Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004517.1 Hibiscus syriacus cultivar Beakdansim tig00009961_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: 154385
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8702 original size:22 final size:21
Alignment explanation
Indices: 8677--8737 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
8667 GAGTGCAAAA
8677 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAGAAAAAGA-AAAAGAAG
*
8699 AGAAA-AAAAATCAGAAAAGAAG
1 AGAAAGAAAAA-GA-AAAAGAAG
8721 A-AAAG-AAAAGAAAAAGA
1 AGAAAGAAAAAGAAAAAGA
8738 GAAAGCAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 6 0.18
20 1 0.03
21 12 0.35
22 15 0.44
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (21 bp):
AGAAAGAAAAAGAAAAAGAAG
Found at i:8707 original size:30 final size:30
Alignment explanation
Indices: 8673--8742 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
8663 ATTGGAGTGC
*
8673 AAAAAGAAAGAAAA-AGACAAAAGAAGAGAA
1 AAAAAGAAAGAAAAGA-ACAAAAGAAAAGAA
* *
8703 AAAAA-ATCAGAAAAGAAGAAAAGAAAAGAA
1 AAAAAGA-AAGAAAAGAACAAAAGAAAAGAA
*
8733 AAAGAGAAAG
1 AAAAAGAAAG
8743 CAAGCCAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
29 1 0.03
30 29 0.91
31 2 0.06
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (30 bp):
AAAAAGAAAGAAAAGAACAAAAGAAAAGAA
Found at i:13717 original size:36 final size:36
Alignment explanation
Indices: 13637--13717 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
13627 TGGCATGAAA
*
13637 GTGATGGAATATGGTGATGATATAGACGTGATAATG
1 GTGATGGACTATGGTGATGATATAGACGTGATAATG
*
13673 GTGATGGACTATGGTGATGATATAGGCGTGATAATG
1 GTGATGGACTATGGTGATGATATAGACGTGATAATG
13709 GTGATGGAC
1 GTGATGGAC
13718 AGATTGTATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
GTGATGGACTATGGTGATGATATAGACGTGATAATG
Found at i:14106 original size:19 final size:20
Alignment explanation
Indices: 14059--14109 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
14049 GAAACCCCTT
**
14059 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
14079 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
14098 TGAAGATACATG
1 TGAAAATACATG
14110 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:21658 original size:20 final size:21
Alignment explanation
Indices: 21635--21678 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
21625 TTCTTTTCTA
*
21635 TGCTTTTTC-TTCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
21655 TGC--TTTCAATCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
21674 TGCTT
1 TGCTT
21679 ATTTTCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
18 4 0.20
19 13 0.65
20 3 0.15
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (21 bp):
TGCTTTTTCAATCTTTTTGAG
Found at i:25075 original size:13 final size:13
Alignment explanation
Indices: 25053--25082 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25043 ACTAAACACC
25053 TTTC-ACATACCT
1 TTTCAACATACCT
25065 TTTCAACATACCT
1 TTTCAACATACCT
25078 TTTCA
1 TTTCA
25083 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:27998 original size:18 final size:19
Alignment explanation
Indices: 27960--27998 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
27950 AAGGAAAAAG
*
27960 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
27979 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
27997 AA
1 AA
27999 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:33535 original size:29 final size:26
Alignment explanation
Indices: 33479--33536 Score: 62
Period size: 29 Copynumber: 2.1 Consensus size: 26
33469 TTTCTTTTCT
*
33479 TTTCTTCTTTTTTTTAAGTGCTGGAA
1 TTTCTTCTTTTTTTTAAGTGCTGCAA
* *
33505 TTTCTTTCTTTATTTTTGGAGTGCTTCAA
1 TTTC-TTCTTT-TTTTT-AAGTGCTGCAA
33534 TTT
1 TTT
33537 TTTTTTCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 6 0.23
28 5 0.19
29 11 0.42
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTTTTTTTAAGTGCTGCAA
Found at i:33847 original size:91 final size:91
Alignment explanation
Indices: 33687--33869 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
33677 CCTAGAACAC
* *
33687 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGTGCCAAGATA
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATA
33752 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * *
33778 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATA
33843 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
33869 C
1 C
33870 ATCAACTACC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATA
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:47551 original size:91 final size:91
Alignment explanation
Indices: 47405--47578 Score: 312
Period size: 91 Copynumber: 1.9 Consensus size: 91
47395 CCCATGCGCC
*
47405 TTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
47470 CTCCCTATTCGGCCAAGCCATGTGTT
66 CTCCCTATTCGGCCAAGCCATGTGTT
* * *
47496 TTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
47561 CTCCCTATTCGGCCAAGC
66 CTCCCTATTCGGCCAAGC
47579 ATCAACTACC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 79 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
CTCCCTATTCGGCCAAGCCATGTGTT
Found at i:54065 original size:8 final size:8
Alignment explanation
Indices: 54054--54078 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54044 TCTTTTTCTT
54054 TTCTTTTC
1 TTCTTTTC
54062 TTCTTTTC
1 TTCTTTTC
54070 TTCTTTTC
1 TTCTTTTC
54078 T
1 T
54079 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:54839 original size:19 final size:21
Alignment explanation
Indices: 54796--54847 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
54786 GAAACCCCTT
54796 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
54817 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
54836 TGAAGATACATG
1 TGAAAATACATG
54848 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:59714 original size:13 final size:13
Alignment explanation
Indices: 59698--59722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59688 TTGAATTTCT
59698 TTTTCTTTTCTTC
1 TTTTCTTTTCTTC
59711 TTTTCTTTTCTT
1 TTTTCTTTTCTT
59723 TGGCACTCCG
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:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:60049 original size:22 final size:21
Alignment explanation
Indices: 60023--60064 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
60013 GGCTGTGGAA
60023 TTGATGGTCTTGATGGATGAAG
1 TTGATGGTCTTGAT-GATGAAG
*
60045 TTGATGGTGTTGATGATGAA
1 TTGATGGTCTTGATGATGAA
60065 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGAAG
Found at i:61478 original size:35 final size:36
Alignment explanation
Indices: 61439--61523 Score: 138
Period size: 35 Copynumber: 2.4 Consensus size: 36
61429 AAATGGAATT
**
61439 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAAA
61474 TGGTGATGATATAGGCGTGATAATGGTGATGGAAAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAAA
61510 TGGTGATGA-ATAGG
1 TGGTGATGATATAGG
61524 TTGTATCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
35 26 0.55
36 21 0.45
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAAA
Found at i:66390 original size:17 final size:19
Alignment explanation
Indices: 66354--66391 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
66344 AACTATATAA
66354 TGCATATAATATAATGATG
1 TGCATATAATATAATGATG
*
66373 TGCATATTATA-AAT-ATG
1 TGCATATAATATAATGATG
66390 TG
1 TG
66392 AACTATAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
TGCATATAATATAATGATG
Found at i:67139 original size:16 final size:15
Alignment explanation
Indices: 67118--67163 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
67108 GGAGTGCAAA
67118 AAGAAAAGACAAAAAG
1 AAGAAAAGA-AAAAAG
67134 AAGAAAAGAAGAAAAG
1 AAGAAAAGAA-AAAAG
67150 AAGAAAAAGAAAAA
1 AAG-AAAAGAAAAA
67164 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.04
16 20 0.71
17 7 0.25
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAAAAG
Found at i:74484 original size:20 final size:21
Alignment explanation
Indices: 74459--74504 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
74449 TGATGTATGA
*
74459 TTTTTTTTCTTTTCTTTTTG-T
1 TTTTTTTTC-TTTCTTGTTGCT
74480 TTTTTTTTCTTTCTTGTTGCT
1 TTTTTTTTCTTTCTTGTTGCT
74501 TTTT
1 TTTT
74505 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.83
Consensus pattern (21 bp):
TTTTTTTTCTTTCTTGTTGCT
Found at i:74485 original size:21 final size:20
Alignment explanation
Indices: 74459--74504 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
74449 TGATGTATGA
* *
74459 TTTTTTTTCTTTTCTTTTTGT
1 TTTTTTTTC-TTTCTTGTTGC
74480 TTTTTTTTCTTTCTTGTTGC
1 TTTTTTTTCTTTCTTGTTGC
74500 TTTTT
1 TTTTT
74505 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.83
Consensus pattern (20 bp):
TTTTTTTTCTTTCTTGTTGC
Found at i:74496 original size:17 final size:17
Alignment explanation
Indices: 74462--74497 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
74452 TGTATGATTT
74462 TTTTTCTTTTCTTTTTG
1 TTTTTCTTTTCTTTTTG
74479 TTTTT-TTTTCTTTCTTG
1 TTTTTCTTTTCTTT-TTG
74496 TT
1 TT
74498 GCTTTTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTG
Found at i:78032 original size:24 final size:21
Alignment explanation
Indices: 77998--78040 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
77988 TGCACAAGAT
*
77998 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
78020 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
78041 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:82598 original size:23 final size:24
Alignment explanation
Indices: 82563--82616 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
82553 AAAATCAGAA
82563 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
82586 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
82610 AAGAAAA
1 AAGAAAA
82617 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:82621 original size:24 final size:23
Alignment explanation
Indices: 82563--82622 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
82553 AAAATCAGAA
82563 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
82586 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
82610 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
82623 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:85402 original size:11 final size:13
Alignment explanation
Indices: 85370--85399 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
85360 TGGCCAAAGA
85370 TGAAAAGGTATGT
1 TGAAAAGGTATGT
85383 TGAAAAGGTATG-
1 TGAAAAGGTATGT
85395 TGAAA
1 TGAAA
85400 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:88366 original size:19 final size:20
Alignment explanation
Indices: 88319--88369 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
88309 GAAACCCCTT
**
88319 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
88339 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
88358 TGAAGATACATG
1 TGAAAATACATG
88370 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:128100 original size:24 final size:21
Alignment explanation
Indices: 128066--128108 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
128056 TGTACAAGAT
*
128066 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
128088 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
128109 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:135268 original size:33 final size:33
Alignment explanation
Indices: 135226--135294 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
135216 GTTGATGAAT
*
135226 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
135259 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
135292 GAA
1 GAA
135295 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:135299 original size:13 final size:12
Alignment explanation
Indices: 135280--135365 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
135270 TTATTGGCGT
135280 GATATGGTGATG
1 GATATGGTGATG
135292 GAATATGGTGAT-
1 G-ATATGGTGATG
*
135304 GATATAGGCG-T-
1 GATAT-GGTGATG
135315 GATAATGGTGATG
1 GAT-ATGGTGATG
135328 GACTATGGTGAT-
1 GA-TATGGTGATG
*
135340 GATATAGGCG-T-
1 GATAT-GGTGATG
135351 GATAATGGTGATG
1 GAT-ATGGTGATG
135364 GA
1 GA
135366 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:135335 original size:36 final size:36
Alignment explanation
Indices: 135265--135366 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
135255 AATGGAAGGA
* * *
135265 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
135300 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
135336 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
135367 AGATTGTATA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 16 0.25
36 47 0.75
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:142296 original size:22 final size:22
Alignment explanation
Indices: 142271--142313 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
142261 GGCCAATCAT
**
142271 AATGGAACATTTGGCCATGCAC
1 AATGGAACATACGGCCATGCAC
*
142293 AATGTAACATACGGCCATGCA
1 AATGGAACATACGGCCATGCA
142314 TGTTCAAGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (22 bp):
AATGGAACATACGGCCATGCAC
Found at i:145596 original size:19 final size:20
Alignment explanation
Indices: 145572--145609 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
145562 TGGCCAAGAG
145572 CATGTATCTTCA-TTAAAAT
1 CATGTATCTTCATTTAAAAT
*
145591 CATGTATTTTCATTTAAAA
1 CATGTATCTTCATTTAAAA
145610 GTTGTGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (20 bp):
CATGTATCTTCATTTAAAAT
Found at i:146363 original size:19 final size:19
Alignment explanation
Indices: 146330--146392 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
146320 AAATTGGAGT
146330 ACAAAAAG-A-AAGAAAAG
