Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold965
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: 131858
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3194 original size:62 final size:62
Alignment explanation
Indices: 3117--3241 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
3107 CATCACATCC
* * *
3117 TCACATATAGGAAGTTGGATAAGTTAGAGATCATTGGTTATTCATACTCTAACTTGGCTTGA
1 TCACATACAGGAAGTTGGATAAGTTAGAGATCATTGGGTATTCAGACTCTAACTTGGCTTGA
*
3179 TCACATACAGGAAGTTGGATAAGTTAGAGATCATTGGGTATTCAGACTCTGACTTGGCTTGA
1 TCACATACAGGAAGTTGGATAAGTTAGAGATCATTGGGTATTCAGACTCTAACTTGGCTTGA
3241 T
1 T
3242 GCCAAAATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (62 bp):
TCACATACAGGAAGTTGGATAAGTTAGAGATCATTGGGTATTCAGACTCTAACTTGGCTTGA
Found at i:4415 original size:17 final size:19
Alignment explanation
Indices: 4393--4443 Score: 79
Period size: 17 Copynumber: 2.7 Consensus size: 19
4383 TTTTACCTAG
4393 ATGTATCGATACATT-AT-
1 ATGTATCGATACATTAATA
4410 ATGTATCGATACATTGAATA
1 ATGTATCGATACATT-AATA
4430 ATGTATCGATACAT
1 ATGTATCGATACAT
4444 CTAGTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.48
19 2 0.06
20 14 0.45
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGTATCGATACATTAATA
Found at i:5193 original size:20 final size:20
Alignment explanation
Indices: 5168--5239 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 20
5158 TACCCTGATG
5168 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
** * * *
5188 TATCGATACACGTATGAATT
1 TATCGATACATTTTTCAATA
* * * *
5208 TATCGATATATTCTACAATG
1 TATCGATACATTTTTCAATA
5228 TATCGATACATT
1 TATCGATACATT
5240 ATGTTTTTTT
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:18978 original size:1 final size:1
Alignment explanation
Indices: 18915--18968 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
18905 CTTTACACCC
* * * * * *
18915 AAAAAAAAACAAAAAAAAACAAAACAAAAAAAACAAAAAAAAAAGAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18969 TAGCAAAAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.89, C:0.07, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:20240 original size:29 final size:29
Alignment explanation
Indices: 20198--21373 Score: 1502
Period size: 28 Copynumber: 40.9 Consensus size: 29
20188 AATGTTCATC
*
20198 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20227 CCTTTCAAAGCCCACAAGACAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
20256 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
20285 CTTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20313 CATTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
20341 CCTTTCAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* *
20372 CCTTTTAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20400 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * *
20428 CCTTGCGAAGCCCACAATTTAATGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* **
20457 -CTTTAAAAGCCCACAAGTCAGTGGTGC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20484 CCTTTCAAAGCCCACACAAGTCAGTGGCACC
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
*
20515 CCTTTTAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
20545 CTTTTCAAAGCCCACGAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20573 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
20602 CTTTTCAAA-CCCATAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
20629 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20658 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
20686 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20715 CCTTTCAAAGCCCACAAGTCAGTGGTACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20744 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20773 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20801 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
20829 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
20858 CTTTTCAAAGCCCACAAATCAGTGGTACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
20887 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
20915 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
20944 CCTTTCAAAGCCCACAAGTCAGTGACACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
20973 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
21002 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
21030 CCTTTCAAAGCCCACGAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
21058 CCTTTCAGAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
21086 CCTTTCGAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * *
21114 CATTGCGAAGCCCACAATTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
21143 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
21170 CCTTTTAAAGGCCACACAAGTCAGTGGCACT
1 CCTTTCAAA-GCC-CACAAGTCAGTGGCACT
* * *
21201 CCTTTTAAAGCTCACGCAAGTCAGTGGTAC-
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACT
*
21231 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
21260 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
21287 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
21315 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
21345 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
21374 ACCCTTTTCG
Statistics
Matches: 1027, Mismatches: 93, Indels: 53
0.88 0.08 0.05
Matches are distributed among these distances:
27 9 0.01
28 500 0.49
29 353 0.34
30 109 0.11
31 56 0.05
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:20756 original size:229 final size:226
Alignment explanation
Indices: 20197--21358 Score: 1607
Period size: 229 Copynumber: 5.1 Consensus size: 226
20187 GAATGTTCAT
* *
20197 CCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGACAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * *
20262 AAAGCCCACAAATCAGTGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCCCA
65 AAAGCCCACAAGTCAGTGGCACTCCTTTTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA
* *
20327 CAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTTAGAGCCCACAAGTC
130 CAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCACTCCTTTCA-AACCCACAAGTC
*
20392 AGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCA
192 AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * * **
20427 CCCTTGCGAAGCCCACAATTTAATGGCACTCTTTAAAAGCCCACAAGTCAGTGGTGC-CCTTTCA
1 CCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
*
20491 AAGCCCACACAAGTCAGTGGCACCCCTTTTAAAGCCCACGCAAGTCAGTGGCACCTTTTCAAAGC
66 AAG-CC-CACAAGTCAGTGGCACTCCTTTTAAAGCCCA--CAAGTCAGTGGCACCTTTTCAAAGC
* * * *
20556 CCACGAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAACCCATAAGTC
