Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1917
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: 56016
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:164 original size:51 final size:50
Alignment explanation
Indices: 16--204 Score: 175
Period size: 51 Copynumber: 3.7 Consensus size: 50
6 TTCTAGAAAG
* * * * *
16 AAATGTATCGATACATTTTTTTTATTGTATTGATACATTCTGG-TTTAATCC
1 AAATGTATCGATACA--TTATTCATTGTATCGATACATTCTGGTTTTGACCC
* * * * *
67 AAATGTATCGACACATTTTTTATTGTATC-ATAAATTTTGGGTTTTTGACCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCT-GG-TTTTGACCC
* * **
118 AAATGTATCGATATATTATTCATTTTATCGATACATTCTAGGTTTTGACAT
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCT-GGTTTTGACCC
* *
169 AAATGTATCGATACATTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATTATTCATTGTATCGATACAT
205 CCAGTTAATT
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
48 7 0.06
49 15 0.13
51 83 0.73
52 9 0.08
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (50 bp):
AAATGTATCGATACATTATTCATTGTATCGATACATTCTGGTTTTGACCC
Found at i:3727 original size:14 final size:14
Alignment explanation
Indices: 3708--3738 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3698 ATTTTATCTC
3708 ATATATATGTATAT
1 ATATATATGTATAT
3722 ATATATATGTATAT
1 ATATATATGTATAT
3736 ATA
1 ATA
3739 CGATACTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:4165 original size:39 final size:38
Alignment explanation
Indices: 4125--4268 Score: 137
Period size: 39 Copynumber: 3.7 Consensus size: 38
4115 AGTTTTCAAG
* *
4125 ATCACATTAATATTTTTATATTAATACATATCTATAAA
1 ATCACATTAATATTTTTATATTAAAATATATCTATAAA
* ** * * *
4163 GATAATTTTAATAATTTTATATTAAAATAAATCTTTAAA
1 -ATCACATTAATATTTTTATATTAAAATATATCTATAAA
* * *
4202 ATCATATTAATACTTTCATATTAAAATATAT-TCATAAA
1 ATCACATTAATATTTTTATATTAAAATATATCT-ATAAA
* *
4240 ATCACTTTAATAATTTCTATATTAAAATA
1 ATCACATTAAT-ATTTTTATATTAAAATA
4269 GAGTCCTTAA
Statistics
Matches: 84, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
37 1 0.01
38 39 0.46
39 44 0.52
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (38 bp):
ATCACATTAATATTTTTATATTAAAATATATCTATAAA
Found at i:4223 original size:38 final size:38
Alignment explanation
Indices: 4125--4268 Score: 139
Period size: 38 Copynumber: 3.7 Consensus size: 38
4115 AGTTTTCAAG
* * * * *
4125 ATCACATTAATATTTTTATATTAATACATATCTATAAA
1 ATCATATTAATAATTTCATATTAAAATATATCTATAAA
* * * * *
4163 GATAATTTTAATAATTTTATATTAAAATAAATCTTTAAA
1 -ATCATATTAATAATTTCATATTAAAATATATCTATAAA
*
4202 ATCATATTAATACTTTCATATTAAAATATAT-TCATAAA
1 ATCATATTAATAATTTCATATTAAAATATATCT-ATAAA
4240 ATCACT-TTAATAATTTCTATATTAAAATA
1 ATCA-TATTAATAATTTC-ATATTAAAATA
4269 GAGTCCTTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
37 1 0.01
38 44 0.51
39 42 0.48
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (38 bp):
ATCATATTAATAATTTCATATTAAAATATATCTATAAA
Found at i:4223 original size:77 final size:77
Alignment explanation
Indices: 4125--4268 Score: 193
Period size: 77 Copynumber: 1.9 Consensus size: 77
4115 AGTTTTCAAG
* * * *
4125 ATCACATTAATATTTTTATATTAATACATA-TCTATAAAGATAATTTTAATAATTT-TATATTAA
1 ATCACATTAATACTTTCATATTAAAACATATTC-ATAAA-ATAACTTTAATAATTTCTATATTAA
4188 AATAAATCTTTAAA
64 AATAAATCTTTAAA
* * *
4202 ATCATATTAATACTTTCATATTAAAATATATTCATAAAATCACTTTAATAATTTCTATATTAAAA
1 ATCACATTAATACTTTCATATTAAAACATATTCATAAAATAACTTTAATAATTTCTATATTAAAA
4267 TA
66 TA
4269 GAGTCCTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
76 14 0.24
77 42 0.72
78 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (77 bp):
ATCACATTAATACTTTCATATTAAAACATATTCATAAAATAACTTTAATAATTTCTATATTAAAA
TAAATCTTTAAA
Found at i:4318 original size:39 final size:40
