Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2264
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: 49580
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:580 original size:40 final size:40
Alignment explanation
Indices: 543--723 Score: 196
Period size: 40 Copynumber: 4.7 Consensus size: 40
533 GCTACTCGTT
*
543 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
583 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * ** *
623 CCAATGCCTTCGGG-CTTAGCCC-GAATCCGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
661 CAAATGCCTTC-GGATCTTAGTCCGGA-TT-GTCATTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
699 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
724 CACATTCGAA
Statistics
Matches: 120, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
37 18 0.15
38 35 0.29
39 15 0.12
40 50 0.42
41 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:686 original size:78 final size:76
Alignment explanation
Indices: 577--721 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 76
567 GTTATAGTAA
* *
577 CTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTA
1 CTCGCACAAATGCCTTCGGGACTTAACCCGGA-TT-GTAACTAGCA-CAAAGCCTTCGGGACTTA
641 GCCCGAATCCGTAT
63 GCCCGAATCCGTAT
** * *
655 CTCGCACAAATGCCTTC-GGATCTTAGTCCGGATTGTCATTAGCACAAAGCCTTCGGGACTTAGC
1 CTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTGTAACTAGCACAAAGCCTTCGGGACTTAGC
719 CCG
65 CCG
722 GACACATTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
75 12 0.20
76 16 0.27
77 5 0.08
78 26 0.44
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (76 bp):
CTCGCACAAATGCCTTCGGGACTTAACCCGGATTGTAACTAGCACAAAGCCTTCGGGACTTAGCC
CGAATCCGTAT
Found at i:8716 original size:40 final size:40
Alignment explanation
Indices: 8672--8863 Score: 185
Period size: 40 Copynumber: 4.8 Consensus size: 40
8662 GGATATAGCT
* *
8672 ACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
8712 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
8752 ACTCGTACCAATGCCTTCGGG-CTTAGCCCAGAATCAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * * * *
8791 TCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGTACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
8831 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGTACAAATGCCTTCGGGACTTAGCCCGGA
8864 CATCATTCGA
Statistics
Matches: 124, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
38 2 0.02
39 29 0.23
40 80 0.65
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:8796 original size:79 final size:79
Alignment explanation
Indices: 8646--8860 Score: 206
Period size: 79 Copynumber: 2.7 Consensus size: 79
8636 AAATCACGTA
* * * *
8646 CCTTCGGAATTTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGT
1 CCTTCGGAACTTAACCGGATATAGCTACTCGTACAAATGCCTTCGGGACATAGCCCAGTAATAGT
8711 AACTCGCACAAATG
66 AACTCGCACAAATG
* * * *
8725 CCTTCGGGACTTAACCCGGATTTAG-TAACTCGTACCAATGCCTTCGGG-CTTAGCCCAG-AATC
1 CCTTCGGAACTTAA-CCGGATATAGCT-ACTCGTACAAATGCCTTCGGGACATAGCCCAGTAAT-
*
8787 AGTATCTCGCACAAATG
63 AGTAACTCGCACAAATG
* * * * * *
8804 CCTTCGGATCTTAGTCCGGATAT-GGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CCTTCGGAACTTA-ACCGGATATAGCT-AC-TCGTACAAATGCCTTCGGGACATAGCCC
8861 GGACATCATT
Statistics
Matches: 112, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.03
79 67 0.60
80 42 0.38
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (79 bp):
CCTTCGGAACTTAACCGGATATAGCTACTCGTACAAATGCCTTCGGGACATAGCCCAGTAATAGT
AACTCGCACAAATG
Found at i:13536 original size:24 final size:24
Alignment explanation
Indices: 13504--13570 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 24
13494 TATATATTTA
*
13504 TATTATATTTTATTATATAACATT
1 TATTATATTTTATTATATAACACT
**
13528 TATTATATTTTTATTATATATTACT
1 TATTATA-TTTTATTATATAACACT
*
13553 TATTATTTTTTATTATAT
1 TATTATATTTTATTATAT
13571 GTTATGTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 18 0.47
25 20 0.53
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTATATTTTATTATATAACACT
Found at i:13565 original size:35 final size:34
Alignment explanation
Indices: 13481--13635 Score: 91
Period size: 35 Copynumber: 4.4 Consensus size: 34
13471 ATTTATCATA
* *
13481 TATTATTTTCCTATATATATTTATATTATATTTTAT
1 TATTATTTT-TTAT-TATATTTATATTATATATTAT
*** *
13517 TATATAACATTTATTATATTTTTATTATATATTACT
1 TAT-TATTTTTTATTATATTTATATTATATATTA-T
* **
13553 TATTATTTTTTATTATATGTTAT-GTATATCGTA-
1 TATTATTTTTTATTATAT-TTATATTATATATTAT
* * * *
13586 TATTATCTATTA-TATTATTTATGTTTTATATTAT
1 TATTATTTTTTATTA-TATTTATATTATATATTAT
13620 TCATTATATTATTTAT
1 T-ATTAT-TT-TTTAT
13636 AATTTTAAAA
Statistics
Matches: 88, Mismatches: 21, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
32 6 0.07
33 19 0.22
34 1 0.01
35 42 0.48
36 14 0.16
37 6 0.07
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (34 bp):