127 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAACCCACAAGTC
20621 AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
192 AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
20656 CTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
1 C-CCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * *
20721 AAAGCCCACAAGTCAGTGGTACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCC
65 AAAGCCCACAAGTCAGTGGCACTCCTTTTAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCC
*
20786 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAACTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCA
129 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA-CCCACAAGTCA
* * *
20850 GTGGCACTCTTTTCAAAGCCCACAAATCAGTGGTA
193 GTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
20885 CTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
1 C-CCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* *
20950 AAAGCCCACAAGTCAGTGACACT-CTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCC
65 AAAGCCCACAAGTCAGTGGCACTCCTTTT-AAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCC
* * * * *
21014 CACAAGTTAGTGGCACCCTTTCAAAGCCCACGAGTTAGTGGCAC-CCTTTCAGAGCCCACAAGTT
128 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA-AACCCACAAGTC
* *
21078 AGTGGCACCCTTTCGAAGCCCACAAGTTAGTGGCA
192 AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * *
21113 CCATTGCGAAGCCCACAATTTAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTTA
1 CCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
* *
21177 AAGGCCACACAAGTCAGTGGCACTCCTTTTAAAGCTCACGCAAGTCAGTGGTACCTTTTCAAAGC
66 AA-GCC-CACAAGTCAGTGGCACTCCTTTTAAAGC-C-CACAAGTCAGTGGCACCTTTTCAAAGC
* *
21242 CCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGT
127 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA-CCCACAAGT
* **
21306 TAGTGGCATTCTTTCAAAGCCCACGCAAGTCAGTGGCA
191 CAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
21344 CCCTTTTAAAGCCCA
1 CCCTTTCAAAGCCCA
21359 TGCAAGTCAA
Statistics
Matches: 832, Mismatches: 80, Indels: 39
0.87 0.08 0.04
Matches are distributed among these distances:
226 8 0.01
227 75 0.09
228 128 0.15
229 398 0.48
230 139 0.17
231 35 0.04
232 49 0.06
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (226 bp):
CCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
AAGCCCACAAGTCAGTGGCACTCCTTTTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCAC
AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAACCCACAAGTCAGTG
GCACCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:21920 original size:20 final size:20
Alignment explanation
Indices: 21892--21966 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
21882 TCATACCCTG
21892 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* ** * *
21912 ATATATCGATACACGTATGA
1 ATGTATCGATACATTTTTCA
* * *
21932 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
21952 ATGTATCGATACATT
1 ATGTATCGATACATT
21967 ATGTTTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:35045 original size:27 final size:29
Alignment explanation
Indices: 35015--35078 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
35005 GTTAAGATAA
35015 ATTATAAATTCT-TGCAAAAT-TAA-AAAC
1 ATTATAAATT-TATGCAAAATATAATAAAC
* * *
35042 ATTATATATTTATGGAAAATATAATAAAT
1 ATTATAAATTTATGCAAAATATAATAAAC
35071 ATTATAAA
1 ATTATAAA
35079 ATAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 16 0.53
28 3 0.10
29 10 0.33
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (29 bp):
ATTATAAATTTATGCAAAATATAATAAAC
Found at i:40065 original size:52 final size:52
Alignment explanation
Indices: 39995--40115 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
39985 GAAAATTTAT
*
39995 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
40047 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
40099 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
40116 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:40128 original size:52 final size:51
Alignment explanation
Indices: 39995--40135 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
39985 GAAAATTTAT
39995 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
40047 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
40099 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
40136 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:40142 original size:13 final size:13
Alignment explanation
Indices: 40124--40148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40114 CAAAGATCAG
40124 TGTATCGATACAA
1 TGTATCGATACAA
40137 TGTATCGATACA
1 TGTATCGATACA
40149 TGTGAGTAAT
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:40232 original size:13 final size:13
Alignment explanation
Indices: 40214--40238 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40204 CAAAAAAATA
40214 TGTATCGATACAT
1 TGTATCGATACAT
40227 TGTATCGATACA
1 TGTATCGATACA
40239 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:40234 original size:33 final size:33
Alignment explanation
Indices: 40192--40258 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
40182 AGTAGCTTAA
40192 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
40225 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
40258 A
1 A
40259 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:43051 original size:19 final size:22
Alignment explanation
Indices: 43027--43069 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
43017 TTCTTGGGAA
43027 TTTTATCT-CC-AAAA-AATTT
1 TTTTATCTACCTAAAACAATTT
43046 TTTTATCTACCTAAAACAATTT
1 TTTTATCTACCTAAAACAATTT
43068 TT
1 TT
43070 AACCTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 4 0.19
22 7 0.33
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTATCTACCTAAAACAATTT
Found at i:47709 original size:13 final size:13
Alignment explanation
Indices: 47691--47717 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47681 ACATTTTGTG
47691 ATGTATCGATACA
1 ATGTATCGATACA
47704 ATGTATCGATACA
1 ATGTATCGATACA
47717 A
1 A
47718 ATTTAGCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:47779 original size:20 final size:20
Alignment explanation
Indices: 47750--47802 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
47740 CCAATGACTT
**
47750 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
* *
47770 GTATCAATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
47790 GTATCGATACATT
1 GTATCGATACATT
47803 GTATCGATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:47826 original size:20 final size:20
Alignment explanation
Indices: 47801--47853 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
