Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 122 of 141
Found at i:38793367 original size:16 final size:17
Alignment explanation
Indices: 38793346--38793383 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
38793336 TCACAAAATT
*
38793346 TAATAAT-ATTTAAAAA
1 TAATAATAAATTAAAAA
38793362 TAATAATAAATTAAAAA
1 TAATAATAAATTAAAAA
*
38793379 CAATA
1 TAATA
38793384 TACCAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TAATAATAAATTAAAAA
Found at i:38793898 original size:3 final size:3
Alignment explanation
Indices: 38793890--38793915 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38793880 CAAGATTAAA
38793890 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
38793916 AAATGGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:38797072 original size:142 final size:143
Alignment explanation
Indices: 38796816--38797100 Score: 563
Period size: 142 Copynumber: 2.0 Consensus size: 143
38796806 ACCAAAATTT
38796816 AAAAGGATAAATTGCACCCTAAACTCCCCTATTTATTATTATTATTTATCCTCTTTTAACACTAA
1 AAAAGGATAAATTGCACCCTAAACTCCCCTATTTATTATTATTATTTATCCTCTTTTAACACTAA
38796881 AAATAGATTGGCCTCTTATCAATTAGTCTAAAAAAAATTTCTACCAAAAAGTATTTTTGTAAGTA
66 AAATAGATTGGCCTCTTATCAATTAGTCTAAAAAAAATTTCTACCAAAAAGTATTTTTGTAAGTA
38796946 AG-CGATTCCAAC
131 AGCCGATTCCAAC
38796958 AAAAGGATAAATTGCACCCTAAACTCCCCTATTTATTATTATTATTTATCCTCTTTTAACACTAA
1 AAAAGGATAAATTGCACCCTAAACTCCCCTATTTATTATTATTATTTATCCTCTTTTAACACTAA
38797023 AAATAGATTGGCCTCTTATCAATTAGTCTAAAAAAAATTTCTACCAAAAAGTATTTTTGTAAGTA
66 AAATAGATTGGCCTCTTATCAATTAGTCTAAAAAAAATTTCTACCAAAAAGTATTTTTGTAAGTA
38797088 AGCCGATTCCAAC
131 AGCCGATTCCAAC
38797101 TGGAAATAAA
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 132 0.93
143 10 0.07
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (143 bp):
AAAAGGATAAATTGCACCCTAAACTCCCCTATTTATTATTATTATTTATCCTCTTTTAACACTAA
AAATAGATTGGCCTCTTATCAATTAGTCTAAAAAAAATTTCTACCAAAAAGTATTTTTGTAAGTA
AGCCGATTCCAAC
Found at i:38802881 original size:45 final size:44
Alignment explanation
Indices: 38802817--38802913 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 44
38802807 AAATAAAAGC
38802817 GTAATGGAATAGAGGCGTAATAGTAAATTAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGT--ATTAATGTGTTTGGTTGAAT
**
38802862 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGTATTAATGTGTTTGGTTGAAT
*
38802906 GGAATGGA
1 GTAATGGA
38802914 GGTGTAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 4 0.08
44 20 0.42
45 24 0.50
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGTATTAATGTGTTTGGTTGAAT
Found at i:38807679 original size:53 final size:53
Alignment explanation
Indices: 38807616--38807721 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
38807606 GCAGTGGATT
* *
38807616 TCAAAAACCACAACAAATGACAGGGAAAAAATGAAAAAATAGACCGAAAGAGA
1 TCAAAAACCACAACAAATGACAAGGAAAAAATGAAAAAAGAGACCGAAAGAGA
*
38807669 TCAAAAACCACAACAAATGACAAGGAAAAAATGAAAAAAGAGACCGAGAGAGA
1 TCAAAAACCACAACAAATGACAAGGAAAAAATGAAAAAAGAGACCGAAAGAGA
38807722 GAATCGGTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.60, C:0.15, G:0.18, T:0.07
Consensus pattern (53 bp):
