Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017625.1 Corchorus olitorius cultivar O-4 contig17658, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 173177
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:503 original size:22 final size:22
Alignment explanation
Indices: 475--626 Score: 142
Period size: 22 Copynumber: 6.5 Consensus size: 22
465 CAACAAGAAG
475 TGCTCTGCAAAGTGGAAAATAA
1 TGCTCTGCAAAGTGGAAAATAA
***
497 TGCTCTGCAAAGATGTTTCCAATAA
1 TGCTCTGCAAAG-TG--GAAAATAA
*** *
522 TGCAAAGCTGAAGTTGAAGAAAATAA
1 TGCTCTGC-AAAG-TG--GAAAATAA
548 TGCACTCTGCAAAGTGGAAAATAA
1 TG--CTCTGCAAAGTGGAAAATAA
*
572 TGCTCTGCAAAGTAGAAAATAA
1 TGCTCTGCAAAGTGGAAAATAA
*
594 TGCTCTGCAAAGTGGTAAATAA
1 TGCTCTGCAAAGTGGAAAATAA
616 TGCTCTGCAAA
1 TGCTCTGCAAA
627 AATGTTTCCA
Statistics
Matches: 104, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
22 62 0.60
23 2 0.02
24 10 0.10
25 10 0.10
26 14 0.13
27 3 0.03
28 3 0.03
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (22 bp):
TGCTCTGCAAAGTGGAAAATAA
Found at i:1254 original size:2 final size:2
Alignment explanation
Indices: 1247--1300 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1237 AGGTTAAAAC
*
1247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1289 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1301 GATACTAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4481 original size:13 final size:12
Alignment explanation
Indices: 4460--4490 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4450 TTTGGTATTT
4460 AGGAAAAAAAAA
1 AGGAAAAAAAAA
4472 AGGAAAAAAAAA
1 AGGAAAAAAAAA
4484 AGGAAAA
1 AGGAAAA
4491 GGAGGTGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AGGAAAAAAAAA
Found at i:5459 original size:31 final size:28
Alignment explanation
Indices: 5390--5469 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
5380 TCTCATTTTT
* * *
5390 AAAAGTTATGGGGTTTATTTGTCCCAAA
1 AAAAGTTAAGGGGCTAATTTGTCCCAAA
5418 AAAAGTTAAGGGGCTAATTTGTCCCAAA
1 AAAAGTTAAGGGGCTAATTTGTCCCAAA
*
5446 ATGGATAGTTAAGGGGCTAATTTG
1 A---AAAGTTAAGGGGCTAATTTG
5470 GGTATTAAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 26 0.58
31 19 0.42
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (28 bp):
AAAAGTTAAGGGGCTAATTTGTCCCAAA
Found at i:12925 original size:6 final size:6
Alignment explanation
Indices: 12914--12949 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
12904 GCTTCAGCAA
12914 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
12950 ATACAAAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.33, G:0.17, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:14225 original size:1 final size:1
Alignment explanation
Indices: 14219--14248 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
14209 GTGTGTGTTG
*
14219 TTTTTTTTTGTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14249 CACTTAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:14235 original size:13 final size:13
Alignment explanation
Indices: 14214--14248 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
14204 TGTGTGTGTG
*
14214 TGTTGTTTTTTTT
1 TGTTTTTTTTTTT
14227 TGTTTTTTTTTTT
1 TGTTTTTTTTTTT
14240 T-TTTTTTTT
1 TGTTTTTTTT
14249 CACTTAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (13 bp):
TGTTTTTTTTTTT
Found at i:20872 original size:52 final size:51
Alignment explanation
Indices: 20770--20872 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 51
20760 GTTCTTCATA
* * **
20770 TTTTCCTTGTTTAGATCTTGTCTCTGGACAAACAAACACTCTTTTAGTGTT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTT
*
20821 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT
20873 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
51 7 0.16
52 36 0.82
53 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (51 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTT
Found at i:23290 original size:19 final size:18
Alignment explanation
Indices: 23247--23291 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
23237 CTTTCTCTTC
23247 CCCTCCTTCCTCCCTCCT
1 CCCTCCTTCCTCCCTCCT
* *
23265 CCTCTCCTTTCTCCCTCGGT
1 CC-CTCCTTCCTCCCTC-CT
23285 CCCTCCT
1 CCCTCCT
23292 CCCTTCCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 18 0.78
20 3 0.13
ACGTcount: A:0.00, C:0.60, G:0.04, T:0.36
Consensus pattern (18 bp):
CCCTCCTTCCTCCCTCCT
Found at i:33389 original size:25 final size:25
Alignment explanation
Indices: 33355--33414 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
