Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009408.1 Hibiscus syriacus cultivar Beakdansim tig00113343_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: 132123
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7077 original size:14 final size:15
Alignment explanation
Indices: 7052--7080 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
7042 AGTCTTACCC
7052 AAAACTATTTAAAAA
1 AAAACTATTTAAAAA
7067 AAAACTA-TTAAAAA
1 AAAACTATTTAAAAA
7081 CAATTGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAACTATTTAAAAA
Found at i:7211 original size:12 final size:12
Alignment explanation
Indices: 7194--7220 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7184 TGCATCTCTT
7194 GAAATATTTTAA
1 GAAATATTTTAA
7206 GAAATATTTTAA
1 GAAATATTTTAA
7218 GAA
1 GAA
7221 TTTAATTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (12 bp):
GAAATATTTTAA
Found at i:23761 original size:21 final size:21
Alignment explanation
Indices: 23735--23774 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23725 CCCCCTTTGA
*
23735 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
23756 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
23775 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:28372 original size:14 final size:14
Alignment explanation
Indices: 28324--28374 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
28314 ATAAACCTTC
*
28324 AAATATAACTTT-A
1 AAATATAATTTTAA
*
28337 AAATATTATTATTATA
1 AAATATAATT-TTA-A
*
28353 ATATATAATTTTAA
1 AAATATAATTTTAA
28367 AAATATAA
1 AAATATAA
28375 AAGTAAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 8 0.27
14 10 0.33
15 3 0.10
16 9 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATAATTTTAA
Found at i:31389 original size:14 final size:14
Alignment explanation
Indices: 31370--31399 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
31360 GAATTCTGGG
31370 TTTTTTTAGGGTAC
1 TTTTTTTAGGGTAC
31384 TTTTTTTAGGGTAC
1 TTTTTTTAGGGTAC
31398 TT
1 TT
31400 CTTAAACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.07, G:0.20, T:0.60
Consensus pattern (14 bp):
TTTTTTTAGGGTAC
Found at i:34357 original size:39 final size:39
Alignment explanation
Indices: 34300--34397 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
34290 AATTGCATAT
* *
34300 CAAGAGCAGAATGTACTTGTCCCTTATACTATCAGATAC
1 CAAGAGCACAATGCACTTGTCCCTTATACTATCAGATAC
*
34339 CAAGAGCACAATGCACTTGTCCCTTATACTATCAGGTAC
1 CAAGAGCACAATGCACTTGTCCCTTATACTATCAGATAC
* *
34378 CAAGAACGCAATGCACTTGT
1 CAAGAGCACAATGCACTTGT
34398 TGTTTATAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (39 bp):
CAAGAGCACAATGCACTTGTCCCTTATACTATCAGATAC
Found at i:42125 original size:53 final size:53
Alignment explanation
Indices: 42058--42162 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
42048 GACGGCTCAC
* * *
42058 AAAGCTTAGACGATTTCAATATGGTGAAAACAGGGGTGAAGTATAAACTAAGT
1 AAAGCTTAGACGATTGCAATATGGTAAAAACAGGGATGAAGTATAAACTAAGT
* *
42111 AAAGCTTAGGCGATTGCAGTATGGTAAAAACAGGGATGAAGTATAAACTAAG
1 AAAGCTTAGACGATTGCAATATGGTAAAAACAGGGATGAAGTATAAACTAAG
42163 CAAAAAACAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (53 bp):
AAAGCTTAGACGATTGCAATATGGTAAAAACAGGGATGAAGTATAAACTAAGT
Found at i:44818 original size:25 final size:25
Alignment explanation
Indices: 44785--44834 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
44775 GCTCCTTCAC
44785 TTCTCCTTTGCTTCTCCTTT-CTTCT
1 TTCTCCTTTG-TTCTCCTTTACTTCT
* *
44810 TTCTTCTTTGTTCTTCTTTACTTCT
1 TTCTCCTTTGTTCTCCTTTACTTCT
44835 GCCGGTCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.02, C:0.30, G:0.04, T:0.64
Consensus pattern (25 bp):
TTCTCCTTTGTTCTCCTTTACTTCT
Found at i:44944 original size:19 final size:18
Alignment explanation
Indices: 44895--44948 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
44885 TATTATTCTC
*
44895 TTGTTTTTCAATTATTTTG
1 TTGTTTTTC-ATTTTTTTG
* *
44914 TTCATTTCTCATTTTTTTCG
1 TT-GTTTTTCATTTTTTT-G
44934 TTGTTTTTCATTTTT
1 TTGTTTTTCATTTTT
44949 CCTTCATTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.70
Consensus pattern (18 bp):
TTGTTTTTCATTTTTTTG
Found at i:45726 original size:15 final size:15
Alignment explanation
Indices: 45700--45749 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