TATTATTTTTTATTATATTTATATTATATATTAT
Found at i:15052 original size:27 final size:27
Alignment explanation
Indices: 15022--15199 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
15012 ATATTGAGCC
* * * *
15022 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
15049 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
15076 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAGTCA-AAT
** * *
15104 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
15131 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
15158 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
15185 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
15200 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:15161 original size:82 final size:81
Alignment explanation
Indices: 15043--15198 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
15033 TGCTATATAA
* * * *
15043 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
15108 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
15125 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
15189 CACTTAGTGC
65 CACTTAGTGC
15199 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20925 original size:14 final size:16
Alignment explanation
Indices: 20906--20942 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
20896 CGATACCCTT
20906 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
20920 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
20936 TTT-CATC
1 TTTGCATC
20943 GCAACCTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Found at i:25606 original size:28 final size:28
Alignment explanation
Indices: 25508--25606 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
25498 CATGAGATTG
* * **
25508 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
25537 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
25565 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
25593 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
25607 GACTTACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 46 0.73
29 17 0.27
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:32536 original size:206 final size:206
Alignment explanation
Indices: 32200--32760 Score: 892
Period size: 206 Copynumber: 2.7 Consensus size: 206
32190 ACTTTAGATA
*
32200 ATTATACTGAAGCAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACA
1 ATTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACA
* * *
32265 TAGCTGCTTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGGTTTGGCATCTTTGTATT
66 TAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATT
* *
32330 GTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTTGACGGAGGCCAGACACATAGCAGAT-TC
131 GTCAGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGCCAGACACATA--AGATATC
32394 -AACCTTCAAATG
194 TAACCTTCAAATG
* *
32406 TTTATACTGAAGCAGATCCAAGATGCTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACA
1 ATTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACA
*
32471 TAGCTGATTTGGCTTTCACGTGCTTATGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATT
66 TAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATT
* *
32536 GTCAGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGATGGAGGGCAGACACATAAGATATCTA
131 GTCAGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGCCAGACACATAAGATATCTA
* *
32601 ACTTTCAGATG
196 ACCTTCAAATG
* * *
32612 ATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTATGCTTACAAGGAGCAAATCGAAGACA
1 ATTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACA
* ** * * *
32677 TAGCTGATTTGGTTTTCATATGCTTACGCTGAAGCAAATCTAAGATGATTTGGTATCTCTATATT
66 TAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATT
32742 GTCAGAGAACAAATCAAAG
131 GTCAGAGAACAAATCAAAG
32761 AAGCAGATTT
Statistics
Matches: 328, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
204 4 0.01
205 2 0.01
206 322 0.98
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (206 bp):
ATTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACA
TAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATT
GTCAGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGCCAGACACATAAGATATCTA
ACCTTCAAATG
Found at i:32975 original size:4 final size:4
Alignment explanation
Indices: 32956--32998 Score: 63
Period size: 4 Copynumber: 11.0 Consensus size: 4
32946 TTACCGGGCC
32956 TAAA TAAA -ACAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TA-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
32999 CATTTATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (4 bp):
TAAA
Found at i:34410 original size:26 final size:24
Alignment explanation
Indices: 34355--34412 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
34345 TATATATATA
34355 ATTTAT-TTATTTTAAAAAACTAT
1 ATTTATATTATTTTAAAAAACTAT
**
34378 ACATATATTATTATTAAAAATACTAT
1 ATTTATATTATT-TTAAAAA-ACTAT
*
34404 TTTTATATT