47791 TATCGATACA
47801 TTGTATCGATACTA-TACAAT
1 TTGTATCGATACTATTA-AAT
47821 TTGTATCGATA-TATTTAAAT
1 TTGTATCGATACTA-TTAAAT
*
47841 GTGTATCGATACT
1 TTGTATCGATACT
47854 TTTCAGGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACTATTAAAT
Found at i:49980 original size:22 final size:21
Alignment explanation
Indices: 49955--49996 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
49945 TTATAGAAAA
49955 TATAAAAACATAAAAATCATAT
1 TATAAAAACATAAAAA-CATAT
*
49977 TATAAAAATATAAAAACATA
1 TATAAAAACATAAAAACATA
49997 AGAGTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (21 bp):
TATAAAAACATAAAAACATAT
Found at i:56384 original size:21 final size:20
Alignment explanation
Indices: 56360--56451 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 20
56350 TATAATTTGA
56360 TAAATTTAATTTAAATTAAAT
1 TAAATTTAA-TTAAATTAAAT
*
56381 TAAA-TTAA--AAATAAAATTTT
1 TAAATTTAATTAAATTAAA---T
* *
56401 TTAATTTAATTAATTTAAAT
1 TAAATTTAATTAAATTAAAT
56421 TAATATTTAATT-AA-TAAAT
1 TAA-ATTTAATTAAATTAAAT
*
56440 AAAATTTAATTA
1 TAAATTTAATTA
56452 TAAAATTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
17 7 0.12
18 8 0.14
19 7 0.12
20 12 0.21
21 16 0.29
23 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATTTAATTAAATTAAAT
Found at i:56448 original size:25 final size:25
Alignment explanation
Indices: 56375--56449 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
56365 TTAATTTAAA
*
56375 TTAA-ATTAAATTAA-AAATAAAAT
1 TTAATATTTAATTAATAAATAAAAT
** *
56398 TTTTTAATTTAATTAAT---TTAAA-
1 TTAAT-ATTTAATTAATAAATAAAAT
56420 TTAATATTTAATTAATAAATAAAAT
1 TTAATATTTAATTAATAAATAAAAT
56445 TTAAT
1 TTAAT
56450 TATAAAATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
21 11 0.29
22 3 0.08
23 6 0.16
24 4 0.11
25 14 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTAATATTTAATTAATAAATAAAAT
Found at i:56457 original size:18 final size:18
Alignment explanation
Indices: 56410--56457 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
56400 TTTAATTTAA
* *
56410 TTAATT-TAAATTAATAT
1 TTAATTATAAAATAAAAT
56427 TTAATTA-ATAAATAAAAT
1 TTAATTATA-AAATAAAAT
56445 TTAATTATAAAAT
1 TTAATTATAAAAT
56458 TAATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 18 0.69
19 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATTATAAAATAAAAT
Found at i:56466 original size:11 final size:11
Alignment explanation
Indices: 56408--56467 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
56398 TTTTTAATTT
*
56408 AATTAAT-TTA
1 AATTAATATAA
**
56418 AATTAATATTT
1 AATTAATATAA
56429 AATTAATAAATAA
1 AATTAAT--ATAA
56442 AATTTAATTATAA
1 AA-TTAA-TATAA
56455 AATTAATATAA
1 AATTAATATAA
56466 AA
1 AA
56468 ATATTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
10 7 0.17
11 16 0.38
12 4 0.10
13 10 0.24
14 4 0.10
15 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTAATATAA
Found at i:56631 original size:14 final size:14
Alignment explanation
Indices: 56614--56660 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
56604 AATAATTTTA
56614 ATAATATAAAAAAT
1 ATAATATAAAAAAT
56628 ATAATATTAAAAAA-
1 ATAATA-TAAAAAAT
56642 ATAATA-AAATATAAT
1 ATAATATAAA-A-AAT
56657 ATAA
1 ATAA
56661 ATTTAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.10
13 1 0.03
14 14 0.48
15 11 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATATAAAAAAT
Found at i:56631 original size:23 final size:24
Alignment explanation
Indices: 56605--56658 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
56595 AGTAGATTTA
* * *
56605 ATAATTTTAATAATATAA-AAAAT
1 ATAATATTAAAAAAATAATAAAAT
56628 ATAATATTAAAAAAATAATAAAAT
1 ATAATATTAAAAAAATAATAAAAT
56652 ATAATAT
1 ATAATAT
56659 AAATTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAATATTAAAAAAATAATAAAAT
Found at i:56712 original size:27 final size:27
Alignment explanation
Indices: 56645--56701 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
56635 TAAAAAAATA
56645 ATAAAATATAATATAAATTTAATATTGT
1 ATAAAA-ATAATATAAATTTAATATTGT
*
56673 ATAAAAATAATATAAATTTGATA-TGT
1 ATAAAAATAATATAAATTTAATATTGT
56699 ATA
1 ATA
56702 TATAAACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 6 0.21
27 16 0.57
28 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (27 bp):
ATAAAAATAATATAAATTTAATATTGT
Found at i:57226 original size:27 final size:25
Alignment explanation
Indices: 57179--57240 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
57169 AATATATATT
* ** *
57179 TTTATTAAATATTACTATATTTGATA
1 TTTATTTAATATTAAAATATTT-AAA
57205 TTTATTTAATATTAAAATTATTTAAA
1 TTTATTTAATATTAAAA-TATTTAAA
57231 TTATATTTAA
1 TT-TATTTAA
57241 ATTTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTATTTAATATTAAAATATTTAAA
Found at i:57254 original size:21 final size:20
Alignment explanation
Indices: 57213--57250 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57203 TATTTATTTA
57213 ATATTAAAATTATTTAAATT
1 ATATTAAAATTATTTAAATT
* *
57233 ATATTTAAATTTTTTAAA
1 ATATTAAAATTATTTAAA
57251 ATTAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTAAAATTATTTAAATT
Found at i:57541 original size:29 final size:26
Alignment explanation
Indices: 57508--57563 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
57498 TTTATTTTTT
57508 TTATA-ATTAAAATTTTTTAAATAATAA
1 TTATATATT-AAATTTTTTAAAT-ATAA
* *
57535 TTATATATTTAATTTTTTACATATAA
1 TTATATATTAAATTTTTTAAATATAA
57561 TTA
1 TTA
57564 ATTATTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 16 0.62
28 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATATATTAAATTTTTTAAATATAA
Found at i:58913 original size:21 final size:22
Alignment explanation
Indices: 58889--58931 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
58879 AAGGTTTCAT
58889 TTTGGTTT-AAGTTAAAA-AATG
1 TTTGGTTTGAA-TTAAAAGAATG
58910 TTTGGTTTGAATTAAAAGAATG
1 TTTGGTTTGAATTAAAAGAATG
58932 AGGCCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (22 bp):
TTTGGTTTGAATTAAAAGAATG
Found at i:59960 original size:2 final size:2
Alignment explanation
Indices: 59953--59977 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59943 TTTCAATCAT
59953 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
59978 TTTTTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60215 original size:18 final size:18
Alignment explanation
Indices: 60181--60220 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
60171 TTCAAGTAAA
*
60181 TTAAATAAATTCGGATAT
1 TTAAATAAATTAGGATAT
60199 TTAAA-AAATTAGTGATAT
1 TTAAATAAATTAG-GATAT
60217 TTAA
1 TTAA
60221 TCCATGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (18 bp):
TTAAATAAATTAGGATAT
Found at i:64807 original size:97 final size:97
