Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2328
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: 83737
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:590 original size:60 final size:61
Alignment explanation
Indices: 524--642 Score: 213
Period size: 61 Copynumber: 2.0 Consensus size: 61
514 TCAATTGGTG
*
524 TAATTTTGATAATAAAAATAAA-TTGAGGTTCAATTGATTTGGGTTAATTTTGTAATAAGA
1 TAATTTTGATAATAAAAATAAAGTTGAGGTTCAATTGATTTGAGTTAATTTTGTAATAAGA
*
584 TAATTTTGATAATAAAGATAAAGTTGAGGTTCAATTGATTTGAGTTAATTTTGTAATAA
1 TAATTTTGATAATAAAAATAAAGTTGAGGTTCAATTGATTTGAGTTAATTTTGTAATAA
643 AATCAAATTG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 21 0.38
61 35 0.62
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.42
Consensus pattern (61 bp):
TAATTTTGATAATAAAAATAAAGTTGAGGTTCAATTGATTTGAGTTAATTTTGTAATAAGA
Found at i:598 original size:17 final size:17
Alignment explanation
Indices: 568--604 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
558 TGATTTGGGT
568 TAATTTTGTAAT-AAGA
1 TAATTTTGTAATAAAGA
584 TAATTTTGATAATAAAGA
1 TAATTTTG-TAATAAAGA
602 TAA
1 TAA
605 AGTTGAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
TAATTTTGTAATAAAGA
Found at i:1584 original size:15 final size:15
Alignment explanation
Indices: 1564--1611 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
1554 TTCTTGTTTT
1564 AAAATTATTTAATAA
1 AAAATTATTTAATAA
* *
1579 AAAATTATTGTATTGA
1 AAAATTATT-TAATAA
*
1595 TAAATTATTT-ATAA
1 AAAATTATTTAATAA
1609 AAA
1 AAA
1612 TATAAATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (15 bp):
AAAATTATTTAATAA
Found at i:1857 original size:87 final size:90
Alignment explanation
Indices: 1683--1863 Score: 253
Period size: 87 Copynumber: 2.0 Consensus size: 90
1673 ATGTTTTTAA
* *
1683 AAATTTTGAGTTATAGATGAATTGCTACATTTACATTTTATTATTTTTTATTTTTAATATGAATA
1 AAATTATGAGTTATAGATGAACTGCTACATTTACATTTTATTATTTTTTATTTTTAATATGAATA
*
1748 TAAATAATAGATACCAATATAATCT
66 TAAATAATAAATACCAATATAATCT
* * *
1773 AAATTATGAGTTATTAGAT-AACTGCTAGATTTA-TTTTTTTTA-TTTTTATTTTT-ATATGAAT
1 AAATTATGAGTTA-TAGATGAACTGCTACATTTACATTTTATTATTTTTTATTTTTAATATGAAT
* *
1834 ATAAATGATAAATATCAATATAATCT
65 ATAAATAATAAATACCAATATAATCT
1860 AAAT
1 AAAT
1864 GAATTAAATT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
87 35 0.43
88 11 0.13
89 7 0.09
90 24 0.29
91 5 0.06
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.48
Consensus pattern (90 bp):
AAATTATGAGTTATAGATGAACTGCTACATTTACATTTTATTATTTTTTATTTTTAATATGAATA
TAAATAATAAATACCAATATAATCT
Found at i:6023 original size:13 final size:13
Alignment explanation
Indices: 6005--6030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5995 CAATTTTTTA
6005 TGTATCGATACAT
1 TGTATCGATACAT
6018 TGTATCGATACAT
1 TGTATCGATACAT
6031 ACTTGCTGTA
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:12286 original size:242 final size:243
Alignment explanation
Indices: 11860--12337 Score: 886
Period size: 242 Copynumber: 2.0 Consensus size: 243
11850 GAATATCTAG
*
11860 TTTTCAAAGTGAAATCGAGAGAGCATTTTTACGTCTCTATGTTTCCCATTTCTCCGGGGCGCATA
1 TTTTCAAAGTGAAATCCAGAGAGCATTTTTACGTCTCTATGTTTCCCATTTCTCCGGGGCGCATA
11925 TGAGATTAAAATTTTATCAAAACCTGGATTTATTTTTTCACAAAATTCATGCATTCAAAGGGGAT
66 TGAGATTAAAATTTTATCAAAACCTGGATTTATTTTTTCACAAAATTCATGCATTCAAAGGGGAT
* * *
11990 CATATTGAAATAATGATAAATCGAAACTAATGTAATCAACATTAAGTCAAAACATTGCTAGTAAG
131 CATATCGAAATAATGATAAATCGAAACCAATGTAATCAACATTAAGTCAAAACATTACTAGTAAG
* *
12055 GTACCAATTTCGGGCGTCGCAAGGAGGTTCGTACCTCTTTGTTCCCCA
196 GTACCAATTTCGGGCATCACAAGGAGGTTCGTACCTCTTTGTTCCCCA
*
12103 TTTTCAAAGTGAAATCCAGAGAGCA-TTTTATGTCTCTATGTTTCCCATTTCTCCGGGGCGCATA
1 TTTTCAAAGTGAAATCCAGAGAGCATTTTTACGTCTCTATGTTTCCCATTTCTCCGGGGCGCATA
12167 TGAGATTAAAATTTTATCAAAACCTGGATTTATTTTTTCACAAAATTCATGCATTCAAAGGGGAT
66 TGAGATTAAAATTTTATCAAAACCTGGATTTATTTTTTCACAAAATTCATGCATTCAAAGGGGAT
12232 CATATCGAAATAATGATAAATCGAAACCAATGTAATCAACATTAAGTCAAAACATTACTAGTAAG
131 CATATCGAAATAATGATAAATCGAAACCAATGTAATCAACATTAAGTCAAAACATTACTAGTAAG
12297 GTACCAATTTCGGGCATCACAAGGAGGTTCGTACCTCTTTG
196 GTACCAATTTCGGGCATCACAAGGAGGTTCGTACCTCTTTG
12338 CGCGTAACCA
Statistics
Matches: 228, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
242 204 0.89
243 24 0.11
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (243 bp):