1 ATTTATATT
34413 TATATAAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 4 0.15
24 5 0.19
25 7 0.26
26 11 0.41
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTATATTATTTTAAAAAACTAT
Found at i:34468 original size:11 final size:11
Alignment explanation
Indices: 34448--34502 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
34438 ATTATTTTCC
34448 TATA-TATATT
1 TATATTATATT
34458 TATATTATATT
1 TATATTATATT
34469 T-TATTATATAAT
1 TATATTATAT--T
*
34481 ATTTATTATATT
1 -TATATTATATT
*
34493 TTTATTATAT
1 TATATTATAT
34503 ATTACTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
10 12 0.30
11 17 0.43
12 2 0.05
13 1 0.03
14 8 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTATATT
Found at i:34495 original size:25 final size:25
Alignment explanation
Indices: 34460--34527 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
34450 TATATATTTA
*
34460 TATTATA-TTTTATTATATAATATT
1 TATTATATTTTTATTATATAATACT
*
34484 TATTATATTTTTATTATATATTACT
1 TATTATATTTTTATTATATAATACT
* *
34509 TATTGTTTTTTTATTATAT
1 TATTATATTTTTATTATAT
34528 GTTATGTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 7 0.18
25 32 0.82
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (25 bp):
TATTATATTTTTATTATATAATACT
Found at i:34512 original size:14 final size:13
Alignment explanation
Indices: 34463--34585 Score: 53
Period size: 14 Copynumber: 9.2 Consensus size: 13
34453 ATATTTATAT
34463 TATATT-TTATTA
1 TATATTATTATTA
*
34475 TATAATATTTATTA
1 TATATTA-TTATTA
34489 TAT-TT-TTATTA
1 TATATTATTATTA
*
34500 TATATTACTTATTG
1 TATATTA-TTATTA
*
34514 T-T-TTTTTATTA
1 TATATTATTATTA
* *
34525 TATGTTATGTATATCG
1 TATATTAT-TAT-T-A
*
34541 TATATTATCTATTG
1 TATATTAT-TATTA
34555 TATTATTTATGT-TT-
1 TA-TA-TTAT-TATTA
34569 TATATTATTCATTA
1 TATATTATT-ATTA
34583 TAT
1 TAT
34586 TATTTATAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
11 16 0.19
12 14 0.16
13 9 0.10
14 26 0.30
15 6 0.07
16 15 0.17
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (13 bp):
TATATTATTATTA
Found at i:34847 original size:7 final size:7
Alignment explanation
Indices: 34828--34863 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
34818 GTAAATTTTT
34828 TTGT-TA
1 TTGTATA
*
34834 TTATATA
1 TTGTATA
34841 TTGTATA
1 TTGTATA
34848 TTGTATA
1 TTGTATA
34855 TTGTATA
1 TTGTATA
34862 TT
1 TT
34864 AAATATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 3 0.11
7 24 0.89
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTGTATA
Found at i:34854 original size:14 final size:14
Alignment explanation
Indices: 34828--34870 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
34818 GTAAATTTTT
34828 TTGT-TATTATATA
1 TTGTATATTATATA
*
34841 TTGTATATTGTATA
1 TTGTATATTATATA
*
34855 TTGTATATTAAATA
1 TTGTATATTATATA
34869 TT
1 TT
34871 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (14 bp):
TTGTATATTATATA
Found at i:34869 original size:21 final size:20
Alignment explanation
Indices: 34828--34870 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
34818 GTAAATTTTT
**
34828 TTGTTATTATATATTGTATA
1 TTGTTATTATATATTAAATA
*
34848 TTGTATATTGTATATTAAATA
1 TTGT-TATTATATATTAAATA
34869 TT
1 TT
34871 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (20 bp):
TTGTTATTATATATTAAATA
Found at i:34889 original size:12 final size:12
Alignment explanation
Indices: 34858--34899 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
34848 TTGTATATTG
34858 TATATTAAATAT
1 TATATTAAATAT
*
34870 TATTTTAAA-AT
1 TATATTAAATAT
34881 TATCATTAAATAT
1 TAT-ATTAAATAT
*
34894 CATATT
1 TATATT
34900 TTTATTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 5 0.20
12 16 0.64
13 4 0.16
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATTAAATAT
Found at i:39257 original size:27 final size:27
Alignment explanation
Indices: 39227--39931 Score: 728
Period size: 27 Copynumber: 26.1 Consensus size: 27
39217 AGTACTCCCG
*
39227 ATTTACAGAATTACCGTTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
** * * *
39254 ATTTGTAAAATTACTATTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
*
39281 ATTTATAGAATTACCATTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
* * * *
39308 GTTTACAGAATTACTATTTAACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
* *
39335 ATTTATAGAATTACCGTTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
** * **
39362 ATTTGTAAAATTACTGTTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
** * * *
39389 ATTTTTAAAATTACCGTTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
*
39416 ATTTACAGAATTACCGTTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
* * *
39443 GTTTATAGAATTACCATTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
39470 ATTTACAGAATTACCATTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
* *
39497 GTTTACAGAATTACTATTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
