Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008907.1 Hibiscus syriacus cultivar Beakdansim tig00112201_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: 66877
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:4693 original size:13 final size:13
Alignment explanation
Indices: 4673--4724 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
4663 GGTCAACATC
4673 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
4686 GATCAACGGGTCG
1 GGTCAACGGGTCG
4699 GGT---CGGGTCG
1 GGTCAACGGGTCG
4709 GGTCAACGGGTCG
1 GGTCAACGGGTCG
4722 GGT
1 GGT
4725 TGTGACCGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 10 0.29
13 24 0.71
ACGTcount: A:0.13, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:4705 original size:23 final size:23
Alignment explanation
Indices: 4679--4724 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
4669 CATCGGTCAA
4679 CGGGTCGGATCAACGGGTCGGGT
1 CGGGTCGGATCAACGGGTCGGGT
*
4702 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGATCAACGGGTCGGGT
4725 TGTGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (23 bp):
CGGGTCGGATCAACGGGTCGGGT
Found at i:4735 original size:23 final size:23
Alignment explanation
Indices: 4688--4737 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4678 ACGGGTCGGA
* *
4688 TCAACGGGTCGGGTCGGGTCGGG
1 TCAACGGGTCGGGTCGGGACCGG
* *
4711 TCAACGGGTCGGGTTGTGACCGG
1 TCAACGGGTCGGGTCGGGACCGG
4734 TCAA
1 TCAA
4738 ACCAGTCACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.22, G:0.44, T:0.20
Consensus pattern (23 bp):
TCAACGGGTCGGGTCGGGACCGG
Found at i:12442 original size:36 final size:36
Alignment explanation
Indices: 12393--12461 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
12383 ATCAATAAGA
* *
12393 AATTACCAACTTGAT-AGGTGTTGAACTTACATAAAG
1 AATTACCAACTTGATCAGAT-TTGAACCTACATAAAG
* *
12429 AATTGCCAGCTTGATCAGATTTGAACCTACATA
1 AATTACCAACTTGATCAGATTTGAACCTACATA
12462 CTCCAGAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 25 0.89
37 3 0.11
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (36 bp):
AATTACCAACTTGATCAGATTTGAACCTACATAAAG
Found at i:13261 original size:27 final size:27
Alignment explanation
Indices: 13201--13261 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
13191 AGGTATATGA
*
13201 GTCATTTTACACTTTAGGGGTATTTTG
1 GTCATTTTACACTTTAAGGGTATTTTG
* **
13228 GTTATTTTACGGTTTAAGGGTATTTAT-
1 GTCATTTTACACTTTAAGGGTATTT-TG
13255 GTCATTT
1 GTCATTT
13262 CCTTCAGTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.20, C:0.08, G:0.21, T:0.51
Consensus pattern (27 bp):
GTCATTTTACACTTTAAGGGTATTTTG
Found at i:14151 original size:20 final size:20
Alignment explanation
Indices: 14126--14177 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
14116 GGTCGGTTAG
14126 GTTGACTCAGACCGATTCGA
1 GTTGACTCAGACCGATTCGA
14146 GTTGACTCAGACCGATTCGA
1 GTTGACTCAGACCGATTCGA
*
14166 GTTAACTCAGAC
1 GTTGACTCAGAC
14178 TAGTTCTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTGACTCAGACCGATTCGA
Found at i:14861 original size:27 final size:27
Alignment explanation
Indices: 14799--14858 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
14789 GGAATGGACA
14799 GGGGTTTCTTGAGAGAATGAGTTTTAG
1 GGGGTTTCTTGAGAGAATGAGTTTTAG
*
14826 GGGGTTTCTTGATAGAATGAGTTTT-G
1 GGGGTTTCTTGAGAGAATGAGTTTTAG
14852 GGGGTTT
1 GGGGTTT
14859 TCTCATTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 8 0.25
27 24 0.75
ACGTcount: A:0.18, C:0.03, G:0.38, T:0.40
Consensus pattern (27 bp):
GGGGTTTCTTGAGAGAATGAGTTTTAG
Found at i:15221 original size:2 final size:2
Alignment explanation
Indices: 15210--15277 Score: 72
Period size: 2 Copynumber: 35.5 Consensus size: 2
15200 ATATTTCAAT
*
15210 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
15249 TGA TA -A TA TA TA TA TA CA TA TA TT TA TA T
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
15278 TATTGTTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
1 4 0.07
2 49 0.89
3 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:15289 original size:32 final size:34
Alignment explanation