45690 ATATTTAGCT
* *
45700 GGGCGTGCGGATGTG
1 GGGCGGGCGGATGCG
*
45715 GGGTGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
45730 GGACGGGCGGATGCG
1 GGGCGGGCGGATGCG
45745 GGGCG
1 GGGCG
45750 AGTAATGTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.08, C:0.16, G:0.64, T:0.12
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:46245 original size:18 final size:19
Alignment explanation
Indices: 46222--46265 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
46212 TATTCGTATT
46222 ATATTAATAAATAAAT-AA
1 ATATTAATAAATAAATAAA
*
46240 ATATTAATAAATATATAAA
1 ATATTAATAAATAAATAAA
46259 ATATTAA
1 ATATTAA
46266 ATATTAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATTAATAAATAAATAAA
Found at i:46464 original size:27 final size:28
Alignment explanation
Indices: 46412--46465 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
46402 TAAAATATAT
* *
46412 TTATTTGTATTTTTTAAAATATATTCATA
1 TTATTTGTA-TTTATAAAACATATTCATA
46441 TTATTTGTA-TTATAAAACATATTCA
1 TTATTTGTATTTATAAAACATATTCA
46466 AGTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
29 9 0.39
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (28 bp):
TTATTTGTATTTATAAAACATATTCATA
Found at i:46548 original size:27 final size:26
Alignment explanation
Indices: 46507--46580 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
46497 TTTATTACAA
* * *
46507 AAAATATAAAAATATATTCGTATTAT
1 AAAATATTAAAATATAATAGTATTAT
* *
46533 AAAATATTAAACATATAATATTTTTAT
1 AAAATATTAAA-ATATAATAGTATTAT
46560 AAAATATATAAAATATTAATA
1 AAAATAT-TAAAATA-TAATA
46581 AATTAAGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.25
27 21 0.52
28 9 0.22
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (26 bp):
AAAATATTAAAATATAATAGTATTAT
Found at i:47793 original size:22 final size:22
Alignment explanation
Indices: 47750--47793 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
47740 AAATTTACAT
*
47750 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
47772 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
47794 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:49805 original size:3 final size:3
Alignment explanation
Indices: 49797--49871 Score: 82
Period size: 3 Copynumber: 24.7 Consensus size: 3
49787 ACATGTATTA
* *
49797 AAT AAT AAT AAT AAT AAT AAT -AT AGTT AAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
*
49842 AAT AAT AAT TAT -AT ATAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AA
49872 AAAAGACCCG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.06
3 51 0.82
4 6 0.10
5 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:50209 original size:43 final size:43
Alignment explanation
Indices: 50058--50319 Score: 135
Period size: 40 Copynumber: 6.1 Consensus size: 43
50048 GTTCTGGTCG
* * * * *
50058 TCTAAGGGTGACATGGTTCCTACGTGATGAGGAAATCTGG---
1 TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGAGCTGGTTA
* * * * * ** **
50098 TCGAGGGTTGACACTGCTCATACGTGATGAAGAGTTCTTGGCCA
1 TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGAGC-TGGTTA
* *
50142 TCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTA
1 TC-TAAGGT--TGACACGGCTCCTACGTGATGAGGA-GAGCTGGTTA
* *
50188 TCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGG---
1 TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGAGCTGGTTA
** * * * ** *
50228 TCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGTCA
1 TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGAGCTGGTTA
* *
50271 TCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTA
1 TCT-AAGGT--TGACACGGCTCCTACGTGATGAGGA-GAGCTGGTTA
50317 TCT
1 TCT
50320 CTAGGGATAA
Statistics
Matches: 167, Mismatches: 39, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
40 61 0.37
41 3 0.02
42 1 0.01
43 30 0.18
44 4 0.02
45 9 0.05
46 36 0.22
47 22 0.13
48 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGAGCTGGTTA
Found at i:50314 original size:46 final size:45
Alignment explanation
Indices: 50108--50319 Score: 145
Period size: 46 Copynumber: 4.8 Consensus size: 45
50098 TCGAGGGTTG
* * * ** *
50108 ACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGC-TGGTCATC-TAAGGTGATA
* * * *