33345 GTGGTCGACT
33355 CCGGGTCGGGGCGTGACAATAAAGA
1 CCGGGTCGGGGCGTGACAATAAAGA
* * *
33380 CCGGGTCGGGGCGTGTCAATACAGG
1 CCGGGTCGGGGCGTGACAATAAAGA
*
33405 CCGGGCCGGG
1 CCGGGTCGGG
33415 TCGGGCTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.45, T:0.12
Consensus pattern (25 bp):
CCGGGTCGGGGCGTGACAATAAAGA
Found at i:34298 original size:22 final size:21
Alignment explanation
Indices: 34258--34298 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
34248 TTGAAGACTT
*
34258 ATTGAAGATAATTTGAAGATC
1 ATTGAAGATAATTTCAAGATC
*
34279 ATTGAAGAATTATTTCAAGA
1 ATTGAAG-ATAATTTCAAGA
34299 AGCAAGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (21 bp):
ATTGAAGATAATTTCAAGATC
Found at i:39116 original size:21 final size:22
Alignment explanation
Indices: 39090--39140 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
39080 AGATATTTTT
**
39090 CAAAATTTTAATGGA-GGCTAC
1 CAAAATTTTAAAAGATGGCTAC
* *
39111 CAAAATTATAAAAGATGGGTAC
1 CAAAATTTTAAAAGATGGCTAC
39133 CAAAATTT
1 CAAAATTT
39141 CAAATGAGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (22 bp):
CAAAATTTTAAAAGATGGCTAC
Found at i:39158 original size:43 final size:43
Alignment explanation
Indices: 39111--39211 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
39101 TGGAGGCTAC
*
39111 CAAAATTATAAA-AGATGGGTACCAAAATTTCAAATGAGGTTAT
1 CAAAATTATAAAGAGAT-AGTACCAAAATTTCAAATGAGGTTAT
* * * * * * *
39154 CAAAATTACAAAGGGCTATTATCAAAGTTTCAATTGAGGTTAT
1 CAAAATTATAAAGAGATAGTACCAAAATTTCAAATGAGGTTAT
39197 CAAAATTATAAAGAG
1 CAAAATTATAAAGAG
39212 CTTTTATACA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 45 0.96
44 2 0.04
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (43 bp):
CAAAATTATAAAGAGATAGTACCAAAATTTCAAATGAGGTTAT
Found at i:39246 original size:43 final size:42
Alignment explanation
Indices: 39135--39244 Score: 139
Period size: 43 Copynumber: 2.5 Consensus size: 42
39125 ATGGGTACCA
* *
39135 AAATTTCAAATGAGGTTATCAAAATTACAAAGGGCTATTATC
1 AAATTTCAAATGAGGTTATCAAAATTATAAAGAGCTATTATC
* *
39177 AAAGTTTCAATTGAGGTTATCAAAATTATAAAGAGCTTTTATAC
1 AAA-TTTCAAATGAGGTTATCAAAATTATAAAGAGCTATTAT-C
* *
39221 AAATTTTAAATGATGGTTTTCAAA
1 AAATTTCAAATGA-GGTTATCAAA
39245 TTTTCAAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 3 0.05
43 42 0.72
44 13 0.22
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (42 bp):
AAATTTCAAATGAGGTTATCAAAATTATAAAGAGCTATTATC
Found at i:39271 original size:22 final size:21
Alignment explanation
Indices: 39221--39312 Score: 60
Period size: 22 Copynumber: 4.2 Consensus size: 21
39211 GCTTTTATAC
* * *
39221 AAATTTTAAATGATGGTTTTCA
1 AAATTTCAAA-GATGATTATCA
* *
39243 AATTTTCAAAGAGTGCTTATCA
1 AAATTTCAAAGA-TGATTATCA
* *
39265 AACTTTCATAAGATGATTGTCA
1 AAATTTCA-AAGATGATTATCA
* *
39287 AAATTTCAATTGAAG-TTATCA
1 AAATTTCAA-AGATGATTATCA
39308 AAATT
1 AAATT
39313 ATAAAGGAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
21 13 0.23
22 39 0.70
23 4 0.07
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
AAATTTCAAAGATGATTATCA
Found at i:48268 original size:19 final size:18
Alignment explanation
Indices: 48235--48270 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48225 TTGAAATTAT
48235 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
48253 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
48271 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:55387 original size:19 final size:18
Alignment explanation
Indices: 55354--55389 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
55344 TTGAAATTAT
55354 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
55372 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
55390 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:56333 original size:33 final size:33
Alignment explanation
Indices: 56291--56367 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
56281 ATCAGTGATA
56291 TCAAAACCATGTATCAGAATCCAAATATTTCTT
1 TCAAAACCATGTATCAGAATCCAAATATTTCTT
* *
56324 TCAAAACCATGTATCATAATCCAAATATTTTTT
1 TCAAAACCATGTATCAGAATCCAAATATTTCTT
56357 TCAAAACCATG
1 TCAAAACCATG
56368 GGCTGCCATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (33 bp):
TCAAAACCATGTATCAGAATCCAAATATTTCTT
Found at i:58186 original size:38 final size:38
Alignment explanation
Indices: 58144--58225 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
58134 TAGCCTGGCA
* *
58144 CGCTGGGCCGCGTGCCTGACCTGCCACTCGGGGCCACG