Indices: 15211--15276 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
15201 TATTTCAATT
*
15211 ATAAT-ATATATATATATATATATATATATTATAG
1 ATAATGATA-ATATATATATACATATATATTATAG
15245 ATAATGATAATATATATATACATATAT-TTATA
1 ATAATGATAATATATATATACATATATATTATA
15277 TTATTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 22 0.73
35 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (34 bp):
ATAATGATAATATATATATACATATATATTATAG
Found at i:18147 original size:10 final size:9
Alignment explanation
Indices: 18132--18204 Score: 69
Period size: 10 Copynumber: 7.8 Consensus size: 9
18122 CAATCAAAAC
18132 AAAAAGAGAA
1 AAAAAGA-AA
18142 AAAAAGAAA
1 AAAAAGAAA
18151 AAAGAA-AAA
1 AAA-AAGAAA
18160 AAAAAGAGAA
1 AAAAAGA-AA
18170 AAAAA-AAA
1 AAAAAGAAA
*
18178 CAAAAGAAA
1 AAAAAGAAA
*
18187 ATTAAAGAAA
1 A-AAAAGAAA
18197 AAAGAAGA
1 AAA-AAGA
18205 CAATATGCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
8 8 0.15
9 17 0.32
10 28 0.53
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:18158 original size:13 final size:13
Alignment explanation
Indices: 18127--18177 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
18117 AGATTCAATC
*
18127 AAAACAAAAAGAG
1 AAAAAAAAAAGAG
*
18140 AAAAAAAGAAAAAAG
1 -AAAAAA-AAAAGAG
18155 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
18168 AAAAAAAAAA
1 AAAAAAAAAA
18178 CAAAAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 16 0.48
14 11 0.33
15 6 0.18
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:18161 original size:18 final size:17
Alignment explanation
Indices: 18140--18202 Score: 72
Period size: 18 Copynumber: 3.6 Consensus size: 17
18130 ACAAAAAGAG
18140 AAAAAAAGAAAAAAGAAA
1 AAAAAAAGAAAAAA-AAA
18158 AAAAAAAGAGAAAAAAAA
1 AAAAAAAGA-AAAAAAAA
* **
18176 AACAAAAGAAAATTAAA
1 AAAAAAAGAAAAAAAAA
*
18193 GAAAAAAGAA
1 AAAAAAAGAA
18203 GACAATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
17 14 0.36
18 20 0.51
19 5 0.13
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAA
Found at i:18162 original size:11 final size:11
Alignment explanation
Indices: 18143--18176 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
18133 AAAAGAGAAA
18143 AAAAGAAAAAAG
1 AAAA-AAAAAAG
18155 AAAAAAAAAAG
1 AAAAAAAAAAG
18166 AGAAAAAAAAA
1 A-AAAAAAAAA
18177 ACAAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:18163 original size:28 final size:29
Alignment explanation
Indices: 18127--18187 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
18117 AGATTCAATC
* *
18127 AAAACAAAAAGAGAAAAAAAGAA-AAAAG
1 AAAAAAAAAAGAGAAAAAAAAAACAAAAG
18155 AAAAAAAAAAGAGAAAAAAAAAACAAAAG
1 AAAAAAAAAAGAGAAAAAAAAAACAAAAG
18184 AAAA
1 AAAA
18188 TTAAAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAGAGAAAAAAAAAACAAAAG
Found at i:18342 original size:69 final size:70
Alignment explanation
Indices: 18260--18398 Score: 217
Period size: 70 Copynumber: 2.0 Consensus size: 70
18250 GATTCAAACT
* *
18260 ATGAGATTGATCAAGCACAATCA-TTTCCGAATCATTGAACCACTTAACTCGAAGATCATAGAGC
1 ATGAGATTGATCAAGCACAATCATTTTCCGAATCACTGAACCACTCAACTCGAAGATCATAGAGC
18324 ATCAA
66 ATCAA
** * *
18329 ATGAGATTGATCAAGCACAATCATTTTTTGAATCACTGAATCACTCCACTCGAAGATCATAGAGC
1 ATGAGATTGATCAAGCACAATCATTTTCCGAATCACTGAACCACTCAACTCGAAGATCATAGAGC
18394 ATCAA
66 ATCAA
18399 GAGAGAGAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
69 23 0.37
70 40 0.63
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (70 bp):
ATGAGATTGATCAAGCACAATCATTTTCCGAATCACTGAACCACTCAACTCGAAGATCATAGAGC
ATCAA
Found at i:19373 original size:33 final size:32
Alignment explanation
Indices: 19321--19402 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 32
19311 TGAGGGCATC
* *
19321 TTTGAAGATTCAAAATCAAATGCTGGGGCATTTT
1 TTTGAA-ATTCAACATCAAATGCTGGGGC-CTTT
* *
19355 TTTGAAATTTAACATCAAATGTTGGGGCCTTT
1 TTTGAAATTCAACATCAAATGCTGGGGCCTTT
*
19387 TTTGAGATTCAACATC
1 TTTGAAATTCAACATC
19403 GAATATTGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 17 0.40
33 19 0.45
34 6 0.14
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (32 bp):
TTTGAAATTCAACATCAAATGCTGGGGCCTTT
Found at i:19401 original size:32 final size:33