TCAAAAACCACAACAAATGACAAGGAAAAAATGAAAAAAGAGACCGAAAGAGA
Found at i:38819682 original size:24 final size:24
Alignment explanation
Indices: 38819647--38819716 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
38819637 CGGATCATCT
* *
38819647 TCTTCATCTTCACCTCCACCCTTG
1 TCTTCATTTTCATCTCCACCCTTG
*
38819671 TAC-TCATTTTCATCTCCACCATTG
1 T-CTTCATTTTCATCTCCACCCTTG
38819695 TCTTCATTTTCATCTCCACCCT
1 TCTTCATTTTCATCTCCACCCT
38819717 CGATTTCATC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.16, C:0.40, G:0.03, T:0.41
Consensus pattern (24 bp):
TCTTCATTTTCATCTCCACCCTTG
Found at i:38822767 original size:12 final size:12
Alignment explanation
Indices: 38822752--38822789 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
38822742 TCTTCTTCTA
*
38822752 TTCAAGTTCTTT
1 TTCAATTTCTTT
*
38822764 TTCAATTTTTTT
1 TTCAATTTCTTT
38822776 TTC-ATTTCTTT
1 TTCAATTTCTTT
38822787 TTC
1 TTC
38822790 TTCGCTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (12 bp):
TTCAATTTCTTT
Found at i:38830002 original size:3 final size:3
Alignment explanation
Indices: 38829994--38830037 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
38829984 AGCTAATTTT
38829994 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38830038 CATTTTGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38837964 original size:19 final size:17
Alignment explanation
Indices: 38837936--38837977 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
38837926 GTTATATTAG
38837936 ATTT-AATACAGTATTTAT
1 ATTTGAATACA-T-TTTAT
*
38837954 ATTTGAATACATTTTGT
1 ATTTGAATACATTTTAT
38837971 ATTTGAA
1 ATTTGAA
38837978 AGTAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 5 0.23
19 6 0.27
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (17 bp):
ATTTGAATACATTTTAT
Found at i:38839438 original size:15 final size:16
Alignment explanation
Indices: 38839418--38839452 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
38839408 TAAATTAATT
*
38839418 TTATTTTTTAAA-ATA
1 TTATTTTTGAAATATA
38839433 TTATTTTTGAAATATA
1 TTATTTTTGAAATATA
38839449 TTAT
1 TTAT
38839453 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATTTTTGAAATATA
Found at i:38839475 original size:25 final size:26
Alignment explanation
Indices: 38839426--38839477 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
38839416 TTTTATTTTT
38839426 TAAAATATTATTTTTGAAATATATTA
1 TAAAATATTATTTTTGAAATATATTA
38839452 TAAAA-ATTAATTATTT-AAAT-TATTA
1 TAAAATATT-ATT-TTTGAAATATATTA
38839477 T
1 T
38839478 CTTTAGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 9 0.38
26 12 0.50
27 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TAAAATATTATTTTTGAAATATATTA
Found at i:38841113 original size:9 final size:9
Alignment explanation
Indices: 38841113--38841171 Score: 73
Period size: 9 Copynumber: 6.4 Consensus size: 9
38841103 TTTATGATTT
38841113 TTTTTATAA
1 TTTTTATAA
38841122 TTTTTATAA
1 TTTTTATAA
38841131 TTTTATATAA
1 TTTT-TATAA
*
38841141 TTTTAATAA
1 TTTTTATAA
* *
38841150 TTTTAATAC
1 TTTTTATAA
*
38841159 TTTTTATGA
1 TTTTTATAA
38841168 TTTT
1 TTTT