TTTTCAAAGTGAAATCCAGAGAGCATTTTTACGTCTCTATGTTTCCCATTTCTCCGGGGCGCATA
TGAGATTAAAATTTTATCAAAACCTGGATTTATTTTTTCACAAAATTCATGCATTCAAAGGGGAT
CATATCGAAATAATGATAAATCGAAACCAATGTAATCAACATTAAGTCAAAACATTACTAGTAAG
GTACCAATTTCGGGCATCACAAGGAGGTTCGTACCTCTTTGTTCCCCA
Found at i:14125 original size:13 final size:13
Alignment explanation
Indices: 14107--14131 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14097 CATTTTATGG
14107 TGTATCGATACAA
1 TGTATCGATACAA
14120 TGTATCGATACA
1 TGTATCGATACA
14132 TACTGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14147 original size:32 final size:33
Alignment explanation
Indices: 14084--14151 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
14074 CGTTATAAGC
**
14084 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
14117 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
14149 CAA
1 CAA
14152 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:16224 original size:21 final size:21
Alignment explanation
Indices: 16193--16244 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
16183 GCGACTAGTG
*
16193 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGG-TGCCCGGTCGCGACC
16215 TGGGGGTG-CCGGTCGCGACC
1 TGGGGGTGCCCGGTCGCGACC
16235 TGGTGGGTGC
1 TGG-GGGTGC
16245 TGCCTAGGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 14 0.52
21 7 0.26
22 6 0.22
ACGTcount: A:0.04, C:0.27, G:0.50, T:0.19
Consensus pattern (21 bp):
TGGGGGTGCCCGGTCGCGACC
Found at i:16537 original size:20 final size:21
Alignment explanation
Indices: 16508--16548 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
16498 TGTTTTTGAT
16508 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
16527 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
16549 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:33378 original size:18 final size:18
Alignment explanation
Indices: 33355--33391 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
33345 CGTCATCCGC
*
33355 CAAAAAAAAACACAACAAA
1 CAAAAATAAA-ACAACAAA
33374 CAAAAATAAAACAACAAA
1 CAAAAATAAAACAACAAA
33392 AAAGGTCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.78, C:0.19, G:0.00, T:0.03
Consensus pattern (18 bp):
CAAAAATAAAACAACAAA
Found at i:34836 original size:29 final size:29
Alignment explanation
Indices: 34790--35266 Score: 603
Period size: 28 Copynumber: 16.8 Consensus size: 29
34780 AGACATTCCT
*
34790 CACC-TTT-AAAAGCTCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGG
*
34817 CATCTTTTCAAAAGCCCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGG
34846 CACCCTTTTCAAAAGCCCACAAGTCAGTGG
1 CA-CCTTTTCAAAAGCCCACAAGTCAGTGG
34876 CAACC--TTCAAAAGCCCACAAGTCAGTGG
1 C-ACCTTTTCAAAAGCCCACAAGTCAGTGG
34904 CACCCTTTTCAAAAGCCCACAAGTCAGTGG
1 CA-CCTTTTCAAAAGCCCACAAGTCAGTGG
*
34934 CACCTTTTC-AAAGCTCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGG
* *
34962 CACCGTTTC-AAAGCCCAAAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGG
*
34990 CAACC--TTCAAAAGCCCACAAGTTAGTGG
1 C-ACCTTTTCAAAAGCCCACAAGTCAGTGG
*
35018 CATCTTTTCAAAAGCCCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGG
*
35047 CAACC--TTCAAAAGCCCACAAGTTAGTGG
1 C-ACCTTTTCAAAAGCCCACAAGTCAGTGG
*
35075 CATCTTTTCAAAAGCCCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGG
35104 CACCCTTTTCAAAAGCCCACAAGTCAGTGG
1 CA-CCTTTTCAAAAGCCCACAAGTCAGTGG
35134 CACCTTTTC-AAAGCCCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGG
* *
35162 CACCCCTTTC-AAAGCCCATAAGTCAGTGG
1 CA-CCTTTTCAAAAGCCCACAAGTCAGTGG
* * *
35191 CAACC--TTCAAAAACCCACAAATTAGTGG
1 C-ACCTTTTCAAAAGCCCACAAGTCAGTGG
* *
35219 CACCTTTTC-AAAGCCCACAAGTTAATGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGG
35247 CAACC--TTC-AAAGCCCACAAG
1 C-ACCTTTTCAAAAGCCCACAAG
35267 GTAGTGACAA
Statistics
Matches: 404, Mismatches: 25, Indels: 42
0.86 0.05 0.09
Matches are distributed among these distances:
27 32 0.08
28 168 0.42
29 118 0.29
30 85 0.21
31 1 0.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.20
Consensus pattern (29 bp):
CACCTTTTCAAAAGCCCACAAGTCAGTGG
Found at i:35041 original size:57 final size:57
Alignment explanation
Indices: 34790--35295 Score: 583
Period size: 57 Copynumber: 8.9 Consensus size: 57
34780 AGACATTCCT
* * *
34790 CACC-TTT-AAAAGCTCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGG
34846 CACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGG
1 CA-CCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGG
*
34904 CACCCTTTTCAAAAGCCCACAAGTCAGTGGC-ACCTTTTC-AAAGCTCACAAGTCAGTGG
1 CA-CCTTTTCAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTCAGTGG
* * *
34962 CACCGTTTC-AAAGCCCAAAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGG
* *
35018 CATCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGG
* *
35075 CATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTCAGTGG
* *
35134 CACCTTTTC-AAAGCCCACAAGTCAGTGGCACCCCTTTC-AAAGCCCATAAGTCAGTGG
1 CACCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACC-TTCAAAAGCCCACAAGTCAGTGG
* * * * *
35191 CAACC--TTCAAAAACCCACAAATTAGTGGC-ACCTTTTC-AAAGCCCACAAGTTAATGG
1 C-ACCTTTTCAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTCAGTGG
* * * *
35247 CAACC--TTC-AAAGCCCACAAGGT-AGTGACAATCTTCAAATGCACACAAGT
1 C-ACCTTTTCAAAAGCCCACAA-GTCAGTGGCAACCTTCAAAAGCCCACAAGT
35296 TGGTGGCATC
Statistics
Matches: 405, Mismatches: 28, Indels: 35
0.87 0.06 0.07
Matches are distributed among these distances:
54 3 0.01
55 31 0.08
56 79 0.20
57 129 0.32
58 105 0.26
59 58 0.14
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.21
Consensus pattern (57 bp):
CACCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGG
Found at i:35424 original size:49 final size:49
Alignment explanation
Indices: 35307--35576 Score: 293
Period size: 49 Copynumber: 5.6 Consensus size: 49
35297 GGTGGCATCT
*
35307 TCTTCTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCA----C-
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCA
* * *
35352 -CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACTTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCA
35400 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-C--TTTCA
* * * **
35452 TCTTCAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCA
* * * * *
35501 TCTTCAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCA-TCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACT-TTCA
* * *
35550 TTTTTAAGTCCGATATCGTTGGCCTTG
1 TCTTTAAGTCCAATATCGCTGGCCTTG
35577 TCTCAGTACA
Statistics
Matches: 189, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
43 35 0.19
44 3 0.02
47 1 0.01
49 103 0.54
50 1 0.01
51 1 0.01
52 45 0.24
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCA
Found at i:35588 original size:49 final size:49
Alignment explanation
Indices: 35356--35621 Score: 255
Period size: 49 Copynumber: 5.3 Consensus size: 49
35346 TGGCACCTTT
* * *
35356 AAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATC-TTCATCTTC
* *
35405 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTTC
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCATCTTC
* * * * *
35457 AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCGTCATCTTC
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTC
* * * * *
35506 AAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCATCTTCATTTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTC
* * ** * *
35555 AAGTCCGATATCGTTGGCCTTGTCTCAGTACATTGTCATTCTTCGCATCTTC
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-TCTT--CATCTTC
* *
35607 GAGCCCAATATCGCT
1 AAGTCCAATATCGCT
35622 AGCTACATAT
Statistics
Matches: 176, Mismatches: 34, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
49 112 0.64
50 4 0.02
52 60 0.34
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (49 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTC
Found at i:35604 original size:150 final size:143
Alignment explanation
Indices: 35307--35624 Score: 379
Period size: 150 Copynumber: 2.2 Consensus size: 143
35297 GGTGGCATCT
* * * *
35307 TCTTCTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTG
1 TCTTC-AAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTAAGACCAATGTCGCTA
*
35372 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
65 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACA
*
35437 TTGGCACCTTTTTCA
130 TTGGCA-CTTTTGCA
* *
35452 TCTTCAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCGTCATCTTCAAGACCAATGT
1 TCTTCAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCA-C--C-T-TT-AAGACCAATGT
* * * **
35517 CGCTAGCCTTGAATCAGCACATTGGCA-TCTTCATTTTTAAGTCCGATATCGTTGGCCTTGTCTC
