGTAAAAAA
Found at i:26987 original size:10 final size:10
Alignment explanation
Indices: 26970--27005 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
26960 AAAAAAATAC
26970 ATATACATAT
1 ATATACATAT
*
26980 ACATACATAT
1 ATATACATAT
*
26990 ATATATATAT
1 ATATACATAT
27000 ATATAC
1 ATATAC
27006 TAGAATAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATACATAT
Found at i:26987 original size:16 final size:16
Alignment explanation
Indices: 26966--26996 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26956 AGAAAAAAAA
26966 ATACATATACATATAC
1 ATACATATACATATAC
*
26982 ATACATATATATATA
1 ATACATATACATATA
26997 TATATATACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
ATACATATACATATAC
Found at i:29093 original size:27 final size:27
Alignment explanation
Indices: 29055--29118 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
29045 TAACAAAATA
29055 TTAATAAACCCAAAATAAATGTTCAGG
1 TTAATAAACCCAAAATAAATGTTCAGG
29082 TTAATAAACCCAAAATAAATGTTCAGG
1 TTAATAAACCCAAAATAAATGTTCAGG
29109 TTAATAAACC
1 TTAATAAACC
29119 ATATAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (27 bp):
TTAATAAACCCAAAATAAATGTTCAGG
Found at i:31358 original size:15 final size:15
Alignment explanation
Indices: 31338--31366 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31328 GTCTGACTTG
31338 TTGTTGTTATATCAC
1 TTGTTGTTATATCAC
31353 TTGTTGTTATATCA
1 TTGTTGTTATATCA
31367 ATTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.14, T:0.55
Consensus pattern (15 bp):
TTGTTGTTATATCAC
Found at i:33295 original size:18 final size:18
Alignment explanation
Indices: 33272--33308 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
33262 ACTTAAAGTG
33272 CTATTTCAAGTACAATTA
1 CTATTTCAAGTACAATTA
33290 CTATTTCAAGTACAATTA
1 CTATTTCAAGTACAATTA
33308 C
1 C
33309 CAAAAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (18 bp):
CTATTTCAAGTACAATTA
Found at i:33761 original size:13 final size:13
Alignment explanation
Indices: 33743--33767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33733 TTCTCAAGAA
33743 CTTCTTCTTCCTT
1 CTTCTTCTTCCTT
33756 CTTCTTCTTCCT
1 CTTCTTCTTCCT
33768 CTCCTCCCGT
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:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
CTTCTTCTTCCTT
Found at i:34321 original size:24 final size:20
Alignment explanation
Indices: 34275--34350 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
34265 ATGCAATTAG
* *
34275 TGCATCGATGCATAGT-GAG
1 TGCATCGATGCACAGTAGAA
*
34294 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACA-G-T-A-GAA
*
34318 TGCATCGATACACAGTAGAA
1 TGCATCGATGCACAGTAGAA
34338 TGCATCGATGCAC
1 TGCATCGATGCAC
34351 TTCAAGGGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 13 0.28
20 15 0.33
21 2 0.04
22 1 0.02
23 1 0.02
24 14 0.30
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (20 bp):
TGCATCGATGCACAGTAGAA
Found at i:35949 original size:18 final size:18
Alignment explanation
Indices: 35878--35950 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
35868 AGGGATTAAC
* *
35878 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCAGGACAT
* *
35896 AGTGGTTCTTCAGAACAAT
1 AGTGGTCCTTCAGGAC-AT
35915 CAGTGGTCCTTCAGGACAT
1 -AGTGGTCCTTCAGGACAT
*
35934 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCAGGACA
35951 AATATTCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 28 0.61
19 4 0.09
20 14 0.30
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:39099 original size:13 final size:13
Alignment explanation
Indices: 39081--39105 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39071 TTCTCAAGAA
39081 CTTCTTCTTCCTT
1 CTTCTTCTTCCTT
39094 CTTCTTCTTCCT
1 CTTCTTCTTCCT
39106 CTCCTCCCAT