50155 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTCATCTAAGGTGATA
* * *
50198 ACACGGCTCCTACGTGATGAGGAGATCTGG---TCT--GGGGATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTCATCTAAGGTGATA
* * **
50238 ACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTCATCT-AAGGTGATA
* *
50284 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTCATCT
50320 CTAGGGATAA
Statistics
Matches: 132, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
38 2 0.02
40 32 0.24
42 1 0.01
43 30 0.23
45 5 0.04
46 40 0.30
47 21 0.16
48 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (45 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTCATCTAAGGTGATA
Found at i:50678 original size:66 final size:63
Alignment explanation
Indices: 50504--50682 Score: 171
Period size: 66 Copynumber: 2.8 Consensus size: 63
50494 CCAAAGCAAC
* * * * * *
50504 TGTCTCGAAAGAGACAAGATTCGTTTCAAAGGAAAC-AACCCAAAGATGGCATTTAAAGGGAAT
1 TGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGACATTTAAAGGGAAT
* ** * * * * *
50567 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGATCGACGTTTCATGGGAA
1 TGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GACATTTAAAGGG-A
50632 AT
62 AT
50634 TGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 TGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
50683 TTTGTTTTGT
Statistics
Matches: 92, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
62 2 0.02
63 14 0.15
64 13 0.14
65 9 0.10
66 34 0.37
67 20 0.22
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (63 bp):
TGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGACATTTAAAGGGAAT
Found at i:50907 original size:15 final size:15
Alignment explanation
Indices: 50883--50926 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
50873 AAGACGATCT
*
50883 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
50898 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
50913 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
50927 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:51188 original size:36 final size:37
Alignment explanation
Indices: 51137--51231 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
51127 GAAACAAACT
* * *
51137 CAAAGATTTT-TTTCAAAAGAAATTGTCTT-TAATAGA
1 CAAA-ATTTTGTTTCAAAAGAAATTATCTTAAAAGAGA
*
51173 TAAAATTTTGTTTCAAAAGAAATTATCTTAAAAGAGA
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAAAGAGA
*
51210 CAAAATTTTGTTTCCAAAGAAA
1 CAAAATTTTGTTTCAAAAGAAA
51232 CAAACTCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
35 5 0.10
36 21 0.41
37 25 0.49
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAATTATCTTAAAAGAGA
Found at i:51256 original size:29 final size:31
Alignment explanation
Indices: 51215--51278 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
51205 AGAGACAAAA
51215 TTTTGTTTCCAAA-GAAACAAACTCAAAGAT
1 TTTTGTTTCCAAAGGAAACAAACTCAAAGAT
*
51245 TTTTGTTT-CAAAGGAAACAATCTCAAAGAT
1 TTTTGTTTCCAAAGGAAACAAACTCAAAGAT
51275 TTTT
1 TTTT
51279 TTCACAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (31 bp):
TTTTGTTTCCAAAGGAAACAAACTCAAAGAT
Found at i:51378 original size:28 final size:29
Alignment explanation
Indices: 51336--51408 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
51326 AGACTCAAAC
*
51336 AACTCACAGATTTTTATTCCAAAGGAACA
1 AACTCAAAGATTTTTATTCCAAAGGAACA
* * *
51365 AACTCCAAGATTTTTATTCAAAAGGAACG
1 AACTCAAAGATTTTTATTCCAAAGGAACA
51394 AACTCAAAGATTTTT
1 AACTCAAAGATTTTT
51409 TCCAAAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (29 bp):
AACTCAAAGATTTTTATTCCAAAGGAACA
Found at i:51433 original size:131 final size:130
Alignment explanation
Indices: 51114--51438 Score: 360
Period size: 131 Copynumber: 2.5 Consensus size: 130
51104 AGAGACAAAA
* * *
51114 TTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAATAGATAAAAT
1 TTTTGATTCAAAGGAAAC-AACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAGAGATAAAAC
* * *
51179 TTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA
65 TTTGTTTCAAAAGAAATTAACTCAAAAGACACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA
51244 T
130 T
* * ** *
51245 TTTTGTTTCAAAGGAAACAATCTCAAAGATTTTTTTC-ACA-AAATTGTCTCAAGAGAGACAAAA
1 TTTTGATTCAAAGGAAACAA-CTCAAAGATTTTTTTCAAAAGAAATTGTCTTTA-AGAGATAAAA
