Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019845.1 Corchorus olitorius cultivar O-4 contig19878, 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: 40081
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:1826 original size:18 final size:19
Alignment explanation
Indices: 1786--1827 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1776 AAGAAAAGAA
*
1786 TAAAAATAAAAAATTAGAG
1 TAAAAATAAAAAATCAGAG
*
1805 -AAAAATAATAAATCA-AG
1 TAAAAATAAAAAATCAGAG
1822 TAAAAA
1 TAAAAA
1828 AGTAATTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (19 bp):
TAAAAATAAAAAATCAGAG
Found at i:3537 original size:9 final size:9
Alignment explanation
Indices: 3523--3550 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3513 ACTATATCTC
3523 TGGCAGGAT
1 TGGCAGGAT
3532 TGGCAGGAT
1 TGGCAGGAT
3541 TGGCAGGAT
1 TGGCAGGAT
3550 T
1 T
3551 AGAGATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.43, T:0.25
Consensus pattern (9 bp):
TGGCAGGAT
Found at i:3825 original size:39 final size:39
Alignment explanation
Indices: 3771--3849 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3761 ATCTGAACAT
3771 TGCATCTATGTATAATGTATTAGTATATTTTGGCTTTAG
1 TGCATCTATGTATAATGTATTAGTATATTTTGGCTTTAG
3810 TGCATCTATGTATAATGTATTAGTATATTTTGGCTTTAG
1 TGCATCTATGTATAATGTATTAGTATATTTTGGCTTTAG
3849 T
1 T
3850 ACTTGCTCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (39 bp):
TGCATCTATGTATAATGTATTAGTATATTTTGGCTTTAG
Found at i:4002 original size:30 final size:30
Alignment explanation
Indices: 3966--4026 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3956 ATTTCCTTAT
* * *
3966 TCATTTCCTTAAGCGATAAATATATACAAC
1 TCATTTCCTTAAACCATAAATATAAACAAC
*
3996 TCATTTCCTTAAACCTTAAATATAAACAAC
1 TCATTTCCTTAAACCATAAATATAAACAAC
4026 T
1 T
4027 ACCAGTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.34
Consensus pattern (30 bp):
TCATTTCCTTAAACCATAAATATAAACAAC
Found at i:10273 original size:2 final size:2
Alignment explanation
Indices: 10266--10290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10256 CATCTCATAA
10266 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10291 CTCTCCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10443 original size:20 final size:18
Alignment explanation
Indices: 10426--10491 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
10416 TTTTTTTTGG
10426 GTTTTTTTTTGGTTTTTTTT
1 GTTTTTTTTTGG--TTTTTT
*
10446 GTTTTTTTTTGGTCTTTT
1 GTTTTTTTTTGGTTTTTT
*
10464 GTTCTTTTTTGGTTCTTTT
1 GTTTTTTTTTGGTT-TTTT
10483 -TTTTTTTTT
1 GTTTTTTTTT
10492 TTTCTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 25 0.61
19 4 0.10
20 12 0.29
ACGTcount: A:0.00, C:0.05, G:0.14, T:0.82
Consensus pattern (18 bp):
GTTTTTTTTTGGTTTTTT
Found at i:10454 original size:10 final size:10
Alignment explanation
Indices: 10416--10494 Score: 65
Period size: 11 Copynumber: 7.9 Consensus size: 10
10406 TTTTATAATC
*
10416 TTTTTTTTGGG
1 TTTTTTTT-TG
10427 TTTTTTTTTG
1 TTTTTTTTTG
*
10437 GTTTTTTTTG
1 TTTTTTTTTG
10447 TTTTTTTTTG
1 TTTTTTTTTG
* *
10457 --GTCTTTTG
1 TTTTTTTTTG
*
10465 TTCTTTTTTGG
1 TT-TTTTTTTG
10476 TTCTTTTTTT-
1 TT-TTTTTTTG
10486 TTTTTTTTT
1 TTTTTTTTT
10495 CTATTTTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
8 6 0.11
9 7 0.12
10 21 0.38
11 22 0.39
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:10463 original size:11 final size:11
Alignment explanation
Indices: 10416--10494 Score: 66
Period size: 10 Copynumber: 7.8 Consensus size: 11
10406 TTTTATAATC
*
10416 TTTTTTTTGGG
1 TTTTTTTTTGG
10427 TTTTTTTTTGG
1 TTTTTTTTTGG
10438 -TTTTTTTT-G
1 TTTTTTTTTGG
10447 TTTTTTTTTGG
1 TTTTTTTTTGG
*
10458 ---TCTTTT-G
1 TTTTTTTTTGG
*
10465 TTCTTTTTTGG
1 TTTTTTTTTGG
10476 TTCTTTTTTT--
1 TT-TTTTTTTGG
10486 TTTTTTTTT
1 TTTTTTTTT
10495 CTATTTTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
7 1 0.02
8 5 0.09
9 8 0.14
10 23 0.40
11 14 0.25
12 6 0.11
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTGG
Found at i:13493 original size:74 final size:74
Alignment explanation
Indices: 13367--13514 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
13357 CAAAGGGAAA
*
13367 GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAGGAAAATCAACGTTTGATAAGGCTATTGT
1 GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAGGAAAATCAACATTTGATAAGGCTATTGT
13432 GGCATTCTT
66 GGCATTCTT
13441 GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAGGAAAATCAACATTTGATAAGGCTATTGT
1 GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAGGAAAATCAACATTTGATAAGGCTATTGT
13506 GGCATTCTT
66 GGCATTCTT
13515 CAATAGGTAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (74 bp):
GAATTGAGCGTTAGGATTGTTACAAGGAGAGCAGCAGGAAAATCAACATTTGATAAGGCTATTGT