60 CGCTAGCCTTGAATCAGCACATTGGCACT-TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATC
* *
35581 AGTACATTGTCA-TTCTTCGCA
124 AGCACATTGGCACTT-TT-GCA
*
35602 TCTTCGAGCCCAATATCGCTAGC
1 TCTTCAAGCCCAATATCGCTAGC
35625 TACATATTAG
Statistics
Matches: 146, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
144 35 0.24
145 6 0.04
147 1 0.01
148 3 0.02
149 5 0.03
150 96 0.66
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (143 bp):
TCTTCAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTAAGACCAATGTCGCTAG
CCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
TGGCACTTTTGCA
Found at i:35606 original size:101 final size:99
Alignment explanation
Indices: 35307--35576 Score: 286
Period size: 101 Copynumber: 2.8 Consensus size: 99
35297 GGTGGCATCT
* * *
35307 TCTTCTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCA--C--C-T-TT-AAGTCCAAT
1 TCTTC-AAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCACTCTTCATCTTCAAGCCCAAT
* * * **
35365 GTTGCTGGCCTTGAATCAGCACATTGGCACTTTCA
65 ATCGTTGGCCTTGAATCAGCACATTGGCACCGTCA
* * * * *
35400 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTTCAAGCCCAA
1 TCTTCAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCA-C-TCTTCATCTTCAAGCCCAA
*
35465 TATCGTTGGCCTTGAATCAGCATATTGGCACCGTCA
64 TATCGTTGGCCTTGAATCAGCACATTGGCACCGTCA
* * * * *
35501 TCTTCAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCA-TCTTCATTTTTAAGTCCGATA
1 TCTTCAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCACTCTTCATCTTCAAGCCCAATA
35565 TCGTTGGCCTTG
66 TCGTTGGCCTTG
35577 TCTCAGTACA
Statistics
Matches: 148, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
92 37 0.25
93 4 0.03
98 29 0.20
99 1 0.01
100 2 0.01
101 75 0.51
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (99 bp):
TCTTCAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCACTCTTCATCTTCAAGCCCAATA
TCGTTGGCCTTGAATCAGCACATTGGCACCGTCA
Found at i:36420 original size:13 final size:13
Alignment explanation
Indices: 36402--36446 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
36392 CATTATTCAA
36402 TGTATCGATACAT
1 TGTATCGATACAT
36415 TGTATCGATACAT
1 TGTATCGATACAT
* *
36428 TATATTGATACAT
1 TGTATCGATACAT
36441 TG-ATCG
1 TGTATCG
36447 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 3 0.11
13 25 0.89
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:36424 original size:33 final size:33
Alignment explanation
Indices: 36382--36511 Score: 99
Period size: 33 Copynumber: 4.0 Consensus size: 33
36372 GCCAAGGAAA
36382 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
** ** * *
36415 TGTATCGATACATTATATTGATACATTGAT-CGT
1 TGTATCGATACATTAT-TCAATGTATCGATACAT
** * *
36448 TGTATCGATACATCTA-GGAATTTTATC--TAGA-
1 TGTATCGATACAT-TATTCAA-TGTATCGATACAT
*
36479 TGTATCGATACATTATTCAATGTATTGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
36512 GCAGGCAAAT
Statistics
Matches: 70, Mismatches: 19, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
30 6 0.09
31 16 0.23
32 4 0.06
33 34 0.49
34 10 0.14
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAT
Found at i:39973 original size:154 final size:153
Alignment explanation
Indices: 39677--40031 Score: 407
Period size: 154 Copynumber: 2.3 Consensus size: 153
39667 CGTTGCGACA
* * * *
39677 GATACCTTCGACATAAAAGTACCCGATACCCCTAAAAGACTTAAAAAGTTTGAAAGAGGATGAAC
1 GATACCTTCGACGTAAAAGTACTCGATATCCTTAAAAGACTTAAAAAGTTTGAAAGAGGATGAAC
* * * * * *
39742 CTATCCTAACTGCCCATCTTTGGCATAAAAATGGACCTAGCAGCAACCTAGTAGCTGGTTTTGAA
66 CTATCCTAACTGCCCACCTTTGGCATAAAAACGGACCCAACAGCAACCTAGTAGCTAGTTTTCAA
***
39807 AAATTTTGAAAATGCCCCTAGGG
131 AAATTACAAAAATGCCCCTAGGG
* * ** * *
39830 GATATCTTTGATTTAAAAGTACTCGATATCCTTAAAGGACTTAAAATGGTTTGAAATG-GGATGA
1 GATACCTTCGACGTAAAAGTACTCGATATCCTTAAAAGACTTAAAA-AGTTTGAAA-GAGGATGA
* *
39894 ACCTATCCTAATTGCCCACCTTTGGCATAAAAACGGACCCAAC-GACAACCTAAG-AGTTAG-TT
64 ACCTATCCTAACTGCCCACCTTTGGCATAAAAACGGACCCAACAG-CAACCT-AGTAGCTAGTTT
39956 TCAAAATATTACAAAAATGCCCCTAGGG
127 TCAAAA-ATTACAAAAATGCCCCTAGGG
*
39984 GATACCTTCGACGTAAAAGTACTTGAT-TCCCTTAAAA-ACCTTAAAAAG
1 GATACCTTCGACGTAAAAGTACTCGATAT-CCTTAAAAGA-CTTAAAAAG
40032 GATAATAGAT
Statistics
Matches: 168, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
153 49 0.29
154 116 0.69
155 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (153 bp):