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:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
CTTCTTCTTCCTT
Found at i:41304 original size:18 final size:18
Alignment explanation
Indices: 41276--41348 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
41266 AGGGATTAAC
41276 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
41294 AGTGATTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
41313 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
41332 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
41349 AATATTCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:41317 original size:38 final size:38
Alignment explanation
Indices: 41275--41349 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
41265 GAGGGATTAA
*
41275 CAGTGGTCCTTCGGGACATAGTGATTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGACATAGTGATCCTTCGGAACAAT
* *
41313 CAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAA
1 CAGTGGTCCTTCGGGACATAGTGATCCTTCGGAACAA
41350 ATATTCAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (38 bp):
CAGTGGTCCTTCGGGACATAGTGATCCTTCGGAACAAT
Found at i:43677 original size:17 final size:18
Alignment explanation
Indices: 43633--43690 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
43623 AACAAGTTAA
43633 TAAAGATAAATATATATTT
1 TAAA-ATAAATATATATTT
** *
43652 TAATTTAAATATCT-TTT
1 TAAAATAAATATATATTT
*
43669 TAAAATAAAT-TTTATTT
1 TAAAATAAATATATATTT
43686 TAAAA
1 TAAAA
43691 AATATAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.06
17 19 0.59
18 8 0.25
19 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TAAAATAAATATATATTT
Found at i:44531 original size:24 final size:22
Alignment explanation
Indices: 44488--44531 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
44478 TTTAAGTTAG
*
44488 TATTTTTTTAAAATAGTTATTA
1 TATTTTTTTAAAATAATTATTA
*
44510 TATTTTATATTAATATAATTAT
1 TATTTT-T-TTAAAATAATTAT
44532 ATAAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 1 0.06
24 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTTTTTTAAAATAATTATTA
Found at i:44551 original size:29 final size:32
Alignment explanation
Indices: 44510--44575 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
44500 ATAGTTATTA
44510 TATTTTATATT-AAT-ATAATTATATAAATAT
1 TATTTTATATTAAATAATAATTATATAAATAT
* *
44540 TATTTT-TATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATAATTATATAAATAT
44572 TATT
1 TATT
44576 ATTTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.13
30 6 0.19
31 3 0.10
32 18 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTTTATATTAAATAATAATTATATAAATAT
Found at i:44575 original size:15 final size:15
Alignment explanation
Indices: 44513--44575 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
44503 GTTATTATAT
*
44513 TTTATATTAATA-TA
1 TTTATATAAATATTA
*
44527 ATTATATAAATATTA
1 TTTATATAAATATTA
* *
44542 TTTTTATTAAAATAATA
1 TTTATA-T-AAATATTA
*
44559 TTTATATAATTATTA
1 TTTATATAAATATTA
44574 TT
1 TT
44576 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 10 0.26
15 14 0.37
16 2 0.05
17 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATATAAATATTA
Found at i:44598 original size:25 final size:24
Alignment explanation
Indices: 44558--44604 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
44548 TTAAAATAAT
44558 ATTTATATAATTATTATTATTTTAA
1 ATTTATATAATTATTATT-TTTTAA
44583 ATTTAT-TAATTAATTATTTTTT
1 ATTTATATAATT-ATTATTTTTT
44605 GTGTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
ATTTATATAATTATTATTTTTTAA
Found at i:44613 original size:20 final size:18
Alignment explanation
Indices: 44588--44624 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
44578 TTTAAATTTA
44588 TTAATTAATTATTTTTTGTG
1 TTAATT-ATT-TTTTTTGTG
44608 TTAATTATTTTTTTTGT