Alignment explanation
Indices: 4169--4327 Score: 125
Period size: 39 Copynumber: 4.1 Consensus size: 40
4159 TAAAGATAAT
* * *
4169 TTTAATAATTT-TATATTAAAATA-AATCTTTAAAATCA-
1 TTTAATAATTTCTAAATTAAAATATATTCATTAAAATCAC
* *
4206 TATTAATACTTTC-ATATTAAAATATATTCA-TAAAATCAC
1 T-TTAATAATTTCTAAATTAAAATATATTCATTAAAATCAC
* * * * ***
4245 TTTAATAATTTCTATATTAAAATAGAGTCCTTAAAATTTT
1 TTTAATAATTTCTAAATTAAAATATATTCATTAAAATCAC
* *
4285 TTTAA-CA-TTCTCAAATTAAAATATATTCATTAAAATCAT
1 TTTAATAATTTCT-AAATTAAAATATATTCATTAAAATCAC
4324 TTTA
1 TTTA
4328 GTAAACTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
37 1 0.01
38 42 0.43
39 44 0.45
40 11 0.11
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (40 bp):
TTTAATAATTTCTAAATTAAAATATATTCATTAAAATCAC
Found at i:4854 original size:16 final size:15
Alignment explanation
Indices: 4833--4875 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
4823 TATGAATGTG
4833 TATATTGATACTAATC
1 TATATTGATAC-AATC
*
4849 TATATTGAT-CAATT
1 TATATTGATACAATC
4863 TATATTGATACAA
1 TATATTGATACAA
4876 ACTTGTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 12 0.48
15 4 0.16
16 9 0.36
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (15 bp):
TATATTGATACAATC
Found at i:6192 original size:24 final size:23
Alignment explanation
Indices: 6165--6210 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6155 CTTTGAAATG
* *
6165 AATTTATTAATATATTTTTATTTC
1 AATTGATTAAT-TATTATTATTTC
6189 AATTGATTAATTATTATTATTT
1 AATTGATTAATTATTATTATTT
6211 AAAATTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
AATTGATTAATTATTATTATTTC
Found at i:7537 original size:23 final size:23
Alignment explanation
Indices: 7483--7541 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
7473 AATAAATAAT
*
7483 ATATATAACAAATTTTAATTTATG
1 ATATATAA-AAATATTAATTTATG
*
7507 A-ATTTAAAAA-ATTACATTTATG
1 ATATATAAAAATATTA-ATTTATG
7529 ATATATAAAAATA
1 ATATATAAAAATA
7542 ATATTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 3 0.10
22 11 0.38
23 13 0.45
24 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (23 bp):
ATATATAAAAATATTAATTTATG
Found at i:7540 original size:22 final size:21
Alignment explanation
Indices: 7483--7540 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
7473 AATAAATAAT
7483 ATATATAACAAATTTTAATTTATG
1 ATATATAA-AAA--TTAATTTATG
*
7507 A-ATTTAAAAAATTACATTTATG
1 ATATAT-AAAAATTA-ATTTATG
7529 ATATATAAAAAT
1 ATATATAAAAAT
7541 AATATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 3 0.10
22 14 0.48
23 9 0.31
24 3 0.10
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
ATATATAAAAATTAATTTATG
Found at i:7547 original size:22 final size:22
Alignment explanation
Indices: 7500--7547 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
7490 ACAAATTTTA
* *
7500 ATTTATGAATTTAAAAAATTAC
1 ATTTATGAATATAAAAAATAAC
*
7522 ATTTATG-ATATATAAAAATAAT
1 ATTTATGAATATA-AAAAATAAC
7544 ATTT
1 ATTT
7548 TAATCTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
ATTTATGAATATAAAAAATAAC
Found at i:11686 original size:97 final size:97
Alignment explanation
Indices: 11548--11785 Score: 352
Period size: 97 Copynumber: 2.5 Consensus size: 97
11538 TTTTTTTGTT
* * *** *
11548 GAAAAATGGGGTTGGAGTATCCCCTTGGAGGGATGGGGTTGGAGTGTCCTCGACAATAATAGTTT
1 GAAAAACGGGGTTGGAGTATCCCCTCGGAATAATGGGGTTGGAGTGTCCTCAACAATAATAGTTT
11613 AGGTAAAAATAAGAATGATCTTGACAAGTTTA
66 AGGTAAAAATAAGAATGATCTTGACAAGTTTA
* * * *
11645 GAAAAACGAGGTTGGAGTATCCCCTCAGAATAATGGAGTTGGACTGTCCTCAACAATAATAGTTT
1 GAAAAACGGGGTTGGAGTATCCCCTCGGAATAATGGGGTTGGAGTGTCCTCAACAATAATAGTTT
*
11710 AGGTAAAAATAAGAATGATCTTGATAAGTTTA
66 AGGTAAAAATAAGAATGATCTTGACAAGTTTA
* *
11742 -AAAAACGGGGATAGAGTATCCCCTCGGAATAATGGGGTTGGAGT