Alignment explanation
Indices: 64641--64822 Score: 337
Period size: 97 Copynumber: 1.9 Consensus size: 97
64631 GTAATATAGC
* *
64641 TCAAAATGTTTGATTTGATTCAGGCTTCAAAAGTTCATTGATTTGTATTTTTTTGGTATGTTGTA
1 TCAAAAGGTTTGATTTGATTCAGGCTTCAAAAGTTCATTGATTTGTATTTCTTTGGTATGTTGTA
64706 CTTTATCTTATGTTTAAGGTTTGATTCAAGCG
66 CTTTATCTTATGTTTAAGGTTTGATTCAAGCG
*
64738 TCAAAAGGTTTGATTTGATTCAGGCTTCAAAAGTTCATTGATTTGTATTTCTTTGGTATGTTGTG
1 TCAAAAGGTTTGATTTGATTCAGGCTTCAAAAGTTCATTGATTTGTATTTCTTTGGTATGTTGTA
64803 CTTTATCTTATGTTTAAGGT
66 CTTTATCTTATGTTTAAGGT
64823 CATCAAAGAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 82 1.00
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.48
Consensus pattern (97 bp):
TCAAAAGGTTTGATTTGATTCAGGCTTCAAAAGTTCATTGATTTGTATTTCTTTGGTATGTTGTA
CTTTATCTTATGTTTAAGGTTTGATTCAAGCG
Found at i:66453 original size:20 final size:22
Alignment explanation
Indices: 66414--66457 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
66404 TGTTCGTATT
66414 ATTTATTTATTTAAAATTTAAA
1 ATTTATTTATTTAAAATTTAAA
*
66436 ATTT-TTTA-TTAAATTTTAAA
1 ATTTATTTATTTAAAATTTAAA
66456 AT
1 AT
66458 ATAAATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 4 0.19
22 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATTTATTTAAAATTTAAA
Found at i:72332 original size:2 final size:2
Alignment explanation
Indices: 72325--72353 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
72315 CAATGCCCTT
72325 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72354 TTTTGGCAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73257 original size:28 final size:28
Alignment explanation
Indices: 73225--73278 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
73215 GCGTTTGGTT
73225 TAAGAATGGAATAAAGAAGG-AATAGTAG
1 TAAGAATGGAATAAAG-AGGAAATAGTAG
73253 TAAGAATGGAATAAAGAGGAAATAGT
1 TAAGAATGGAATAAAGAGGAAATAGT
73279 TATTCCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.54, C:0.00, G:0.28, T:0.19
Consensus pattern (28 bp):
TAAGAATGGAATAAAGAGGAAATAGTAG
Found at i:74179 original size:2 final size:2
Alignment explanation
Indices: 74172--74241 Score: 59
Period size: 2 Copynumber: 34.0 Consensus size: 2
74162 TTGGTCTGAA
* * * * * * *
74172 AT AT AT AT AC AT AT AT AT AT AT AT AT AC AT GAG AT TT GT CT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
74215 AT AT AT AT ACT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT
74242 TTGCTATCAC
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
2 51 0.94
3 3 0.06
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:79760 original size:12 final size:13
Alignment explanation
Indices: 79725--79771 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
79715 TTACAAATAA
* *
79725 AAAATGTATTTAT
1 AAAATATATATAT
*
79738 AAATTATATATAT
1 AAAATATATATAT
79751 AAAATA-ATATAT
1 AAAATATATATAT
*
79763 AAATTATAT
1 AAAATATAT
79772 TTCAAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AAAATATATATAT
Found at i:93910 original size:20 final size:20
Alignment explanation
Indices: 93885--93938 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
93875 TATTTTAGGC
* * *
93885 ATGTATCGATACATTCATTT
1 ATGTATCGATACAGTCACTA
*
93905 ATGTATCGATATAGTCACTA
1 ATGTATCGATACAGTCACTA
93925 ATTGTATCGATACA
1 A-TGTATCGATACA
93939 AATCATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAGTCACTA
Found at i:94744 original size:61 final size:61
Alignment explanation
Indices: 94575--95308 Score: 232
Period size: 61 Copynumber: 12.8 Consensus size: 61
94565 GGACTTAAAG
* * ** *
94575 ATAA-AAAGAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGCACTTAAAGATGTGAAGA
1 ATAATAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * *
94636 ATGATAAAGGTGTCAATATGCTGATTCACGGCTAGCGATATCT-GGCTTGAAA-ATGAGAAGA
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT-TGGGCTT-AAAGATGAGAAGA
*
94697 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTT--A-AT-----G-
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * * * * * *
94749 TTAACAAAGATGCCAATGTGCTAATTCAAGGCCAACGACATTGGACTTAAAGAT-----G-
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * * ** * *
94804 ---ACAAAGATGCCAATATGTTGATTTAAGGGTAGTGATATTGGACTT--A-A-GA-AAG-
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * * *
94856 A-AA-AAA-GTGCCAATGTGTTGATTCAAGGCCATCGACATTGGAC-T-----T-A-AA-A
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * * * *
94905 ATAA-AAAGAGTGCCAATGTGCTGATTTAAGGCAAACGACATTGGACTTAAAGAT-ACGAAGA
1 ATAATAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGA-GAAGA
* * * * * * * *
94966 ATGATAAAGGTCCCAATATGCTGATTTACGGCTAGCG--ATCGGGCTTGAAGATGATAAGA
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * * * * *
95025 ATGA-GAAGAATGCCAATATGCTGATTCAAGGCTAGCAACATAGGG-TT-----T-A-AA-A
1 ATAATAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
** * * * ** * *
95077 ATGGTAAAGGTGCCAATATGCTGATTCAAGGCTAGCAATATCGGATTTAAAGA-AACAAG-
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * * * * * * *
95136 AT-TTGACAA-GTGCCAATGTGTTGATTCAGGGCTAACGACATTGGGCTTGAAGATGAGAAAA
1 ATAAT-A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * ** * * *
95197 ATGATAAAGGTACCAATATGCTGATTCAAGGCCAGTGATATTGAACTTAAAGATAATAAGG
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
* * * * * * *
95258 ATGAGAATGATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAA
1 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
95309 AATGGTAAAT
Statistics
Matches: 520, Mismatches: 105, Indels: 96
0.72 0.15 0.13
Matches are distributed among these distances:
49 5 0.01
50 6 0.01
51 1 0.00
52 176 0.34
53 12 0.02
54 3 0.01
55 4 0.01
58 10 0.02
59 82 0.16
60 13 0.03
61 195 0.38
62 13 0.03
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (61 bp):
ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAAGA
Found at i:94785 original size:52 final size:52
Alignment explanation
Indices: 94697--94959 Score: 269
Period size: 52 Copynumber: 5.1 Consensus size: 52
94687 AATGAGAAGA
* * * * * *
94697 ATAATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAATG
1 ATAACAAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAG
* *
94749 TTAACAAAGATGCCAATGTGCTAATTCAAGGCCAACGACATTGGACTTAAAG
1 ATAACAAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAG
* * * * ** ** * *
94801 ATGACAAAGATGCCAATATGTTGATTTAAGGGTAGTGATATTGGACTTAAGAA
1 ATAACAAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAA-AG
* * * * *
94854 AGAAAAAAG-TGCCAATGTGTTGATTCAAGGCCATCGACATTGGACTTAAAA
1 ATAACAAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAG
* *
94905 ATAA-AAAGAGTGCCAATGTGCTGATTTAAGGCAAACGACATTGGACTTAAAG