* * *
51308 CTTTGTTTC-AAAGTAAA-TAGACTCAAACA-ACTCACAGATTTT-TATTCCAAAGGAACAAACT
64 CTTTGTTTCAAAAG-AAATTA-ACTCAAA-AGACACA-AAATTTTGT-TTCCAAAGAAACAAACT
*
51369 CCAAGAT
124 CAAAGAT
*
51376 TTTT-ATTCAAAAGG-AACGAACTCAAAGATTTTTTCCAAAAGAAATTGTCTTTAAGAGATAAAA
1 TTTTGATTC-AAAGGAAAC-AACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAGAGATAAAA
51439 ATCGTTTTAA
Statistics
Matches: 164, Mismatches: 19, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
129 16 0.10
130 53 0.32
131 85 0.52
132 10 0.06
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (130 bp):
TTTTGATTCAAAGGAAACAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAGAGATAAAACT
TTGTTTCAAAAGAAATTAACTCAAAAGACACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGAT
Found at i:51704 original size:34 final size:32
Alignment explanation
Indices: 51657--51784 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 32
51647 AGAAAATGAT
**
51657 GTCTCAAGCGAGACGAAATTTGCTTTAAGATATA
1 GTCTCAAATGAGAC-AAATTTG-TTTAAGATATA
**
51691 GTCTCAAATGAGACAAAGTTTGTTTTTGATATA
1 GTCTCAAATGAGACAAA-TTTGTTTAAGATATA
* *
51724 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAATGAGAC-AAATTTG--TTTA-AGATATA
**
51760 GTCTCAAGCGAGACAAAGTTTGTTT
1 GTCTCAAATGAGACAAA-TTTGTTT
51785 TTGAGAAACG
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
33 30 0.38
34 22 0.28
35 6 0.08
36 20 0.26
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (32 bp):
GTCTCAAATGAGACAAATTTGTTTAAGATATA
Found at i:51780 original size:69 final size:67
Alignment explanation
Indices: 51657--51788 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 67
51647 AGAAAATGAT
* * * *
51657 GTCTCAAGCGAGACGAAATTTGCTTTAAGATATAGTCTCAAATGAGACAAAGTTTGTTTTTGATA
1 GTCTCAAACGAGACAAAATTTGCTTTAAGAAATAGTCTCAAACGAGACAAAGTTTGTTTTTGATA
51722 TA
66 TA
* * * *
51724 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTTGA
1 GTCTCAAACGAGACAAAATTTG-CTTTA-AGAAATAGTCTCAAACGAGACAAAGTTTGTTTTTGA
51789 GAAACGATCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 19 0.35
68 4 0.07
69 32 0.58
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (67 bp):
GTCTCAAACGAGACAAAATTTGCTTTAAGAAATAGTCTCAAACGAGACAAAGTTTGTTTTTGATA
TA
Found at i:51819 original size:35 final size:33
Alignment explanation
Indices: 51690--51807 Score: 137
Period size: 33 Copynumber: 3.4 Consensus size: 33
51680 TTTAAGATAT
* *
51690 AGTCTCAAATGAGACAAAGTTTGTTTTTGATAT
1 AGTCTCAAATGAGACAAAGTTTGTTTTTGAGAA
*
51723 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAA
1 AGTCTCAAATGAGACAAAGTTTGTTTTT-GAGAA
**
51757 ATTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAA
1 A--GTCTCAAATGAGACAAAGTTTGTTTTTGAGAA
*
51792 ACGATCTCAAGTGAGA
1 A-G-TCTCAAATGAGA
51808 TCAACTTTGT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
33 27 0.37
34 5 0.07
35 17 0.23
36 24 0.33
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (33 bp):
AGTCTCAAATGAGACAAAGTTTGTTTTTGAGAA
Found at i:51873 original size:101 final size:99
Alignment explanation
Indices: 51760--51987 Score: 250
Period size: 101 Copynumber: 2.3 Consensus size: 99
51750 TAGAGAAATT
* *
51760 GTCTCAAGCGAGACAAAGTTTGTTTTTG-AGAAAC--GATCTCAA-GTGAGATCAACTTTGTTTA
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAAGAAACAACATCT-AAGGTGAGAT----TTTGTTTA
* *
51821 -ATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
60 TA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
51861 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTTTGTTTTTAGT
1 GTCTCAAGCGAGACAAAATTTGTTTTG-AAGAAACAAC-ATCTAAGGTGAGATTTTGTTTATAGT
* * *
51926 GAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
64 GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
51962 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
51988 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
100 5 0.05
101 85 0.77
102 7 0.06
104 2 0.02
105 11 0.10
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (99 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAGAAACAACATCTAAGGTGAGATTTTGTTTATAGTGA
AACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:52150 original size:36 final size:36
Alignment explanation
Indices: 52110--52208 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