1 ACAAAAAGAAGAAGAAAAG
146347 ACAAAAAGAAGAAGAAAAG
1 ACAAAAAGAAGAAGAAAAG
*
146366 AAGAAAAAGAAAAGAAGAAAAG
1 -ACAAAAAG--AAGAAGAAAAG
146388 A-AAAA
1 ACAAAA
146393 GAAATTCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 8 0.20
18 1 0.03
19 8 0.20
20 11 0.28
21 1 0.03
22 11 0.28
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (19 bp):
ACAAAAAGAAGAAGAAAAG
Found at i:146364 original size:11 final size:11
Alignment explanation
Indices: 146350--146396 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
146340 AGAAAAGACA
146350 AAAAGAAGAAG
1 AAAAGAAGAAG
146361 AAAAGAAGAA-
1 AAAAGAAGAAG
*
146371 AAAGAAAAGAAG
1 AAA-AGAAGAAG
*
146383 AAAAGAAAAAG
1 AAAAGAAGAAG
146394 AAA
1 AAA
146397 TTCAAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 3 0.10
11 25 0.81
12 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:146366 original size:8 final size:8
Alignment explanation
Indices: 146355--146389 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
146345 AGACAAAAAG
146355 AAGAAGAA
1 AAGAAGAA
146363 AAGAAG-A
1 AAGAAGAA
146370 AA-AAGAA
1 AAGAAGAA
146377 AAGAAGAA
1 AAGAAGAA
146385 AAGAA
1 AAGAA
146390 AAAGAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 6 0.24
8 16 0.64
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:146369 original size:14 final size:13
Alignment explanation
Indices: 146333--146391 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 13
146323 TTGGAGTACA
146333 AAAAGAAAGAAAAG
1 AAAAG-AAGAAAAG
146347 ACAAA-AAGAAGAAG
1 A-AAAGAAGAA-AAG
146361 AAAAGAAGAAAAAG
1 AAAAGAAG-AAAAG
146375 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
146388 AAAA
1 AAAA
146392 AGAAATTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
13 17 0.41
14 19 0.46
15 5 0.12
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:146392 original size:28 final size:29
Alignment explanation
Indices: 146332--146396 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
146322 ATTGGAGTAC
146332 AAAAAGAAAGAAAAGACAAAAAGAAGAAG
1 AAAAAGAAAGAAAAGACAAAAAGAAGAAG
146361 -AAAAG-AAGAAAAAGA-AAAGAAGAA-AAG
1 AAAAAGAAAG-AAAAGACAAA-AAGAAGAAG
146388 AAAAAGAAA
1 AAAAAGAAA
146397 TTCAAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
27 9 0.28
28 21 0.66
29 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAGAAAAGACAAAAAGAAGAAG
Found at i:146393 original size:19 final size:19
Alignment explanation
Indices: 146333--146396 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 19
146323 TTGGAGTACA
146333 AAAAGAAAGAAAAGACAAAAAG
1 AAAAG-AAGAAAAG--AAAAAG
146355 AAGAAGAA-AAGAAGAAAAAG
1 AA-AAGAAGAA-AAGAAAAAG
146375 AAAAGAAGAAAAGAAAAAG
1 AAAAGAAGAAAAGAAAAAG
146394 AAA
1 AAA
146397 TTCAAAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
19 17 0.44
20 10 0.26
21 2 0.05
22 7 0.18
23 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAAAGAAAAAG
Found at i:146623 original size:17 final size:18
Alignment explanation
Indices: 146601--146634 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
146591 CCTTTAAATG
*
146601 ATTTCTTTTA-TCTTTCC
1 ATTTCTTATATTCTTTCC
146618 ATTTCTTATATTCTTTC
1 ATTTCTTATATTCTTTC
146635 TACCCTAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTCTTATATTCTTTCC
Found at i:149550 original size:21 final size:20
Alignment explanation
Indices: 149501--149557 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
149491 TTATTCGTCC
*
149501 AAAAG-CATGTATCTTCATT
1 AAAAGTCATGTATTTTCATT
149520 AAAA-TCATGTATTTTCATTT
1 AAAAGTCATGTATTTTCA-TT
149540 AAAAGTCATGTATTTTCA
1 AAAAGTCATGTATTTTCA
149558 AAGGGGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
20 6 0.18
21 13 0.38
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (20 bp):
AAAAGTCATGTATTTTCATT
Found at i:150005 original size:18 final size:19
Alignment explanation
Indices: 149969--150006 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
149959 TATCCTTTCT
*
149969 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATACTTA
*
149988 TTATTT-ATTTTATACTTA
1 TTATTTCATTTCATACTTA
150006 T
1 T
150007 ATTATTATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTCATTTCATACTTA
Found at i:150934 original size:19 final size:21
Alignment explanation
Indices: 150891--150942 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
150881 GAAACCCCTT
150891 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
150912 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
150931 TGAAGATACATG
1 TGAAAATACATG
150943 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Done.