1 ATAACAAAGA-TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAG
94957 ATA
1 ATA
94960 CGAAGAATGA
Statistics
Matches: 172, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
50 4 0.02
51 5 0.03
52 156 0.91
53 7 0.04
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (52 bp):
ATAACAAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAG
Found at i:94942 original size:156 final size:166
Alignment explanation
Indices: 94534--95417 Score: 492
Period size: 172 Copynumber: 5.2 Consensus size: 166
94524 GTCTGTGATA
* *
94534 TGCCAATGTGTAGATTCAAGGCC-TAC-ACACTGGACTTAAAGATAAAAAGAGTGCCAATGTGCT
1 TGCCAATGTGTTGATTCAAGGCCAT-CGACATTGGACTTAAAGATAAAAAGAGTGCCAATGTGCT
* * *
94597 GATTCAAGGCCAGCGACATTGCACTTAAAGATGTGAAGAATGATAAAGGTGTCAATATGCTGATT
65 GATTCAAGGCCAACGACATTGGACTTAAAGA--TGAAGAATG---AA-GTGCCAATATGCTGATT
*
94662 CACGGCTAGCGATATCTGGCTTGAAAATGAGAAGAATAATAAAGG
124 CAAGGCTAGCGATATCTGGCTT--AAATGAGAAGAATAATAAAGG
* * * * * * *
94707 TGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAATGTTAACAAAGA-TGCCAATGTGCT
1 TGCCAATGTGTTGATTCAAGGCCATCGACATTGGACTTAAAGATAA-AAAGAGTGCCAATGTGCT
* * *
94771 AATTCAAGGCCAACGACATTGGACTTAAAGATGACA-AA-G-A-TGCCAATATGTTGATTTAAGG
65 GATTCAAGGCCAACGACATTGGACTTAAAGATGA-AGAATGAAGTGCCAATATGCTGATTCAAGG
* *
94832 GTAGTGATAT-TGGACTT-AA-GA-AAG-A-AA-AAA-G
129 CTAGCGATATCTGG-CTTAAATGAGAAGAATAATAAAGG
*
94863 TGCCAATGTGTTGATTCAAGGCCATCGACATTGGACTTAAAAATAAAAAGAGTGCCAATGTGCTG
1 TGCCAATGTGTTGATTCAAGGCCATCGACATTGGACTTAAAGATAAAAAGAGTGCCAATGTGCTG
* * * *
94928 ATTTAAGGCAAACGACATTGGACTTAAAGATACGAAGAATGATAAAGGTCCCAATATGCTGATTT
66 ATTCAAGGCCAACGACATTGGACTTAAAGAT--GAAGAATG---AA-GTGCCAATATGCTGATTC
* * * * * *
94993 ACGGCTAGCG--ATCGGGCTTGAAGATGATAAGAATGA-GAAGAA
125 AAGGCTAGCGATATCTGGCTT-AA-ATGAGAAGAATAATAAAG-G
* * * * * * ** * ** *
95035 TGCCAATATGCTGATTCAAGGCTAGCAACATAGGGTTTAAAAATGGTAAAG-GTGCCAATATGCT
1 TGCCAATGTGTTGATTCAAGGCCATCGACATTGGACTTAAAGAT-AAAAAGAGTGCCAATGTGCT
* * * * * * ** * * *
95099 GATTCAAGGCTAGCAATATCGGATTTAAAGAAACAAGATTTGACAAGTGCCAATGTGTTGATTCA
65 GATTCAAGGCCAACGACATTGGACTTAAAG-ATGAAGA-ATG--AAGTGCCAATATGCTGATTCA
* * * * *
95164 GGGCTAACGACAT-TGGGCTTGAAGATGAGAAAAATGATAAAGG
126 AGGCTAGCGATATCT-GGCTT-AA-ATGAGAAGAATAATAAAGG
* * * * *
95207 TACCAATATGCTGATTCAAGGCCAGT-GATATTGAACTTAAAGATAATAAGGATGAGAATGATGC
1 TGCCAATGTGTTGATTCAAGGCCA-TCGACATTGGACTTAAAGAT-A-AA--A--AG-A-G-TGC
* * * * * *
95271 TAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAATG--GTAA--ATGTGCCAATATACT
56 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAG-AATGAAGTGCCAATATGCT
* * * * * *
95332 GATTCAAGGCCACCGATATC-GGACTTAAA-GA-AAGAAGATTTGACGAG
120 GATTCAAGGCTAGCGATATCTGG-CTTAAATGAGAAGAATA-ATAAAG-G
* * *
95379 TGCCAATGTGTTGATTCAAAGCCAACGACATTGGGCTTA
1 TGCCAATGTGTTGATTCAAGGCCATCGACATTGGACTTA
95418 GAAGGGTTGC
Statistics
Matches: 543, Mismatches: 119, Indels: 99
0.71 0.16 0.13
Matches are distributed among these distances:
155 5 0.01
156 80 0.15
157 4 0.01
158 6 0.01
159 2 0.00
160 3 0.01
161 2 0.00
162 2 0.00
163 6 0.01
164 5 0.01
165 51 0.09
166 1 0.00
167 3 0.01
168 3 0.01
169 1 0.00
170 29 0.05
171 12 0.02
172 165 0.30
173 35 0.06
174 83 0.15
175 6 0.01
177 2 0.00
178 1 0.00
179 1 0.00
180 2 0.00
181 33 0.06
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (166 bp):
TGCCAATGTGTTGATTCAAGGCCATCGACATTGGACTTAAAGATAAAAAGAGTGCCAATGTGCTG
ATTCAAGGCCAACGACATTGGACTTAAAGATGAAGAATGAAGTGCCAATATGCTGATTCAAGGCT
AGCGATATCTGGCTTAAATGAGAAGAATAATAAAGG
Found at i:95336 original size:233 final size:231
Alignment explanation
Indices: 94913--95421 Score: 653
Period size: 233 Copynumber: 2.2 Consensus size: 231
94903 AAATAAAAAG
* * * * * *
94913 AGTGCCAATGTGCTGATTTAAGGCAAACGACATTGGACTTAAAGATACGAAGAATGATAAAGGTC
1 AGTGCCAATGTGTTGATTCAAGGCAAACGACATTGGGCTTGAAGATACGAAAAATGATAAAGGTA
* * * ** * *
94978 CCAATATGCTGATTTACGGCTAGCGATCGGGCTTGAAGATGATAAGAATGAGAAGAATGCCAATA
66 CCAATATGCTGATTCAAGGCCAGCGATCGAACTTAAAGATAATAAGAATGAGAAGAATGCCAATA
* * *
95043 TGCTGATTCAAGGCTAGCAACATAGGGTTTAAAAATGGTAAAGGTGCCAATATGCTGATTCAAGG
131 TGCTGATTCAAGGCCAGCAACATAGGGCTTAAAAATGGTAAAGGTGCCAATATACTGATTCAAGG
* * *
95108 CTAGCAATATCGGATTTAAAGAAACAAGATTTGACA
196 CCACCAATATCGGACTTAAAGAAACAAGATTTGACA
* *
95144 AGTGCCAATGTGTTGATTCAGGGCTAACGACATTGGGCTTGAAGATGA-GAAAAATGATAAAGGT
1 AGTGCCAATGTGTTGATTCAAGGCAAACGACATTGGGCTTGAAGAT-ACGAAAAATGATAAAGGT
* * * *
95208 ACCAATATGCTGATTCAAGGCCAGTGATATTGAACTTAAAGATAATAAGGATGAGAATG-ATGCT
65 ACCAATATGCTGATTCAAGGCCAGCG--ATCGAACTTAAAGATAATAAGAATGAGAA-GAATGCC
* * * *
95272 AATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAATGGTAAATGTGCCAATATACTGATTC
127 AATATGCTGATTCAAGGCCAGCAACATAGGGCTTAAAAATGGTAAAGGTGCCAATATACTGATTC
* * *
95337 AAGGCCACCGATATCGGACTTAAAGAAAGAAGATTTGACG
192 AAGGCCACCAATATCGGACTTAAAGAAACAAGATTTGACA
* *
95377 AGTGCCAATGTGTTGATTCAAAGCCAACGACATTGGGCTTAGAAG
1 AGTGCCAATGTGTTGATTCAAGGCAAACGACATTGGGCTT-GAAG
95422 GGTTGCCACC
Statistics
Matches: 238, Mismatches: 35, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
231 76 0.32
232 1 0.00
233 156 0.66
234 5 0.02
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (231 bp):
AGTGCCAATGTGTTGATTCAAGGCAAACGACATTGGGCTTGAAGATACGAAAAATGATAAAGGTA
CCAATATGCTGATTCAAGGCCAGCGATCGAACTTAAAGATAATAAGAATGAGAAGAATGCCAATA
TGCTGATTCAAGGCCAGCAACATAGGGCTTAAAAATGGTAAAGGTGCCAATATACTGATTCAAGG
CCACCAATATCGGACTTAAAGAAACAAGATTTGACA
Found at i:95342 original size:113 final size:111
Alignment explanation
Indices: 95193--95417 Score: 272
Period size: 113 Copynumber: 2.0 Consensus size: 111
95183 TGAAGATGAG
* ** * *
95193 AAAAATGATAAAGGTACCAATATGCTGATTCAAGGCCAGTGATATTGAACTTAAAGATAATAAGG
1 AAAAATGATAAAGGTACCAATATACTGATTCAAGGCCACCGATATCGAACTTAAAGA-AAGAA-G
* * * *
95258 ATGAGAATGA-TGCTAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
64 ATGAG-ACGAGTGCCAATGTGCTGATTCAAAGCCAACGACATTGGGCTT
* * * *
95306 AAAAATGGTAAATGTGCCAATATACTGATTCAAGGCCACCGATATCGGACTTAAAGAAAGAAGAT
1 AAAAATGATAAAGGTACCAATATACTGATTCAAGGCCACCGATATCGAACTTAAAGAAAGAAGAT
** *
95371 TTGACGAGTGCCAATGTGTTGATTCAAAGCCAACGACATTGGGCTT
66 GAGACGAGTGCCAATGTGCTGATTCAAAGCCAACGACATTGGGCTT
95417 A
1 A
95418 GAAGGGTTGC
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
110 3 0.03
111 39 0.41
112 4 0.04
113 49 0.52
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (111 bp):
AAAAATGATAAAGGTACCAATATACTGATTCAAGGCCACCGATATCGAACTTAAAGAAAGAAGAT
GAGACGAGTGCCAATGTGCTGATTCAAAGCCAACGACATTGGGCTT
Found at i:95534 original size:33 final size:33
Alignment explanation
Indices: 95410--95704 Score: 274
Period size: 32 Copynumber: 9.2 Consensus size: 33