38841172 ATAGAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
9 35 0.80
10 9 0.20
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:38841139 original size:19 final size:19
Alignment explanation
Indices: 38841112--38841174 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
38841102 TTTTATGATT
*
38841112 TTTTTTATAATTTTTATAA
1 TTTTATATAATTTTTATAA
*
38841131 TTTTATATAATTTTAATAA
1 TTTTATATAATTTTTATAA
* *
38841150 TTTTA-ATACTTTTTATGA
1 TTTTATATAATTTTTATAA
38841168 TTTTATA
1 TTTTATA
38841175 GAAATTTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
18 15 0.39
19 23 0.61
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATATAATTTTTATAA
Found at i:38841163 original size:37 final size:37
Alignment explanation
Indices: 38841113--38841184 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
38841103 TTTATGATTT
* * *
38841113 TTTTTATAATTTTTATAATTTTATATAATTTTAATAA
1 TTTTAATAATTTTTATAATTTTATAGAAATTTAATAA
* *
38841150 TTTTAATACTTTTTATGATTTTATAGAAATTTAAT
1 TTTTAATAATTTTTATAATTTTATAGAAATTTAAT
38841185 GGGCAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (37 bp):
TTTTAATAATTTTTATAATTTTATAGAAATTTAATAA
Found at i:38841366 original size:25 final size:25
Alignment explanation
Indices: 38841328--38841386 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
38841318 TCAATTTTCA
* *
38841328 TATATTTTTTATATTTAATCATTTT
1 TATATTTTTGATATTTAATCATATT
** *
38841353 TATATTTTTGATATTTTCTGATATT
1 TATATTTTTGATATTTAATCATATT
38841378 TATATTTTT
1 TATATTTTT
38841387 TTATTATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (25 bp):
TATATTTTTGATATTTAATCATATT
Found at i:38841398 original size:9 final size:8
Alignment explanation
Indices: 38841328--38841399 Score: 56
Period size: 9 Copynumber: 8.4 Consensus size: 8
38841318 TCAATTTTCA
38841328 TATATTTT
1 TATATTTT
38841336 T-TATATTT
1 TATAT-TTT
*
38841344 AATCATTTT
1 TAT-ATTTT
38841353 TATATTTT
1 TATATTTT
38841361 TGATATTTT
1 T-ATATTTT
*
38841370 CTGATATTTA
1 -T-ATATTTT
*
38841380 TATTTTTT
1 TATATTTT
38841388 TATTATTTT
1 TA-TATTTT
38841397 TAT
1 TAT
38841400 GGGAAAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
7 3 0.06
8 18 0.35
9 21 0.40
10 10 0.19
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (8 bp):
TATATTTT
Found at i:38845044 original size:102 final size:102
Alignment explanation
Indices: 38844921--38845124 Score: 302
Period size: 102 Copynumber: 2.0 Consensus size: 102
38844911 ATTTACATTA
* * *
38844921 TCCCATTTTTTTCAGAGTCATTATAAATGAGCTTAAATGAATAAAGCTTTTCAAGCTT-AAGGGT
1 TCCCATTTTTTTCACAGTCATTACAAATGAGCTTAAATGAATAAAGCTTTTCAAG-TTCAAAGGT
*
38844985 CAAAGTGGATAAAAAAAAGTTCAGGGGTCAAAAGTTAC
65 CAAAGTGGATAAAAAAAAGTGCAGGGGTCAAAAGTTAC
* * * * *
38845023 TCCCATTTTTTTCACAGTCATTGCAAATGAGCTTAAATGAATAACGGTTTTTAAGTTCAAAGGTT
1 TCCCATTTTTTTCACAGTCATTACAAATGAGCTTAAATGAATAAAGCTTTTCAAGTTCAAAGGTC
*
38845088 AAAGTGGCTAAAAAAAAGTGCAGGGGTCAAAAGTTAC
66 AAAGTGGATAAAAAAAAGTGCAGGGGTCAAAAGTTAC
38845125 CTTATCCCTA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 2 0.02
102 89 0.98
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