1 TTAATTATTTTTTTTGT
44625 CTACAGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (18 bp):
TTAATTATTTTTTTTGTG
Found at i:52772 original size:18 final size:17
Alignment explanation
Indices: 52718--52772 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
52708 TTATATAAAA
* *
52718 TATAGTTTTATTATAAT
1 TATATTTTTATTATATT
* *
52735 TATATTTTTTTGTATTTT
1 TATATTTTTAT-TATATT
52753 TATATTTTTATTATAGTT
1 TATATTTTTATTATA-TT
52771 TA
1 TA
52773 AATCGATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.67
Consensus pattern (17 bp):
TATATTTTTATTATATT
Found at i:53313 original size:36 final size:35
Alignment explanation
Indices: 53255--53330 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 35
53245 ATAATGTCTA
*
53255 TGGTTCAGCCATTGTTCCTTCTTCTT-TTGCTTCTTT
1 TGGTTCAGCCATTGTT-CTTCTTCTTCTTG-TTCTTC
53291 TGGTTCAGCCATTGGCTT-TTCTTCTTCTTGTTCTTC
1 TGGTTCAGCCATT-G-TTCTTCTTCTTCTTGTTCTTC
53327 TGGT
1 TGGT
53331 GTATGATGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
36 30 0.83
37 4 0.11
38 2 0.06
ACGTcount: A:0.05, C:0.24, G:0.17, T:0.54
Consensus pattern (35 bp):
TGGTTCAGCCATTGTTCTTCTTCTTCTTGTTCTTC
Found at i:55536 original size:3 final size:3
Alignment explanation
Indices: 55528--55589 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
55518 TAACCTTTTG
* *
55528 TTA TTA TTA TTA TTA TTA TT- TTA TTTA TCTA TT- TTC TT- TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA
55572 -TA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
55590 ACTAATATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
2 7 0.14
3 38 0.75
4 6 0.12
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:60472 original size:16 final size:16
Alignment explanation
Indices: 60451--60483 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
60441 ATTAAGAGCA
*
60451 TCACATTCATTATTTT
1 TCACATACATTATTTT
60467 TCACATACATTATTTT
1 TCACATACATTATTTT
60483 T
1 T
60484 TACAGCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (16 bp):
TCACATACATTATTTT
Found at i:61248 original size:84 final size:83
Alignment explanation
Indices: 60876--61436 Score: 483
Period size: 84 Copynumber: 6.7 Consensus size: 83
60866 TTTTATACAA
* **
60876 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTAACT
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG-TAACCAAAGACCTTCGAGTTCGACT
* * * *
60941 ATACTCAACTCTAATGTAC
65 ACACTCAGCTCTAAGGCAC
* * * * * * *
60960 ATCATTTGCGGAATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTT-GAGTTCAATT
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTAACCAAAGA-CCTTCGAGTTCGACT
* * *
61021 AGACTCAGCT-TCGAGGCCAT
65 ACACTCAGCTCT-AAGG-CAC
* * * * * *
61041 ATCATTTACATCATAACTCAAGGCTAGAAGGGTTATCTCTGACCAAAAGACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTAACC-AAAGACCTTCGAGTTCGACT
* *
61106 ACACTCAGCTTTGAGGGCAC
65 ACACTCAGCTCT-AAGGCAC
* * * *
61126 ACCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCGACC
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGT-AACCAAAGACCTTCGAGTTCGACT
* *
61191 ACGCTCAGCTCTAAGACAC
65 ACACTCAGCTCTAAGGCAC
* * * * *
61210 ATCATTTGCAGTATAACTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGATTA
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
* *
61272 CACTCAGCTTCGAGGGCAC
66 CACTCAGC-TCTAAGGCAC
* * * * * *
61291 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGAACTTCGAGTTCGACTA
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
** *
61356 TGCTCAGCTCCAAGGCAC
66 CACTCAGCTCTAAGGCAC
* ** * * * *
61374 ATAATTTACAATACAACTTAAGTCAAGAAGGGTTATCTGCCAACCGAAGACC-TCTGAGTTCGA
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG-TAACCAAAGACCTTC-GAGTTCGA
61437 TTATATTCAG
Statistics
Matches: 382, Mismatches: 79, Indels: 32
0.77 0.16 0.06