* *
39524 ATTTATAGAATTACCGTTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
** * ** *
39551 ATTTGTAAAATTACTGTTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
39578 ATTTACAGAATTACCATTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
* * *
39605 GTTTACAGAATTACTATTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
*
39632 ATTTATAGAATTACCATTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
** * * *
39659 ATTTGTAAAATTACTATTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
*
39686 ATTTACAGAATTACCGTTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
* **
39713 GTTTACAGAATTACCATTTTACCCTTG
1 ATTTACAGAATTACCATTTTACCCTCA
*
39740 ATTTACAGAATTATCATTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
* ** *
39767 GTTTACAGAATTACTGTTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
** *
39794 ATTTACAGAATTACTGTTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
** * * * *
39821 ATTTGTAAAATTATCGTTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
* ***
39848 ATTTATAGAATTACTGGTTTACCCTCA
1 ATTTACAGAATTACCATTTTACCCTCA
* * * * *
39875 GTTTACAAAATTATCGTTTTACCCTCG
1 ATTTACAGAATTACCATTTTACCCTCA
*
39902 ATTTACTA-AATTACTATTTTACCCTCA
1 ATTTAC-AGAATTACCATTTTACCCTCA
39929 ATT
1 ATT
39932 GTGAAATTAC
Statistics
Matches: 569, Mismatches: 108, Indels: 2
0.84 0.16 0.00
Matches are distributed among these distances:
27 568 1.00
28 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (27 bp):
ATTTACAGAATTACCATTTTACCCTCA
Found at i:39370 original size:108 final size:107
Alignment explanation
Indices: 39227--39928 Score: 802
Period size: 108 Copynumber: 6.5 Consensus size: 107
39217 AGTACTCCCG
* * ** * *
39227 ATTTACAGAATTACCGTTTTACCCTCAATTTGTAAAATTACTATTTTACCCTC-GATTTATAGAA
1 ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCAG-TTTACAGAA
* *
39291 TTACCATTTTACCCTC-AGTTTACAGAATTACTATTTAACCCTC
65 TTACCATTTTACCCTCGA-TTTACAGAATTACCATTTTACCCTC
* ** * * * ** *
39334 GATTTATAGAATTACCGTTTTACCCTCAATTTGTAAAATTACTGTTTTACCCTCAATTTTTAAAA
1 -ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCAGTTTACAGAA
* *
39399 TTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTC
65 TTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTC
* *
39442 AGTTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCAGTTTACAGAA
1 A-TTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCAGTTTACAGAA
* * * *
39507 TTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTC
65 TTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTC
* * * *
39550 AATTTGTAAAATTACTGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCAGTTTACAGAA
1 -ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCAGTTTACAGAA
* *
39615 TTACTATTTTACCCTCGATTTATAGAATTACCATTTTACCCTC
65 TTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTC
* * ** **
39658 AATTTGTAAAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAA
1 -ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCAGTTTACAGAA
* *
39723 TTACCATTTTACCCTTGATTTACAGAATTATCATTTTACCCTC
65 TTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTC
* * * *
39766 AGTTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTGTA-A-
1 A-TTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTC-AGTT-TACAG
* * * ***
39829 AATTATCGTTTTACCCTCGATTTATAGAATTACTGGTTTACCCTC
63 AATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTC
* * *
39874 AGTTTACAAAATTATCGTTTTACCCTCGATTTACTA-AATTACTATTTTACCCTCA
1 A-TTTATAGAATTACCGTTTTACCCTCGATTTAC-AGAATTACTATTTTACCCTCA
39929 ATTGTGAAAT
Statistics
Matches: 532, Mismatches: 54, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
107 3 0.01
108 520 0.98
109 7 0.01
110 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (107 bp):
ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCAGTTTACAGAAT
TACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTC
Found at i:39974 original size:27 final size:27
Alignment explanation
Indices: 39944--40103 Score: 205
Period size: 27 Copynumber: 6.0 Consensus size: 27
39934 GAAATTACTA
*
39944 AAATACCGCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
39971 AAATACCACTATAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
39998 AAATACCCCCGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * *
40025 AAATACCCTTGTAGGG-AGAAATACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
40051 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* ** *
40078 AGATACCTTTGTAGGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
40104 ATTTTGCCCC
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
26 22 0.19
27 92 0.81
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:40084 original size:53 final size:54
Alignment explanation
Indices: 39934--40099 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 54
39924 CCTCAATTGT