GGCATTCTT
Found at i:14576 original size:2 final size:2
Alignment explanation
Indices: 14569--14604 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
14559 ATGAATCAGG
*
14569 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14605 GCATTGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:15942 original size:30 final size:30
Alignment explanation
Indices: 15907--15993 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
15897 AAGATCAAAC
15907 TTTTAAGTAATTTGTGAATAAAGGTTGGAT
1 TTTTAAGTAATTTGTGAATAAAGGTTGGAT
* *
15937 TTTTAA-TAA------AA-AAA--TTGAAGC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGA-T
15958 TTTTAAGTAATTTGTGAATAAAGGTTGGAT
1 TTTTAAGTAATTTGTGAATAAAGGTTGGAT
15988 TTTTAA
1 TTTTAA
15994 TTAAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 22
0.62 0.06 0.32
Matches are distributed among these distances:
20 4 0.10
21 6 0.14
22 6 0.14
23 2 0.05
28 2 0.05
29 6 0.14
30 12 0.29
31 4 0.10
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (30 bp):
TTTTAAGTAATTTGTGAATAAAGGTTGGAT
Found at i:16296 original size:51 final size:51
Alignment explanation
Indices: 15753--16337 Score: 781
Period size: 51 Copynumber: 11.4 Consensus size: 51
15743 AGATCAATCT
* * *
15753 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTTATTTAAAAGA-T-CATC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGA-TTTTTAATTAAAAGATTGAAGC
* *
15803 TTTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTTAATTAAAAGA-TCAAAC
1 -TTTTAAGTAATTTGTGAATAAAGGTTGGA-TTTTTAATTAAAAGATTGAAGC
* *
15855 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTTTAATTAAAAGA-TCAAAC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGA--TTTTTAATTAAAAGATTGAAGC
* *
15907 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATAAAAAAATTGAAGC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAGC
*
15958 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAATATTGAAGC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAGC
16009 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAA-AGTTGAAGC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGA-TTGAAGC
* *
16060 TTTTAAGTAATTTGTGAATAAGGGTTGGATTTTTAATTAAAAAATTGAAGC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAGC
* *
16111 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGA-TCAAAC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAGC
** *
16161 TTTTAAGTAATTTGTGAATAAAATTTGGATTTTTAATTAAAAAATTGAAGC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAGC
* **
16212 TTTTAAGTAATTTGTGAATAAAGATCAGATTTTTAATTAAAAGATTGAA-C
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAGC
* * * * *
16262 TTTTAAGTAATTTGTAAATGAAGATT-GATTTTTTTTTAATTAAAGGATTGAATC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGA----TTTTTAATTAAAAGATTGAAGC
* *
16316 TTTTAAGTAGTTTGTAAATAAA
1 TTTTAAGTAATTTGTGAATAAA
16338 AAAGAGAAGA
Statistics
Matches: 493, Mismatches: 30, Indels: 19
0.91 0.06 0.04
Matches are distributed among these distances:
49 2 0.00
50 83 0.17
51 314 0.64
52 54 0.11
53 19 0.04
54 21 0.04
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (51 bp):
TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAGC
Found at i:16334 original size:54 final size:50
Alignment explanation
Indices: 15753--16437 Score: 502
Period size: 51 Copynumber: 13.4 Consensus size: 50
15743 AGATCAATCT
* * ** * * *
15753 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTTATTTAAAAGA-TCATC
1 TTTTAAGTAATTTGTAAATAAAGATCAGA-TTTTTAATTAAAAGATTGAAC
* * ** **
15803 TTTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTTAATTAAAAGATCAAAC
1 -TTTTAAGTAATTTGTAAATAAAGATCAGA-TTTTTAATTAAAAGATTGAAC
* * ** **
15855 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTTTAATTAAAAGATCAAAC
1 TTTTAAGTAATTTGTAAATAAAGATCAGA--TTTTTAATTAAAAGATTGAAC
* * ** * *
15907 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATAAAAAAATTGAAGC
1 TTTTAAGTAATTTGTAAATAAAGATCAGATTTTTAATTAAAAGATTGAA-C
* * ** *
15958 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAATATTGAAGC
1 TTTTAAGTAATTTGTAAATAAAGATCAGATTTTTAATTAAAAGATTGAA-C
* * **
16009 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAA-AGTTGAAGC
1 TTTTAAGTAATTTGTAAATAAAGATCAGATTTTTAATTAAAAGA-TTGAA-C
* * * ** *
16060 TTTTAAGTAATTTGTGAATAAGGGTTGGATTTTTAATTAAAAAATTGAAGC
1 TTTTAAGTAATTTGTAAATAAAGATCAGATTTTTAATTAAAAGATTGAA-C
* * ** **
16111 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATCAAAC
1 TTTTAAGTAATTTGTAAATAAAGATCAGATTTTTAATTAAAAGATTGAAC
* ** *
16161 TTTTAAGTAATTTGTGAATAAA-ATTTGGATTTTTAATTAAAAAATTGAAGC
1 TTTTAAGTAATTTGTAAATAAAGA-TCAGATTTTTAATTAAAAGATTGAA-C
*