Matches are distributed among these distances:
79 1 0.00
80 51 0.13
81 73 0.19
83 43 0.11
84 123 0.32
85 85 0.22
86 6 0.02
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (83 bp):
ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
CACTCAGCTCTAAGGCAC
Found at i:61276 original size:165 final size:164
Alignment explanation
Indices: 61086--61416 Score: 455
Period size: 164 Copynumber: 2.0 Consensus size: 164
61076 TCTCTGACCA
* * * * * *
61086 AAAGACCTTCGAGTTCGACTACACTCAGCTTTGAGGGCACACCATTTGCAGCATAACTTAAGTCG
1 AAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGCACACCATTTACAACATAACTCAAGGCG
* * * *
61151 AGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCGACCACGCTCAGCTCTAAGACACATCATT
66 AGAAGGGTTATCTGT-AACCAAAGAACTTCGAGTTCGACCACGCTCAGCTCCAAGACACATAATT
* * * *
61216 TGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCC
130 TACAATACAACTTAAGTCAAGAAGGGCTATCTGCC
* * *
61251 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGCACACCATTTACAACATAACTCAAGGCG
* * * *
61316 AGAAGGGTTATCTGTTACCAAAGAACTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATAATTT
66 AGAAGGGTTATCTGTAACCAAAGAACTTCGAGTTCGACCACGCTCAGCTCCAAGACACATAATTT
*
61381 ACAATACAACTTAAGTCAAGAAGGGTTATCTGCC
131 ACAATACAACTTAAGTCAAGAAGGGCTATCTGCC
61415 AA
1 AA
61417 CCGAAGACCT
Statistics
Matches: 144, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
164 73 0.51
165 71 0.49
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (164 bp):
AAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGCACACCATTTACAACATAACTCAAGGCG
AGAAGGGTTATCTGTAACCAAAGAACTTCGAGTTCGACCACGCTCAGCTCCAAGACACATAATTT
ACAATACAACTTAAGTCAAGAAGGGCTATCTGCC
Found at i:61325 original size:250 final size:248
Alignment explanation
Indices: 60878--61436 Score: 769
Period size: 250 Copynumber: 2.2 Consensus size: 248
60868 TTATACAAAT
* ** * *
60878 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTAACTAT
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACCAC
* * *
60943 ACTCAACTCTAATGTACATCATTTGCGGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 ACTCAACTCTAATGCACATCATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * *
61008 CTTGAGTTCAATTAGACTCAGCTTCGAGGCCATATCATTTACATCATAACTCAAGGCTAGAAGGG
131 CTCGAGTTCAATTACACTCAGCTTCGAGGCCACATCATTTACAACATAACTCAAGGCTAGAAGGG
* ** *
61073 TTATCTCTGACCAAAAGACCTTCGAGTTCGACTACACTCAGCTTTGAGGGCACAC
196 TTATCTCTGACC-AAAGAACTTCGAGTTCGACTACACTCAGC-TCCAAGGCACAC
* *
61128 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCGACCAC
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACCAC
* * *
61193 GCTCAGCTCTAA-GACACATCATTTGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 ACTCAACTCTAATG-CACATCATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* *
61257 CCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGG
130 CCTCGAGTTCAATTACACTCAGCTTCGAGGCCACATCATTTACAACATAACTCAAGGCTAGAAGG
* * ** *
61322 GTTATCTGTTACCAAAGAACTTCGAGTTCGACTATGCTCAGCTCCAAGGCACAT
195 GTTATCTCTGACCAAAGAACTTCGAGTTCGACTACACTCAGCTCCAAGGCACAC
* ** * * * *
61376 AATTTACAATACAACTTAAGTCAAGAAGGGTTATCTGCCAACCGAAGACCTCTGAGTTCGA
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGA
61437 TTATATTCAG
Statistics
Matches: 271, Mismatches: 37, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
248 60 0.22
249 27 0.10
250 184 0.68
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (248 bp):
CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACCAC
ACTCAACTCTAATGCACATCATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCAATTACACTCAGCTTCGAGGCCACATCATTTACAACATAACTCAAGGCTAGAAGGG
TTATCTCTGACCAAAGAACTTCGAGTTCGACTACACTCAGCTCCAAGGCACAC
Found at i:64157 original size:31 final size:31
Alignment explanation