Alignment explanation
Indices: 19321--19412 Score: 105
Period size: 32 Copynumber: 2.8 Consensus size: 33
19311 TGAGGGCATC
* * *
19321 TTTGAAGATTCAAAATCAAATGCTGGGGCATTTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCACTTT
* *
19355 TTTGAAATTTAACATCAAATGTTGGGGC-CTTT
1 TTTGAGATTCAACATCAAATGTTGGGGCACTTT
* *
19387 TTTGAGATTCAACATCGAATATTGGG
1 TTTGAGATTCAACATCAAATGTTGGG
19413 CCATCTTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 25 0.51
33 20 0.41
34 4 0.08
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (33 bp):
TTTGAGATTCAACATCAAATGTTGGGGCACTTT
Found at i:20677 original size:36 final size:36
Alignment explanation
Indices: 20623--20698 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
20613 AGACAATTTC
*
20623 CAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAA
1 CAAATTTTATCTCCCTTGAGACAATTTCCCTTGAAA
* *
20659 CAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAA
1 CAAATTTTATCTCCCTTGAGACAATTTCCCTTGAAA
20695 CAAA
1 CAAA
20699 ATCTTTGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.36
Consensus pattern (36 bp):
CAAATTTTATCTCCCTTGAGACAATTTCCCTTGAAA
Found at i:20812 original size:36 final size:36
Alignment explanation
Indices: 20716--20944 Score: 224
Period size: 36 Copynumber: 6.3 Consensus size: 36
20706 AATTTGTTTT
* ** *
20716 CCTTGAAACTAATTTCGTCTCCCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCCCTTGAGACAATTTC
** * * * * *
20752 TTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAAC-AAATTTTATCTCCCTTGAGACAATTTC
* * * *
20789 TCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCCCTTGAGACAATTTC
* * * *
20825 CCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCCCTTGAGACAATTTC
* * *
20861 TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCCCTTGAGACAATTTC
* * *
20897 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCCCTTGAGACAATTTC
20933 CCTTGAAACAAA
1 CCTTGAAACAAA
20945 ATAATTAAAT
Statistics
Matches: 175, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
36 145 0.83
37 30 0.17
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (36 bp):
CCTTGAAACAAATTTTATCTCCCTTGAGACAATTTC
Found at i:20869 original size:72 final size:72
Alignment explanation
Indices: 20711--20944 Score: 360
Period size: 72 Copynumber: 3.2 Consensus size: 72
20701 CTTTGAATTT
* * * ** * *
20711 GTTTTCCTTGAAACTAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
20776 TTGAGACA
65 TTGAGACA
* *
20784 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
*
20849 TAAGACA
66 TGAGACA
*
20856 GTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
20921 TGAGACA
66 TGAGACA
20928 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
20945 ATAATTAAAT
Statistics
Matches: 148, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 106 0.72
73 42 0.28
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (72 bp):
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
TGAGACA
Found at i:21128 original size:36 final size:36
Alignment explanation
Indices: 21060--21128 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
21050 ATTGAAAACA
* *
21060 TTTTCCTTGAAATGAATTTTGTCACTCATGAGATCG
1 TTTTCCTTGAAATAAATTTTGTCACCCATGAGATCG
* *
21096 TTTTCCTTGAAATAAATTTTGTCTCCCTTGAGA
1 TTTTCCTTGAAATAAATTTTGTCACCCATGAGA
21129 CAGTTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTCCTTGAAATAAATTTTGTCACCCATGAGATCG
Found at i:21137 original size:101 final size:100
Alignment explanation
Indices: 20765--21176 Score: 386
Period size: 101 Copynumber: 4.0 Consensus size: 100
20755 TGGAACTAAG
* * *
20765 TTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 TTTTGTCTCCCTTGAGACAGTTTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
* * * * * *
20829 GAAACA-AATTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACAAA
65 GAAACATAA-----AC-AT-TGAAAACATTTTC-CTTGAAA-TAA
* * *
20873 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCCCTTGAGACAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
* * *
20938 AAACA-AAATAATT-AAATCTGTTTTCCTTGAAACTAA
66 AAACATAAA-CATTGAAAAC-ATTTTCCTTGAAA-TAA
* * * *