52100 AAAGTGAAAA
**
52110 TGTCTCAAATGAGACAAAATTTGTTTTGAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
52146 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
52182 TGTCTCAAGCGAGACAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTT
52209 TAGAAAAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
Found at i:52572 original size:4 final size:4
Alignment explanation
Indices: 52563--52628 Score: 73
Period size: 4 Copynumber: 17.0 Consensus size: 4
52553 TTTATGTATC
* * *
52563 ATGT ATGT A--T ATGT ATGT ATGT ATAT ATGT ATAT ATGT ACGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
52609 ATAT ACGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT
52629 GTATACTCTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
4 48 0.96
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:53820 original size:13 final size:14
Alignment explanation
Indices: 53804--53835 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
53794 TCTTTGTCCT
53804 CTTTTGTTCTTTG-
1 CTTTTGTTCTTTGA
53817 CTTTT-TTCTTTGA
1 CTTTTGTTCTTTGA
53830 CTTTTG
1 CTTTTG
53836 CTTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.03, C:0.16, G:0.12, T:0.69
Consensus pattern (14 bp):
CTTTTGTTCTTTGA
Found at i:53827 original size:12 final size:12
Alignment explanation
Indices: 53804--53927 Score: 80
Period size: 12 Copynumber: 10.5 Consensus size: 12
53794 TCTTTGTCCT
53804 CTTTTGTTCTTTG
1 CTTTT-TTCTTTG
53817 CTTTTTTCTTTG
1 CTTTTTTCTTTG
*
53829 AC-TTTTGCTTTG
1 -CTTTTTTCTTTG
*
53841 -ATTTTTCTTTG
1 CTTTTTTCTTTG
*
53852 -TTTTTGCTTTG
1 CTTTTTTCTTTG
* *
53863 ATTTTTT-TTTT
1 CTTTTTTCTTTG
* **
53874 CTCTGCTCTTTG
1 CTTTTTTCTTTG
*
53886 TTTTTTTCTTTG
1 CTTTTTTCTTTG
53898 CTCTTTTCTCTTTG
1 CT-TTTT-TCTTTG
*
53912 -ATTTTTCTTTG
1 CTTTTTTCTTTG
53923 -TTTTT
1 CTTTTT
53928 GATTGGATCT
Statistics
Matches: 87, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
11 34 0.39
12 37 0.43
13 10 0.11
14 6 0.07
ACGTcount: A:0.03, C:0.15, G:0.10, T:0.72
Consensus pattern (12 bp):
CTTTTTTCTTTG
Found at i:53845 original size:11 final size:11
Alignment explanation
Indices: 53819--53867 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
53809 GTTCTTTGCT
*
53819 TTTTTCTTTGA
1 TTTTGCTTTGA
53830 CTTTTGCTTTGA
1 -TTTTGCTTTGA
* *
53842 TTTTTCTTTGT
1 TTTTGCTTTGA
53853 TTTTGCTTTGA
1 TTTTGCTTTGA
53864 TTTT
1 TTTT
53868 TTTTTTCTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (11 bp):
TTTTGCTTTGA
Found at i:53856 original size:22 final size:22
Alignment explanation
Indices: 53819--53928 Score: 98
Period size: 23 Copynumber: 4.7 Consensus size: 22
53809 GTTCTTTGCT
*
53819 TTTTTCTTTGACTTTTGCTTTGA
1 TTTTTCTTTG-TTTTTGCTTTGA
53842 TTTTTCTTTGTTTTTGCTTTGA
1 TTTTTCTTTGTTTTTGCTTTGA
* *
53864 TTTTT-TTT-TTCTCTGCTCTTTGTT
1 TTTTTCTTTGTT-TTTG--CTTTG-A
*
53888 TTTTTCTTTGCTCTTTTCTCTTTGA
1 TTTTTCTTTG-T-TTTT-GCTTTGA
53913 TTTTTCTTTGTTTTTG
1 TTTTTCTTTGTTTTTG
53929 ATTGGATCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
20 2 0.03
21 6 0.08
22 16 0.23
23 19 0.27
24 6 0.08
25 13 0.18
26 5 0.07
27 3 0.04
28 1 0.01
ACGTcount: A:0.04, C:0.14, G:0.11, T:0.72
Consensus pattern (22 bp):
TTTTTCTTTGTTTTTGCTTTGA
Found at i:53862 original size:34 final size:35
Alignment explanation
Indices: 53810--53928 Score: 100
Period size: 34 Copynumber: 3.4 Consensus size: 35
53800 TCCTCTTTTG
* *
53810 TTCTTTGCTTTTTTCTTTGACTTTTGCTTTGATTT
1 TTCTTTGCTTTTTGCTTTGACTTTTTCTTTGATTT
* ** *
53845 TTCTTTG-TTTTTGCTTTGA-TTTTTTTTTTCTCTG
1 TTCTTTGCTTTTTGCTTTGACTTTTTCTTTGAT-TT
* * * *
53879 CTCTTTGTTTTTTTCTTTGCTCTTTTCTCTTTGATTT
1 TTCTTTGCTTTTTGCTTTG-ACTTTT-TCTTTGATTT
53916 TTCTTTG-TTTTTG
1 TTCTTTGCTTTTTG
53929 ATTGGATCTT
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
33 8 0.12
34 18 0.28
35 17 0.27
36 5 0.08
37 11 0.17
38 5 0.08
ACGTcount: A:0.03, C:0.14, G:0.11, T:0.71
Consensus pattern (35 bp):
TTCTTTGCTTTTTGCTTTGACTTTTTCTTTGATTT
Found at i:53891 original size:19 final size:19
Alignment explanation
Indices: 53867--53903 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53857 GCTTTGATTT
53867 TTTTTTTCTCTGCTCTTTG
1 TTTTTTTCTCTGCTCTTTG
*
53886 TTTTTTTCTTTGCTCTTT
1 TTTTTTTCTCTGCTCTTT