GATACCTTCGACGTAAAAGTACTCGATATCCTTAAAAGACTTAAAAAGTTTGAAAGAGGATGAAC
CTATCCTAACTGCCCACCTTTGGCATAAAAACGGACCCAACAGCAACCTAGTAGCTAGTTTTCAA
AAATTACAAAAATGCCCCTAGGG
Found at i:40812 original size:161 final size:162
Alignment explanation
Indices: 40562--40959 Score: 591
Period size: 161 Copynumber: 2.5 Consensus size: 162
40552 AATATAAAAG
* * * * * * *
40562 ATTAAAATTTTTCTCAAAAATAGCAATTCAATTTAATTTTATTGATTTTCAAAAATACCATTTCG
1 ATTAGAATTTATCCCAAGAATACCAATTTAATTTAATTTTATTTATTTTCAAAAATACCATTTCG
** * * *
40627 TGCCCTAATGGAAGCCCGAAAGAATACTAAAGGTTTCTGAAATCTTTTATACCCCTACGGATACC
66 TATCCTAATGAAAGCCCAAAAGAATACGAAAGGTTTCTGAAATCTTTTATACCCCTACGGATACC
40692 CATAGGAATACAAAAGATTAGAAAAAATAAAT
131 CATAGGAATACAAAAGATTAGAAAAAATAAAT
* * * *
40724 ATTAGAATTTATCCCAAGAATACTAATTTAATTTAATTTAATTTATTTTC-GAAATACGATTTCG
1 ATTAGAATTTATCCCAAGAATACCAATTTAATTTAATTTTATTTATTTTCAAAAATACCATTTCG
* * * * *
40788 TATCATAATGAAAGCCTAAAAGAATACGAAAGGTTTTTGAAATCTTTTATACCCTTACGGATGCC
66 TATCCTAATGAAAGCCCAAAAGAATACGAAAGGTTTCTGAAATCTTTTATACCCCTACGGATACC
40853 CATAGGAATACAAAAGATTAGAAAAAATAAAT
131 CATAGGAATACAAAAGATTAGAAAAAATAAAT
*
40885 ATTAGAATTTATCCCAAGAATACCAATTTAATTTAATTTTATTTATTTTCAAAAATACCATTTTG
1 ATTAGAATTTATCCCAAGAATACCAATTTAATTTAATTTTATTTATTTTCAAAAATACCATTTCG
40950 TATCCTAATG
66 TATCCTAATG
40960 GAAGTGTAGA
Statistics
Matches: 208, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
161 147 0.71
162 61 0.29
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (162 bp):
ATTAGAATTTATCCCAAGAATACCAATTTAATTTAATTTTATTTATTTTCAAAAATACCATTTCG
TATCCTAATGAAAGCCCAAAAGAATACGAAAGGTTTCTGAAATCTTTTATACCCCTACGGATACC
CATAGGAATACAAAAGATTAGAAAAAATAAAT
Found at i:41792 original size:20 final size:20
Alignment explanation
Indices: 41767--41824 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
41757 TTTTTACCCA
41767 AATGTATAGATACATTTTTC
1 AATGTATAGATACATTTTTC
41787 AATGTATAGATACATTTTTC
1 AATGTATAGATACATTTTTC
*
41807 AATGTATAGATATATTTT
1 AATGTATAGATACATTTT
41825 GTCTTTTACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (20 bp):
AATGTATAGATACATTTTTC
Found at i:41863 original size:50 final size:51
Alignment explanation
Indices: 41788--41922 Score: 209
Period size: 51 Copynumber: 2.7 Consensus size: 51
41778 ACATTTTTCA
* * * * *
41788 ATGTATAGATACATTTTTCAATGTATAGATATATTTTGTC-TTTTACCCAG
1 ATGTATCGATACATTTTTCAATGTATTGATACATTCTATCTTTTTACCCAG
*
41838 ATGTATCGATACATTTTTCAATGTATTGATACGTTCTATCTTTTTACCCAG
1 ATGTATCGATACATTTTTCAATGTATTGATACATTCTATCTTTTTACCCAG
41889 ATGTATCGATACATTTTTCAATGTATTGATACAT
1 ATGTATCGATACATTTTTCAATGTATTGATACAT
41923 CTAGTTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 34 0.44
51 43 0.56
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (51 bp):
ATGTATCGATACATTTTTCAATGTATTGATACATTCTATCTTTTTACCCAG
Found at i:55503 original size:17 final size:16
Alignment explanation
Indices: 55474--55525 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
55464 CCTTCATACC
*
55474 AAAATAAAACAAAAAA
1 AAAAAAAAACAAAAAA
*
55490 AAAAAAAAACCAAAAA
1 AAAAAAAAACAAAAAA
* * *
55506 ACAAACAATCAAAAATA
1 AAAAAAAAACAAAAA-A
55523 AAA
1 AAA
55526 GGGTCTAGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.83, C:0.12, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAAAAAAACAAAAAA
Found at i:56792 original size:13 final size:12
Alignment explanation
Indices: 56715--56796 Score: 58
Period size: 14 Copynumber: 6.3 Consensus size: 12
56705 CCAATTCACC
56715 ATTTGTCAAGAA
1 ATTTGTCAAGAA
56727 ATGGTTGTCAAGAA
1 AT--TTGTCAAGAA
*
56741 ATTATCATCAAGAA
1 ATT-T-GTCAAGAA
* *
56755 CTTCTGTCGAGAA
1 ATT-TGTCAAGAA
*
56768 TGTTTGTC-AGAA
1 -ATTTGTCAAGAA
56780 ACTTTGTCAAGAA
1 A-TTTGTCAAGAA
56793 ATTT
1 ATTT
56797 TTATCAATAC
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
12 16 0.29
13 16 0.29
14 24 0.43
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (12 bp):
ATTTGTCAAGAA
Found at i:56845 original size:28 final size:28
Alignment explanation
Indices: 56811--57536 Score: 815
Period size: 28 Copynumber: 25.6 Consensus size: 28
56801 CAATACGACC
56811 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
56839 CATTTCAAAGCCTACAAGTTAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*
56867 CCTTTCAAAGCCCATAAGGT-AGTGGCAT
1 CCTTTCAAAGCCCACAA-GTCAGTGGCAT
*
56895 CCTTTCAAAGCCCATAAGGT-AGTGGCAT