16212 TTTTAAGTAATTTGTGAATAAAGATCAGATTTTTAATTAAAAGATTGAAC
1 TTTTAAGTAATTTGTAAATAAAGATCAGATTTTTAATTAAAAGATTGAAC
* * *
16262 TTTTAAGTAATTTGTAAATGAAGAT-TGATTTTTTTTTAATTAAAGGATTGAATC
1 TTTTAAGTAATTTGTAAATAAAGATCAGA----TTTTTAATTAAAAGATTGAA-C
* * ** *** * *
16316 TTTTAAGTAGTTTGTAAATAAAAAAGAGAAGATTAAGTAAAAGA-TGTACC
1 TTTTAAGTAATTTGTAAATAAAGATCAGATTTTTAATTAAAAGATTG-AAC
* * * * * * *
16366 TTTTAATTAAGTTGTAAATAAA-AGTAAGATCTTTAAGTAAATGACT-AATC
1 TTTTAAGTAATTTGTAAATAAAGA-TCAGATTTTTAATTAAAAGATTGAA-C
16416 TTTTTAAGTAATTTGTAAATAA
1 -TTTTAAGTAATTTGTAAATAA
16438 GAATGAGGTC
Statistics
Matches: 566, Mismatches: 49, Indels: 38
0.87 0.08 0.06
Matches are distributed among these distances:
49 4 0.01
50 123 0.22
51 341 0.60
52 55 0.10
53 19 0.03
54 22 0.04
55 2 0.00
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.41
Consensus pattern (50 bp):
TTTTAAGTAATTTGTAAATAAAGATCAGATTTTTAATTAAAAGATTGAAC
Found at i:16488 original size:52 final size:51
Alignment explanation
Indices: 16377--16525 Score: 133
Period size: 52 Copynumber: 2.9 Consensus size: 51
16367 TTTAATTAAG
* * * * * * *
16377 TTGTAAATAAAAGTAAGATCTTT-AAGTAAATGACTA-ATCTTTTTAAGTAAT
1 TTGTAAATAAAATTGAGATCTTTGAACTAAAAGA-TAGAACTTTTGAA-TAAC
* * * *
16428 TTGTAAATAAGAA-TGAGGTCTTTGGAGTGAAAGATAGAACCTTTTGAATAAC
1 TTGTAAATAA-AATTGAGATCTTTGAACTAAAAGATAGAA-CTTTTGAATAAC
*
16480 TTGTAAATAAAATTGAGATCTTTGAACTAAAAGATTGAACTTTTGA
1 TTGTAAATAAAATTGAGATCTTTGAACTAAAAGATAGAACTTTTGA
16526 TAAAACTGGA
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
51 29 0.36
52 44 0.55
53 7 0.09
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (51 bp):
TTGTAAATAAAATTGAGATCTTTGAACTAAAAGATAGAACTTTTGAATAAC
Found at i:17279 original size:20 final size:20
Alignment explanation
Indices: 17254--17293 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17244 TCGGAAGGTG
*
17254 TTGTTTTCAATATTTTATTC
1 TTGTTTCCAATATTTTATTC
*
17274 TTGTTTCCAATGTTTTATTC
1 TTGTTTCCAATATTTTATTC
17294 CCGTTTTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.62
Consensus pattern (20 bp):
TTGTTTCCAATATTTTATTC
Found at i:17280 original size:48 final size:48
Alignment explanation
Indices: 17077--17279 Score: 318
Period size: 48 Copynumber: 4.2 Consensus size: 48
17067 TTTTCTTCAA
*
17077 TATTCCTGTTTTGCCCTTCCCGGTTGGAAGGTGTTGTTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
* * *
17125 TATTCCTGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTGTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
*
17173 TATT-CTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
1 TATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
* *
17221 TATTCCCGTTTCGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
*
17269 TATTCTTGTTT
1 TATTCCTGTTT
17280 CCAATGTTTT
Statistics
Matches: 140, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
47 2 0.01
48 137 0.98
49 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (48 bp):
TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
Found at i:17299 original size:20 final size:20
Alignment explanation
Indices: 17256--17299 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
17246 GGAAGGTGTT
* **
17256 GTTTTCAATATTTTATTCTT
1 GTTTCCAATATTTTATTCCC
*
17276 GTTTCCAATGTTTTATTCCC
1 GTTTCCAATATTTTATTCCC
17296 GTTT
1 GTTT
17300 TGCCCTTCCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.59
Consensus pattern (20 bp):
GTTTCCAATATTTTATTCCC
Found at i:17315 original size:68 final size:68
Alignment explanation
Indices: 17207--17644 Score: 698
Period size: 68 Copynumber: 6.4 Consensus size: 68
17197 CGGAAGGTGT
*
17207 TGTTTTCAATGTTTTATTCCCGTTTCGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
*
17272 TCT
66 TCA
*
17275 TGTTTCCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
17340 TCA
66 TCA
* * * * * *
17343 TGTTTTCAATTTTTTATTCCCATTTTGCCCTTCTCGGTCGGAAGGAGTTGTCTTCAAAATTTTAC
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTA-
17408 TTC-
65 TTCA
*
17411 TGTTTTCAATGTTCTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
*
17476 TCC
66 TCA
* * *
17479 TGTTTTGCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGTAAGGAGTTGTTTTGAATATTTTA
1 TGTTTT-CAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTA
*
17544 TTCC
65 TTCA
* *
17548 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGATTGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
17613 TCA
66 TCA
17616 TGTTTTCAATGTTTTATTCCCGTTTTGCC
1 TGTTTTCAATGTTTTATTCCCGTTTTGCC
17645 TATTCTCTTC
Statistics
Matches: 340, Mismatches: 27, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
67 3 0.01
68 270 0.79
69 67 0.20
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (68 bp):
TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
TCA
Found at i:17348 original size:20 final size:20
Alignment explanation
Indices: 17323--17361 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17313 CGGAAGGTGT
17323 TGTTTTCAATATTTTATTCA
1 TGTTTTCAATATTTTATTCA
*
17343 TGTTTTCAATTTTTTATTC
1 TGTTTTCAATATTTTATTC
17362 CCATTTTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCA
Found at i:17368 original size:20 final size:20
Alignment explanation
Indices: 17325--17368 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
17315 GAAGGTGTTG
**
17325 TTTTCAATATTTTATTCATG
1 TTTTCAATATTTTATTCACA
* *
17345 TTTTCAATTTTTTATTCCCA
1 TTTTCAATATTTTATTCACA
17365 TTTT
1 TTTT
17369 GCCCTTCTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTCAATATTTTATTCACA
Found at i:17494 original size:21 final size:21
Alignment explanation
Indices: 17459--17507 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
17449 CGGAAGGTGT
17459 TGTTTT-CAATATTTTATTCC
1 TGTTTTGCAATATTTTATTCC
*
17479 TGTTTTGCAATGTTTTATTCC
1 TGTTTTGCAATATTTTATTCC
*
17500 CGTTTTGC
1 TGTTTTGC
17508 CCTTCCCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.57
Consensus pattern (21 bp):
TGTTTTGCAATATTTTATTCC
Found at i:17553 original size:20 final size:20
Alignment explanation
Indices: 17528--17574 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17518 CGTAAGGAGT
17528 TGTTTTGAATATTTTATTCC
1 TGTTTTGAATATTTTATTCC
* *
17548 TGTTTTCAATGTTTTATTCC
1 TGTTTTGAATATTTTATTCC
*
17568 CGTTTTG
1 TGTTTTG
17575 CCCTTCCCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.60
Consensus pattern (20 bp):
TGTTTTGAATATTTTATTCC
Found at i:17621 original size:20 final size:20
Alignment explanation
Indices: 17596--17634 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17586 TGGAAGGTGT
17596 TGTTTTCAATATTTTATTCA
1 TGTTTTCAATATTTTATTCA
*
17616 TGTTTTCAATGTTTTATTC
1 TGTTTTCAATATTTTATTC
17635 CCGTTTTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.62
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCA
Found at i:17640 original size:20 final size:20
Alignment explanation
Indices: 17597--17641 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
17587 GGAAGGTGTT
*
17597 GTTTTCAATATTTTATTCAT
1 GTTTTCAATATTTTATTCAC
* *
17617 GTTTTCAATGTTTTATTCCC
1 GTTTTCAATATTTTATTCAC
17637 GTTTT
1 GTTTT
17642 GCCTATTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (20 bp):
GTTTTCAATATTTTATTCAC
Found at i:25361 original size:155 final size:155
Alignment explanation
Indices: 25075--25385 Score: 577
Period size: 155 Copynumber: 2.0 Consensus size: 155
25065 TATCAGAATT
* * *
25075 TCAAGCCTTTTGGATGGGATGGTGAAGATAAGGATCAGCAGGGTCAGGAAGAAGAAGAGATGGAT
1 TCAAGCCTTCTGGATGGGATGGTGAAGATAAGGATCAGCAAGGTCAAGAAGAAGAAGAGATGGAT
25140 CAGAAGATGAAAGGACTTGCCATCAATGCAGTGACTGAGGAGGAACCCGAGTCTCACCCCTGGGT
66 CAGAAGATGAAAGGACTTGCCATCAATGCAGTGACTGAGGAGGAACCCGAGTCTCACCCCTGGGT
25205 CTATCCAATGGCTCCAGGAGAAGAG
131 CTATCCAATGGCTCCAGGAGAAGAG
*
25230 TCAAGCCTTCTGGATGGGATGGTGAAGATGAGGATCAGCAAGGTCAAGAAGAAGAAGAGATGGAT
1 TCAAGCCTTCTGGATGGGATGGTGAAGATAAGGATCAGCAAGGTCAAGAAGAAGAAGAGATGGAT
*
25295 CAGAAGATGAAAGGACTTGCCATCAATGCAGTGACTGAGGAGGAACCCGAGTCTCACCCCTTGGT
66 CAGAAGATGAAAGGACTTGCCATCAATGCAGTGACTGAGGAGGAACCCGAGTCTCACCCCTGGGT
25360 CTATCCAATGGCTCCAGGAGAAGAG
131 CTATCCAATGGCTCCAGGAGAAGAG
25385 T
1 T
25386 TGGACAACTG
Statistics
Matches: 151, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 151 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (155 bp):
TCAAGCCTTCTGGATGGGATGGTGAAGATAAGGATCAGCAAGGTCAAGAAGAAGAAGAGATGGAT
CAGAAGATGAAAGGACTTGCCATCAATGCAGTGACTGAGGAGGAACCCGAGTCTCACCCCTGGGT
CTATCCAATGGCTCCAGGAGAAGAG
Found at i:30927 original size:12 final size:12
Alignment explanation
Indices: 30910--30935 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30900 AAAATTGGAA
30910 AAACATAGGATT
1 AAACATAGGATT
30922 AAACATAGGATT
1 AAACATAGGATT
30934 AA
1 AA
30936 CGGTGAGATT
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:0.08, G:0.15, T:0.23
Consensus pattern (12 bp):
AAACATAGGATT
Found at i:32133 original size:51 final size:50
Alignment explanation
Indices: 31691--32175 Score: 609
Period size: 51 Copynumber: 9.4 Consensus size: 50
31681 AAATCAATCT
* *
31691 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTTAATTAAAAGA-TCATC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGA-TTTTTAATTAAAAGATTGAAC
** **
31741 TTTTTAAGTAATTTGTGAATAAATATTGGATTTTTTAATTAAAAGATCAAAC
1 -TTTTAAGTAATTTGTGAATAAAGGTTGGA-TTTTTAATTAAAAGATTGAAC
**
31793 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTTAATTAAAAGATCAAAC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGA-TTTTTAATTAAAAGATTGAAC