1 CGCTGGCCCGCGTGCCTGACCTGCCACGCGGGGCCACG
* * * *
58182 CGCTGGCCCGCGTGCCTGGCCTGGCACGCTGGGCCGCG
1 CGCTGGCCCGCGTGCCTGACCTGCCACGCGGGGCCACG
58220 CGCTGG
1 CGCTGG
58226 TGTGGCCCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.05, C:0.41, G:0.40, T:0.13
Consensus pattern (38 bp):
CGCTGGCCCGCGTGCCTGACCTGCCACGCGGGGCCACG
Found at i:61655 original size:22 final size:24
Alignment explanation
Indices: 61616--61662 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
61606 ACGCAGAATT
61616 TTTTTTTTAAATTAAAAAATGCAAA
1 TTTTTTTT-AATTAAAAAATGCAAA
61641 TTTTTTTT-ATT-AAAAATGCAAA
1 TTTTTTTTAATTAAAAAATGCAAA
61663 AAACAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.50
23 3 0.14
25 8 0.36
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTTTTTTAATTAAAAAATGCAAA
Found at i:68381 original size:18 final size:17
Alignment explanation
Indices: 68350--68385 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
68340 TTTCTCTTCA
68350 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
*
68367 TCTAGTTTTTGTTCTAGT
1 TCTA-TTTTTCTTCTAGT
68385 T
1 T
68386 TTAGGGCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:69813 original size:29 final size:29
Alignment explanation
Indices: 69771--69826 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
69761 AACCTAGGTT
69771 TTTCAAACACATACTTGATCAGATCTAAC
1 TTTCAAACACATACTTGATCAGATCTAAC
*
69800 TTTCAAACACATACTTGATCGGATCTA
1 TTTCAAACACATACTTGATCAGATCTA
69827 CCTTGGAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (29 bp):
TTTCAAACACATACTTGATCAGATCTAAC
Found at i:73771 original size:47 final size:47
Alignment explanation
Indices: 73701--73880 Score: 263
Period size: 47 Copynumber: 3.8 Consensus size: 47
73691 TCTTTCAACA
*
73701 TTCCCAAATTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTT
1 TTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGCTT
* *
73748 TTCCCAGATTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTGCTT
1 TTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGCTT
*
73795 TTTCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGCTT
1 TTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGCTT
* * * * *
73842 TT-TCGAGTGTGCCCTTTCCCACCGGAAGGTGTTGTTTAA
1 TTCCCAAAT-TGCCCTTCCCCATCGGAAGGTGTTGTTTAA
73881 ATTCCCAGTT
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
46 3 0.02
47 118 0.98
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (47 bp):
TTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGCTT
Found at i:73940 original size:41 final size:41
Alignment explanation
Indices: 73851--74326 Score: 521
Period size: 41 Copynumber: 11.7 Consensus size: 41
73841 TTTTCGAGTG
* ** *
73851 TGCCCTTTCCCACCGGAAGGTGTTGTTTA-AATTCCCAGTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
** * * *
73891 TGCCCTTCCCGGCTGGAAGGTCTTGTTTGCTTTTCCCAGTC
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
* *
73932 TGCACTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAATC
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
* * *
73973 TGCCCTTCCCCGCCGGAAGGTGTTGTTTACATTT-CAAGTC
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
* *
74013 TGCTCTTCCCCACCAGAAGGTGTTGTTTACTTTTCCCAGTC
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
* * * * * * *
74054 CGGCCTTCCCCACCAGAAGCTGTTGTTCACTTCTCCCAGTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
***
74095 TGCCCTTCCCTGTCGGAAGGTGTTGTTTACTTTT-CCAGTC
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
*
74135 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTCTT-CCAGTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTT-TTCCCAGTC
*** * *
74176 TGCCCTTCCCGGTCTGAAAGTGTTGTTTACTTTTCCCAGTC
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
* * *
74217 TCCCCTTCCCCACCGGAAGGTGTTGTTTACTTCTCCCAGTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
*** *
74258 TGCCCTTCCCGGTCAGAAGGTGTTGTTTACTTTT-CCAGTC
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
* * * *
74298 TACCCTTCCCCACTGGAAGATATTGTTTA
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTA
74327 AATTCCCAGT
Statistics
Matches: 356, Mismatches: 76, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
40 119 0.33
41 237 0.67
ACGTcount: A:0.14, C:0.31, G:0.20, T:0.36
Consensus pattern (41 bp):
TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTC
Found at i:73956 original size:81 final size:81
Alignment explanation
Indices: 73859--74246 Score: 287
Period size: 81 Copynumber: 4.8 Consensus size: 81