1 CCTTTCAAAGCCCACAA-GTCAGTGGCAT
*
56923 CCTTTCAAAGCCCACAAGTTAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*
56951 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
56979 CCTTTCAAAGCCTACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
57007 CCTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CC-TTTCAAAGCCCACAAGTCAGTGGCAT
* *
57036 ACCCTTTCAAAGCCCATAAGTC-GATGGCAC
1 --CCTTTCAAAGCCCACAAGTCAG-TGGCAT
*
57066 CCTTTCAAA-CACCACAAGACAGTGGCAT
1 CCTTTCAAAGC-CCACAAGTCAGTGGCAT
* *
57094 CCTTTTAAAGCCCATAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
57122 CATTTCAAAGCCTACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
57150 CCTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CC-TTTCAAAGCCCACAAGTCAGTGGCAT
* * *
57179 ACCCTTTCAAAACCCACAAGTC-GATCGCAC
1 --CCTTTCAAAGCCCACAAGTCAG-TGGCAT
* *
57209 CCTTTCAAA-CCCAGCATGACAGTGGCAT
1 CCTTTCAAAGCCCA-CAAGTCAGTGGCAT
* *
57237 CCTTTCATAGCCCACAAGTTAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
57265 CATTTCAAAGCCCACAAGTTAGTGGCA-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
57292 CCATTTCGAAGCCCATAAGTTAGTGGCA-
1 CC-TTTCAAAGCCCACAAGTCAGTGGCAT
** * *
57320 CCATTTTGAAGCCCAAAAGTTAGTGGCAT
1 CC-TTTCAAAGCCCACAAGTCAGTGGCAT
* *
57349 ACTTTCAAAACCCACAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*
57377 CCTTTCAAAGCCCACAATTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
57405 CCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
57432 CTATTTCAAAGCCCACAAGTTAATGGCAT
1 C-CTTTCAAAGCCCACAAGTCAGTGGCAT
*
57461 CAC-TTCAAAGCCCACAAGTTAGTGGCAT
1 C-CTTTCAAAGCCCACAAGTCAGTGGCAT
* *
57489 CCTTTCAAAGCCCACACAAGTCATTGGTAACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGG-CA-T
*
57521 CTTTTCAAAGCCCACA
1 CCTTTCAAAGCCCACA
57537 CAAGTTAGTG
Statistics
Matches: 607, Mismatches: 66, Indels: 48
0.84 0.09 0.07
Matches are distributed among these distances:
27 10 0.02
28 459 0.76
29 63 0.10
30 58 0.10
31 7 0.01
32 10 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (28 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:57675 original size:45 final size:48
Alignment explanation
Indices: 57624--57732 Score: 134
Period size: 49 Copynumber: 2.3 Consensus size: 48
57614 AAGTTCGATA
* *
57624 TCGCTGGCATTGAATCAACATATTGG-CAC-CTTT-ATTAGCCCAATG
1 TCGCTGGCCTTGAATCAACACATTGGCCACTCTTTGATTAGCCCAATG
* * *
57669 TCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTTGCTTAGCCCAATG
1 TCGCTGGCCTTGAATCAACACATTGG-CCACTCTTTGATTAGCCCAATG
*
57718 TCTCTGGCCTTGAAT
1 TCGCTGGCCTTGAAT
57733 TGGCACATTG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
45 23 0.43
47 3 0.06
48 3 0.06
49 25 0.46
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (48 bp):
TCGCTGGCCTTGAATCAACACATTGGCCACTCTTTGATTAGCCCAATG
Found at i:58767 original size:20 final size:20
Alignment explanation
Indices: 58742--58779 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58732 TTTTTACCCA
*
58742 AATGTATTGATACATTTTTC
1 AATGTATCGATACATTTTTC
58762 AATGTATCGATACATTTT
1 AATGTATCGATACATTTT
58780 GCCTTTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:58797 original size:30 final size:31
Alignment explanation
Indices: 58763--58842 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 31
58753 ACATTTTTCA
58763 ATGTATCGATACATTTTG-CCTTTTACCCAG
1 ATGTATCGATACATTTTGTCCTTTTACCCAG
**
58793 ATGTATCGATACATATTCTGTTTTTTTACCCAG
1 ATGTATCGATACAT-TT-TGTCCTTTTACCCAG
58826 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
58843 TCAATGTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
30 14 0.31
31 3 0.07
32 4 0.09
33 24 0.53
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (31 bp):
ATGTATCGATACATTTTGTCCTTTTACCCAG
Found at i:63168 original size:13 final size:13
Alignment explanation
Indices: 63150--63175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63140 TACACCAAGT
63150 ATGTATCGATACA
1 ATGTATCGATACA
63163 ATGTATCGATACA
1 ATGTATCGATACA
63176 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:63173 original size:32 final size:33
Alignment explanation
Indices: 63132--63195 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
63122 TAGCCAAACT
* **
63132 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
63164 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