53904 TCTCTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.08, T:0.73
Consensus pattern (19 bp):
TTTTTTTCTCTGCTCTTTG
Found at i:54607 original size:26 final size:26
Alignment explanation
Indices: 54529--54608 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
54519 TTTCAAAGTG
*
54529 GAAAGAATATTTCCAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
54555 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
54576 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
54601 GATAGAAT
1 GAAAGAAT
54609 GTCAAAATTG
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 19 0.47
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:54609 original size:46 final size:45
Alignment explanation
Indices: 54517--54610 Score: 134
Period size: 46 Copynumber: 2.1 Consensus size: 45
54507 ATAAATGCAG
* * *
54517 TGTTTCAAAGTGGAAAGAATATTTCCAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAAGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
* *
54562 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAAGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
54608 TGT
1 TGT
54611 CAAAATTGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 10 0.23
46 33 0.77
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (45 bp):
TGTTTCAAAGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:56036 original size:30 final size:29
Alignment explanation
Indices: 56000--56061 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
55990 TGACAAAATG
56000 ACACAAACAAAAGAGAAGAAATAAGTTAGT
1 ACACAAACAAAAGAGAA-AAATAAGTTAGT
*
56030 ACACAAACAAAAGAGAAACATAAGTTAGT
1 ACACAAACAAAAGAGAAAAATAAGTTAGT
56059 ACA
1 ACA
56062 TGTAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.60, C:0.13, G:0.15, T:0.13
Consensus pattern (29 bp):
ACACAAACAAAAGAGAAAAATAAGTTAGT
Found at i:57610 original size:22 final size:22
Alignment explanation
Indices: 57567--57610 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
57557 AAATTTACAT
*
57567 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
57589 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
57611 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:59621 original size:3 final size:3
Alignment explanation
Indices: 59613--59687 Score: 82
Period size: 3 Copynumber: 24.7 Consensus size: 3
59603 ACATGTATTA
* *
59613 AAT AAT AAT AAT AAT AAT AAT -AT AGTT AAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
*
59658 AAT AAT AAT TAT -AT ATAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AA
59688 AAAAGACCCG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.06
3 51 0.82
4 6 0.10
5 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:70106 original size:3 final size:3
Alignment explanation
Indices: 70100--70140 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
70090 AATAAAGTAT
70100 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
70141 TGAATAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:74979 original size:17 final size:17
Alignment explanation
Indices: 74957--75000 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
74947 ATGTAAAAAT
74957 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
74974 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
74991 AAATATTTAA
1 AAATATTTAA
75001 TCAAGAAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:76873 original size:16 final size:16
Alignment explanation
Indices: 76852--76891 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
76842 AGCTATGTGA
76852 CATATGAATATGAATT
1 CATATGAATATGAATT
76868 CATATGAATATGAATT
1 CATATGAATATGAATT
76884 CATATGAA
1 CATATGAA
76892 AAGTGACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (16 bp):
CATATGAATATGAATT
Found at i:77283 original size:24 final size:23
Alignment explanation
Indices: 77205--77292 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
77195 CAATCTTATA
*
77205 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
77228 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
77251 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
77275 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
77293 TATATAAGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.02
23 35 0.64
24 18 0.33