* * *
39934 GAAATTACTAAAATACCGCTGTAGGGTAGAATTACCGAAATACCAC-TATAGGGTA
1 GAAA-TACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACC-CTTGTAGGGTA
* * * *
39989 GAATTACCGAAATACCCCCGTAGGGTAGAATTATCGAAATACCCTTGTAGGG-A
1 GAAATACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTA
* *
40042 GAAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCTTTGTAGGGTA
1 GAAATACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTA
40096 -AAAT
1 GAAAT
40100 TACCATTTTG
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
53 52 0.54
54 41 0.43
55 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (54 bp):
GAAATACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTA
Found at i:40092 original size:80 final size:81
Alignment explanation
Indices: 39944--40101 Score: 212
Period size: 80 Copynumber: 2.0 Consensus size: 81
39934 GAAATTACTA
*
39944 AAATACCGCTGTAGGGTAGAATTACCGAAATACCACTATAGGGTAGAATTACCGAAATACCCCCG
1 AAATACCGCTGTAGGGTAGAAATACCGAAATACCACTATAGGGTAGAATTACCGAAATACCCCCG
*
40009 TAGGGTAGAATTATCG
66 TAGGGTAAAATTATCG
* * * * ***
40025 AAATACC-CTTGTAGGG-AGAAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCTTT
1 AAATACCGC-TGTAGGGTAGAAATACCGAAATACCACTATAGGGTAGAATTACCGAAATACCCCC
40088 GTAGGGTAAAATTA
65 GTAGGGTAAAATTA
40102 CCATTTTGCC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 53 0.79
81 14 0.21
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (81 bp):
AAATACCGCTGTAGGGTAGAAATACCGAAATACCACTATAGGGTAGAATTACCGAAATACCCCCG
TAGGGTAAAATTATCG
Found at i:40340 original size:27 final size:26
Alignment explanation
Indices: 40302--40384 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
40292 CGGAGGAAGC
*
40302 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
40329 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
40355 GTATCTAGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
40382 GTT
1 GTT
40385 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:40727 original size:27 final size:26
Alignment explanation
Indices: 40697--40768 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
40687 GGTGGGTTTT
*
40697 CCACAGTATCTGATTCTGGTGGCTCTG
1 CCACAGTATCTG-TTCTGGTGACTCTG
*
40724 CCACAATATCTGTATCTGGTGACTCTG
1 CCACAGTATCTGT-TCTGGTGACTCTG
*
40751 TCAC-GATATCTGTTCTGG
1 CCACAG-TATCTGTTCTGG
40769 CAGCCATGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 6 0.15
27 33 0.85
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (26 bp):
CCACAGTATCTGTTCTGGTGACTCTG
Found at i:40892 original size:6 final size:6
Alignment explanation
Indices: 40883--40984 Score: 95
Period size: 6 Copynumber: 16.8 Consensus size: 6
40873 TTGCATTCAC
* *
40883 ATTCTG ATTCTG ATTCT- ATCACCTA ATTCTG ATTCTG ATTCTG ATTCT-
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
40931 ATTACTA ATAT-TG ATTCTG ATTCTG ATTCT- TTTACTG ATTCTG ATTCTG
1 ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
40980 ATTCT
1 ATTCT
40985 CATTTTGGTT
Statistics
Matches: 81, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
5 8 0.10
6 64 0.79
7 6 0.07
8 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:40946 original size:30 final size:30
Alignment explanation
Indices: 40883--40984 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
40873 TTGCATTCAC
*
40883 ATTCTGATTCTGATTCTATCACCTAATTCTG
1 ATTCTGATTCTGATTCTATTA-CTAATTCTG
40914 ATTCTGATTCTGATTCTATTACTAATAT-TG
1 ATTCTGATTCTGATTCTATTACTAAT-TCTG
* *
40944 ATTCTGATTCTGATTCTTTTACTGATTCTG
1 ATTCTGATTCTGATTCTATTACTAATTCTG
40974 ATTCTGATTCT
1 ATTCTGATTCT
40985 CATTTTGGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
29 1 0.02
30 44 0.67
31 21 0.32
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.50
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTATTACTAATTCTG
Found at i:43070 original size:27 final size:27
Alignment explanation
Indices: 42985--43628 Score: 497
Period size: 26 Copynumber: 24.9 Consensus size: 27
42975 GTACTCTCGA
* * *
42985 TTACAGAATTACCGTTTTACCTTCA-A
1 TTACAGAATTACCATTTTACCCTCAGT
* **
43011 TT-GA-AATTACTGTTTTACCCTC-GAT
1 TTACAGAATTACCATTTTACCCTCAG-T
43036 TTACAGAATTACCATATTTACCCTCAGT
1 TTACAGAATTACCAT-TTTACCCTCAGT
43064 TTA-AGAATTA-CATTTTACCCTC-GAT
1 TTACAGAATTACCATTTTACCCTCAG-T
* *
43089 TTACAGAATTACC-GTTTACCCTCAAT
1 TTACAGAATTACCATTTTACCCTCAGT
* * *
43115 TTATAAAATTA--TTTTTACCCTC-GAT
1 TTACAGAATTACCATTTTACCCTCAG-T
*
43140 TTA-AGAA-TACCGTTTTACCCTCA-T
1 TTACAGAATTACCATTTTACCCTCAGT
43164 TTACAGAATTACCATTTTACCCTCAGT
1 TTACAGAATTACCATTTTACCCTCAGT
43191 TTACAGAATTACCATTTTACCCTCA-T
1 TTACAGAATTACCATTTTACCCTCAGT
*
43217 TTATAGAATTACCATTTTACCCTCA-T
1 TTACAGAATTACCATTTTACCCTCAGT
*
43243 TTACAGAATTACTA-TTTACCCTC-GAT
1 TTACAGAATTACCATTTTACCCTCAG-T
* * *
43269 TTATAGAATTACCGTTTTACCCTCAATT
1 TTACAGAATTACCATTTTACCCTC-AGT
**
43297 TGTA-AGAATTA-TGTTTTACCCTCA-T