Indices: 64068--64164 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
64058 TGTAATACAG
* *
64068 TCCCCCAACATTTAGTCCGTTTATAATATGA
1 TCCCCCAACATTTAGTCCATTTACAATATGA
* * *
64099 TACCCCAACATTTAGTCTATTTTCAATATGA
1 TCCCCCAACATTTAGTCCATTTACAATATGA
* *
64130 TCCCCCAACATTTAGTCCATTTGCAATATGG
1 TCCCCCAACATTTAGTCCATTTACAATATGA
64161 TCCC
1 TCCC
64165 TAATGTAACT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCATTTACAATATGA
Found at i:66275 original size:2 final size:2
Alignment explanation
Indices: 66262--66311 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
66252 CAATAATTAT
*
66262 TA TA TG 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
66304 TA TA TA TA
1 TA TA TA TA
66312 AATTTGAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66467 original size:38 final size:38
Alignment explanation
Indices: 66416--66491 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
66406 TCGACGTTTC
66416 ACTTCTCTTCTAAATTCCGTAAATGCTTCACCAATGGT
1 ACTTCTCTTCTAAATTCCGTAAATGCTTCACCAATGGT
*
66454 ACTTCTCTTCTAAATTTCGTAAATGCTTCACCAATGGT
1 ACTTCTCTTCTAAATTCCGTAAATGCTTCACCAATGGT
66492 TGGCAGGGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (38 bp):
ACTTCTCTTCTAAATTCCGTAAATGCTTCACCAATGGT
Found at i:66604 original size:16 final size:16
Alignment explanation
Indices: 66583--66618 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
66573 TCATTATTGA
66583 GGTGAGTTATAAACTT
1 GGTGAGTTATAAACTT
66599 GGTGAGTTATAAACTT
1 GGTGAGTTATAAACTT
66615 GGTG
1 GGTG
66619 TGTTCCACGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.06, G:0.31, T:0.36
Consensus pattern (16 bp):
GGTGAGTTATAAACTT
Found at i:70786 original size:45 final size:45
Alignment explanation
Indices: 70676--70797 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
70666 CATTGTATGT
70676 ATCGATGCACATATCATGCATCGATGCACTCAGGTTTCTATGAAAAC
1 ATCGATGCAC-T-TCATGCATCGATGCACTCAGGTTTCTATGAAAAC
* *
70723 ATCGAATGCATTTGATGCATCGATGCACTCAGGCTATT-T-TG-AAAC
1 ATCG-ATGCACTTCATGCATCGATGCACTCAGG-T-TTCTATGAAAAC
70768 ATCAGATGCACTTCATGCATCGATGCACTC
1 ATC-GATGCACTTCATGCATCGATGCACTC
70798 TTAGTGCACC
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
45 30 0.45
46 23 0.34
47 7 0.10
48 7 0.10
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (45 bp):
ATCGATGCACTTCATGCATCGATGCACTCAGGTTTCTATGAAAAC
Found at i:70794 original size:17 final size:19
Alignment explanation
Indices: 70767--70815 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
70757 TATTTTGAAA
70767 CATCAGATGCACT-TCA-TG
1 CATC-GATGCACTCTCAGTG
*
70785 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
70804 CACCGATGCACT
1 CATCGATGCACT
70816 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:72039 original size:29 final size:27
Alignment explanation
Indices: 72007--72063 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
71997 ATTTCAAAAT
72007 TATAATTATGAAA-AAAATATATTAATTTA
1 TATAATTAT-AAATAAAATAT-TT-ATTTA
*
72036 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTTATTTA
72063 T
1 T
72064 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 6 0.23
28 5 0.19
29 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TATAATTATAAATAAAATATTTATTTA
Found at i:72262 original size:149 final size:144
Alignment explanation
Indices: 72021--72291 Score: 375
Period size: 149 Copynumber: 1.8 Consensus size: 144
72011 ATTATGAAAA
* * *
72021 AAATATATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACT
1 AAATAAATTAATTTATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACA
* *
72086 TCTAGGTGCCTTAAGACAGCTCTTTTCTTAATATTAAAAAATAAATAAATATTAAAATAACATCT
66 TCCAGGTGCCTTAAGACAGCTCATTTCTTAATATTAAAAAATAAATAAATATTAAAATAACATCT
72151 TTCTAAAAATAATT
131 TTCTAAAAATAATT