95400 CCAACGACAT
*
95410 TGGGC-TTAGAAG--GGTTGCCACCGACGTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
** *
95440 TGGGCTTTAG-AGAAGGTTATCACCAACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
* *
95472 TGGGCTTTAG-A-AAGATTGCCA-CTAGCTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGA-CTTGTG
* *
95503 TGGGCTTTAGAAGGAGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
* *
95536 TGGGCTTTGGAAAAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
* * *
95569 TGGGCTTTGGAAAAAGGTTGCCACCGGCTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
* *
95602 TGGGCTTTTAG-AG-GGGTTACCACC-AGCTTGTG
1 TGGGC-TTTAGAAGAAGGTTGCCACCGA-CTTGTG
* * *
95634 TGGTCTTTTAG-AG-GGGTTGCCACCGGCTTGTG
1 TGGGC-TTTAGAAGAAGGTTGCCACCGACTTGTG
* * *
95666 TGGGCTTTAG-AGAAGCTTTCCATCGACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
95698 TGGGCTT
1 TGGGCTT
95705 GGCAGTATGC
Statistics
Matches: 224, Mismatches: 30, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
30 9 0.04
31 34 0.15
32 94 0.42
33 81 0.36
34 6 0.03
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.30
Consensus pattern (33 bp):
TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
Found at i:95739 original size:20 final size:20
Alignment explanation
Indices: 95714--95758 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
95704 TGGCAGTATG
*
95714 CATTTACTAATGTATCGATA
1 CATTTACAAATGTATCGATA
95734 CATTTACAAATGTATCGATA
1 CATTTACAAATGTATCGATA
*
95754 TATTT
1 CATTT
95759 CCTTGGCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (20 bp):
CATTTACAAATGTATCGATA
Found at i:97383 original size:57 final size:57
Alignment explanation
Indices: 97283--97559 Score: 288
Period size: 57 Copynumber: 4.8 Consensus size: 57
97273 AAAATACAAG
* * * *
97283 AAATTTTCATGAAAA-TCTCTAGATCATAGAAAATAACTTAAATGACCCCAACATAAAT
1 AAATTTGCAT-AAAAGTCCCTAGATCATA-AAAATGACCTAAATGACCCCAACATAAAT
** * *
97341 AAATTTGCATAAAAGTCTTTAGATTATAAAAATGACCTAAATGACCCCAACATACAT
1 AAATTTGCATAAAAGTCCCTAGATCATAAAAATGACCTAAATGACCCCAACATAAAT
* * * *
97398 AAATTTGCATAAAAGTCCCAAGATCATAAAGATGACCTAAATGACCTCAATA-AATAT
1 AAATTTGCATAAAAGTCCCTAGATCATAAAAATGACCTAAATGACCCCAACATAA-AT
* * * * * *
97455 AAATTTACATAAAAGTACCTAGATCATAAAAAATGACCTAAATGATCCTAACACACAT
1 AAATTTGCATAAAAGTCCCTAGATCAT-AAAAATGACCTAAATGACCCCAACATAAAT
* * * *
97513 AAATATGCAAAAAAAGTCCCTAAATCATAAAAAATGACCTAAGTGAC
1 AAATTTGC-ATAAAAGTCCCTAGATCAT-AAAAATGACCTAAATGAC
97560 ATCAAAAATC
Statistics
Matches: 184, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
56 1 0.01
57 101 0.55
58 48 0.26
59 34 0.18
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.25
Consensus pattern (57 bp):
AAATTTGCATAAAAGTCCCTAGATCATAAAAATGACCTAAATGACCCCAACATAAAT
Found at i:97604 original size:117 final size:114
Alignment explanation
Indices: 97360--97617 Score: 304
Period size: 117 Copynumber: 2.2 Consensus size: 114
97350 TAAAAGTCTT
* * *
97360 TAGATTATAAAAATGACCTAAATGACCCCAACATACATAAATTTGCATAAAAGTCCCAAGATCAT
1 TAGATTATAAAAATGACCTAAATGACCCCAACACACATAAATATGCAAAAAAGTCCCAAGATCAT
* * * *
97425 AAAGATGACCTAAATGACCTCAATAAATATAAATTTACATAAAAGTACC
66 AAAAATGACCTAAATGACATCAATAAATACAAAATTACATAAAAGTACC
* * *
97474 TAGATCATAAAAAATGACCTAAATGATCCTAACACACATAAATATGCAAAAAAAGTCCCTAA-AT
1 TAGATTAT-AAAAATGACCTAAATGACCCCAACACACATAAATATGC-AAAAAAGTCCC-AAGAT
* ** *
97538 CATAAAAAATGACCTAAGTGACATCAA-AAATCACAAAATTACATCTAAGTCCC
63 CAT-AAAAATGACCTAAATGACATCAATAAAT-ACAAAATTACATAAAAGTACC
* *
97591 TAGATTATGAAAAATAAACTAAATGAC
1 TAGATTAT-AAAAATGACCTAAATGAC
97618 ATAAAATTTC
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
114 7 0.06
115 34 0.28
116 19 0.16
117 60 0.50
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (114 bp):
TAGATTATAAAAATGACCTAAATGACCCCAACACACATAAATATGCAAAAAAGTCCCAAGATCAT
AAAAATGACCTAAATGACATCAATAAATACAAAATTACATAAAAGTACC
Found at i:97707 original size:58 final size:58
Alignment explanation
Indices: 97339--97708 Score: 205
Period size: 58 Copynumber: 6.4 Consensus size: 58
97329 CCCAACATAA
* * * * *** * *
97339 ATAAATTTGCATAAAAGTCTTTAGATTA-TAAAAATGACCTAAATGACCCCAACATAC
1 ATAAAATTACATAAAAGTCCTTAGATTACGAAAAATGACCTAAATGACATTAAAATTC
* * ** * * * * * *
97396 ATAAATTTGCATAAAAGTCCCAAGATCA-TAAAGATGACCTAAATGACCTCAATAAAT-
1 ATAAAATTACATAAAAGTCCTTAGATTACGAAAAATGACCTAAATGACATTAA-AATTC
* * ** * * **
97453 ATAAATTTACATAAAAGTACC-TAGATCATAAAAAATGACCTAAATGATC-CTAACACAC
1 ATAAAATTACATAAAAGT-CCTTAGATTACGAAAAATGACCTAAATGA-CATTAAAATTC
* * * * * ** * * *
97511 AT-AAATATGCAAAAAAAGTCCCTAAATCATAAAAAATGACCTAAGTGACATCAAAAATC
1 ATAAAAT-TAC-ATAAAAGTCCTTAGATTACGAAAAATGACCTAAATGACATTAAAATTC
* ** * * * *
97570 ACAAAATTACATCTAAGTCCCTAGATTATGAAAAATAAACTAAATGACA-TAAAATTTC
1 ATAAAATTACATAAAAGTCCTTAGATTACGAAAAATGACCTAAATGACATTAAAA-TTC
* *
97628 ATAAAATTACATTAAATTCCTTAGATTACGAAAAATGACCTAAATGACATTAAAATTC
1 ATAAAATTACATAAAAGTCCTTAGATTACGAAAAATGACCTAAATGACATTAAAATTC
* *
97686 ATGAAATGACATAAAAGTCCTTA
1 ATAAAATTACATAAAAGTCCTTA
97709 AGTCATGGAA
Statistics
Matches: 248, Mismatches: 53, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
57 77 0.31
58 123 0.50
59 44 0.18
60 4 0.02
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.26
Consensus pattern (58 bp):
ATAAAATTACATAAAAGTCCTTAGATTACGAAAAATGACCTAAATGACATTAAAATTC
Found at i:99635 original size:57 final size:57
Alignment explanation
Indices: 99566--99688 Score: 230
Period size: 57 Copynumber: 2.2 Consensus size: 57
99556 GTGGTTTTGC
99566 TTTTTGGA-TTAAAAGAGTTGCAAGCAATTAATGGAATGGTAAGGCTATGGTTTTATG
1 TTTTT-GATTTAAAAGAGTTGCAAGCAATTAATGGAATGGTAAGGCTATGGTTTTATG
99623 TTTTTGATTTAAAAGAGTTGCAAGCAATTAATGGAATGGTAAGGCTATGGTTTTATG
1 TTTTTGATTTAAAAGAGTTGCAAGCAATTAATGGAATGGTAAGGCTATGGTTTTATG
99680 TTTTTGATT
1 TTTTTGATT
99689 CTAGATGGGT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 2 0.03
57 63 0.97
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (57 bp):
TTTTTGATTTAAAAGAGTTGCAAGCAATTAATGGAATGGTAAGGCTATGGTTTTATG
Found at i:100371 original size:20 final size:21
Alignment explanation
Indices: 100348--100400 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
100338 ACAATTCAAA
** *
100348 GTATCGATACATGTTACA-AT
1 GTATCGATACATGAAAAAGAT
100368 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAAGAT
100389 GTATCGATACAT
1 GTATCGATACAT
100401 TTCATTGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
GTATCGATACATGAAAAAGAT
Found at i:100468 original size:13 final size:13
Alignment explanation
Indices: 100450--100475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100440 TACACAAAGT
100450 ATGTATCGATACA
1 ATGTATCGATACA
100463 ATGTATCGATACA
1 ATGTATCGATACA