1 T-TACAGAATTACCATTTTACCCTCAGT
43322 TTACA-AATTA-CA-TTTACCCTC-GT
1 TTACAGAATTACCATTTTACCCTCAGT
*
43345 TTACAGAATTACTATTTTACCCTC-GAT
1 TTACAGAATTACCATTTTACCCTCAG-T
*
43372 TTACAGAATTATCATTTTACCCTC-GAT
1 TTACAGAATTACCATTTTACCCTCAG-T
** * *
43399 TTGTA-AATTACTATTTTACCCTC-GA
1 TTACAGAATTACCATTTTACCCTCAGT
*
43424 TTACAGAATTACCGTTTTA-CCTCAGT
1 TTACAGAATTACCATTTTACCCTCAGT
* *
43450 TTACAGAATTA-CA-TTTACCCTTGATT
1 TTACAGAATTACCATTTTACCC-TCAGT
* *
43476 TTACA-AATTATCGTTTTACCCTCA-T
1 TTACAGAATTACCATTTTACCCTCAGT
* *
43501 TTACAGAATTACTATTTTACCCTCGATT
1 TTACAGAATTACCATTTTACCCTC-AGT
* *
43529 TGTA-A-AATTACCGTTTTACCCT-TGAT
1 T-TACAGAATTACCATTTTACCCTCAG-T
* ***
43555 TTATAGAATTACTGGTTTACCCTCAGT
1 TTACAGAATTACCATTTTACCCTCAGT
* * *
43582 TTACAAAATTATC-GTTTACCCTC-GAT
1 TTACAGAATTACCATTTTACCCTCAG-T
*
43608 TT-TAGAATTA-CATTTTACCCT
1 TTACAGAATTACCATTTTACCCT
43629 TGATTGTGAA
Statistics
Matches: 511, Mismatches: 61, Indels: 93
0.77 0.09 0.14
Matches are distributed among these distances:
23 17 0.03
24 41 0.08
25 94 0.18
26 190 0.37
27 138 0.27
28 26 0.05
29 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (27 bp):
TTACAGAATTACCATTTTACCCTCAGT
Found at i:43696 original size:26 final size:27
Alignment explanation
Indices: 43638--43821 Score: 192
Period size: 27 Copynumber: 7.2 Consensus size: 27
43628 TTGATTGTGA
43638 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
43665 AATTACTGAAATACCCCTATA-GGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
43691 AATTACTGAAATACCCTTATA-GGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
43717 AATTAC---AATA-CCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
43740 AATT-C--AAATACCCTTGTA--GTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
43762 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
43789 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
43816 AATTAC
1 AATTAC
43822 CATTTTGCCC
Statistics
Matches: 137, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.09
23 18 0.13
24 6 0.04
25 12 0.09
26 36 0.26
27 52 0.38
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:43730 original size:23 final size:24
Alignment explanation
Indices: 43646--43794 Score: 117
Period size: 26 Copynumber: 6.0 Consensus size: 24
43636 GAAATTACTG
* *
43646 AAATACCCCTGTAGGGTAGAATTAC
1 AAATACCCTTATA-GGTAGAATTAC
*
43671 TGAAATACCCCTATAGGTAGAATTAC
1 --AAATACCCTTATAGGTAGAATTAC
43697 TGAAATACCCTTATAGGTAGAATTAC
1 --AAATACCCTTATAGGTAGAATTAC
*
43723 -AATACCCTGTA-GGGTAGAATT-C
1 AAATACCCT-TATAGGTAGAATTAC
* *
43745 AAATACCCTTGTA-GTAGAAATACC
1 AAATACCCTTATAGGTAGAATTA-C
* *
43769 GAAATACCCCTGTAGGGTAGAATTAC
1 -AAATACCCTTATA-GGTAGAATTAC
43795 CGAGATACCC
Statistics
Matches: 106, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
22 9 0.08
23 25 0.24
24 3 0.03
25 12 0.11
26 37 0.35
27 20 0.19
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
AAATACCCTTATAGGTAGAATTAC
Found at i:44056 original size:27 final size:26
Alignment explanation
Indices: 44018--44098 Score: 110
Period size: 25 Copynumber: 3.1 Consensus size: 26
44008 CGGAGGAAGC
*
44018 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
44045 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
44071 G-TATGGTGACTCTGTCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
44096 GTT
1 GTT
44099 GACCGATCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
25 22 0.45
26 9 0.18
27 18 0.37
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:45331 original size:6 final size:6
Alignment explanation
Indices: 45320--45421 Score: 86
Period size: 6 Copynumber: 16.8 Consensus size: 6
45310 AACCAAAATG
* *
45320 AGAATC AGAATC ATAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* * *
45368 AGTAA-C AGAATC AAAATC AGAATC AGAATT AGTTGAT- AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AG--AATC AGAATC AGAATC
45417 AGAAT
1 AGAAT
45422 GTGAATGCTA
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
5 7 0.09
6 63 0.81
7 5 0.06
8 3 0.04
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.23
Consensus pattern (6 bp):
AGAATC
Found at i:45356 original size:30 final size:29
Alignment explanation
Indices: 45320--45421 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 29
45310 AACCAAAATG
*
45320 AGAATCAGAATCATAATCAGTAACAGAATC
1 AGAATCAGAATCA-AATTAGTAACAGAATC
45350 AGAATCAGAATCAATATTAGTAACAGAATC
1 AGAATCAGAATCAA-ATTAGTAACAGAATC
* * *
45380 AAAATCAGAATCAGAATTAGTTGATAGAATC
1 AGAATCAGAATCA-AATTAG-TAACAGAATC
45411 AGAATCAGAAT
1 AGAATCAGAAT
45422 GTGAATGCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.02
30 44 0.69
31 19 0.30
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.23
Consensus pattern (29 bp):
AGAATCAGAATCAAATTAGTAACAGAATC
Found at i:45604 original size:26 final size:27
Alignment explanation
Indices: 45542--45613 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