20974 TTCTGTCTCCCTTGAGACAG-TTTCTTTTGGAACAATATTTTGTCTCCCTTAAGACAGTTTCTCT
1 TTTTGTCTCCCTTGAGACAGTTTTC-CTTGAAACAA-ATTTTGTCTCCCTTGAGACAGTTTCTCT
21038 TGAAACATAAACATTGAAAACATTTTCCTTGAAATGAA
64 TGAAACATAAACATTGAAAACATTTTCCTTGAAAT-AA
* * * *
21076 TTTTGTCACTCATGAGATC-GTTTTCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
1 TTTTGTCTCCCTTGAGA-CAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
* * *
21140 GAAGCATAAACTTTGAAAACAGTTTCCTTTGAAATAA
65 GAAACATAAACATTGAAAACATTTTCC-TTGAAATAA
21177 AATCTTTGAA
Statistics
Matches: 262, Mismatches: 31, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
100 3 0.01
101 95 0.36
102 82 0.31
103 13 0.05
108 66 0.25
109 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (100 bp):
TTTTGTCTCCCTTGAGACAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
AAACATAAACATTGAAAACATTTTCCTTGAAATAA
Found at i:21141 original size:36 final size:36
Alignment explanation
Indices: 21061--21142 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
21051 TTGAAAACAT
* *
21061 TTTC-CTTGAAATGAATTTTGTCACTCATGAGATCG
1 TTTCTCTTGAAATAAATTTTGTCACCCATGAGATCG
* *
21096 TTT-TCCTTGAAATAAATTTTGTCTCCCTTGAGA-CAG
1 TTTCT-CTTGAAATAAATTTTGTCACCCATGAGATC-G
21132 TTTCTCTTGAA
1 TTTCTCTTGAA
21143 GCATAAACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
35 4 0.10
36 34 0.87
37 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAATAAATTTTGTCACCCATGAGATCG
Found at i:21368 original size:35 final size:35
Alignment explanation
Indices: 21326--21412 Score: 156
Period size: 35 Copynumber: 2.5 Consensus size: 35
21316 CTTGGAATAC
*
21326 TGTTTCTCTTGAAACACAAAAAAAACCTTTGAAAT
1 TGTTTCTCTTGAAACACAAAAAAAACCTTTGAAAA
*
21361 TGTTTCTCTTGAAACACACAAAAAACCTTTGAAAA
1 TGTTTCTCTTGAAACACAAAAAAAACCTTTGAAAA
21396 TGTTTCTCTTGAAACAC
1 TGTTTCTCTTGAAACAC
21413 CAAACCCTCG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (35 bp):
TGTTTCTCTTGAAACACAAAAAAAACCTTTGAAAA
Found at i:22189 original size:37 final size:37
Alignment explanation
Indices: 22148--22255 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
22138 AACATAGCGT
22148 TAGAGTTTCACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTCACTAGGATTCAAACTCCTAAAAATATGA
*
22185 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTCACTAGGATTCAAACTCCTAAAAATATGA
**
22222 TAGAG-TTCTACTATAATTCAAACTCCTAAAAATA
1 TAGAGTTTC-ACTAGGATTCAAACTCCTAAAAATA
22256 GGATCCATAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 2 0.03
37 64 0.97
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (37 bp):
TAGAGTTTCACTAGGATTCAAACTCCTAAAAATATGA
Found at i:22610 original size:2 final size:2
Alignment explanation
Indices: 22605--22638 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22595 ACACACACAC
22605 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
22639 TAATTTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22814 original size:30 final size:30
Alignment explanation
Indices: 22780--22836 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
22770 ATTTATTTAT
*
22780 TTATTTACTATGTATA-TATTTTTTTCACCA
1 TTATTTACTA-GTATATTATTTATTTCACCA
*
22810 TTATTTTCTAGTATATTATTTATTTCA
1 TTATTTACTAGTATATTATTTATTTCA
22837 TTTGCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.60
Consensus pattern (30 bp):
TTATTTACTAGTATATTATTTATTTCACCA
Found at i:22853 original size:23 final size:21
Alignment explanation
Indices: 22827--22869 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
22817 CTAGTATATT
22827 ATTTATTTCATTTGCTTTTATGG
1 ATTTATTTCATTT--TTTTATGG
* *
22850 ATTTTTTTTATTTTTTTATG
1 ATTTATTTCATTTTTTTATG
22870 TCTTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (21 bp):
ATTTATTTCATTTTTTTATGG
Found at i:22865 original size:8 final size:8
Alignment explanation
Indices: 22852--22887 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
22842 TTTTATGGAT
22852 TTTTTTTA
1 TTTTTTTA
22860 TTTTTTTA
1 TTTTTTTA
*
22868 TGTCTTTTA
1 T-TTTTTTA
22877 TTTTTTTA
1 TTTTTTTA
22885 TTT
1 TTT
22888 AATTTACTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:22875 original size:21 final size:21