73849 TGTGCCCTTT
* * * * * *
73859 CCCACCGGAAGGTGTTGTTTA-AATTCCCAGTTTGCCCTTCCCGGCTGGAAGGTCTTGTTTGCTT
1 CCCACCGGAAGGTGTTGTTTACAATTCCCAATCTGCCCTTCCCCGCCGGAAGGTCTTGTTTACAT
*
73923 TTCCCAGTCTGCACTTC
66 TT-CAAGTCTGCACTTC
** *
73940 CCCACCGGAAGGTGTTGTTTACTTTTCCCAATCTGCCCTTCCCCGCCGGAAGGTGTTGTTTACAT
1 CCCACCGGAAGGTGTTGTTTACAATTCCCAATCTGCCCTTCCCCGCCGGAAGGTCTTGTTTACAT
*
74005 TTCAAGTCTGCTCTTC
66 TTCAAGTCTGCACTTC
* ** * * * * * * * *
74021 CCCACCAGAAGGTGTTGTTTACTTTTCCCAGTCCGGCCTTCCCCACCAGAAGCTGTTGTTCAC-T
1 CCCACCGGAAGGTGTTGTTTACAATTCCCAATCTGCCCTTCCCCGCCGGAAGGTCTTGTTTACAT
* * *
74085 TCTCCCAGTTTGCCCTTC
66 T-T-CAAGTCTGCACTTC
*** * * * * * *
74103 CCTGTCGGAAGGTGTTGTTTAC-TTTTCCAGTCTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
1 CCCACCGGAAGGTGTTGTTTACAATTCCCAATCTGCCCTTCCCCGCCGGAAGGTCTTGTTTACAT
* * *
74167 CTTCCAGTTTGCCCTTC
66 -TTCAAGTCTGCACTTC
*** * * ** * * * *
74184 CCGGTCTGAAAGTGTTGTTTACTTTTCCCAGTCTCCCCTTCCCCACCGGAAGGTGTTGTTTAC
1 CCCACCGGAAGGTGTTGTTTACAATTCCCAATCTGCCCTTCCCCGCCGGAAGGTCTTGTTTAC
74247 TTCTCCCAGT
Statistics
Matches: 264, Mismatches: 37, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
80 2 0.01
81 156 0.59
82 105 0.40
83 1 0.00
ACGTcount: A:0.14, C:0.31, G:0.20, T:0.35
Consensus pattern (81 bp):
CCCACCGGAAGGTGTTGTTTACAATTCCCAATCTGCCCTTCCCCGCCGGAAGGTCTTGTTTACAT
TTCAAGTCTGCACTTC
Found at i:74021 original size:122 final size:121
Alignment explanation
Indices: 73804--74326 Score: 526
Period size: 122 Copynumber: 4.2 Consensus size: 121
73794 TTTTCCAAAT
* * * * *
73804 TGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGCTTTTTCGAGTGTGCCCTTTCCCACCGGAA
1 TGCCCTTCCCCACCGGAAGGTGTTGTTT-A-----CTTTTCCCAGTCTGCCCTTCCCCACCGGAA
* * * ** ** * *
73869 GGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCGGCTGGAAGGTCTTGTTTGCTTTTCCCAGTC
60 GGTGTTGTTTACATTTCCAGTCTGCCCTTCCCCACCAGAAGGTGTTGTTTACTTTT-CCAGTC
* * *
73932 TGCACTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAATCTGCCCTTCCCCGCCGGAAGGTGTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTCTGCCCTTCCCCACCGGAAGGTGTT
* *
73997 GTTTACATTTCAAGTCTGCTCTTCCCCACCAGAAGGTGTTGTTTACTTTTCCCAGTC
66 GTTTACATTTCCAGTCTGCCCTTCCCCACCAGAAGGTGTTGTTTACTTTT-CCAGTC
* * * * * * * ***
74054 CGGCCTTCCCCACCAGAAGCTGTTGTTCACTTCTCCCAGTTTGCCCTTCCCTGTCGGAAGGTGTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTCTGCCCTTCCCCACCGGAAGGTGTT
* * *
74119 GTTTACTTTTCCAGTCTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTCTTCCAGTT
66 GTTTACATTTCCAGTCTGCCCTTCCCCACCAGAAGGTGTTGTTTACTT-TTCCAGTC
*** * * *
74176 TGCCCTTCCCGGTCTGAAAGTGTTGTTTACTTTTCCCAGTCTCCCCTTCCCCACCGGAAGGTGTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTCTGCCCTTCCCCACCGGAAGGTGTT
* ***
74241 GTTTAC-TTCTCCCAGTTTGCCCTTCCCGGTCAGAAGGTGTTGTTTACTTTTCCAGTC
66 GTTTACATT-T-CCAGTCTGCCCTTCCCCACCAGAAGGTGTTGTTTACTTTTCCAGTC
* * * *
74298 TACCCTTCCCCACTGGAAGATATTGTTTA
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTA
74327 AATTCCCAGT
Statistics
Matches: 327, Mismatches: 65, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
121 2 0.01
122 263 0.80
123 35 0.11
127 1 0.00
128 26 0.08
ACGTcount: A:0.14, C:0.30, G:0.20, T:0.36
Consensus pattern (121 bp):
TGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTCTGCCCTTCCCCACCGGAAGGTGTT
GTTTACATTTCCAGTCTGCCCTTCCCCACCAGAAGGTGTTGTTTACTTTTCCAGTC
Found at i:74114 original size:163 final size:163
Alignment explanation
Indices: 73945--74326 Score: 543
Period size: 163 Copynumber: 2.3 Consensus size: 163
73935 ACTTCCCCAC
* *
73945 CGGAAGGTGTTGTTTACTTTTCCCAATCTGCCCTTCCCCGCCGGAAGGTGTTGTTTACAT-TTCA
1 CGGAAGGTGTTGTTTACTTTT-CCAGTCTGCCCTTCCCCACCGGAAGGTGTTGTTTACATCTTCA
* * *
74009 AGTCTGCTCTTCCCCACCAGAAGGTGTTGTTTACTTTTCCCAGTC-CGGCCTTCCCCACCAGAAG
65 AGTCTGCCCTTCCCCACCAGAAAGTGTTGTTTACTTTTCCCAGTCTC-CCCTTCCCCACCAGAAG
*
74073 CTGTTGTTCACTTCTCCCAGTTTGCCCTTCCCTGT
129 CTGTTGTTCACTTCTCCCAGTTTGCCCTTCCCGGT
* *
74108 CGGAAGGTGTTGTTTACTTTTCCAGTCTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTCTTCCA
1 CGGAAGGTGTTGTTTACTTTTCCAGTCTGCCCTTCCCCACCGGAAGGTGTTGTTTACATCTTCAA
* *** * * *
74173 GTTTGCCCTTCCCGGTCTGAAAGTGTTGTTTACTTTTCCCAGTCTCCCCTTCCCCACCGGAAGGT
66 GTCTGCCCTTCCCCACCAGAAAGTGTTGTTTACTTTTCCCAGTCTCCCCTTCCCCACCAGAAGCT
*
74238 GTTGTTTACTTCTCCCAGTTTGCCCTTCCCGGT
131 GTTGTTCACTTCTCCCAGTTTGCCCTTCCCGGT
* * * * *
74271 CAGAAGGTGTTGTTTACTTTTCCAGTCTACCCTTCCCCACTGGAAGATATTGTTTA