100476 CGAAAAATTG
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:100473 original size:32 final size:33
Alignment explanation
Indices: 100432--100495 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
100422 TAGCCAAACT
*
100432 TGTATCGATACAC--AAAGTATGTATCGATACAA
1 TGTATCGATACACGAAAAAT-TGTATCGATACAA
100464 TGTATCGATACACGAAAAATTGTATCGATACA
1 TGTATCGATACACGAAAAATTGTATCGATACA
100496 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 12 0.41
34 4 0.14
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACGAAAAATTGTATCGATACAA
Found at i:100493 original size:33 final size:32
Alignment explanation
Indices: 100432--100495 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
100422 TAGCCAAACT
*
100432 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAATATGTATCGATACAA
100464 TGTATCGATACACGAAAA-ATTGTATCGATACA
1 TGTATCGATACAC-AAAATA-TGTATCGATACA
100496 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAATATGTATCGATACAA
Found at i:110752 original size:330 final size:329
Alignment explanation
Indices: 110032--110827 Score: 721
Period size: 330 Copynumber: 2.4 Consensus size: 329
110022 CAATTTTCAT
* * * * * *
110032 TAAATTAGTTTTT-CAAAATTCTTTTTGTTTCCTCAGTTTTTCATTTTTCT-TTTGAAAACTTCC
1 TAAATTA-TTTTTGAAAAATTCTTTTTATTTCATAAGTTTTTCATTTTTTTCTTTG-AAA-TTCT
* * * * * * * * *
110095 CGT-TTTC-GAAATACAAAGTTTTCTTCATCGTATATTTTTTCG-GGAAGATTTTTATTGGTTTA
63 CGTATTTCTGAAATACAGAGTTTTCTACTTAGTAAATGTTTTCGAGG-GGATTTTTCTTAGTTTA
* *
110157 AAATTTTAATATTTATAAAATATTATCACTTAGTTACCATCAAATCAGTTTCAAAAAAATTATTT
127 AATTTTTAA-ATTTATAAAATATCATCACTTAGTTACCATCAAATCAGTTTCAAAAAAATTATTT
** * * *** **
110222 TATTCCATGAGTTTTTGATTTTCTTTTGGAATTCCTTCTGTTTTCGAAATACAGAGCTTTATTCT
191 TATTCCATGAAATTTTCATTTTCTCTCAAAATT-CTTCTGTTTTCGAAATACAGAAATTTATTCT
** * *
110287 CCATAATGTTTTTGGGAGGATTTTCTTTGGTTTAAGATTTTTAAAATTCATCAAATATTATTACT
255 CCATAATGTTTTCAGGAGGATTTTCTTTGATTTAAGATTTTTAAAATTCATCAAATATCATTACT
*
110352 TAATCACCAT
320 TAATCACCAG
* * * * * ** * * *
110362 TTAATAAGTTTTGAGAATTTCTTTTTATTTCACGAGTTTTTCA-GTTTTTCCTTAAAATTCTAC-
1 TAAATTATTTTTGAAAAATTCTTTTTATTTCATAAGTTTTTCATTTTTTTCTTTGAAATTCT-CG
*
110425 TATTTCTGAAATACAGAGTTTTCTACTTTGTAAATGTTTTCGAGGGGATTTTTCTTAGTTTATAA
65 TATTTCTGAAATACAGAGTTTTCTACTTAGTAAATGTTTTCGAGGGGATTTTTCTTAGTTTA-AA
* * * * **
110490 TTTTTAAATTTATCAAATATCATCATTTAATTTA-CATGAAATCAGTTTTGAAAAAATTATTTTA
129 TTTTTAAATTTATAAAATATCATCACTT-AGTTACCATCAAATCAGTTTCAAAAAAATTATTTTA
* *
110554 TTTCATGAAATTTTCATTTT-TCTCAAAATT-TTCCTGTTTAT-GAAATAC-GAAATTTTTTACT
193 TTCCATGAAATTTTCATTTTCTCTCAAAATTCTT-CTGTTT-TCGAAATACAGAAATTTATT-CT
* *
110615 CCGTAAATGTTTTCAGGAGGAATTTTC-TTGATTTATA-ATTTTTATAATTCATCAAATATCATT
255 CCAT-AATGTTTTCAGGAGG-ATTTTCTTTGATTTA-AGATTTTTAAAATTCATCAAATATCATT
* * *
110678 ATTTTATTCA-TAG
317 A-CTTAATCACCAG
*
110691 TAAATTATTTTTGAAAAATTC-TTTTATTTTCATAAGTTTTTCATTTTTTTCTTTGAAATTCTCT
1 TAAATTATTTTTGAAAAATTCTTTTTA-TTTCATAAGTTTTTCATTTTTTTCTTTGAAATTCTCG
* * * * *
110755 TATTT-TCGAAAAACTGAGTTTTCTA-TTCAATAAATGTTTTTGAGAGGATTTTTCTCTA-TTTA
65 TATTTCT-GAAATACAGAGTTTTCTACTT-AGTAAATGTTTTCGAGGGGATTTTTCT-TAGTTT-
110817 AAATTTTTAAA
126 AAATTTTTAAA
110828 ATTCATCTAA
Statistics
Matches: 375, Mismatches: 69, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
327 9 0.02
328 27 0.07
329 103 0.27
330 219 0.58
331 17 0.05
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (329 bp):
TAAATTATTTTTGAAAAATTCTTTTTATTTCATAAGTTTTTCATTTTTTTCTTTGAAATTCTCGT
ATTTCTGAAATACAGAGTTTTCTACTTAGTAAATGTTTTCGAGGGGATTTTTCTTAGTTTAAATT
TTTAAATTTATAAAATATCATCACTTAGTTACCATCAAATCAGTTTCAAAAAAATTATTTTATTC
CATGAAATTTTCATTTTCTCTCAAAATTCTTCTGTTTTCGAAATACAGAAATTTATTCTCCATAA
TGTTTTCAGGAGGATTTTCTTTGATTTAAGATTTTTAAAATTCATCAAATATCATTACTTAATCA
CCAG
Found at i:114684 original size:158 final size:158
Alignment explanation
Indices: 114456--115014 Score: 605
Period size: 158 Copynumber: 3.6 Consensus size: 158
114446 TTTCCTAAGA
* * * * * *
114456 GATACTCTAACCCTATTTTTATTTCCAAAATATTGAATTTTTCATCTTCG-GGATATTCCAGCCC
1 GATACTCTAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATC-TCGAGGATACTCTAACCC
* * *
114520 CATCAATTCTGAGGGGATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTTGG
65 CATCAATTCTGAGGGGATACTCCAACCTCAGTTTTATTTTCAAAATATTAAATTTTTCATCTTGG
* *
114585 AGATACTCTAACCCCATCAATTCTGAGGG
130 AGATACTCCAACCTCATCAATTCTGAGGG
**** *
114614 GATACTCTAACCTTGGTTTTATTTCCAAAATATTAAATTTTTCATCTCGAGGATACTTTAACCCC
1 GATACTCTAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCTCGAGGATACTCTAACCCC
* * * * *
114679 GTCAATTCCGAGGGGATACTCTAACCTCAGTTTTATTTTTAAAATATTAAATTTTTCATC-TCGA
66 ATCAATTCTGAGGGGATACTCCAACCTCAGTTTTATTTTCAAAATATTAAATTTTTCATCTTGGA
* * *
114743 GGATACTCCAAGCTCATTAATTCTGAGGA
131 -GATACTCCAACCTCATCAATTCTGAGGG
* * * * ** * * *
114772 GATACTCCAACCTCGCTTTTGTTTCCAAAATATT-AATTTTTTTTCTTGGGGATACTCTAACCTC
1 GATACTCTAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCTCGAGGATACTCTAACCCC
* * * * * * *
114836 GTTATTTTTAAGGAGATATTCCAACCTC-GTTTTATTTTCAAAATATTAAATTTTTCATCTTGG-
66 ATCAATTCTGAGGGGATACTCCAACCTCAGTTTTATTTTCAAAATATTAAATTTTTCATCTTGGA
**
114899 GATACTCCAACCTCATCAATTCCAAGGG
131 GATACTCCAACCTCATCAATTCTGAGGG
** **
114927 GATACTCTAACCCCACTCATATTTCCAAAATGCTAAATTTTTCATCTCGA-GATAC-CTAACCCC
1 GATACTCTAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCTCGAGGATACTCTAACCCC
* *
114990 AT--ATTCGGAGGGGATACTCTAACCT
66 ATCAATTCTGAGGGGATACTCCAACCT
115015 TGTTTCTTTT
Statistics
Matches: 330, Mismatches: 67, Indels: 14
0.80 0.16 0.03
Matches are distributed among these distances:
152 16 0.05
154 8 0.02
155 54 0.16
156 41 0.12
157 52 0.16
158 159 0.48
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (158 bp):
GATACTCTAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCTCGAGGATACTCTAACCCC
ATCAATTCTGAGGGGATACTCCAACCTCAGTTTTATTTTCAAAATATTAAATTTTTCATCTTGGA
GATACTCCAACCTCATCAATTCTGAGGG
Found at i:114964 original size:78 final size:78
Alignment explanation
Indices: 114456--115014 Score: 538
Period size: 79 Copynumber: 7.2 Consensus size: 78
114446 TTTCCTAAGA
* * * *
114456 GATACTCTAACC-CTATTTTTATTTCCAAAATATTGAATTTTTCATCTTCGGGATATTCCAGCCC
1 GATACTCTAACCTC-AGTTTTATTTCCAAAATATTAAATTTTTCATCTT-GGGATACTCCAACCC
114520 CATCAATTCTGAGGG
64 CATCAATTCTGAGGG
* * * * * *
114535 GATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTTGGAGATACTCTAACCCC
1 GATACTCTAACCTCAGTTTTATTTCCAAAATATTAAATTTTTCATCTTGG-GATACTCCAACCCC
114600 ATCAATTCTGAGGG
65 ATCAATTCTGAGGG
** * **
114614 GATACTCTAACCTTGGTTTTATTTCCAAAATATTAAATTTTTCATCTCGAGGATACTTTAACCCC
1 GATACTCTAACCTCAGTTTTATTTCCAAAATATTAAATTTTTCATCTTG-GGATACTCCAACCCC