72165 AAATAAATTAATATATATATAATTTATAAA-AATATGATATTTATTTATTTAAAAATATCAGAAA
1 AAATAAATTAAT-T-TATAT-ATTTATAAATAA-A--ATATTTATTTATTTAAAAATATCAGAAA
* ** * *
72229 ATGGACATCCAGTTGTTTTAAGACTGC-CATTTCTTAATATTGAAAAATAAATAAATATTAAAA
60 A-GGACATCCAGGTGCCTTAAGACAGCTCATTTCTTAATATTAAAAAATAAATAAATATTAAAA
72292 CAGAATTAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
144 11 0.10
145 1 0.01
146 7 0.06
147 10 0.09
149 62 0.56
150 19 0.17
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (144 bp):
AAATAAATTAATTTATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACA
TCCAGGTGCCTTAAGACAGCTCATTTCTTAATATTAAAAAATAAATAAATATTAAAATAACATCT
TTCTAAAAATAATT
Found at i:72320 original size:149 final size:147
Alignment explanation
Indices: 72052--72329 Score: 337
Period size: 149 Copynumber: 1.9 Consensus size: 147
72042 TATAAATAAA
* * * *
72052 ATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTAA
1 ATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACAGCTCATTTCTTAA
* ***
72117 TATTAAAAAATAAATAAATATTAAAATAACATCTTTCTAAAAATAATTAAATAAATTAATATATA
66 TATTAAAAAATAAATAAATATTAAAACAACATCTAAATAAAAATAATTAAATAAA-T-ATATATA
72182 TATAATTTATAAAAATATG
129 TATAATTTATAAAAATATG
* ** *
72201 ATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTTTAAGACTGC-CATTTCTTA
1 ATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGCCTTAAGACAGCTCATTTCTTA
* * * * *
72265 ATATTGAAAAATAAATAAATATTAAAACAGA-AT-TAAATAATTATTTATTATATAAATATATAT
65 ATATTAAAAAATAAATAAATATTAAAACA-ACATCTAAATAA-AAATAATTAAATAAATATATAT
72328 AT
128 AT
72330 TTATGGCTAA
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
147 8 0.07
148 5 0.05
149 76 0.70
150 20 0.18
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (147 bp):
ATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACAGCTCATTTCTTAA
TATTAAAAAATAAATAAATATTAAAACAACATCTAAATAAAAATAATTAAATAAATATATATATA
TAATTTATAAAAATATG
Found at i:73727 original size:3 final size:3
Alignment explanation
Indices: 73721--73773 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
73711 ATTATTTATT
* * *
73721 TAA TAA TAA TAA T-A TAA T-A TTA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
73765 TAA TAA TAA
1 TAA TAA TAA
73774 ATAAAACAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
2 8 0.19
3 35 0.81
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:73746 original size:22 final size:21
Alignment explanation
Indices: 73699--73777 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 21
73689 ATTGGGCCTG
*
73699 TAATAATAATAAATTAT-TTA
1 TAATAATAATAAATAATATTA
73719 TTTAATAATAATAATATAATATTA
1 --TAATAATAATAA-ATAATATTA
* *
73743 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATTA
73762 TAATAATAATAAATAA
1 TAATAATAATAAATAA
73778 AACAAATGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 14 0.29
20 3 0.06
21 2 0.04
22 23 0.47
23 4 0.08
24 3 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAATAATAAATAATATTA
Found at i:73784 original size:22 final size:22
Alignment explanation
Indices: 73721--73783 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
73711 ATTATTTATT
* * * *
73721 TAATAATAATAATATAATATTA
1 TAATAATAATAAAACAAAATAA
*
73743 TAATAATATTAAAACAAAATAA
1 TAATAATAATAAAACAAAATAA
73765 TAATAATAAATAAAACAAA
1 TAATAAT-AATAAAACAAA
73784 TGAAAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 24 0.71
23 10 0.29
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAATAAAACAAAATAA
Found at i:74275 original size:113 final size:113
Alignment explanation
Indices: 74037--74690 Score: 962
Period size: 113 Copynumber: 5.8 Consensus size: 113
74027 TTCAGATGAG
* * **
74037 TTCTTCTCATTATGAACTTCCTATTCCTTCTTCA-AGTGAGTTCTTCTCATTATGAACACT-TCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA-TGAGTTCTTCTCATTATGAACTTTCTCT