1 GAAAAACGGGGTTGGAGTATCCCCTCGGAATAATGGGGTTGGAGT
11786 ATCTCCGATA
Statistics
Matches: 124, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
96 38 0.31
97 86 0.69
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.26
Consensus pattern (97 bp):
GAAAAACGGGGTTGGAGTATCCCCTCGGAATAATGGGGTTGGAGTGTCCTCAACAATAATAGTTT
AGGTAAAAATAAGAATGATCTTGACAAGTTTA
Found at i:15130 original size:61 final size:61
Alignment explanation
Indices: 15032--15168 Score: 197
Period size: 61 Copynumber: 2.2 Consensus size: 61
15022 AAAGATGATG
*
15032 AAGATGAGAAGAGTGATAAAGATGCCAATATGCTGATTC-AGAGCCAGAGATATTGGGCTTA
1 AAGATGAGAAGAATGATAAAGATGCCAATATGCTGATTCAAG-GCCAGAGATATTGGGCTTA
* * *
15093 AAGATGATGAAGAATGATAAAGGT-CCAATATGTTGATTCAAGGCCAGCGATATTGGGCTTA
1 AAGATGA-GAAGAATGATAAAGATGCCAATATGCTGATTCAAGGCCAGAGATATTGGGCTTA
*
15154 AAGATGCGAAGAATG
1 AAGATGAGAAGAATG
15169 TTAATGTGCT
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
60 8 0.12
61 45 0.65
62 16 0.23
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (61 bp):
AAGATGAGAAGAATGATAAAGATGCCAATATGCTGATTCAAGGCCAGAGATATTGGGCTTA
Found at i:15299 original size:49 final size:49
Alignment explanation
Indices: 15112--15590 Score: 439
Period size: 49 Copynumber: 10.0 Consensus size: 49
15102 AAGAATGATA
* * * *
15112 AAGGT-CCAATATGTTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGCG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--G
* ** * * *
15162 AAGAATGTTAATGTGCTGATTTACGGCCAACGACATT-GAGCTT--AG--G
1 AAG-GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGA-CTTAAAGATG
* * * * * *
15208 AA--TGCCAATATGTTGATTCAAGGCCAGCGATATCGGATTTAAAGATA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* *
15255 AAGGTGCCAATGTGCTGATTCAAGGCTAACGACATTGGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * *
15304 AAGGTGCCAATGTGCTGATTGAAGGCCA-CTGACATCGAACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGC-GACATTGGACTTAAAGATG
* *
15353 AAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* *
15402 AAGGTGCCAATGTGCTGATTCAAAGCCAGCGACATTAGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * * *
15451 AAGATGCCAATGTGCTGATTCAGGGCCAGTGACATTGG-GTT-TAG--G
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * * ** *
15496 AA--TGCCAATATGATGATTCAAGGCCAGCAATATCAGACTTAAAGATA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
** *
15543 AAGGTGCCAATGTGCTGATTCAAGGTTAGCAACATTGGACTTAGAAGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
15591 GTTGCCATCG
Statistics
Matches: 345, Mismatches: 65, Indels: 38
0.77 0.15 0.08
Matches are distributed among these distances:
43 51 0.15
44 4 0.01
45 7 0.02
46 3 0.01
47 6 0.02
48 3 0.01
49 234 0.68
50 10 0.03
51 2 0.01
52 25 0.07
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (49 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
Found at i:15397 original size:147 final size:141
Alignment explanation
Indices: 15108--15590 Score: 540
Period size: 147 Copynumber: 3.4 Consensus size: 141
15098 GATGAAGAAT
* * * * * **
15108 GATAAAGGT-CCAATATGTTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGCGAAGAATGTTA
1 GATAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGAT--GAAG-ATGCCA
* * * *
15172 ATGTGCTGATTTACGGCCAAC-GACATTGAGCTT-AGGAATGCCAATATGTTGATTCAAGGCCAG
63 ATGTGCTGATTCAAGGCC-ACTGACATCGA-CTTAAGGAATGCCAATATGATGATTCAAGGCCAG
* *
15235 CGATATCGGATTTAAA
126 CGATATCAGACTTAAA
* *
15251 GATAAAGGTGCCAATGTGCTGATTCAAGGCTAACGACATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAGATGCCAATG
* * *
15316 TGCTGATTGAAGGCCACTGACATCGAACTTAAAGATGAAAGTGCCAATGTGCTGATTCAAGGCCA
66 TGCTGATTCAAGGCCACTGACATCG-ACTT-AAG--G-AA-TGCCAATATGATGATTCAAGGCCA
* *
15381 GCGACATTAGACTTAAA