Alignment explanation
Indices: 22842--22888 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
22832 TTTCATTTGC
22842 TTTTATGGATTTT-TTTTATTT
1 TTTTATGGATTTTATTTT-TTT
**
22863 TTTTATGTCTTTTATTTTTTT
1 TTTTATGGATTTTATTTTTTT
*
22884 ATTTA
1 TTTTA
22889 ATTTACTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTTATGGATTTTATTTTTTT
Found at i:24251 original size:2 final size:2
Alignment explanation
Indices: 24246--24337 Score: 175
Period size: 2 Copynumber: 45.5 Consensus size: 2
24236 AAAAATATGA
24246 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
24288 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
24330 AT CAT AT A
1 AT -AT AT A
24338 CGATTAGAGA
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 87 0.98
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24794 original size:24 final size:24
Alignment explanation
Indices: 24759--24835 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
24749 CCTGGATTTG
*
24759 AGCATCAGGAATGCCATAAGTGTC
1 AGCATCAAGAATGCCATAAGTGTC
24783 AGCATCAAGAATGCCATAAGTGTC
1 AGCATCAAGAATGCCATAAGTGTC
*
24807 AGCATCAAGAATGCCA-AAGGTGTA
1 AGCATCAAGAATGCCATAA-GTGTC
24831 AGCAT
1 AGCAT
24836 TCAATATCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 2 0.04
24 48 0.96
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (24 bp):
AGCATCAAGAATGCCATAAGTGTC
Found at i:26526 original size:21 final size:21
Alignment explanation
Indices: 26509--26560 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
26499 ACGAAAAGAA
26509 AAATAAAAGACATAAAAAAAT
1 AAATAAAAGACATAAAAAAAT
**
26530 AAATAAAATCCATAAAAGCAAAT
1 AAATAAAAGACATAAAA--AAAT
26553 GAAATAAA
1 -AAATAAA
26561 TAAAATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
23 4 0.15
24 7 0.27
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.15
Consensus pattern (21 bp):
AAATAAAAGACATAAAAAAAT
Found at i:26576 original size:15 final size:17
Alignment explanation
Indices: 26558--26599 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
26548 CAAATGAAAT
26558 AAATAAA-ATAC-TAGA
1 AAATAAATATACATAGA
*
26573 AAATAATATATACATAGT
1 AAATAA-ATATACATAGA
26591 AAATAAATA
1 AAATAAATA
26600 AATAAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 1 0.04
17 7 0.30
18 9 0.39
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
AAATAAATATACATAGA
Found at i:26740 original size:2 final size:2
Alignment explanation
Indices: 26733--26836 Score: 208
Period size: 2 Copynumber: 52.0 Consensus size: 2
26723 ATGAAAATTA
26733 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
26775 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
26817 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
26837 GTGTGTGTGT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27249 original size:37 final size:37
Alignment explanation
Indices: 27194--27305 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
27184 ATGCTTCTGG
* *
27194 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
**
27231 ATCCTATTTTTAAAAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
27268 ATCCTATTTATAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
27305 A
1 A
27306 ACGCTATGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:27434 original size:2 final size:2
Alignment explanation
Indices: 27427--27462 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27417 TATTTAAAAT
27427 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
27463 ATCAGGTCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31870 original size:2 final size:2
Alignment explanation
Indices: 31863--31895 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
31853 ATTTTAAATA
31863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31896 TAAATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:31902 original size:12 final size:13
Alignment explanation
Indices: 31857--31909 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 13
31847 ACCGAAATTT
*
31857 TAAATAATATATA
1 TAAATATTATATA
*
31870 TATATATATATATA
1 TAAATAT-TATATA
*
31884 TATATATTATAT-
1 TAAATATTATATA
*
31896 TAAATATTAAATA
1 TAAATATTATATA