25 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:78489 original size:29 final size:28
Alignment explanation
Indices: 78455--78518 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 28
78445 ACTTAATTCG
78455 AAATAAATAAATTACAT-TCCATTAATTT
1 AAATAAATAAATTACATCT-CATTAATTT
78483 AAAATAAATAAATTACATCTCATTAATTT
1 -AAATAAATAAATTACATCTCATTAATTT
78512 AAATAAA
1 AAATAAA
78519 AATAACAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 7 0.21
29 26 0.76
30 1 0.03
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATAAATAAATTACATCTCATTAATTT
Found at i:80053 original size:2 final size:2
Alignment explanation
Indices: 80043--80088 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
80033 TTTTTTATTA
*
80043 AT AT GAT AT AT -T A- AT AT AT A- AT TT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80083 AT AT AT
1 AT AT AT
80089 TGAAAATGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87481 original size:2 final size:2
Alignment explanation
Indices: 87476--87520 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
87466 AACATCATCA
87476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87518 AT A
1 AT A
87521 GTTTGTATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89513 original size:155 final size:155
Alignment explanation
Indices: 89230--89519 Score: 454
Period size: 155 Copynumber: 1.9 Consensus size: 155
89220 AGTTATATTT
* * * *
89230 TGGTTCAAATTTGGTTAAAAAATGGACTTAAAATGAATGAGAAATTGAAGAAACAATAAAATCAA
1 TGGTTCAAATTTAGTAAAAAAATAGACTTAAAATGAATGAGAAATTGAAGAAACAATAAAACCAA
* * *
89295 GGACTAAATCGTAAAACTATCAAAATACTTAGTCAAATTTTTGGTTTTTCGAGTAACTTAAAAAT
66 GGACTAAATCGTAAAACTATCAAAATACTTAGTCAAATTTTTGATTTTTCGAATAACTCAAAAAT
89360 TCAAATTTTTCGGTTTAGGAGCATG
131 TCAAATTTTTCGGTTTAGGAGCATG
* *
89385 TGGTTCAAATTTAGTAAAAAAATAGACTTAAAATGAATGAGAAATTGAAGAAATAATGAAACCAA
1 TGGTTCAAATTTAGTAAAAAAATAGACTTAAAATGAATGAGAAATTGAAGAAACAATAAAACCAA
* ** * *
89450 TGACTAAATCGTAAAACTATCAAAATTTTTGGTCAAATTTTTGATTTTTTGAATAACTCAAAAAT
66 GGACTAAATCGTAAAACTATCAAAATACTTAGTCAAATTTTTGATTTTTCGAATAACTCAAAAAT
89515 TCAAA
131 TCAAA
89520 ATTTCAACTC
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
155 121 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.32
Consensus pattern (155 bp):
TGGTTCAAATTTAGTAAAAAAATAGACTTAAAATGAATGAGAAATTGAAGAAACAATAAAACCAA
GGACTAAATCGTAAAACTATCAAAATACTTAGTCAAATTTTTGATTTTTCGAATAACTCAAAAAT
TCAAATTTTTCGGTTTAGGAGCATG
Found at i:92127 original size:31 final size:31
Alignment explanation
Indices: 92092--92168 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
92082 ATGATTTTGA
* **
92092 AAAATTGA-AAGTTTATATACTTAAACGGACC
1 AAAATTGATAA-TTTAGATACAAAAACGGACC
92123 AAAATTGATAATTTAGATACAAAAACGGACC
1 AAAATTGATAATTTAGATACAAAAACGGACC
* *
92154 AAGATTGATATTTTA
1 AAAATTGATAATTTA
92169 AGCACTAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (31 bp):
AAAATTGATAATTTAGATACAAAAACGGACC
Found at i:99257 original size:157 final size:157
Alignment explanation
Indices: 98963--99273 Score: 543
Period size: 157 Copynumber: 2.0 Consensus size: 157
98953 AAAATGTTTT
*
98963 CTCTAATTTTAAATAATTATTATTCTCCTAAGCATGATCGTTCAACAAACAAATGGAAAAACAAC
1 CTCTAATTTTAAATAATTATTATTCTCCTAAGCATGATCGTTCAACAAACAAATGCAAAAACAAC
* * *
99028 ATATTAATCAATTGATCAGAAAAAACTATTTCACAGAACAAGCAAGCATATGCAACCTTTTTTAT
66 ATATTAATCAATTGATCAGAAAAAACTATTTCACAGAACAAGCAAGCAAATACAACCTTTTTTAA
*
99093 AACAAAAAAATAATTCCAGACACTTTC
131 AACAAAAAAATAATTCCAAACACTTTC
* *
99120 CTCTAATTTTCAATAATTATTATTCTCCTAAGCATGATCGTTCAACAAACAAATGCTAAAACAAC
1 CTCTAATTTTAAATAATTATTATTCTCCTAAGCATGATCGTTCAACAAACAAATGCAAAAACAAC
*
99185 ATATTAATCAATTGATCAG-AAAAACTATTTCACAGAACACGCAAGCAAATACAACCTTTTTTAA
66 ATATTAATCAATTGATCAGAAAAAACTATTTCACAGAACAAGCAAGCAAATACAACCTTTTTTAA
99249 AACAAAAAAATAATTCCAAACACTT
131 AACAAAAAAATAATTCCAAACACTT
99274 CCTGATCGTG
Statistics
Matches: 146, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
156 65 0.45
157 81 0.55
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (157 bp):
CTCTAATTTTAAATAATTATTATTCTCCTAAGCATGATCGTTCAACAAACAAATGCAAAAACAAC
ATATTAATCAATTGATCAGAAAAAACTATTTCACAGAACAAGCAAGCAAATACAACCTTTTTTAA
AACAAAAAAATAATTCCAAACACTTTC
Found at i:104037 original size:14 final size:14