125 GCGATATCAGACTTAAA
* * * *
15398 GATGAAGGTGCCAATGTGCTGATTCAAAGCCAGCGACATTAGACTTAAAGATGAAGATGCCAATG
1 GATAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAGATGCCAATG
* * * ** * *
15463 TGCTGATTCAGGGCCAGTGACATTGGGTTTAGGAATGCCAATATGATGATTCAAGGCCAGCAATA
66 TGCTGATTCAAGGCCACTGACATCGACTTAAGGAATGCCAATATGATGATTCAAGGCCAGCGATA
15528 TCAGACTTAAA
131 TCAGACTTAAA
* *
15539 GATAAAGGTGCCAATGTGCTGATTCAAGGTTAGCAACATTGGACTTAGAAGA
1 GATAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTA-AAGA
15591 GTTGCCATCG
Statistics
Matches: 288, Mismatches: 42, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
140 2 0.01
141 105 0.36
142 11 0.04
143 12 0.04
144 36 0.12
145 3 0.01
146 4 0.01
147 115 0.40
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (141 bp):
GATAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAGATGCCAATG
TGCTGATTCAAGGCCACTGACATCGACTTAAGGAATGCCAATATGATGATTCAAGGCCAGCGATA
TCAGACTTAAA
Found at i:15698 original size:33 final size:32
Alignment explanation
Indices: 15650--16131 Score: 438
Period size: 27 Copynumber: 15.9 Consensus size: 32
15640 TAGGCTTTTG
*
15650 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAAA
1 AAGG-AAAAGGTGCCACAGAGTTGTGGACTT-AA
* * *
15684 AAGGAAAAGATGCCACAGAGTTATGGACTTGA
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
*
15716 AAGGAAAAAGGTGCCACAGAGTTGTGGACTTGA
1 AAGG-AAAAGGTGCCACAGAGTTGTGGACTTAA
* *
15749 AAGGAAAAAGGTGCCACGGAATTGTGGACTT--
1 AAGG-AAAAGGTGCCACAGAGTTGTGGACTTAA
**
15780 -A--AAAAGGTGCCACAGAGTTGCAGACTT--
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
* * *
15807 -A--AAAAGGTGTCACGGAGTTATGGACTTAA
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
* * *
15836 AAAGAAAAGGTGTCATAGAGTTGTGGACTT-A
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
* *
15867 AA--AAAAGGTGCCACGGAGTTGTGGGCTTAA
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
* *
15897 AAGGAACAAGTTGCCACAGAGTTATGGACTT--
1 AAGGAA-AAGGTGCCACAGAGTTGTGGACTTAA
*
15928 -A--AAAAGGTGCCACAAAGTTGTGGACTTAA
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
15957 AAGGAAAAGGTGCCA-AGGAGTTGTGGACTTAA
1 AAGGAAAAGGTGCCACA-GAGTTGTGGACTTAA
15989 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
* *
16021 AA-G----GGTGCCACGGAGTTATGGACTTAA
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
* *
16048 AA-G----GGTGCCACGGAGATGTGGACTTAA
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
*
16075 AA-G---A-GTGCCATAGAGTTGTGGACTTAA
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
*
16102 AAGGAAAAGATGCCACAGAGTTGTGGACTT
1 AAGGAAAAGGTGCCACAGAGTTGTGGACTT
16132 TTAAGAAAAA
Statistics
Matches: 384, Mismatches: 41, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
27 137 0.36
28 3 0.01
29 22 0.06
30 7 0.02
31 6 0.02
32 106 0.28
33 99 0.26
34 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (32 bp):
AAGGAAAAGGTGCCACAGAGTTGTGGACTTAA
Found at i:15843 original size:87 final size:87
Alignment explanation
Indices: 15720--16131 Score: 269
Period size: 86 Copynumber: 4.7 Consensus size: 87
15710 ACTTGAAAGG
* * * *
15720 AAAAAGGTGCCACAGAGTTGTGGACTTGAAAGGAAAAAGGTGCCACGGAATTGTGGACTT-AAAA
1 AAAAAGGTGCCACAGAGTTATGGACTTAAAAAG-AAAAGGTGCCACAGAATTGTGGACTTAAAAA
15784 AGGTGCCACAGAGTTGCAGACTT
65 AGGTGCCACAGAGTTGCAGACTT
* * * * *
15807 AAAAAGGTGTCACGGAGTTATGGACTTAAAAAGAAAAGGTGTCATAGAGTTGTGGACTTAAAAAA
1 AAAAAGGTGCCACAGAGTTATGGACTTAAAAAGAAAAGGTGCCACAGAATTGTGGACTT-AAAAA
* ** *
15872 AGGTGCCACGGAGTTGTGGGCTT
65 AGGTGCCACAGAGTTGCAGACTT
*
15895 AAAAGGAACAAGTTGCCACAGAGTTATGGACTT----A-AAAAGGTGCCACA-AAGTTGTGGACT
1 ---A--AA-AAGGTGCCACAGAGTTATGGACTTAAAAAGAAAAGGTGCCACAGAA-TTGTGGACT
**
15954 TAAAAGGAAAAGGTGCCA-AGGAGTTGTGGACTT