31909 T
1 T
31910 TTTGGCTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 10 0.29
13 11 0.32
14 13 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATATTATATA
Found at i:34541 original size:15 final size:15
Alignment explanation
Indices: 34506--34534 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34496 ATATACAGAA
34506 AATAATTTGAAATTG
1 AATAATTTGAAATTG
34521 AATAATTTGAAATT
1 AATAATTTGAAATT
34535 AATTAATAAT
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:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
AATAATTTGAAATTG
Found at i:34658 original size:21 final size:22
Alignment explanation
Indices: 34634--34682 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 22
34624 TAAAAACTGG
34634 TATTTAAAATATATTT-ATATA
1 TATTTAAAATATATTTCATATA
*
34655 TATTT--AATATTTTTCATATA
1 TATTTAAAATATATTTCATATA
34675 TAGTTTAA
1 TA-TTTAA
34683 TAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTAAAATATATTTCATATA
Found at i:34884 original size:22 final size:21
Alignment explanation
Indices: 34850--34892 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
34840 ATGTAAAAAG
34850 AAAAAATAAATA-TTTAATTT
1 AAAAAATAAATATTTTAATTT
34870 AAAAAATATACATATTTTAATTT
1 AAAAAATA-A-ATATTTTAATTT
34893 TAAATTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 3 0.15
23 8 0.40
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAAATAAATATTTTAATTT
Found at i:34959 original size:65 final size:63
Alignment explanation
Indices: 34842--34969 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 63
34832 AACTATAAAT
* * *
34842 GTAAAAAGAAAAAATAAATATTTAATTTAAAAAATATACATATTTTAATTTTAAATTTTGAAG
1 GTAAAAAGAAAAAATAAAGATTAAATTTAAAAAATATACATATTTTAATTTTAAAATTTGAAG
34905 GTAAAAAG-AAAAATAAAGATTAAATTTAGTTTAAAAA-ATACATATTTTAATTTTAAAATTTGA
1 GTAAAAAGAAAAAATAAAGATTAAATTTA----AAAAATATACATATTTTAATTTTAAAATTTGA
34968 AG
62 AG
34970 ATGGAATTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
62 18 0.31
63 8 0.14
65 27 0.47
66 5 0.09
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (63 bp):
GTAAAAAGAAAAAATAAAGATTAAATTTAAAAAATATACATATTTTAATTTTAAAATTTGAAG
Found at i:35132 original size:27 final size:27
Alignment explanation
Indices: 35102--35155 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
35092 TGTCTTCTTT
35102 GTAGCTTATTTTTCTTCAACTAGATTA
1 GTAGCTTATTTTTCTTCAACTAGATTA
35129 GTAGCTTATTTTTCTTCAACTAGATTA
1 GTAGCTTATTTTTCTTCAACTAGATTA
35156 TGAGATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (27 bp):
GTAGCTTATTTTTCTTCAACTAGATTA
Found at i:43427 original size:5 final size:5
Alignment explanation
Indices: 43417--43442 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43407 ATCATCACTT
43417 AGTTC AGTTC AGTTC AGTTC AGTTC A
1 AGTTC AGTTC AGTTC AGTTC AGTTC A
43443 ATTTTAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
AGTTC
Found at i:50625 original size:3 final size:3
Alignment explanation
Indices: 50617--50750 Score: 223
Period size: 3 Copynumber: 44.7 Consensus size: 3
50607 ATTTAATATT
50617 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
50665 TAA TAT TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
50713 TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
50751 TGGATAAAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 121 1.00
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:51236 original size:119 final size:119
Alignment explanation
Indices: 50998--51914 Score: 1514
Period size: 119 Copynumber: 7.9 Consensus size: 119
50988 TCTTGATGAG
*
50998 TTCTTCTCATTATGAAC-T-TT-TT-CTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
* * * *
51055 C-CTGGTAATGTTGATCCATCAA-ATGATGAATTCAAGC-AAAGGTTGAACAAA
66 CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
*
51106 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTGTGAACTCTTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
51171 CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
66 CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
51225 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
* *