1 CGGAAGGTGTTGTTTACTTTTCCAGTCTGCCCTTCCCCACCGGAAGGTGTTGTTTA
74327 AATTCCCAGT
Statistics
Matches: 196, Mismatches: 21, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
162 35 0.18
163 160 0.82
164 1 0.01
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.36
Consensus pattern (163 bp):
CGGAAGGTGTTGTTTACTTTTCCAGTCTGCCCTTCCCCACCGGAAGGTGTTGTTTACATCTTCAA
GTCTGCCCTTCCCCACCAGAAAGTGTTGTTTACTTTTCCCAGTCTCCCCTTCCCCACCAGAAGCT
GTTGTTCACTTCTCCCAGTTTGCCCTTCCCGGT
Found at i:74475 original size:65 final size:66
Alignment explanation
Indices: 74372--74526 Score: 163
Period size: 65 Copynumber: 2.3 Consensus size: 66
74362 TTGCAAAATA
* * * *
74372 CCCTGTCGGACAAAGGGTCAGTTTTGTCACTCTCCTTGCATTTAG-G-TTCTAGTTTTCCCAAAA
1 CCCTTTCGGACAAAGGGTCAGTCTAGTCACTCTCCTTGCATTTAGAGTTTCTA-ATTTCCCAAAA
74435 CG
65 CG
* * *
74437 CCCTTTCGGACAAAGGGTTAGTCTAGTCACAT-TTCTTGCTTTTAGACTTAGTTTCTAATTTCCC
1 CCCTTTCGGACAAAGGGTCAGTCTAGTCAC-TCTCCTTGCATTTAG----AGTTTCTAATTTCCC
*
74501 AAAATG
61 AAAACG
74507 CCCTTTCGGACAAAGGGTCA
1 CCCTTTCGGACAAAGGGTCA
74527 ATCTTCTCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
65 37 0.50
66 1 0.01
70 31 0.42
71 5 0.07
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (66 bp):
CCCTTTCGGACAAAGGGTCAGTCTAGTCACTCTCCTTGCATTTAGAGTTTCTAATTTCCCAAAAC
G
Found at i:76416 original size:19 final size:18
Alignment explanation
Indices: 76392--76431 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
76382 TTGAAGATTT
*
76392 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
76411 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
76429 ATT
1 ATT
76432 ATCTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:89817 original size:16 final size:16
Alignment explanation
Indices: 89779--89818 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
89769 ACCCGAACCA
*
89779 GAACCCGAAATTACCC
1 GAACCCGAAAATACCC
* *
89795 GAGCCCGAAAATACCT
1 GAACCCGAAAATACCC
89811 GAACCCGA
1 GAACCCGA
89819 CCCGAGCCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.35, G:0.17, T:0.10
Consensus pattern (16 bp):
GAACCCGAAAATACCC
Found at i:90349 original size:31 final size:31
Alignment explanation
Indices: 90278--90349 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
90268 GTCTATCATC
*
90278 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
90309 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
90339 GTTTTAATTTG
1 -TTTTAATTTG
90350 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:91773 original size:21 final size:19
Alignment explanation
Indices: 91742--91781 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
91732 CTATAATTCT
91742 TTTTTTCTAATCTGGCCCCC
1 TTTTTTCTAAT-TGGCCCCC
*
91762 TTTTTTCTTAATTTGCCCCC
1 TTTTTTC-TAATTGGCCCCC
91782 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.33, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTTTTCTAATTGGCCCCC
Found at i:91805 original size:23 final size:24
Alignment explanation
Indices: 91762--91806 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
91752 TCTGGCCCCC
*
91762 TTTTTTCTTAATTTGCCCCCATAT
1 TTTTTTCTTAATTTGCACCCATAT
*
91786 TTTTTTTTTAATTTG-ACCCAT
1 TTTTTTCTTAATTTGCACCCAT
91807 TGATAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.18, C:0.20, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTTTTCTTAATTTGCACCCATAT
Found at i:94113 original size:10 final size:10
Alignment explanation
Indices: 94098--94123 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
94088 TTCATCACGA
94098 GTTCTTACTC
1 GTTCTTACTC
94108 GTTCTTACTC
1 GTTCTTACTC
94118 GTTCTT
1 GTTCTT
94124 TAATATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.27, G:0.12, T:0.54
Consensus pattern (10 bp):
GTTCTTACTC
Found at i:96913 original size:86 final size:86
Alignment explanation
Indices: 96752--96913 Score: 263
Period size: 86 Copynumber: 1.9 Consensus size: 86
96742 AATTAAAATA
*
96752 GTAAAATGGTCAAAGAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTCTCA
1 GTAAAATGGTAAAAGAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTCTCA
* *
96817 GTTGAGTAAAATAGTAAAGTG
66 GTAGAATAAAATAGTAAAGTG
*
96838 GTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTT-TCT
1 GTAAAATGGTAAAAGAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTCTC-
*
96902 GGTAGAATAAAA
65 AGTAGAATAAAA
96914 CTGCAAAAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
85 2 0.03
86 68 0.97
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (86 bp):
GTAAAATGGTAAAAGAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTCTCA
GTAGAATAAAATAGTAAAGTG
Found at i:97299 original size:140 final size:138
Alignment explanation
Indices: 97154--97407 Score: 400
Period size: 140 Copynumber: 1.8 Consensus size: 138
97144 CATTATTTAA
*
97154 ACTTTTATAGTTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATCTAATACCCTTATAAA
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATACCCTTAT-AA
* *
97219 ATATTTTATTTTTACCATTATACTATTTTAATTAAAAAACTTATATATATATATATATTAGAATT
65 ATATTTTATTTTTACCATTATACTAATTTAATT-AAAAACTTAGATATATATATATATTAGAATT
97284 TTTTAAATAT
129 TTTTAAATAT
* * * **
97294 ACTTTTATAGTTTTGCTCAACTAAAAACTCTATTTTTATTTAATTAATTCTAATATCCTTATACC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATACCCTTATAAA
* *
97359 TATTTTATTTTTACCGTTTTACTAATTTAATTAAAAACTTAGATATATA
66 TATTTTATTTTTACCATTATACTAATTTAATTAAAAACTTAGATATATA
97408 ATAATTTTTA
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
138 16 0.15
139 30 0.29
140 58 0.56
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.49
Consensus pattern (138 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATACCCTTATAAA
TATTTTATTTTTACCATTATACTAATTTAATTAAAAACTTAGATATATATATATATTAGAATTTT
TTAAATAT
Found at i:99226 original size:31 final size:31
Alignment explanation
Indices: 99185--99246 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
99175 GGGCATATAA
* *
99185 TGGCTAAATGTTCAATTC-TAGATATAACGTT
1 TGGCCAAATGTTCAATTCAT-GATACAACGTT
99216 TGGCCAAATGTTCAATTCATGATACAACGTT
1 TGGCCAAATGTTCAATTCATGATACAACGTT
99247 ACAAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (31 bp):
TGGCCAAATGTTCAATTCATGATACAACGTT
Found at i:103121 original size:32 final size:33
Alignment explanation
Indices: 103080--103187 Score: 103
Period size: 32 Copynumber: 3.3 Consensus size: 33
103070 AAATTCTCAG
*
103080 TGCCGCCCTAGGAAGGCGGCA-AGCCATGGCCA
1 TGCCGCCCTACGAAGGCGGCATAGCCATGGCCA
* * *
103112 TGCCGCCCTACGAGGGCGGCATGGCCATGG-CT
1 TGCCGCCCTACGAAGGCGGCATAGCCATGGCCA
* * * * *
103144 TGCCACCCTCCTAAGGCGGCATGGGCCATGGTCA
1 TGCCGCCCTACGAAGGCGGCAT-AGCCATGGCCA
*
103178 TGCCTCCCTA
1 TGCCGCCCTA
103188 ACAGGGCGGC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 38 0.61
33 15 0.24
34 9 0.15
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (33 bp):
TGCCGCCCTACGAAGGCGGCATAGCCATGGCCA
Found at i:109841 original size:33 final size:33
Alignment explanation
Indices: 109794--109867 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
109784 ATAAAATTGC
*
109794 CTGTACCGTCCTGGTAGGGCGGCACGGCCATGG
1 CTGTGCCGTCCTGGTAGGGCGGCACGGCCATGG
* *
109827 TTGTGCCGTCCTGGTGGGGCGGCACGGCCATGG
1 CTGTGCCGTCCTGGTAGGGCGGCACGGCCATGG
109860 CTGTGCCG
1 CTGTGCCG
109868 CACCATCTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.08, C:0.30, G:0.42, T:0.20
Consensus pattern (33 bp):
CTGTGCCGTCCTGGTAGGGCGGCACGGCCATGG
Found at i:109883 original size:33 final size:33
Alignment explanation
Indices: 109846--109971 Score: 152
Period size: 33 Copynumber: 3.9 Consensus size: 33
109836 CCTGGTGGGG
* *
109846 CGGCACGGCCATGGCTGTGCCGCACCATCTGGA
1 CGGCACCGCCGTGGCTGTGCCGCACCATCTGGA
109879 CGGCACCGCCGTGGCTGTGCCGCACCATCTGGA
1 CGGCACCGCCGTGGCTGTGCCGCACCATCTGGA
* * * *
109912 CGGCACCGCCGTGGC-ATGCCGCA--GTGATGGTG
1 CGGCACCGCCGTGGCTGTGCCGCACCAT-CTGG-A
109944 CGGCACCGCCGTGG-TGTGCCGCACCATC
1 CGGCACCGCCGTGGCTGTGCCGCACCATC
109972 ACTGCGGCAC
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
30 1 0.01
31 3 0.04
32 28 0.35
33 46 0.58
34 1 0.01
ACGTcount: A:0.13, C:0.37, G:0.35, T:0.15
Consensus pattern (33 bp):
CGGCACCGCCGTGGCTGTGCCGCACCATCTGGA
Found at i:110282 original size:29 final size:30
Alignment explanation
Indices: 110225--110310 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 30
110215 GCACAAAATG
* *
110225 ATAACGTTGTATCCTGAAAT-CACACTTTT-
1 ATAACGTTGTATCCTGAATTGAACA-TTTTC
*
110254 ATAACGTTGCATCCTGAATTGAACATTTTGCC
1 ATAACGTTGTATCCTGAATTGAACATTTT--C
*
110286 A-AACGTTATATCCTGAATTGAACAT
1 ATAACGTTGTATCCTGAATTGAACAT
110311 CTAGCCGGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
29 22 0.46
30 3 0.06
31 22 0.46
32 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (30 bp):
ATAACGTTGTATCCTGAATTGAACATTTTC
Found at i:114732 original size:66 final size:66
Alignment explanation
Indices: 114626--114877 Score: 450
Period size: 66 Copynumber: 3.8 Consensus size: 66
114616 CCAATTGGAA
*
114626 GACATGTTATTCTCCTTCACTGCACCCTCTTCGACATCCCCCCATCCAGTAGGATGAATACAGTA