59 T--AA--AAAAGGTGCCACA-GAGTTGCAGACTT
* * * *
15987 AAAAGGAAAAGGTGCCACAGAGTTGTGGACTT-AAAAG----GGTGCCACGGAGTTATGGACTT-
1 ---A--AAAAGGTGCCACAGAGTTATGGACTTAAAAAGAAAAGGTGCCACAGAATTGTGGACTTA
* * * **
16046 AAAAGGGTGCCACGGAGATGTGGACTT
61 AAAAAGGTGCCACAGAGTTGCAGACTT
* * * * *
16073 -AAAAGAGTGCCATAGAGTTGTGGACTTAAAAGGAAAAGATGCCACAGAGTTGTGGACTT
1 AAAAAG-GTGCCACAGAGTTATGGACTTAAAAAGAAAAGGTGCCACAGAATTGTGGACTT
16132 TTAAGAAAAA
Statistics
Matches: 266, Mismatches: 34, Indels: 51
0.76 0.10 0.15
Matches are distributed among these distances:
80 5 0.02
81 20 0.08
82 4 0.02
86 63 0.24
87 28 0.11
88 25 0.09
89 21 0.08
90 4 0.02
91 40 0.15
92 32 0.12
93 2 0.01
94 22 0.08
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (87 bp):
AAAAAGGTGCCACAGAGTTATGGACTTAAAAAGAAAAGGTGCCACAGAATTGTGGACTTAAAAAA
GGTGCCACAGAGTTGCAGACTT
Found at i:16043 original size:91 final size:90
Alignment explanation
Indices: 15852--16140 Score: 330
Period size: 91 Copynumber: 3.3 Consensus size: 90
15842 AAGGTGTCAT
* *
15852 AGAGTTGTGGACTT-AAA-AAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGTTGCCACA
1 AGAGTTGTGGACTTAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA-AAGGTGCCACA
* *
15915 GAGTTATGGACTTAAAAAGGTGCCAC
65 GAGTTGTGGACTTAAAAGGGTGCCAC
* *
15941 AAAGTTGTGGACTTAAAAGGAAAAGGTGCCAAGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACA
1 AGAGTTGTGGACTTAAAA-GAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACA
16006 GAGTTGTGGACTTAAAAGGGTGCCAC
65 GAGTTGTGGACTTAAAAGGGTGCCAC
* * * *
16032 GGAGTTATGGACTTAAAAG----GGTGCCACGGAGATGTGGACTTAAAA-G---A-GTGCCATAG
1 AGAGTTGTGGACTTAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACAG
16088 AGTTGTGGACTTAAAAGGAAAAGATGCCAC
66 AGTTGTGGACTTAAAAGG----G-TGCCAC
**
16118 AGAGTTGTGGACTTTTAAGAAAA
1 AGAGTTGTGGACTTAAAAGAAAA
16141 ATGATGCCAC
Statistics
Matches: 172, Mismatches: 16, Indels: 23
0.82 0.08 0.11
Matches are distributed among these distances:
81 26 0.15
82 1 0.01
85 2 0.01
86 45 0.26
89 13 0.08
90 4 0.02
91 49 0.28
92 32 0.19
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (90 bp):
AGAGTTGTGGACTTAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACAG
AGTTGTGGACTTAAAAGGGTGCCAC
Found at i:16180 original size:63 final size:63
Alignment explanation
Indices: 16109--16259 Score: 180
Period size: 63 Copynumber: 2.4 Consensus size: 63
16099 TAAAAGGAAA
** * * *
16109 AGATGCCACAGAGTTGTGGACTTTTAAGAAAAATGATGCCACTGAG-TAGTGGCCTTGGAAAAG
1 AGATGCCACAGAGTCATGGACTTTGAAGAAAAAGGATGCCACTGAGTTA-TGGACTTGGAAAAG
* * *
16172 AGATGCCACTA-AGTCATGGTCTTAGAAGAAAAAGGATGCCACTGAGTTATGGATTTGGAAAAG
1 AGATGCCAC-AGAGTCATGGACTTTGAAGAAAAAGGATGCCACTGAGTTATGGACTTGGAAAAG
* *
16235 AGATGTCACTGAGTCATGGACTTTG
1 AGATGCCACAGAGTCATGGACTTTG
16260 GGAAGGGTGC
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
63 70 0.96
64 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (63 bp):
AGATGCCACAGAGTCATGGACTTTGAAGAAAAAGGATGCCACTGAGTTATGGACTTGGAAAAG
Found at i:16274 original size:29 final size:30
Alignment explanation
Indices: 16138--16286 Score: 126
Period size: 30 Copynumber: 4.9 Consensus size: 30
16128 ACTTTTAAGA
* *
16138 AAAATGATGCCACTGAGT-AGTGG-CCTTGG
1 AAAAGGATGCCACTGAGTCA-TGGACTTTGG
* * *
16167 AAAAGAGATGCCACTAAGTCATGGTCTTAGAAG
1 AAAAG-GATGCCACTGAGTCATGGACTTTG--G
*
16200 AAAAAGGATGCCACTGAGTTATGGA-TTTGG
1 -AAAAGGATGCCACTGAGTCATGGACTTTGG
*
16230 AAAAGAGATGTCACTGAGTCATGGACTTTGG
1 AAAAG-GATGCCACTGAGTCATGGACTTTGG
* * *
16261 -GAAGGGTGCCACTGAGTCGTGGACTT
1 AAAAGGATGCCACTGAGTCATGGACTT
16287 AGAAGAAAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
29 28 0.29
30 36 0.37
31 9 0.09
32 3 0.03
33 17 0.17
34 5 0.05
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (30 bp):