51290 CTCTGGAAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAG
66 CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
51344 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTT-
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
51404 CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
66 CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
51458 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTC-TCTCATTATGAACTCTTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
*
51522 CTCTGGAAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
66 CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
51576 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
* *
51641 CTCTGGAAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAG
66 CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
51695 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC-CTT-
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
* * * * *
51758 CTCTGGAAAAGAATGATCCATCAA-GTGATGAATTTAAACAAAAGGTTGAACAAG
66 CTCTGGAAACG-ATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
51812 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
* *
51877 CTCTGAAAATGAATGATCCATCAATTTGATGAATTCAA
66 CTCTGGAAACG-ATGATCCATCAATTTGATGAATTCAA
51915 ATCTTTGCTA
Statistics
Matches: 766, Mismatches: 22, Indels: 30
0.94 0.03 0.04
Matches are distributed among these distances:
108 17 0.02
109 1 0.00
110 2 0.00
111 2 0.00
112 11 0.01
114 89 0.12
115 23 0.03
116 36 0.05
117 123 0.16
118 131 0.17
119 320 0.42
120 11 0.01
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (119 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
CTCTGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:51662 original size:351 final size:351
Alignment explanation
Indices: 50996--51914 Score: 1600
Period size: 351 Copynumber: 2.6 Consensus size: 351
50986 GCTCTTGATG
*
50996 AGTTCTTCTCATTATGAAC-T-TT-TT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-CT
* * *
51056 CTGGTAATGTTGATCCATCAAATGATGAATTCAAGC-AAAGGTTGAACAAATTCTTCTCATTATG
65 CTGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
* *
51120 AACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTGTGAACTCTTCCTCTGGAAACGATG
130 AACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAACAATG
51185 ATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
195 ATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
51250 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAACAATGATCCATCAATT
260 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAACAATGATCCATCAATT
51315 TGATGAATTCAAGCAAAAGGTTGAACA
325 TGATGAATTCAAGCAAAAGGTTGAACA
51342 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* *
51407 TGGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
66 TGGAAAAGATGATCCATCAA-ATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
51472 AACTTCTTCTTCCTTCTTCAGATGACGAGTTC-TCTCATTATGAACTCTTCCTCTGGAAACAATG
130 AACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAACAATG
51536 ATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
195 ATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
51601 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAACAATGATCCATCAATT
260 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAACAATGATCCATCAATT
51666 TGATGAATTCAAGCAAAAGGTTGAACA
325 TGATGAATTCAAGCAAAAGGTTGAACA
51693 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACCTT
* * * *
51758 CTCTGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATT
63 CTCTGGAAAAG-ATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATT
* *
51823 ATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGAAAATG
127 ATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAA-C
51888 AATGATCCATCAATTTGATGAATTCAA
191 AATGATCCATCAATTTGATGAATTCAA
51915 ATCTTTGCTA
Statistics
Matches: 546, Mismatches: 14, Indels: 16
0.95 0.02 0.03
Matches are distributed among these distances:
346 19 0.03
347 1 0.00
348 2 0.00
349 3 0.01
350 51 0.09
351 240 0.44
352 60 0.11
354 105 0.19
355 38 0.07
356 27 0.05