45532 ATGACTGCCA
* *
45542 AGAA-CAGAATATCGTGACAGAGTCACC
1 AGAATCAG-ATATTGTGGCAGAGTCACC
45569 AGATAT-AGATATTGTGGCAGAG-CACC
1 AGA-ATCAGATATTGTGGCAGAGTCACC
*
45595 AGAATCAGATAGTGTGGCA
1 AGAATCAGATATTGTGGCA
45614 AACCCACACT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 2 0.05
26 19 0.49
27 15 0.38
28 3 0.08
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (27 bp):
AGAATCAGATATTGTGGCAGAGTCACC
Found at i:45829 original size:22 final size:21
Alignment explanation
Indices: 45779--45836 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
45769 AGGTAATACT
*
45779 TTGGCACGAAGCCATATCAAG
1 TTGGCACAAAGCCATATCAAG
* * *
45800 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATA-TCAAG
*
45822 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
45837 TAATAACGGG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (21 bp):
TTGGCACAAAGCCATATCAAG
Found at i:45975 original size:26 final size:27
Alignment explanation
Indices: 45924--46005 Score: 96
Period size: 26 Copynumber: 3.0 Consensus size: 27
45914 CGATCGGGTC
* *
45924 AACAGATATTGTGACAGAGTCA-CAGA
1 AACAGATATTGTGGCAGAGCCACCAGA
* *
45950 TAGAGATA-TGTGGCAGAGCCACCAGA
1 AACAGATATTGTGGCAGAGCCACCAGA
45976 AACAGATATTTGTGGCATGAGCCACCAGA
1 AACAGATA-TTGTGGCA-GAGCCACCAGA
46005 A
1 A
46006 CGCTCCTCCG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
25 11 0.24
26 16 0.35
28 7 0.15
29 12 0.26
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (27 bp):
AACAGATATTGTGGCAGAGCCACCAGA
Found at i:46251 original size:27 final size:27
Alignment explanation
Indices: 46202--46386 Score: 173
Period size: 27 Copynumber: 7.0 Consensus size: 27
46192 GGGGCAAAAT
* * ** *
46202 GGTAATTTTACCCCACAAAGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
46229 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
46256 AGATATTTCTACCCTACAAGGGTATTTC
1 -GGTAATTCTACCCTACAGGGGTATTTC
*
46284 GATAA-T-TACCCTAC-GGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
46308 -GTAA-TCTACCCTATAAGGGTATTTTT
1 GGTAATTCTACCCTACAGGGGTA-TTTC
* * *
46334 AGTAATTCTACCCTATAGTGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
46361 AGTAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAGGGGTATTT
46387 AGTAATTTCA
Statistics
Matches: 133, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
23 4 0.03
24 16 0.12
25 13 0.10
26 4 0.03
27 57 0.43
28 39 0.29
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:46268 original size:28 final size:26
Alignment explanation
Indices: 46233--46390 Score: 155
Period size: 28 Copynumber: 6.0 Consensus size: 26
46223 TATCTCGGTA
46233 ATTCTACCCTACAGGGGTATTTCAGAT
1 ATTCTACCCTACAGGGGTATTTCAG-T
*
46260 ATTTCTACCCTACAAGGGTATTTC-GAT
1 A-TTCTACCCTACAGGGGTATTTCAG-T
*
46287 AAT-TACCCTAC-GGGGTATTTC-GT
1 ATTCTACCCTACAGGGGTATTTCAGT
* * * *
46310 AATCTACCCTATAAGGGTATTTTTAGT
1 ATTCTACCCTACAGGGGTA-TTTCAGT
* *
46337 AATTCTACCCTATAGTGGTATTTCAGT
1 -ATTCTACCCTACAGGGGTATTTCAGT
46364 AATTCTACCCTACAGGGGTATTT-AGT
1 -ATTCTACCCTACAGGGGTATTTCAGT
46390 A
1 A
46391 ATTTCACAAT
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
23 4 0.04
24 17 0.15
25 14 0.12
26 7 0.06
27 34 0.30
28 37 0.33
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (26 bp):
ATTCTACCCTACAGGGGTATTTCAGT
Found at i:46367 original size:77 final size:80
Alignment explanation
Indices: 46221--46392 Score: 194
Period size: 77 Copynumber: 2.2 Consensus size: 80
46211 ACCCCACAAA
* * *
46221 GGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGATATTTCTACCCTACAAGGGTATTTCGA
1 GGTATTTC-GTAA-TCTACCCTACAAGGGTATTTCAGATAATTCTACCCTACAAGGGTATTTCGA
46286 TAA-T-TACCCTAC-GG
64 TAATTCTACCCTACAGG
* * *
46300 GGTATTTCGTAATCTACCCTATAAGGGTATTTTTAG-TAATTCTACCCTA-TAGTGGTATTTC-A
1 GGTATTTCGTAATCTACCCTACAAGGGTA-TTTCAGATAATTCTACCCTACAAG-GGTATTTCGA
46362 GTAATTCTACCCTACAGG
64 -TAATTCTACCCTACAGG
*
46380 GGTATTTAGTAAT
1 GGTATTTCGTAAT
46393 TTCACAATTG
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
76 3 0.04
77 38 0.47
78 10 0.12
79 15 0.19
80 14 0.17
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (80 bp):
GGTATTTCGTAATCTACCCTACAAGGGTATTTCAGATAATTCTACCCTACAAGGGTATTTCGATA
ATTCTACCCTACAGG
Found at i:46436 original size:27 final size:27
Alignment explanation
Indices: 46402--46687 Score: 164
Period size: 27 Copynumber: 10.4 Consensus size: 27
46392 TTTCACAATT
46402 GAGGGTAAAATAGTAATTCTGTAAATC
1 GAGGGTAAAATAGTAATTCTGTAAATC
* * *
46429 GAGGGTAAAAGA-TAATTTTTGTAAACC
1 GAGGGTAAAATAGTAA-TTCTGTAAATC
** * *
46456 GACGGGTAAACCAGTAATTCTATTAAATA
1 GA-GGGTAAAATAGTAATTCT-GTAAATC
* **
46485 GAGGGTAAAA-GGTAATT-TACAAATC
1 GAGGGTAAAATAGTAATTCTGTAAATC
**
46510 GAGGGTATAAA-ACAAAATTCTGTAAATC
1 GAGGGTA-AAATA-GTAATTCTGTAAATC
* *
46538 GAGGG-AAAATAGTGTAATTCTATAAAAC
1 GAGGGTAAAATA--GTAATTCTGTAAATC
* *