*
31844 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAAATTGAAGC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAA-C
*
31895 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAAATTGAAGC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAA-C
**
31946 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATCAAAC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAC
*
31996 TTTTAAGTAATTTTTGTGAATAAAGGTTGGATTTTTAATTAAAAAATTGAAGC
1 TTTTAAGTAA--TTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAA-C
* *
32049 CTTTAAGTAATTTGTGAATAAA-GATGAGATTTTTAATTAAAAGATTGAAC
1 TTTTAAGTAATTTGTGAATAAAGGTTG-GATTTTTAATTAAAAGATTGAAC
* * *
32099 TTTTAAGTAATTTGT-AATGAAGATT-GATTTTTTTTTTTAATTAAAGGATTGAATC
1 TTTTAAGTAATTTGTGAATAAAGGTTGGA------TTTTTAATTAAAAGATTGAA-C
* *
32154 TTTTAAGTAGTTTGTAAATAAA
1 TTTTAAGTAATTTGTGAATAAA
32176 AATGAGAAGA
Statistics
Matches: 393, Mismatches: 26, Indels: 25
0.89 0.06 0.06
Matches are distributed among these distances:
48 2 0.01
49 5 0.01
50 47 0.12
51 252 0.64
52 38 0.10
53 10 0.03
54 19 0.05
55 15 0.04
56 5 0.01
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.43
Consensus pattern (50 bp):
TTTTAAGTAATTTGTGAATAAAGGTTGGATTTTTAATTAAAAGATTGAAC
Found at i:32219 original size:105 final size:105
Alignment explanation
Indices: 32027--32220 Score: 237
Period size: 105 Copynumber: 1.8 Consensus size: 105
32017 AAAGGTTGGA
* * *** *
32027 TTTTTAATTAAAAAATTGAAGCCTTTAAGTAATTTGTGAATAAAGATGAGATTTTTAATTAAAAG
1 TTTTTAATTAAAAAATTGAAGCCTTTAAGTAATTTGTAAATAAAAATGAGAAGATTAAGTAAAAG
*
32092 ATTGAACTTTTAAGTAATTTGTAATGAAGATTGATTTTTT
66 ATTGAACTTTTAAGTAAGTTGTAATGAAGATTGATTTTTT
** * * *
32132 TTTTTAATTAAAGGATTGAATCTTTTAAGTAGTTTGTAAATAAAAATGAGAAGATTAAGTAAAAG
1 TTTTTAATTAAAAAATTGAAGCCTTTAAGTAATTTGTAAATAAAAATGAGAAGATTAAGTAAAAG
* * *
32197 A-TGTACCTTTTGATTAAGTTGTAA
66 ATTG-AACTTTTAAGTAAGTTGTAA
32221 ATAAAAGTAA
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
104 2 0.03
105 71 0.97
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (105 bp):
TTTTTAATTAAAAAATTGAAGCCTTTAAGTAATTTGTAAATAAAAATGAGAAGATTAAGTAAAAG
ATTGAACTTTTAAGTAAGTTGTAATGAAGATTGATTTTTT
Found at i:32273 original size:101 final size:103
Alignment explanation
Indices: 32134--32340 Score: 262
Period size: 101 Copynumber: 2.0 Consensus size: 103
32124 GATTTTTTTT
* *
32134 TTTAATTAAAGGATTGAATCTTTTAAGTAGTTTGTAAATAAAAATGAGAAG-A-TT-AAGTAAAA
1 TTTAATTAAAGGACTGAATCTTTTAAGTAATTTGTAAATAAAAATGAG--GTATTTGAAGTAAAA
* *
32196 GAT-GTACCTTTTGATTAAGTTGTAAATAAAAGTAAGATC
64 GATCGAACCTTTTGATTAACTTGTAAATAAAAGTAAGATC
* * *
32235 TTTAATTAAAGGACT-AATCTTTTTAAGTAATTTGTAAATAAGAATGAGGTATTTGGAGTGAAAG
1 TTTAATTAAAGGACTGAATC-TTTTAAGTAATTTGTAAATAAAAATGAGGTATTTGAAGTAAAAG
* * *
32299 ATCGAACCTTTTGATTAACTTGTATATAAAATTGAGATC
65 ATCGAACCTTTTGATTAACTTGTAAATAAAAGTAAGATC
32338 TTT
1 TTT
32341 GAACTAAAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
99 1 0.01
100 5 0.05
101 42 0.46
102 9 0.10
103 34 0.37
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (103 bp):
TTTAATTAAAGGACTGAATCTTTTAAGTAATTTGTAAATAAAAATGAGGTATTTGAAGTAAAAGA
TCGAACCTTTTGATTAACTTGTAAATAAAAGTAAGATC
Found at i:32352 original size:52 final size:51
Alignment explanation
Indices: 32165--32364 Score: 131
Period size: 52 Copynumber: 3.9 Consensus size: 51
32155 TTTAAGTAGT
*** * * *
32165 TTGTAAATAAAAATGAGAAGATT-AAGTAAAAGAT-GTACCTTTTGATTAAG
1 TTGTAAAT-AAAATGAGATCTTTGAACTAAAAGATCGAACCTTTTGATTAAC
* * * * * * * *
32215 TTGTAAATAAAAGTAAGATCTTT-AATTAAAGGA-CTAATCTTTTTAAGTAAT
1 TTGTAAATAAAA-TGAGATCTTTGAACTAAAAGATCGAA-CCTTTTGATTAAC
* * * * *
32266 TTGTAAATAAGAATGAGGTATTTGGAGTGAAAGATCGAACCTTTTGATTAAC
1 TTGTAAATAA-AATGAGATCTTTGAACTAAAAGATCGAACCTTTTGATTAAC
* *
32318 TTGTATATAAAATTGAGATCTTTGAACTAAAAGATTGAA-CTTTTGAT
1 TTGTAAATAAAA-TGAGATCTTTGAACTAAAAGATCGAACCTTTTGAT
32365 AAAACTGGAA
Statistics
Matches: 112, Mismatches: 31, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
49 4 0.04
50 23 0.21
51 36 0.32
52 46 0.41
53 3 0.03
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (51 bp):
TTGTAAATAAAATGAGATCTTTGAACTAAAAGATCGAACCTTTTGATTAAC
Found at i:32973 original size:48 final size:48
Alignment explanation
Indices: 32915--33118 Score: 322
Period size: 48 Copynumber: 4.2 Consensus size: 48
32905 TTTTCTTCAA
32915 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGAG-GTTGTTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAG-GTGTTGTTTTCAATATTT
*
32963 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTGTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
* *
33011 TATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGATT-TTTTCAATGTTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTG-TTGTTTTCAATATTT