Alignment explanation
Indices: 104018--104046 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
104008 ATGATAGGTA
104018 TGAATAAAATAAAT
1 TGAATAAAATAAAT
104032 TGAATAAAATAAAT
1 TGAATAAAATAAAT
104046 T
1 T
104047 AAGTTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (14 bp):
TGAATAAAATAAAT
Found at i:106688 original size:44 final size:44
Alignment explanation
Indices: 106638--106722 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
106628 GAGATCAAAC
*
106638 ATAATTATGTTTATAACACGTACAAGAACGCATATGTTTTATAT
1 ATAATTATGTTTATAACACGTACAAGAACGCATATATTTTATAT
106682 ATAATTATGTTTATAACACGTACAAGAACGCATATATTTTA
1 ATAATTATGTTTATAACACGTACAAGAACGCATATATTTTA
106723 CAGAAACAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (44 bp):
ATAATTATGTTTATAACACGTACAAGAACGCATATATTTTATAT
Found at i:109367 original size:14 final size:14
Alignment explanation
Indices: 109348--109385 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
109338 TGTTCGGTAA
109348 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
109362 TATGTTCGTTCGTT
1 TATGTTCGTTCATT
109376 TATGTTCGTT
1 TATGTTCGTT
109386 TATATGCGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.18, T:0.58
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:109654 original size:23 final size:23
Alignment explanation
Indices: 109624--109725 Score: 82
Period size: 23 Copynumber: 4.3 Consensus size: 23
109614 GTTTGTTCGT
109624 TTGTGTTCATTTACGTTCGTTTA
1 TTGTGTTCATTTACGTTCGTTTA
* * *
109647 TTGTGTTCGTTTACATCCGTTCGT-
1 TTGTGTTCATTTACGTTCGTT--TA
*
109671 TTGTGTT-ATTTAACGTTCATTTA
1 TTGTGTTCATTT-ACGTTCGTTTA
* * * *
109694 TTGTATTCGTTTATGTTCGTTCA
1 TTGTGTTCATTTACGTTCGTTTA
109717 TTTGTGTTC
1 -TTGTGTTC
109726 GCTTATCATT
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
22 1 0.02
23 35 0.58
24 23 0.38
25 1 0.02
ACGTcount: A:0.13, C:0.14, G:0.18, T:0.56
Consensus pattern (23 bp):
TTGTGTTCATTTACGTTCGTTTA
Found at i:109669 original size:47 final size:48
Alignment explanation
Indices: 109591--109725 Score: 157
Period size: 47 Copynumber: 2.9 Consensus size: 48
109581 GTTCGTTTAT
** * **
109591 GTTCATTTATTGTATTTTTTTACGTTTGTTCGTTTGTGTTCATTT-AC
1 GTTCATTTATTGTATTCGTTTACATCCGTTCGTTTGTGTTCATTTAAC
* *
109638 GTTCGTTTATTGTGTTCGTTTACATCCGTTCGTTTGTGTT-ATTTAAC
1 GTTCATTTATTGTATTCGTTTACATCCGTTCGTTTGTGTTCATTTAAC
** * *
109685 GTTCATTTATTGTATTCGTTTATGTTCGTTCATTTGTGTTC
1 GTTCATTTATTGTATTCGTTTACATCCGTTCGTTTGTGTTC
109726 GCTTATCATT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
46 4 0.05
47 69 0.95
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.58
Consensus pattern (48 bp):
GTTCATTTATTGTATTCGTTTACATCCGTTCGTTTGTGTTCATTTAAC
Found at i:113229 original size:31 final size:29
Alignment explanation
Indices: 113173--113269 Score: 90
Period size: 28 Copynumber: 3.3 Consensus size: 29
113163 TAAGTATTTA
113173 AAATACCT-AAAGTATTTTTTATCAAAAT
1 AAATACCTAAAAGTATTTTTTATCAAAAT
*
113201 AAATACCTAAAATTATATTTTTAGTCAAAAT
1 AAATACCTAAAAGTAT-TTTTTA-TCAAAAT
** * * * *
113232 ATGTACCT-AAAGCATTGTATGTCAAAAT
1 AAATACCTAAAAGTATTTTTTATCAAAAT
*
113260 AGATACCTAA
1 AAATACCTAA
113270 GCTATTCAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
28 21 0.38
29 10 0.18
30 11 0.20
31 13 0.24
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (29 bp):
AAATACCTAAAAGTATTTTTTATCAAAAT
Found at i:113795 original size:37 final size:37
Alignment explanation
Indices: 113722--113796 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
113712 GTTGGAAAAT
* *
113722 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* **
113759 ATTTATATACTTTTTTTTACGAAATTAAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTAAAAAATTAAAAATCATAAA
113796 A
1 A
113797 CATATTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 15 0.47
38 17 0.53
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:117985 original size:18 final size:19
Alignment explanation
Indices: 117962--117997 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
117952 TTATTTTAAA
117962 TAAAAAAAAT-TAAAATTT
1 TAAAAAAAATATAAAATTT
*
117980 TAAAAATAATATAAAATT
1 TAAAAAAAATATAAAATT
117998 AAATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAAAAATATAAAATTT
Done.