AAAAGGATGCCACTGAGTCATGGACTTTGG
Found at i:16307 original size:33 final size:32
Alignment explanation
Indices: 16073--16307 Score: 148
Period size: 33 Copynumber: 7.4 Consensus size: 32
16063 ATGTGGACTT
* * *
16073 AAAAGAGTGCCA-TAGAGTTGTGGACTTAAAAGG
1 AAAAGA-TGCCACT-GAGTCGTGGACTTAGAAGA
* * **
16106 AAAAGATGCCACAGAGTTGTGGACTTTTAAGA
1 AAAAGATGCCACTGAGTCGTGGACTTAGAAGA
* *
16138 AAAATGATGCCACTGAGTAGTGGCCTT-G--GA
1 AAAA-GATGCCACTGAGTCGTGGACTTAGAAGA
* * *
16168 AAAGAGATGCCACTAAGTCATGGTCTTAGAAGA
1 AAA-AGATGCCACTGAGTCGTGGACTTAGAAGA
** *
16201 AAAAGGATGCCACTGAGTTATGGA-TTTG--GA
1 AAAA-GATGCCACTGAGTCGTGGACTTAGAAGA
* * *
16231 AAAGAGATGTCACTGAGTCATGGACTTTG--G-
1 AAA-AGATGCCACTGAGTCGTGGACTTAGAAGA
* * *
16261 GAAGGGTGCCACTGAGTCGTGGACTTAGAAGA
1 AAAAGATGCCACTGAGTCGTGGACTTAGAAGA
16293 AAAAGTATGCCACTG
1 AAAAG-ATGCCACTG
16308 TATAGTGGAC
Statistics
Matches: 162, Mismatches: 27, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
29 20 0.12
30 47 0.29
31 9 0.06
32 32 0.20
33 54 0.33
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (32 bp):
AAAAGATGCCACTGAGTCGTGGACTTAGAAGA
Found at i:17139 original size:13 final size:13
Alignment explanation
Indices: 17121--17177 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
17111 CATAAAGTGT
17121 TGTATCGATACAA
1 TGTATCGATACAA
17134 TGTATCGATACATAA
1 TGTATCGATAC--AA
17149 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
17166 TGTATCGATACA
1 TGTATCGATACA
17178 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:17156 original size:32 final size:32
Alignment explanation
Indices: 17101--17198 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
17091 TTCAACGATT
17101 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
17134 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
17166 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
17198 T
1 T
17199 ATAAGCTACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:17158 original size:19 final size:18
Alignment explanation
Indices: 17099--17196 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
17089 ATTTCAACGA
17099 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
17118 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
17134 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
17150 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
17166 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
17182 TTTTGTATCAATACA
1 -TTTGTATCGATACA
17197 ATATAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:17255 original size:13 final size:13
Alignment explanation
Indices: 17237--17261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17227 ACATTTCAAA
17237 TGTATCGATACAT
1 TGTATCGATACAT
17250 TGTATCGATACA
1 TGTATCGATACA
17262 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17306 original size:52 final size:52
Alignment explanation
Indices: 17270--17398 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
17260 CACTGATCTT
*
17270 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
17322 TGTATCGATACATGCAAGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
17374 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
17399 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:21521 original size:19 final size:19
Alignment explanation
Indices: 21478--21533 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
21468 CTGCCAGTTT
*
21478 CATGTATCGATACATTTGAG
1 CATGTATCGATACA-ATGAG
*
21498 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
21517 CATGTATCGATACAATG
1 CATGTATCGATACAATG
21534 TATTGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:28499 original size:15 final size:15
Alignment explanation