* *
33059 TATTCCCGTTTCGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
*
33107 TATTACTGTTTT
1 TATTCCTGTTTT
33119 CAATGTTTTA
Statistics
Matches: 144, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
47 3 0.02
48 139 0.97
49 2 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.45
Consensus pattern (48 bp):
TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
Found at i:33118 original size:20 final size:20
Alignment explanation
Indices: 33093--33130 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33083 CGGAAGGTGT
33093 TGTTTTCAATATTTTATTAC
1 TGTTTTCAATATTTTATTAC
*
33113 TGTTTTCAATGTTTTATT
1 TGTTTTCAATATTTTATT
33131 CCAGTTTTGC
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:0.21, C:0.08, G:0.08, T:0.63
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTAC
Found at i:33137 original size:20 final size:20
Alignment explanation
Indices: 33094--33138 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
33084 GGAAGGTGTT
*
33094 GTTTTCAATATTTTATTACT
1 GTTTTCAATATTTTATTACA
* *
33114 GTTTTCAATGTTTTATTCCA
1 GTTTTCAATATTTTATTACA
33134 GTTTT
1 GTTTT
33139 GCCCTTGCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (20 bp):
GTTTTCAATATTTTATTACA
Found at i:33186 original size:20 final size:20
Alignment explanation
Indices: 33161--33206 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
33151 CAGAAGGTGT
*
33161 TGTTTTTAATATTTTATTCC
1 TGTTTTCAATATTTTATTCC
33181 TGTTTTCAATATTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
33201 CGTTTT
1 TGTTTT
33207 GCCCTTCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.07, T:0.63
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCC
Found at i:33247 original size:68 final size:68
Alignment explanation
Indices: 33047--33253 Score: 333
Period size: 68 Copynumber: 3.0 Consensus size: 68
33037 GAAGGTGATT
* *
33047 TTTTCAATGTTTTATTCCCGTTTCGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTA
1 TTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTC
33112 CTG
66 CTG
* * * *
33115 TTTTCAATGTTTTATTCCAGTTTTGCCCTTGCCGGTCAGAAGGTGTTGTTTTTAATATTTTATTC
1 TTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTC
33180 CTG
66 CTG
* *
33183 TTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
1 TTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTC
*
33248 CCG
66 CTG
33251 TTT
1 TTT
33254 CGCGCCGGTC
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 126 1.00
ACGTcount: A:0.14, C:0.19, G:0.17, T:0.49
Consensus pattern (68 bp):
TTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTC
CTG
Found at i:33277 original size:44 final size:47
Alignment explanation
Indices: 33181--33291 Score: 165
Period size: 44 Copynumber: 2.4 Consensus size: 47
33171 ATTTTATTCC
33181 TGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGT
1 TGTTTTCAATATTTTATTCCCGTTTTGCCC-TCCCGGTCGGAAGGTGT
* * *
33229 TGTTTTCAATGTTTTATTCCCG-TTT-CGC-GCCGGTCGGAAGGTGT
1 TGTTTTCAATATTTTATTCCCGTTTTGCCCTCCCGGTCGGAAGGTGT
33273 TGTTTTCAATATTTTATTC
1 TGTTTTCAATATTTTATTC
33292 TTGTTTTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
44 33 0.56
46 2 0.03
47 3 0.05
48 21 0.36
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.46
Consensus pattern (47 bp):
TGTTTTCAATATTTTATTCCCGTTTTGCCCTCCCGGTCGGAAGGTGT
Found at i:33287 original size:112 final size:115
Alignment explanation
Indices: 33113--33359 Score: 392
Period size: 112 Copynumber: 2.2 Consensus size: 115
33103 ATTTTATTAC
*
33113 TGTTTTCAATGTTTTATTCCAGTTTTGCCCTTGCCGGTCAGAAGGTGTTGTTTTTAATATTTTAT
1 TGTTTTCAATGTTTTATTCCAGTTTTGCCC-TGCCGGTCAGAAGGTGTTGTTTTCAATATTTTAT
*
33178 TCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGT
65 TCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGT
* * *
33229 TGTTTTCAATGTTTTATTCCCG-TTT-CGC-GCCGGTCGGAAGGTGTTGTTTTCAATATTTTATT
1 TGTTTTCAATGTTTTATTCCAGTTTTGCCCTGCCGGTCAGAAGGTGTTGTTTTCAATATTTTATT
* *
33291 CTTGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGT
66 CCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGT
*
33341 TGTTTTCAATATTTTATTC
1 TGTTTTCAATGTTTTATTC
33360 TTGTTTTCAA
Statistics
Matches: 123, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
112 97 0.79
114 2 0.02
115 3 0.02
116 21 0.17
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (115 bp):
TGTTTTCAATGTTTTATTCCAGTTTTGCCCTGCCGGTCAGAAGGTGTTGTTTTCAATATTTTATT
CCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGT
Found at i:33297 original size:20 final size:20
Alignment explanation
Indices: 33272--33311 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
33262 TCGGAAGGTG