1 GACATGTTATTCTCCTTCACTGCACCCTCTTCGGCATCCCCCCATCCAGTAGGATGAATACAGTA
114691 G
66 G
* *
114692 GACATGTTATTCTCCTTAACTGCACCCTCTTCGGCATCCCCCCATCCAGTAGGACGAATACAGTA
1 GACATGTTATTCTCCTTCACTGCACCCTCTTCGGCATCCCCCCATCCAGTAGGATGAATACAGTA
114757 G
66 G
* * *
114758 GGCGTGTTATTCTCCTTCACTGCAACCTCTTCGGCATCCCCCCATCCAGTAGGATGAATACAGTA
1 GACATGTTATTCTCCTTCACTGCACCCTCTTCGGCATCCCCCCATCCAGTAGGATGAATACAGTA
114823 G
66 G
114824 GACATGTTATTCTCCTTCACTGCACCCTCTTCGGCATCCCCCCATCCAGTAGGA
1 GACATGTTATTCTCCTTCACTGCACCCTCTTCGGCATCCCCCCATCCAGTAGGA
114878 CCTATAAACG
Statistics
Matches: 175, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 175 1.00
ACGTcount: A:0.22, C:0.34, G:0.17, T:0.27
Consensus pattern (66 bp):
GACATGTTATTCTCCTTCACTGCACCCTCTTCGGCATCCCCCCATCCAGTAGGATGAATACAGTA
G
Found at i:115976 original size:167 final size:166
Alignment explanation
Indices: 115443--116225 Score: 803
Period size: 167 Copynumber: 4.7 Consensus size: 166
115433 AATTCCAAAA
** * * * * *
115443 ACAGCTGATTCACAATCCATTTATGGCAAAACCTAGAAAACGACAGTAAAATGAGTATGCCAGCG
1 ACAGCTGATTCGTAAGCTATTTATGGAAAAACCTAGAAAACGACAGCAAAATGAATATGCCAGCG
* * * * * *
115508 TAAGCAGGCCAATTTGGAACACCACCGTGTACA-AACTAGTTGGAGGACAGTTCCAAGCAATATT
66 TAAGCAAGCAAATTTGGACCAACACCGTGTGCACAA-TAGTTGGAGGACAGTTCCAAGCATTATT
** * *
115572 ATATAATGATTGTCAGCTGCAATACTTTAACTTCATAT
130 ATATAATGATACTCAGCTGGAATACTTTAACTCCA-AT
* * * * * *
115610 ACAGCTAATCCGCAAGCTATTTATGGAAAAACCTAGAAAACGACAGTAAAATAAATATGCCAGCA
1 ACAGCTGATTCGTAAGCTATTTATGGAAAAACCTAGAAAACGACAGCAAAATGAATATGCCAGCG
* * * *
115675 TATGCAAG-AAAGTTT-GATCCAACACCGTGTGCAC---A--TGGAAGACAATT-CAAGCGTTAT
66 TAAGCAAGCAAA-TTTGGA-CCAACACCGTGTGCACAATAGTTGGAGGACAGTTCCAAGCATTAT
* * * *
115732 TATATAATGATGCTCAGCTGGACTACTTTTAACCCCGAAC
129 TATATAATGATACTCAGCTGGAATAC-TTTAACTCC-AAT
* * * * *
115772 ACAGCTGATACGTAAGCTATTTATGGAAAATCCTAGAAAACGACAGCAAAATGAATACGCCATCA
1 ACAGCTGATTCGTAAGCTATTTATGGAAAAACCTAGAAAACGACAGCAAAATGAATATGCCAGCG
*
115837 TAAGCAAGCAAATTTGGACCAACACTGTGTGCACAATAGTTGGAGGACAGTTCCAAGCATTATTA
66 TAAGCAAGCAAATTTGGACCAACACCGTGTGCACAATAGTTGGAGGACAGTTCCAAGCATTATTA
* * *
115902 TATAGTGATACTCAGCTGGACTACTTTAACTACTAAT
131 TATAATGATACTCAGCTGGAATACTTTAACT-CCAAT
* *
115939 ACAGCTGATTCGTAAGCTATTTATGGGAAAACCTAGAAAACGACAGGAAAATGAATATGCCAGCG
1 ACAGCTGATTCGTAAGCTATTTATGGAAAAACCTAGAAAACGACAGCAAAATGAATATGCCAGCG
* * **
116004 TAAGCAAGAAAATTTGGTGACCAACACTC-TGTGCACACTAGTTACAGGACAGTTCCAAGCATTA
66 TAAGCAAGCAAATTT-G-GACCAACAC-CGTGTGCACAATAGTTGGAGGACAGTTCCAAGCATTA
* **
116068 TCATATGAAACATACTCAGCTGGAATACTTTAACTCCAAAT
128 TTATAT-AATGATACTCAGCTGGAATACTTTAACTCC-AAT
* * * * * ** **
116109 GCTGCGGATTTGTAAGCTATTTATGGAAAAACCTAGAAAATGACAGCAAAATGAATACACCAATG
1 ACAGCTGATTCGTAAGCTATTTATGGAAAAACCTAGAAAACGACAGCAAAATGAATATGCCAGCG
* * * * * **
116174 TAAGCAAGCAGATTTGGATCAACACCATGTGCATACTAGTTACAGGACAGTT
66 TAAGCAAGCAAATTTGGACCAACACCGTGTGCACAATAGTTGGAGGACAGTT
116226 ACAAAAGCAA
Statistics
Matches: 519, Mismatches: 77, Indels: 39
0.82 0.12 0.06
Matches are distributed among these distances:
161 30 0.06
162 100 0.19
163 6 0.01
164 1 0.00
165 1 0.00
166 4 0.01
167 168 0.32
168 67 0.13
169 48 0.09
170 94 0.18
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (166 bp):
ACAGCTGATTCGTAAGCTATTTATGGAAAAACCTAGAAAACGACAGCAAAATGAATATGCCAGCG
TAAGCAAGCAAATTTGGACCAACACCGTGTGCACAATAGTTGGAGGACAGTTCCAAGCATTATTA
TATAATGATACTCAGCTGGAATACTTTAACTCCAAT
Found at i:116308 original size:80 final size:79
Alignment explanation
Indices: 116156--116308 Score: 180
Period size: 80 Copynumber: 1.9 Consensus size: 79
116146 AAATGACAGC
* * * * * * *
116156 AAAATGAATACACCAATGTAAGCAAGCAGATTTGGATCAACACCATGTGCATACTAGTTACAGGA
1 AAAATGAAAACACCAATGTAAGCAAGCAAATTTAGACCAACACCATGTGAACACTAGTTACAAGA
*
116221 CAGTTACAAAAGCA
66 CAATTACAAAAGCA
* * ** *
116235 AAAATGAAAACACCCAGTGTAAGCAAGCAAATTTAGACCAATACTGTGTGAACACTAGTTAGAAG
1 AAAATGAAAACA-CCAATGTAAGCAAGCAAATTTAGACCAACACCATGTGAACACTAGTTACAAG
116300 ACAATTACA
65 ACAATTACA
116309 GGCATTATAT
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
79 11 0.18
80 49 0.82
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (79 bp):
AAAATGAAAACACCAATGTAAGCAAGCAAATTTAGACCAACACCATGTGAACACTAGTTACAAGA
CAATTACAAAAGCA
Found at i:127198 original size:18 final size:18
Alignment explanation
Indices: 127175--127213 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
127165 CAAAAATACA