Indices: 28481--28512 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28471 CGAGTCAACC
28481 TCATCATTATCATCA
1 TCATCATTATCATCA
*
28496 TCATCATTTTCATCA
1 TCATCATTATCATCA
28511 TC
1 TC
28513 TTTGACAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:30156 original size:33 final size:33
Alignment explanation
Indices: 30096--30162 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
30086 GCCGTGGGGC
* *
30096 ATAATGTATCGATACAATTCTTCATGTATTGAT
1 ATAATGTATCGATACAATTCCTCATGTATCGAT
* *
30129 ATAATGTATTGATACATTATCCT-ATGTATCGAT
1 ATAATGTATCGATACAAT-TCCTCATGTATCGAT
30162 A
1 A
30163 CATTTCACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (33 bp):
ATAATGTATCGATACAATTCCTCATGTATCGAT
Found at i:30219 original size:20 final size:19
Alignment explanation
Indices: 30194--30248 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
30184 TGTCAGTTTA
* *
30194 ATGTATCGATACATTTGAGT
1 ATGTATCGATACA-ATGAGC
*
30214 ATGTATCAATACAATGAGC
1 ATGTATCGATACAATGAGC
*
30233 ATATATCGATACAATG
1 ATGTATCGATACAATG
30249 TATCGATACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAGC
Found at i:37151 original size:21 final size:20
Alignment explanation
Indices: 37118--37158 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
37108 GAGGTGTTGG
37118 ACATACTAAAAATGCATGAA
1 ACATACTAAAAATGCATGAA
*
37138 ACATAGCTCAAAATGCATGAA
1 ACATA-CTAAAAATGCATGAA
37159 CATGGGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (20 bp):
ACATACTAAAAATGCATGAA
Found at i:38084 original size:20 final size:20
Alignment explanation
Indices: 38059--38112 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
38049 ATTTGCCTGC
*
38059 ATGTATCGATGCATTGAATA
1 ATGTATCGATGCATTCAATA
**
38079 ATGTATCGACACATTCAATA
1 ATGTATCGATGCATTCAATA
38099 ATGTATCGATGCAT
1 ATGTATCGATGCAT
38113 CTGGGTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (20 bp):
ATGTATCGATGCATTCAATA
Found at i:38201 original size:15 final size:13
Alignment explanation
Indices: 38170--38195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38160 ACAAAACTTA
38170 TGTATCGATACAT
1 TGTATCGATACAT
38183 TGTATCGATACAT
1 TGTATCGATACAT
38196 ATTGTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:39719 original size:33 final size:33
Alignment explanation
Indices: 39681--39747 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
39671 GTTACAAGCT
39681 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
*
39714 ATGTATTGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
39747 A
1 A
39748 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:39802 original size:21 final size:21
Alignment explanation
Indices: 39776--39831 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
39766 CTGCCAGTTT
**
39776 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
39797 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
39816 CATGTATCGATACAAT
1 CATGTATCGATACAAT
39832 GTATCGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:39835 original size:13 final size:13
Alignment explanation
Indices: 39817--39843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39807 TACATTGAAC
39817 ATGTATCGATACA
1 ATGTATCGATACA
39830 ATGTATCGATACA
1 ATGTATCGATACA
39843 A
1 A
39844 GGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:40406 original size:17 final size:19
Alignment explanation
Indices: 40384--40428 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
40374 TTTCGTTTTT
40384 CCTTAAA-AAAT-TCTCCC
1 CCTTAAACAAATATCTCCC
*
40401 CCTTAAACGAATATCTCCC
1 CCTTAAACAAATATCTCCC
40420 CCTTAAACA
1 CCTTAAACA
40429 GTTATCTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 3 0.12
19 14 0.58
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (19 bp):