* *
114679 GTCAATTCCGAGGG
65 ATCAATTCTGAGGG
** * * *
114693 GATACTCTAACCTCAGTTTTATTTTTAAAATATTAAATTTTTCATCTCGAGGATACTCCAAGCTC
1 GATACTCTAACCTCAGTTTTATTTCCAAAATATTAAATTTTTCATCTTG-GGATACTCCAACCCC
* *
114758 ATTAATTCTGAGGA
65 ATCAATTCTGAGGG
* * ** * *
114772 GATACTCCAACCTC-GCTTTTGTTTCCAAAATATT-AATTTTTTTTCTTGGGGATACTCTAACCT
1 GATACTCTAACCTCAG-TTTTATTTCCAAAATATTAAATTTTTCATCTT-GGGATACTCCAACCC
* * * * * *
114835 CGTTATTTTTAAGGA
64 CATCAATTCTGAGGG
* * * *
114850 GATATTCCAACCTC-GTTTTATTTTCAAAATATTAAATTTTTCATCTTGGGATACTCCAACCTCA
1 GATACTCTAACCTCAGTTTTATTTCCAAAATATTAAATTTTTCATCTTGGGATACTCCAACCCCA
**
114914 TCAATTCCAAGGG
66 TCAATTCTGAGGG
* * ** ** * * *
114927 GATACTCTAACCCCACTCATATTTCCAAAATGCTAAATTTTTCATCTCGAGATAC-CTAACCCCA
1 GATACTCTAACCTCAGTTTTATTTCCAAAATATTAAATTTTTCATCTTGGGATACTCCAACCCCA
*
114991 T--ATTCGGAGGG
66 TCAATTCTGAGGG
115002 GATACTCTAACCT
1 GATACTCTAACCT
115015 TGTTTCTTTT
Statistics
Matches: 402, Mismatches: 71, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
75 20 0.05
77 58 0.14
78 93 0.23
79 229 0.57
80 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (78 bp):
GATACTCTAACCTCAGTTTTATTTCCAAAATATTAAATTTTTCATCTTGGGATACTCCAACCCCA
TCAATTCTGAGGG
Found at i:117499 original size:166 final size:164
Alignment explanation
Indices: 117147--117552 Score: 440
Period size: 166 Copynumber: 2.5 Consensus size: 164
117137 ATTTCCATTG
* * * * *
117147 GTTTAAAATTTTTAAAATTCATCAAATATTAATATTTAATTTATAGTAAATCATTTTTCAAAAAT
1 GTTT-AAATTTTTAAAATTCATCAAATATTATTATTTAACTCATATTAAATCATTTTTGAAAAAT
* ** * *
117212 TCATTTA-TTTCATGAGTTTTTCATTTTTTCCTTAAAATTTTCTTTTTTCGAAAAATTGAGTTTT
65 TCATTTATTTTCATGAGTTTTTAATTTTTTCCTTAAAATTGCCTTTTTCCGAAAAATTGACTTTT
* * * * * *
117276 TTATTCCATAAAGGTTTTTGAGGGGATTTTTCTCA
130 ATACTACACAAAGATTTTCGAGGGGATTTTTCTCA
* * * * * *
117311 GTTCGAAATTTTTAATATTCATCAAATCTCATTATTTAACTCGTATTAAATTATTTTTGAAAAAT
1 GTT-TAAATTTTTAAAATTCATCAAATATTATTATTTAACTCATATTAAATCATTTTTGAAAAAT
* * *
117376 TCATTTATTTTGATGAGTTTTTAATTTTTTCCTTGAAA-TGCCTATGTTTCCGGAAAATTGACTT
65 TCATTTATTTTCATGAGTTTTTAATTTTTTCCTTAAAATTGCCT-T-TTTCCGAAAAATTGACTT
* *
117440 TTATACTATACAAATATTTTCGAGGGGATTTTTCTC-
128 TTATACTACACAAAGATTTTCGAGGGGATTTTTCTCA
* ** * *
117476 GATTTAAATTTTTTAAAATTCATCTAATATTATTATTTAACTCCCATTAAATCAATTTTGAAAAC
1 G-TTTAAA-TTTTTAAAATTCATCAAATATTATTATTTAACTCATATTAAATCATTTTTGAAAAA
117541 TTCAATTTATTT
64 TTC-ATTTATTT
117553 CATAAATTTT
Statistics
Matches: 198, Mismatches: 37, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
164 63 0.32
165 32 0.16
166 95 0.48
167 8 0.04
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (164 bp):
GTTTAAATTTTTAAAATTCATCAAATATTATTATTTAACTCATATTAAATCATTTTTGAAAAATT
CATTTATTTTCATGAGTTTTTAATTTTTTCCTTAAAATTGCCTTTTTCCGAAAAATTGACTTTTA
TACTACACAAAGATTTTCGAGGGGATTTTTCTCA
Found at i:119015 original size:16 final size:16
Alignment explanation
Indices: 118996--119039 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
118986 AACAAAAGCA
118996 AAATTAAATATTAAAT
1 AAATTAAATATTAAAT
**
119012 AAATTAAATAAAAAAAT
1 AAATTAAAT-ATTAAAT
119029 AAA-TAAATATT
1 AAATTAAATATT
119040 CTTATCAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 8 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTAAATATTAAAT
Found at i:121634 original size:156 final size:155
Alignment explanation
Indices: 121410--121847 Score: 484
Period size: 156 Copynumber: 2.8 Consensus size: 155
121400 AGGTATCAAA
** * * * * * *
121410 CTTAGGGGCATTTTCATTTTTTTTTTAAATTGAGTCCTAAGCTATCATCAGGTCCATTTTTATGC
1 CTTAGGGGCATTTTCATAATTTTTTTAAAATGAGTCCTAGGTTGTCATCGGGTCCACTTTTATGC
* * * * *
121475 CAAATGTGGGTATTTAGGATAGGTTCATCCCATTTATAATCATTTTTAGGTCTTTTAGAGGTACC
66 CAAAGGTGGGTATTTAGGATAGGTTCATTCCATCTATAATC-TTTTTAAGTCCTTTAGAGGTACC
*
121540 AAGCACTTGTAAGTCGAAGATATC-C
130 AAGCACTTCTAAGTCGAAGATATCAC
* * * *
121565 CTTAGGGGTATTTTCATAATTTTTTTATAACTGAGTCTTAGGTTGTCATCGGGTCTACTTTTATG
1 CTTAGGGGCATTTTCATAATTTTTTTA-AAATGAGTCCTAGGTTGTCATCGGGTCCACTTTTATG
* * * * *
121630 CCAAAGGTAGGTATCTAGGATAGGTTCATTCCATCTATGATCCTTTTTAAGTCCTTTAGGGGTAT
65 CCAAAGGTGGGTATTTAGGATAGGTTCATTCCATCTATAAT-CTTTTTAAGTCCTTTAGAGGTAC
* * *
121695 CAGGCACTTCTAAGTTGAAGGTATCAGAC
129 CAAGCACTTCTAAGTCGAAGATATC--AC
* * * * * *
121724 C-TAAGGACATTTTTTAAAATTTTATTAGAAATGAGTCCTAGGTTGTCATCGGATCCACTTTTAT
1 CTTAGGGGCA-TTTTCATAATTTTTTTA-AAATGAGTCCTAGGTTGTCATCGGGTCCACTTTTAT
* *
121788 GCCGAAGGTGGGTATTTCGGATAGGTTCATTCCATCTATAATTCTTTTTAAGTCCTTTAG
64 GCCAAAGGTGGGTATTTAGGATAGGTTCATTCCATCTATAA-TCTTTTTAAGTCCTTTAG
121848 GATCACTGGA
Statistics
Matches: 235, Mismatches: 41, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
155 24 0.10
156 103 0.44
157 1 0.00
158 5 0.02
159 101 0.43
160 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (155 bp):
CTTAGGGGCATTTTCATAATTTTTTTAAAATGAGTCCTAGGTTGTCATCGGGTCCACTTTTATGC
CAAAGGTGGGTATTTAGGATAGGTTCATTCCATCTATAATCTTTTTAAGTCCTTTAGAGGTACCA
AGCACTTCTAAGTCGAAGATATCAC
Found at i:121802 original size:159 final size:155
Alignment explanation
Indices: 121440--121848 Score: 460
Period size: 159 Copynumber: 2.6 Consensus size: 155
121430 TTTTTTAAAT
* * * * * *
121440 TGAGTCCTAAGCTATCATCAGGTCCATTTTTATGCCAAATGTGGGTATTTAGGATAGGTTCATCC
1 TGAGTCCTAGGTTGTCATC-GGTCCACTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATTC
* * * * * * *
121505 CATTTATAATCATTTTTAGGTCTTTTAGAGGTACCAAGCACTTGTAAGTCGAAGATATCCCTTAG
65 CATCTATAATCCTTTTTAAGTCCTTTAGGGGTACCAAGCACTTCTAAGTCGAAGATATCCCTAAG
** * * * *
121570 GGGTATTTTCATAATTTTTTTATAAC
130 GCATATTTTCAAAATTTTATTAGAAA
* * * *
121596 TGAGTCTTAGGTTGTCATCGGGTCTACTTTTATGCCAAAGGTAGGTATCTAGGATAGGTTCATTC
1 TGAGTCCTAGGTTGTCATC-GGTCCACTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATTC
* * * * *
121661 CATCTATGATCCTTTTTAAGTCCTTTAGGGGTATCAGGCACTTCTAAGTTGAAGGTATCAGACCT
65 CATCTATAATCCTTTTTAAGTCCTTTAGGGGTACCAAGCACTTCTAAGTCGAAGATATC---CCT
*
121726 AAGGACAT-TTTTTAAAATTTTATTAGAAA
127 AAGG-CATATTTTCAAAATTTTATTAGAAA
* *
121755 TGAGTCCTAGGTTGTCATCGGATCCACTTTTATGCCGAAGGTGGGTATTTCGGATAGGTTCATTC
1 TGAGTCCTAGGTTGTCATCGG-TCCACTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATTC
*
121820 CATCTATAATTCTTTTTAAGTCCTTTAGG
65 CATCTATAATCCTTTTTAAGTCCTTTAGG
121849 ATCACTGGAC
Statistics
Matches: 210, Mismatches: 38, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
156 102 0.49
158 2 0.01
159 105 0.50
160 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (155 bp):
TGAGTCCTAGGTTGTCATCGGTCCACTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATTCC
ATCTATAATCCTTTTTAAGTCCTTTAGGGGTACCAAGCACTTCTAAGTCGAAGATATCCCTAAGG
CATATTTTCAAAATTTTATTAGAAA
Done.