33272 TTGTTTTCAATATTTTATTC
1 TTGTTTTCAATATTTTATTC
*
33292 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATATTTTATTC
33312 CCGTTTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.65
Consensus pattern (20 bp):
TTGTTTTCAATATTTTATTC
Found at i:33317 original size:20 final size:20
Alignment explanation
Indices: 33274--33318 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
33264 GGAAGGTGTT
**
33274 GTTTTCAATATTTTATTCTT
1 GTTTTCAATATTTTATTCCC
*
33294 GTTTTCAATGTTTTATTCCC
1 GTTTTCAATATTTTATTCCC
33314 GTTTT
1 GTTTT
33319 GCCCTTCCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (20 bp):
GTTTTCAATATTTTATTCCC
Found at i:33339 original size:180 final size:182
Alignment explanation
Indices: 32997--33637 Score: 768
Period size: 180 Copynumber: 3.4 Consensus size: 182
32987 CGGAAGGTGT
*
32997 TGTTGTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGATT-TTTTCAATGTTTTA
1 TGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTG-TTGTTTTCAATGTTTTA
33061 TTCCCGTTTCGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTACTGTTTTCAATGTT
65 TTCCCGTTTCG-CC-TCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTACTGTTTTCAATGTT
* * *
33126 TTATTCCAGTTTTGCCCTTGCCGGTCAGAAGGTGTTGTTTTTAATATTTTATTCC
128 TTATTCCAGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCC
33181 TGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
*
33246 TCCCGTTTCG-C-GCCGGTCGGAAGGTGTTGTTTTCAATATTTTATT-CTTGTTTTCAATGTTTT
66 TCCCGTTTCGCCTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTAC-TGTTTTCAATGTTTT
* * *
33308 ATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATATTTTATTCT
130 ATTCCAGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCC
* ** * * * *
33361 TGTTTTCAATGTTTTATTCTTGTTTTGCCCTTCCCGGTCCGAAGGAGTTGTTTTCAATATTTTGT
1 TGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
* *
33426 TCCTGTTTTCAATGTTTTATTCCCGTTTTTCCCTTTCCGGTCGGAAGGTCTTGTTTTCAATATTT
66 TCC------C---G---T-TT--CG------CC-TCCCGGTCGGAAGGTGTTGTTTTCAATATTT
* * * * * *
33491 TATTCCTGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGAGTTGTTTTCGATA
109 TATTACTGTTTTCAATGTTTTATTCCAGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATA
33556 TTTTATTCC
174 TTTTATTCC
* * * *
33565 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCTCGGTCGGACGGTATTGTTTTCAATGTTTTAT
1 TGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
*
33630 TCCTGTTT
66 TCCCGTTT
33638 TCAATGTTTT
Statistics
Matches: 399, Mismatches: 31, Indels: 47
0.84 0.06 0.10
Matches are distributed among these distances:
179 1 0.00
180 156 0.39
182 1 0.00
183 2 0.01
184 71 0.18
186 1 0.00
189 1 0.00
191 2 0.01
192 2 0.01
193 2 0.01
195 3 0.01
202 1 0.00
204 155 0.39
205 1 0.00
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.49
Consensus pattern (182 bp):
TGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
TCCCGTTTCGCCTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTACTGTTTTCAATGTTTTA
TTCCAGTTTTGCCCTTCCCGATCAGAAGGTGTTGTTTTCAATATTTTATTCC
Found at i:33355 original size:68 final size:68
Alignment explanation
Indices: 33229--33685 Score: 679
Period size: 68 Copynumber: 6.8 Consensus size: 68
33219 CGGAAGGTGT
* *
33229 TGTTTTCAATGTTTTATTCCCG-TTT-CGC--GCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
*
33290 TCT
66 TCC
*
33293 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
*
33358 TCT
66 TCC
** * * *
33361 TGTTTTCAATGTTTTATTCTTGTTTTGCCCTTCCCGGTCCGAAGGAGTTGTTTTCAATATTTTGT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
33426 TCC
66 TCC
* * *
33429 TGTTTTCAATGTTTTATTCCCGTTTTTCCCTTTCCGGTCGGAAGGTCTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
33494 TCC
66 TCC
* *
33497 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGAGTTGTTTTCGATATTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
33562 TCC
66 TCC
* * * *
33565 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCTCGGTCGGACGGTATTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
33630 TCC
66 TCC
** * *
33633 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCCATCGAAAGGGGTTGTTT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTT
33686 CTATTCTCTT
Statistics
Matches: 353, Mismatches: 36, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
64 22 0.06
65 3 0.01
66 2 0.01
68 326 0.92
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (68 bp):
TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
TCC
Found at i:33365 original size:20 final size:20
Alignment explanation
Indices: 33340--33386 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
33330 TCGGAAGGTG
33340 TTGTTTTCAATATTTTATTC
1 TTGTTTTCAATATTTTATTC
*