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (351 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAACAATGA
TCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAACAATGATCCATCAATTT
GATGAATTCAAGCAAAAGGTTGAACA
Found at i:52643 original size:52 final size:52
Alignment explanation
Indices: 52543--52902 Score: 650
Period size: 52 Copynumber: 6.9 Consensus size: 52
52533 CTATCCAATT
* *
52543 AGATCAGATATCTCAAAGAACAACTTCCAGAAGATGTTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAAC-ACTTCCAGAAGATGCTATGTTCTGTCCAACC
52596 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
*
52648 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACC
52700 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
*
52752 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
*
52804 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTATCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
52856 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTC
52903 GCTTTTCCAT
Statistics
Matches: 297, Mismatches: 8, Indels: 5
0.96 0.03 0.02
Matches are distributed among these distances:
51 1 0.00
52 275 0.93
53 21 0.07
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACC
Found at i:53881 original size:6 final size:6
Alignment explanation
Indices: 53870--53954 Score: 57
Period size: 6 Copynumber: 13.0 Consensus size: 6
53860 CTTGACCCCC
*
53870 TTTCTT TTTCTT TTTCTTCT TTTCCTTT TTTCTT TTTTTCT TTTCTTT
1 TTTCTT TTTCTT TTTC-T-T TTT-C-TT TTTCTT TTTCT-T TTTC-TT
*
53918 CTCTTCTT TTTC-T TTTCTTT TTTCCT TTT-TT TTTCTT
1 -T-TTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT
53955 CAAGCATAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
5 9 0.14
6 25 0.38
7 13 0.20
8 12 0.18
9 6 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:53889 original size:9 final size:9
Alignment explanation
Indices: 53877--53931 Score: 53
Period size: 8 Copynumber: 6.2 Consensus size: 9
53867 CCCTTTCTTT
53877 TTCTTTTTC
1 TTCTTTTTC
53886 TTC-TTTTC
1 TTCTTTTTC
*
53894 CT-TTTTTC
1 TTCTTTTTC
53902 TT-TTTTTC
1 TTCTTTTTC
*
53910 TTTTCTTTCTC
1 --TTCTTTTTC
53921 TTCTTTTTC
1 TTCTTTTTC
53930 TT
1 TT
53932 TTCTTTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 18 0.47
9 13 0.34
10 2 0.05
11 5 0.13
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:53915 original size:41 final size:41
Alignment explanation
Indices: 53870--53949 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
53860 CTTGACCCCC
*
53870 TTTCTTTTTCTT-TTTCTTCTTTTCCTTTTTT-CTTTTTTTCT
1 TTTCTTTCTCTTCTTT-TTCTTTT-CTTTTTTCCTTTTTTTCT
53911 TTTCTTTCTCTTCTTTTTCTTTTCTTTTTTCCTTTTTTT
1 TTTCTTTCTCTTCTTTTTCTTTTCTTTTTTCCTTTTTTT
53950 TTCTTCAAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
40 7 0.19
41 26 0.72
42 3 0.08
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (41 bp):
TTTCTTTCTCTTCTTTTTCTTTTCTTTTTTCCTTTTTTTCT
Found at i:53923 original size:35 final size:33
Alignment explanation
Indices: 53870--53955 Score: 111
Period size: 33 Copynumber: 2.5 Consensus size: 33
53860 CTTGACCCCC
*
53870 TTTCTTTTTCTTTTTCTTCTTTTCCTTTTTTCTTTT
1 TTTC-TTTTCTTTTTCTTCTTTT--TCTTTTCTTTT
*
53906 TTTCTTTTCTTTCTCTTCTTTTTCTTTTCTTTT
1 TTTCTTTTCTTTTTCTTCTTTTTCTTTTCTTTT
*
53939 TTCCTTTT-TTTTTCTTC
1 TTTCTTTTCTTTTTCTTC
53956 AAGCATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 8 0.17
33 17 0.37
35 17 0.37
36 4 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (33 bp):
TTTCTTTTCTTTTTCTTCTTTTTCTTTTCTTTT
Found at i:66620 original size:3 final size:3
Alignment explanation
Indices: 66612--66728 Score: 165
Period size: 3 Copynumber: 40.7 Consensus size: 3
66602 TTAATATATT
*
66612 TAA TAA TAA -AA -AA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
66658 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA T-A TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66704 TAA TAA T-A TAA TTAA T-A TAA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TA
66729 TGGATAAAAA
Statistics
Matches: 104, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
2 12 0.12
3 89 0.86
4 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Done.