63196 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:67267 original size:15 final size:15
Alignment explanation
Indices: 67247--67277 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
67237 TAAAAATGTC
*
67247 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
67262 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
67277 C
1 C
67278 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:69366 original size:13 final size:13
Alignment explanation
Indices: 69348--69385 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
69338 CATTTTTCTT
69348 TGTATCGATACAA
1 TGTATCGATACAA
* *
69361 TGTATCAATACAC
1 TGTATCGATACAA
69374 TGTATCGATACA
1 TGTATCGATACA
69386 GGGGGATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:71972 original size:13 final size:13
Alignment explanation
Indices: 71954--71979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71944 TACACCAAGT
71954 ATGTATCGATACA
1 ATGTATCGATACA
71967 ATGTATCGATACA
1 ATGTATCGATACA
71980 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:71977 original size:32 final size:33
Alignment explanation
Indices: 71936--71999 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
71926 TAGCCAAACT
* **
71936 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
71968 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
72000 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:73415 original size:165 final size:160
Alignment explanation
Indices: 73230--73756 Score: 460
Period size: 165 Copynumber: 3.2 Consensus size: 160
73220 ATGGGATTTC
*
73230 AATGACAATATTATATGAATTTTAAAAATTTTAAACTGAGAAAAATCCTCCCAAAAAAATTTAAA
1 AATGACAATATTAGATGAATTTTAAAAATTTTAAACT-AGAAAAATCC-CCCAAAAAAATTTAAA
*
73295 AAGAAGAAAACTTCGTTTCTCGAGAAAAAAG-ATTTCAAAGAAAAAATTC-AAAACTCTTGAAAA
64 AAGAAGAAAAC-TCGTTT-TCGA-AAAAAAGAATTTCAAAGAAAAAATTCAAAAACTCATGAAAA
* * **
73358 TGAATTAATTTTTCAAAACTGAATAAAATTTGAGTTT
126 TGAATTAATTTTTAAAAACTG-ATAAAATATGA-AAT
** * **
73395 AATGACAATATTAGATGAATTTTAAAAATTTTAAATCTAGAAACCTCCCCCCTCGAAAACCTTT-
1 AATGACAATATTAGATGAATTTTAAAAATTTTAAA-CTAGAAAAAT--CCCC-CAAAAAAATTTA
*** *
73459 ATGGGAAAGAAAACTCGGTTTTTCGAAAAAAAGAAAATTTCAAGGAAAAAATTCAAAAACTCATG
62 AAAAG-AAGAAAACTC-G-TTTTCGAAAAAAAG--AATTTCAAAGAAAAAATTCAAAAACTCATG
* **
73524 AAAATAAATT-ATTTTTAAAAACTGATTCAATATGAAAT
122 AAAATGAATTAATTTTTAAAAACTGATAAAATATGAAAT
* ** * *
73562 AA-G-CAATGATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCTCAAAAAAAATTA
1 AATGAC-A--ATATTAGATGAATTTTAAAAATTTTAAACT-AGAAAAATCCCCCAAAAAAATTTA
* * *
73625 CAAAGTAGAAAACAACGTATTTCGAAAAAAGAAGAATTTC-AAGAAAAAATTCAAAAACTCATGA
62 AAAAGAAGAAAAC-TCGT-TTTCG-AAAAA-AAGAATTTCAAAGAAAAAATTCAAAAACTCATGA
* * **
73689 AAATGAGTTAATTTTTGAAAAA-AGATTTAATAT-AAAT
123 AAATGAATTAATTTTT-AAAAACTGATAAAATATGAAAT
* * *
73726 AAATAATAATATTTGATGAATTTTAAAAATT
1 -AATGACAATATTAGATGAATTTTAAAAATT
73757 AAAAATAAAA
Statistics
Matches: 296, Mismatches: 41, Indels: 51
0.76 0.11 0.13
Matches are distributed among these distances:
164 58 0.20
165 84 0.28
166 33 0.11
167 31 0.10
168 42 0.14
169 30 0.10
170 18 0.06
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (160 bp):
AATGACAATATTAGATGAATTTTAAAAATTTTAAACTAGAAAAATCCCCCAAAAAAATTTAAAAA
GAAGAAAACTCGTTTTCGAAAAAAAGAATTTCAAAGAAAAAATTCAAAAACTCATGAAAATGAAT
TAATTTTTAAAAACTGATAAAATATGAAAT
Found at i:73684 original size:164 final size:163
Alignment explanation
Indices: 73479--73781 Score: 461
Period size: 164 Copynumber: 1.9 Consensus size: 163
73469 AAACTCGGTT
73479 TTTCGAAAAAAAGAAAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATAAATT-ATTTTT-AA
1 TTTCGAAAAAAAGAAAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATAAATTAATTTTTGAA
* * *
73542 AAACTGATTCAATATGAAATAAGCAATGATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAA
66 AAA-AGATTCAATAT-AAATAAACAATAATATTTGATGAATTTTAAAAATTAAAAA-TAA-AAAA
73607 ATCCCTCAAAAAAAATTACAAAGTAGAAAACAACGTA
127 ATCCCTCAAAAAAAATTACAAAGTAGAAAACAACGTA
* *
73644 TTTCG-AAAAAAGAAGAATTTCAA-GAAAAAATTCAAAAACTCATGAAAATGAGTTAATTTTTGA
1 TTTCGAAAAAAAGAA-AATTTCAAGGAAAAAATTCAAAAACTCATGAAAATAAATTAATTTTTGA
* *
73707 AAAAAGATTTAATATAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAATAAAAAAATC
65 AAAAAGATTCAATATAAATAAACAATAATATTTGATGAATTTTAAAAATTAAAAATAAAAAAATC
*
73772 TCTCAAAAAA
130 CCTCAAAAAA