127175 AAATTAGGCATCCCATGT
1 AAATTAGGCATCCCATGT
127193 AAATTAGGCATCCCATGT
1 AAATTAGGCATCCCATGT
127211 AAA
1 AAA
127214 ATTGGAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (18 bp):
AAATTAGGCATCCCATGT
Found at i:128543 original size:32 final size:34
Alignment explanation
Indices: 128493--128555 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 34
128483 ATATCAACTG
*
128493 CTTTTTTTACTTGATTTATTATTTTTTTCTCAAA
1 CTTTTTTTACTTGATTTATTATTTTCTTCTCAAA
* *
128527 CTTTTTTTA-TT-TTTTATTCTTTTCTTCTC
1 CTTTTTTTACTTGATTTATTATTTTCTTCTC
128556 CGTTTTCTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 15 0.58
33 2 0.08
34 9 0.35
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (34 bp):
CTTTTTTTACTTGATTTATTATTTTCTTCTCAAA
Found at i:141213 original size:21 final size:21
Alignment explanation
Indices: 141189--141228 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
141179 TGAATTTGGA
*
141189 GATG-ATTGTAGACGAGCTTTT
1 GATGAATTGAAGA-GAGCTTTT
141210 GATGAATTGAAGAGAGCTT
1 GATGAATTGAAGAGAGCTT
141229 CGACCTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (21 bp):
GATGAATTGAAGAGAGCTTTT
Found at i:165354 original size:10 final size:10
Alignment explanation
Indices: 165341--165385 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
165331 CGATACCTCG
*
165341 ATATCTGTAA
1 ATATCTATAA
165351 ATATCTATAA
1 ATATCTATAA
*
165361 ATATCCATAA
1 ATATCTATAA
*
165371 ATATCTGTAA
1 ATATCTATAA
165381 ATATC
1 ATATC
165386 CATATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (10 bp):
ATATCTATAA
Found at i:165371 original size:20 final size:20
Alignment explanation
Indices: 165348--165389 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
165338 TCGATATCTG
165348 TAAATATCTATAAATATCCA
1 TAAATATCTATAAATATCCA
*
165368 TAAATATCTGTAAATATCCA
1 TAAATATCTATAAATATCCA
165388 TA
1 TA
165390 TTAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAATATCTATAAATATCCA
Found at i:167037 original size:22 final size:22
Alignment explanation
Indices: 167012--167062 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
167002 GAAAAATGTC
*
167012 CAAAACATACAAGTTGAGGGAG
1 CAAAACATACAAGTTCAGGGAG
* *
167034 C-AAACGTACAAGTTCAGGGGG
1 CAAAACATACAAGTTCAGGGAG
167055 CAAAACAT
1 CAAAACAT
167063 CCAAAACTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (22 bp):
CAAAACATACAAGTTCAGGGAG
Found at i:167189 original size:29 final size:30
Alignment explanation
Indices: 167149--167209 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
167139 ACAGAGGCGC
* *
167149 AAATTGAGAGTTCAGGGGGCAAAATGTCCA
1 AAATTGAGAGTTCAAGGGGCAAAACGTCCA
167179 AAATTGA-AGTTCAAGGGGCAAAACGTCCA
1 AAATTGAGAGTTCAAGGGGCAAAACGTCCA
167208 AA
1 AA
167210 CGCTATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (30 bp):
AAATTGAGAGTTCAAGGGGCAAAACGTCCA
Found at i:168806 original size:35 final size:35
Alignment explanation
Indices: 168767--168837 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
168757 ATTAACTCTC
*
168767 AATTGATGAGGTTTGCCTCTTTTTTGCATATAACA
1 AATTGATGAGGTTTGCCTCTTTTTTGCACATAACA
*
168802 AATTGATGAGGTTTGGCTCTTTTTTGCACATAACA
1 AATTGATGAGGTTTGCCTCTTTTTTGCACATAACA
168837 A
1 A
168838 GTATACTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (35 bp):
AATTGATGAGGTTTGCCTCTTTTTTGCACATAACA
Found at i:170400 original size:27 final size:27
Alignment explanation
Indices: 170370--170423 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
170360 CCAAAACATT
*
170370 ACCTTAAATAACTTACTTAACAAACTA
1 ACCTTAAATAACCTACTTAACAAACTA
170397 ACCTTAAATAACCTACTTAACAAACTA
1 ACCTTAAATAACCTACTTAACAAACTA
170424 CCAAACAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (27 bp):
ACCTTAAATAACCTACTTAACAAACTA
Found at i:170440 original size:12 final size:12
Alignment explanation
Indices: 170425--170454 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
170415 AACAAACTAC
170425 CAAACAAATAAA
1 CAAACAAATAAA
170437 CAAACAAATAAA
1 CAAACAAATAAA
170449 CTAAAC
1 C-AAAC
170455 TTACATTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.70, C:0.20, G:0.00, T:0.10
Consensus pattern (12 bp):
CAAACAAATAAA
Found at i:172431 original size:14 final size:14
Alignment explanation
Indices: 172412--172438 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
172402 ACATATGAAT
172412 GTATTAATTCAATC
1 GTATTAATTCAATC
172426 GTATTAATTCAAT
1 GTATTAATTCAAT
172439 ATTTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (14 bp):
GTATTAATTCAATC
Done.