33360 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATATTTTATTC
33380 TTGTTTT
1 TTGTTTT
33387 GCCCTTCCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.09, G:0.09, T:0.68
Consensus pattern (20 bp):
TTGTTTTCAATATTTTATTC
Found at i:33434 original size:20 final size:20
Alignment explanation
Indices: 33409--33454 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
33399 CCGAAGGAGT
*
33409 TGTTTTCAATATTTTGTTCC
1 TGTTTTCAATATTTTATTCC
*
33429 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
33449 CGTTTT
1 TGTTTT
33455 TCCCTTTCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.15, G:0.11, T:0.61
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCC
Found at i:33485 original size:248 final size:248
Alignment explanation
Indices: 33047--33501 Score: 759
Period size: 248 Copynumber: 1.8 Consensus size: 248
33037 GAAGGTGATT
*
33047 TTTTCAATGTTTTATTCCCGTTTCGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTA
1 TTTTCAATGTTTTATTCCCGTTTCGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATATTTTATTA
* * *
33112 CTGTTTTCAATGTTTTATTCCAGTTTTGCCCTTGCCGGTCAGAAGGTGTTGTTTTTAATATTTTA
66 CTGTTTTCAATGTTTTATTCCAGTTTTGCCCTTCCCGGTCAGAAGGAGTTGTTTTCAATATTTTA
* *
33177 TTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTT
131 TTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTCTTGTTTTCAATATT
33242 TTATTCCCGTTTCGCGCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCTTG
196 TTATTCCCGTTTCGCGCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCTTG
*
33295 TTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATATTTTATT-
1 TTTTCAATGTTTTATTCCCGTTTCGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATATTTTATTA
** *
33359 CTTGTTTTCAATGTTTTATTCTTGTTTTGCCCTTCCCGGTCCGAAGGAGTTGTTTTCAATATTTT
66 C-TGTTTTCAATGTTTTATTCCAGTTTTGCCCTTCCCGGTCAGAAGGAGTTGTTTTCAATATTTT
* * * *
33424 GTTCCTGTTTTCAATGTTTTATTCCCGTTTTTCCCTTTCCGGTCGGAAGGTCTTGTTTTCAATAT
130 ATTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTCTTGTTTTCAATAT
*
33489 TTTATTCCTGTTT
195 TTTATTCCCGTTT
33502 TCAATGTTTT
Statistics
Matches: 191, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
247 1 0.01
248 190 0.99
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.49
Consensus pattern (248 bp):
TTTTCAATGTTTTATTCCCGTTTCGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATATTTTATTA
CTGTTTTCAATGTTTTATTCCAGTTTTGCCCTTCCCGGTCAGAAGGAGTTGTTTTCAATATTTTA
TTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTCTTGTTTTCAATATT
TTATTCCCGTTTCGCGCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCTTG
Found at i:33502 original size:20 final size:20
Alignment explanation
Indices: 33477--33522 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
33467 CGGAAGGTCT
33477 TGTTTTCAATATTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
33497 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
33517 CGTTTT
1 TGTTTT
33523 GCCCTTCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCC
Found at i:33570 original size:20 final size:20
Alignment explanation
Indices: 33545--33590 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
33535 CGGAAGGAGT
*
33545 TGTTTTCGATATTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
33565 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
33585 CGTTTT
1 TGTTTT
33591 GCCCTTCTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.15, G:0.11, T:0.61
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCC
Found at i:33638 original size:20 final size:20
Alignment explanation
Indices: 33613--33658 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
33603 CGGACGGTAT
33613 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
33633 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
*
33653 CGTTTT
1 TGTTTT
33659 GCCCTTCCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.11, T:0.61
Consensus pattern (20 bp):
TGTTTTCAATGTTTTATTCC
Found at i:38541 original size:21 final size:21
Alignment explanation
Indices: 38517--38565 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
38507 ATAGTTTAGA
*
38517 TTTAATTTACTTTGC-TTTATT
1 TTTAATTTA-ATTGCTTTTATT
* *
38538 TTTAGTTTAATTGCTTTTCTT
1 TTTAATTTAATTGCTTTTATT
38559 TTTAATT
1 TTTAATT
38566 GCTATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTAATTTAATTGCTTTTATT
Found at i:39013 original size:16 final size:15
Alignment explanation
Indices: 38975--39016 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
38965 ACAGAGATTG
*
38975 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
38990 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
39005 ACTAGAAAACAA
1 AC-AGAAAACAA
39017 AGCAGAGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.