* *
74100 GGCAATA-CTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
65 GG-AAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
* *
74149 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * ** * *
74214 GAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
66 GAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
* * *
74262 CTCTTCTCATTATGAATTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
74327 GAAAAGCTGATCCATCGAA-TGATGAATTCAAACAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATC-AAGTGATGAATTCAAACAAAAGGTTGAACAAA
*
74375 TTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-TTCTCATTATGAACTTTCTCT
* * ** *
74440 GTAAAA-CTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAAC-AA
65 GGAAAAGC-TGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
*
74488 TCTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 T-TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
74553 GGAAAAGCTGATCCATCGAA-TGATGAATTCAAACAAAAGGTTGAACAAA
65 GGAAAAGCTGATCCATC-AAGTGATGAATTCAAACAAAAGGTTGAACAAA
74602 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
74667 GAAAAGCTGATCCAACGAGTGATG
66 GAAAAGCTGATCCATCAAGTGATG
74691 GATTTGAATC
Statistics
Matches: 486, Mismatches: 44, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
112 56 0.12
113 325 0.67
114 105 0.22
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:74512 original size:227 final size:226
Alignment explanation
Indices: 74038--74697 Score: 1089
Period size: 227 Copynumber: 2.9 Consensus size: 226
74028 TCAGATGAGT
* * * **
74038 TCTTCTCATTATGAACTTCCTATTCCTTCTTCA-AGTGAGTTCTTCTCATTATGAACACT-TCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGA-TGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
74101 GCAATA-CTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTTATTATGAA
65 G-AAAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
*
74165 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT-TGAAA-TGCTGATCCA
129 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGTAAAACT--TGATCCA
74228 TCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
192 TCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
*
74263 TCTTCTCATTATGAATTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
74328 AAAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 AAAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
74393 TCTTCTTCCTTTTTCAGATGAGTTCTTTCTCATTATGAACTTTCTCTGTAAAACTTGATCCATCA
131 TCTTCTTCCTTCTTCAGATGAGTTC-TTCTCATTATGAACTTTCTCTGTAAAACTTGATCCATCA
*
74458 AGTGATGGATTTGAGCAAAAGGTTGAACAATC
195 AGTGATGGATTTGAGCAAAAGGTTGAACAAGC
74490 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
74555 AAAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 AAAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
* * *
74620 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGC-TGATCCAACG
131 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGTAAAA-CTTGATCCATCA
74684 AGTGATGGATTTGA
195 AGTGATGGATTTGA
74698 ATCTTTGCTA
Statistics
Matches: 411, Mismatches: 17, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
225 54 0.13
226 136 0.33
227 216 0.53
228 4 0.01
229 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (226 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGTAAAACTTGATCCATCAA
GTGATGGATTTGAGCAAAAGGTTGAACAAGC
Found at i:76239 original size:20 final size:20
Alignment explanation
Indices: 76214--76259 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
76204 GACCCTCCTT
76214 TTTTTTCTTCTTTCATTTCA
1 TTTTTTCTTCTTTCATTTCA
76234 TTTTTTCTTCTTTCATTTCA
1 TTTTTTCTTCTTTCATTTCA
76254 TTTTTT
1 TTTTTT
76260 ATTCAAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTCTTCTTTCATTTCA
Done.