73782 TTTACAGAGA
Statistics
Matches: 127, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
162 16 0.13
163 3 0.02
164 75 0.59
165 28 0.22
166 5 0.04
ACGTcount: A:0.56, C:0.08, G:0.09, T:0.28
Consensus pattern (163 bp):
TTTCGAAAAAAAGAAAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATAAATTAATTTTTGAA
AAAAGATTCAATATAAATAAACAATAATATTTGATGAATTTTAAAAATTAAAAATAAAAAAATCC
CTCAAAAAAAATTACAAAGTAGAAAACAACGTA
Found at i:73835 original size:164 final size:165
Alignment explanation
Indices: 73236--73781 Score: 454
Period size: 164 Copynumber: 3.3 Consensus size: 165
73226 TTTCAATGAC
** * * * *
73236 AATATTAT-ATGAATTTTAAAAATTTTAAACTGAGAAAAATCCTCCCAAAAAAATTTAAAAAGAA
1 AATATT-TGATGAATTTTAAAAATTAAAAACTAAGAAAAATCC-CTCAAAAAAAATTACAAAGAA
** * * *
73300 GAAAACTTCGT-TTCTCGAGAAAA-AAG-ATTTCAAAGAAAAAATTC-AAAACTCTTGAAAATGA
64 GAAAACAACGTATT-TCGAAAAAAGAAGAATTTCAAAGAAAAAATTCAAAAACTCATGAAAATAA
* * ** * ** * ** *
73361 ATTAATTTTTCAAAACTGAATAAAATTTGAGTTTAATGAC
128 ATT-ATTTTTAAAAACAG-ATTCAATATGAAATAAACAAT
* * * ** * *** ***
73401 AATATTAGATGAATTTTAAAAATTTTAAATCT-AGAAACCTCCCCCCTCGAAAACCTTTA-TGGG
1 AATATTTGATGAATTTTAAAAA-TTAAAAACTAAGAAAAAT---CCCTCAAAAAAAATTACAAAG
* * *
73464 AAAGAAAAC-TCGGTTTTTCGAAAAAAAGAA-AATTTCAAGGAAAAAATTCAAAAACTCATGAAA
62 -AAGAAAACAAC-GTATTTCG-AAAAAAGAAGAATTTCAAAGAAAAAATTCAAAAACTCATGAAA
* *
73527 ATAAATTATTTTTAAAAACTGATTCAATATGAAATAAGCAAT
124 ATAAATTATTTTTAAAAACAGATTCAATATGAAATAAACAAT
* *
73569 GATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCTCAAAAAAAATTACAAAGTAGA
1 AATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCTCAAAAAAAATTACAAAGAAGA
* *
73634 AAACAACGTATTTCGAAAAAAGAAGAATTTC-AAGAAAAAATTCAAAAACTCATGAAAATGAGTT
66 AAACAACGTATTTCGAAAAAAGAAGAATTTCAAAGAAAAAATTCAAAAACTCATGAAAATAAATT
* *
73698 AATTTTTGAAAAA-AGATTTAATAT-AAATAAATAAT
131 -ATTTTT-AAAAACAGATTCAATATGAAATAAACAAT
*
73733 AATATTTGATGAATTTTAAAAATTAAAAA-TAA-AAAAATCTCTCAAAAAA
1 AATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCTCAAAAAA
73782 TTTACAGAGA
Statistics
Matches: 311, Mismatches: 52, Indels: 39
0.77 0.13 0.10
Matches are distributed among these distances:
162 16 0.05
163 3 0.01
164 76 0.24
165 73 0.23
166 17 0.05
167 30 0.10
168 46 0.15
169 32 0.10
170 18 0.06
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (165 bp):
AATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCTCAAAAAAAATTACAAAGAAGA
AAACAACGTATTTCGAAAAAAGAAGAATTTCAAAGAAAAAATTCAAAAACTCATGAAAATAAATT
ATTTTTAAAAACAGATTCAATATGAAATAAACAAT
Found at i:80210 original size:36 final size:36
Alignment explanation
Indices: 80163--80236 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
80153 ATGAAATGAA
*
80163 AGTAAGATGGATAAAAAAATTATTGTTTTCAACAAT
1 AGTAAGATGGATAAAAAAATTATTATTTTCAACAAT
80199 AGTAAGATGGATAAAAAAATTATTATTTTCAACAAT
1 AGTAAGATGGATAAAAAAATTATTATTTTCAACAAT
80235 AG
1 AG
80237 GTGTTAGGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (36 bp):
AGTAAGATGGATAAAAAAATTATTATTTTCAACAAT
Found at i:82537 original size:35 final size:35
Alignment explanation
Indices: 82498--82568 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
82488 TTTCATTTGA
*
82498 TTCAAGATCAAGTCTCAAAGAACCTTGAAGCAAAT
1 TTCAAGATCAAGTCTCAAAGAACCTTGAAACAAAT
* * *
82533 TTCAAGATCAAGTTTCCAAGACCCTTGAAACAAAT
1 TTCAAGATCAAGTCTCAAAGAACCTTGAAACAAAT
82568 T
1 T
82569 GAAGTCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (35 bp):
TTCAAGATCAAGTCTCAAAGAACCTTGAAACAAAT
Found at i:82561 original size:79 final size:77
Alignment explanation
Indices: 82399--82562 Score: 177
Period size: 79 Copynumber: 2.1 Consensus size: 77
82389 AATAGAAAAT
* * **
82399 CCTTGAAATTGATCTCATTGATTCAAGATTAAGTCTTGAAAACCTTAAAAGAAATCTCAAGATCA
1 CCTTGAAATAGATCTCATTGATTCAAGATCAAGTCTCAAAAACCTTAAAAGAAATCTCAAGATCA
* *
82464 AGTCTAGAATAC
66 AGTCTACAAGAC
* * * * *
82476 CTTTGAAGTAGATTTCATTTGATTCAAGATCAAGTCTCAAAGAACCTT-GAAGCAAATTTCAAGA
1 CCTTGAAATAGATCTCA-TTGATTCAAGATCAAGTCTCAAA-AACCTTAAAAG-AAATCTCAAGA
* *
82540 TCAAGTTTCCAAGAC
63 TCAAGTCTACAAGAC
82555 CCTTGAAA
1 CCTTGAAA
82563 CAAATTGAAG
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
77 13 0.19
78 23 0.33
79 33 0.48
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (77 bp):
CCTTGAAATAGATCTCATTGATTCAAGATCAAGTCTCAAAAACCTTAAAAGAAATCTCAAGATCA
AGTCTACAAGAC
Done.