46566 TGA-GGTGAAA-CGATAATTCTGTAAATC
1 -GAGGGTAAAATAG-TAATTCTGTAAATC
46593 GAGGGTAAAAATAGTAATTTCTGTAAAT-
1 GAGGGT-AAAATAGTAA-TTCTGTAAATC
* *
46621 GAGGGGTAAAAGA-TAATATCTAT-AATC
1 GA-GGGTAAAATAGTAAT-TCTGTAAATC
46648 TGAAAGGGTAAAATAGTAATT-TGTACAAAT-
1 -G--AGGGTAAAATAGTAATTCTGT--AAATC
46678 GAGGGTAAAA
1 GAGGGTAAAA
46688 CGATTAATTC
Statistics
Matches: 199, Mismatches: 34, Indels: 52
0.70 0.12 0.18
Matches are distributed among these distances:
25 11 0.06
26 17 0.09
27 65 0.33
28 58 0.29
29 40 0.20
30 5 0.03
31 3 0.02
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (27 bp):
GAGGGTAAAATAGTAATTCTGTAAATC
Found at i:46636 original size:55 final size:54
Alignment explanation
Indices: 46386--46698 Score: 191
Period size: 55 Copynumber: 5.7 Consensus size: 54
46376 CAGGGGTATT
* * *
46386 TAGTAATTTC-ACAATTGA-GGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAA
1 TAGTAATTTCTATAAATGAGGGGTAAAAGA-TAATTCTGTAAATCGAGGGTAAAA
* * * * * * *
46439 GA-TAATTTTTGTAAACCGACGGGTAAACCAG-TAATTCTATTAAATAGAGGGTAAAA
1 TAGTAATTTCTATAAA-TGAGGGGTAAA--AGATAATTCT-GTAAATCGAGGGTAAAA
* * * * *
46495 -GGTAA-TT-TACAAATCGAGGGTATAAAACAAAATTCTGTAAATCGAGGG-AAAA
1 TAGTAATTTCTATAAAT-GAGGG-GTAAAAGATAATTCTGTAAATCGAGGGTAAAA
* *
46547 TAGTGTAA-TTCTATAAAACTGAGGTG-AAACGATAATTCTGTAAATCGAGGGTAAAAA
1 TA--GTAATTTCTAT-AAA-TGAGGGGTAAAAGATAATTCTGTAAATCGAGGGT-AAAA
* *
46604 TAGTAATTTCTGTAAATGAGGGGTAAAAGATAATATCTAT-AATCTGAAAGGGTAAAA
1 TAGTAATTTCTATAAATGAGGGGTAAAAGATAAT-TCTGTAAATC-G--AGGGTAAAA
* *
46661 TAGTAATTTGTACAAATGA-GGGTAAAACGATTAATTCT
1 TAGTAATTTCTATAAATGAGGGGTAAAA-GA-TAATTCT
46699 ATAATCAATA
Statistics
Matches: 201, Mismatches: 33, Indels: 48
0.71 0.12 0.17
Matches are distributed among these distances:
52 10 0.05
53 14 0.07
54 22 0.11
55 68 0.34
56 38 0.19
57 39 0.19
58 10 0.05
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.29
Consensus pattern (54 bp):
TAGTAATTTCTATAAATGAGGGGTAAAAGATAATTCTGTAAATCGAGGGTAAAA
Found at i:46661 original size:57 final size:58
Alignment explanation
Indices: 46594--46704 Score: 156
Period size: 57 Copynumber: 1.9 Consensus size: 58
46584 CTGTAAATCG
**
46594 AGGGTAAAAATAGTAATTTCTGTAAATGAGGGGTAAAA-GA-TAATATCTATAATCTGAA
1 AGGGTAAAAATAGTAATTTCTACAAATGA-GGGTAAAACGATTAAT-TCTATAATCTGAA
*
46652 AGGGT-AAAATAGTAATTTGTACAAATGAGGGTAAAACGATTAATTCTATAATC
1 AGGGTAAAAATAGTAATTTCTACAAATGAGGGTAAAACGATTAATTCTATAATC
46705 AATAGCGGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
56 8 0.17
57 31 0.65
58 9 0.19
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (58 bp):
AGGGTAAAAATAGTAATTTCTACAAATGAGGGTAAAACGATTAATTCTATAATCTGAA
Found at i:46785 original size:27 final size:27
Alignment explanation
Indices: 46755--46911 Score: 165
Period size: 27 Copynumber: 5.6 Consensus size: 27
46745 AAAATACAAA
46755 GGTAAAATGGTAATTCTATAAACTGAG
1 GGTAAAATGGTAATTCTATAAACTGAG
* *
46782 GGTAAAATGGTAATTCTGTAATC-GAG
1 GGTAAAATGGTAATTCTATAAACTGAG
* * *
46808 CGGTTAAAATCAGTAATTGTAACTTAAATTGAG
1 -GG-TAAAAT-GGTAATTCT-A--TAAACTGAG
*
46841 GGTAAAACGGTAATTCTATAAA-TCGAG
1 GGTAAAATGGTAATTCTATAAACT-GAG
* *
46868 GGTAAAATAGTAATTCTGTAAACTGAG
1 GGTAAAATGGTAATTCTATAAACTGAG
46895 GGTAAAATGGTAATTCT
1 GGTAAAATGGTAATTCT
46912 TGTAAATCAG
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
26 4 0.04
27 68 0.64
28 7 0.07
29 8 0.07
30 7 0.07
31 5 0.05
32 5 0.05
33 3 0.03
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (27 bp):
GGTAAAATGGTAATTCTATAAACTGAG
Found at i:46841 original size:59 final size:53
Alignment explanation
Indices: 46755--46916 Score: 191
Period size: 54 Copynumber: 2.9 Consensus size: 53
46745 AAAATACAAA
* *
46755 GGTAAAATGGTAATTCTATAAACTGAGGGTAAAATGGTAATTCTGTAATCGAG
1 GGTAAAATAGTAATTCTGTAAACTGAGGGTAAAATGGTAATTCTGTAATCGAG
* * *
46808 CGGTTAAAATCAGTAATTGTAACT-TAAATTGAGGGTAAAACGGTAATTCTATAAATCGAG
1 -GG-TAAAAT-AGTAA-T-T--CTGTAAACTGAGGGTAAAATGGTAATTCTGT-AATCGAG
46868 GGTAAAATAGTAATTCTGTAAACTGAGGGTAAAATGGTAATTCTTGTAA
1 GGTAAAATAGTAATTCTGTAAACTGAGGGTAAAATGGTAATTC-TGTAA
46917 ATCAGTAAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
53 2 0.02
54 27 0.29
55 9 0.10
56 5 0.05
57 6 0.07
58 7 0.08
59 27 0.29
60 9 0.10
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (53 bp):
GGTAAAATAGTAATTCTGTAAACTGAGGGTAAAATGGTAATTCTGTAATCGAG
Found at i:49352 original size:27 final size:28
Alignment explanation
Indices: 49286--49353 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
49276 CAGCATGGCT
*
49286 CCAGAA-CAGGATATCGTGACAGAAGTCA
1 CCAGAATCA-GATATCGTGACAGAAGCCA
* *
49314 CCAGATAT-AGATATTGTGGCAG-AGCCA
1 CCAGA-ATCAGATATCGTGACAGAAGCCA
49341 CCAGAATCAGATA
1 CCAGAATCAGATA
49354 CAGTGGCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 2 0.06
27 14 0.41
28 16 0.47
29 2 0.06
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGAATCAGATATCGTGACAGAAGCCA
Done.