CCTTAAACAAATATCTCCC
Found at i:40442 original size:22 final size:19
Alignment explanation
Indices: 40394--40446 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
40384 CCTTAAAAAA
40394 TTCTCCCCCTTAAACGAAT
1 TTCTCCCCCTTAAACGAAT
* *
40413 ATCTCCCCCTTAAACAGTTAT
1 TTCTCCCCCTTAAAC-G-AAT
40434 CTTCTCCCCCTTA
1 -TTCTCCCCCTTA
40447 TGTAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.50
20 1 0.04
21 2 0.07
22 11 0.39
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.34
Consensus pattern (19 bp):
TTCTCCCCCTTAAACGAAT
Found at i:40472 original size:13 final size:12
Alignment explanation
Indices: 40444--40469 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40434 CTTCTCCCCC
40444 TTATGTAAAAAA
1 TTATGTAAAAAA
40456 TTATGTAAAAAA
1 TTATGTAAAAAA
40468 TT
1 TT
40470 TATTTTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
TTATGTAAAAAA
Found at i:42314 original size:13 final size:13
Alignment explanation
Indices: 42296--42323 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42286 AAATAGTACC
42296 CAATGTATCGATA
1 CAATGTATCGATA
42309 CAATGTATCGATA
1 CAATGTATCGATA
42322 CA
1 CA
42324 GGGAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:48194 original size:18 final size:19
Alignment explanation
Indices: 48162--48201 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
48152 CAATGAAAAC
48162 AAAAGCTCTTGGAAATGTG
1 AAAAGCTCTTGGAAATGTG
* *
48181 AAAA-CTCTTTGAAATTTG
1 AAAAGCTCTTGGAAATGTG
48199 AAA
1 AAA
48202 GAAAGCTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (19 bp):
AAAAGCTCTTGGAAATGTG
Found at i:48478 original size:13 final size:13
Alignment explanation
Indices: 48460--48492 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
48450 ACATTTCTTC
48460 ATGTATCGATACA
1 ATGTATCGATACA
48473 ATGTATCGATACA
1 ATGTATCGATACA
*
48486 TTGTATC
1 ATGTATC
48493 ATGTATCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:48478 original size:33 final size:33
Alignment explanation
Indices: 48440--48506 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
48430 ATTACAAGCT
*
48440 ATGTATCGATACATT-TCTTCATGTATCGATACA
1 ATGTATCGATACATTGT-ATCATGTATCGATACA
48473 ATGTATCGATACATTGTATCATGTATCGATACA
1 ATGTATCGATACATTGTATCATGTATCGATACA
48506 A
1 A
48507 ATAGCAATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTATCATGTATCGATACA
Found at i:48987 original size:12 final size:12
Alignment explanation
Indices: 48970--49001 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
48960 CAAAAACGTT
48970 ATGGTTTTTTTA
1 ATGGTTTTTTTA
48982 ATGGTTTTTTTA
1 ATGGTTTTTTTA
*
48994 ATGCTTTT
1 ATGGTTTT
49002 CATGGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.03, G:0.16, T:0.66
Consensus pattern (12 bp):
ATGGTTTTTTTA
Found at i:49545 original size:50 final size:51
Alignment explanation
Indices: 49490--49604 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
49480 TGAATAGTAC
* *
49490 ATGTATCGATATATTCTA-TTTTTTACCCAGATGTATCGATATATTTTTCA
1 ATGTATCGATACATTCTATTTTTTTACCCAGATGTATCGATACATTTTTCA
* *
49540 ATGTATTGATACGTTCTATTTTTTTACCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTATTTTTTTACCCAGATGTATCGATACATTTTTCA
49591 ATGTATCGATACAT
1 ATGTATCGATACAT
49605 CTAGTTAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 15 0.26
51 43 0.74
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (51 bp):
ATGTATCGATACATTCTATTTTTTTACCCAGATGTATCGATACATTTTTCA
Found at i:54828 original size:2 final size:2
Alignment explanation
Indices: 54823--54855 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54813 AAAGTGTGTG
54823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54856 GTGTGTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.