TCCCATTTTTTTCACAGTCATTACAAATGAGCTTAAATGAATAAAGCTTTTCAAGTTCAAAGGTC
AAAGTGGATAAAAAAAAGTGCAGGGGTCAAAAGTTAC
Found at i:38848885 original size:19 final size:19
Alignment explanation
Indices: 38848871--38848933 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
38848861 TTTTATGATT
*
38848871 TTTTTATAATTTTATATAA
1 TTTTAATAATTTTATATAA
*
38848890 TTTTAATAATTTTA-ATAC
1 TTTTAATAATTTTATATAA
* * *
38848908 TTTTTATGATTTTATAGAA
1 TTTTAATAATTTTATATAA
*
38848927 ATTTAAT
1 TTTTAAT
38848934 GGGCAAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 15 0.43
19 20 0.57
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTAATAATTTTATATAA
Found at i:38848912 original size:10 final size:9
Alignment explanation
Indices: 38848871--38848921 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
38848861 TTTTATGATT
*
38848871 TTTTTATAA
1 TTTTAATAA
38848880 TTTTATATAA
1 TTTTA-ATAA
38848890 TTTTAATAA
1 TTTTAATAA
*
38848899 TTTTAATAC
1 TTTTAATAA
* *
38848908 TTTTTATGA
1 TTTTAATAA
38848917 TTTTA
1 TTTTA
38848922 TAGAAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 26 0.74
10 9 0.26
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTAATAA
Found at i:38850147 original size:18 final size:17
Alignment explanation
Indices: 38850124--38850165 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
38850114 AATTTTTAAA
* *
38850124 TATATTTTATTTATTTT
1 TATATTTTAATCATTTT
38850141 T-TATATTTAATCATTTT
1 TATAT-TTTAATCATTTT
38850158 TATATTTT
1 TATATTTT
38850166 TGATATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTTTAATCATTTT
Found at i:38850184 original size:25 final size:24
Alignment explanation
Indices: 38850131--38850196 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
38850121 AAATATATTT
*
38850131 TATTTAT-TTTTTATATTTAATCA
1 TATTTATATTTTTATATTTTATCA
* * *
38850154 TTTTTATATTTTTGATATTTTCTGA
1 TATTTATATTTTT-ATATTTTATCA
38850179 TATTTATAATTTTT-TATT
1 TATTTAT-ATTTTTATATT
38850197 ATTTTTATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.17
24 9 0.26
25 14 0.40
26 6 0.17
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (24 bp):
TATTTATATTTTTATATTTTATCA
Found at i:38851420 original size:107 final size:107
Alignment explanation
Indices: 38851144--38851471 Score: 412
Period size: 107 Copynumber: 3.1 Consensus size: 107
38851134 ATGACATGGA
* * *
38851144 TTGAAA-TTT-AAGAGGATATTTGGCTATTTAGTCGAACAAGAAATCGAAACCCAGCACGTTAGG
1 TTGAAAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGG
* * * * **
38851207 GCCCGTTCTCTCGAATTTCCAAATGCAAAACATTGCCTCGTT
66 GCACGTTTTCTCGAATTTCCAAATGCGAAATATTGCCTTATT
** *** * * *
38851249 TTGAAA-TTTTGAAAGGATATTCAACTATTTGGTCAAACGAGTAATCGAAACCCAACACGTTAGG
1 TTGAAAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGG
*
38851313 GCACGTTTTCTCGAATTTTCAAACT-CGAAATATTGCCTTATT
66 GCACGTTTTCTCGAATTTCCAAA-TGCGAAATATTGCCTTATT
* * *
38851355 TTGAAAGTTTAAAAATGATATTTGGCTATTCGGTCGAACGAGAAACCGAAACCCAGCACGTTAGG
1 TTGAAAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGG
*
38851420 GCACGTTTTCTCGAGTTTCCAAATGCGAAATATTGCCTTATT
66 GCACGTTTTCTCGAATTTCCAAATGCGAAATATTGCCTTATT
*
38851462 TTTAAAGTTT
1 TTGAAAGTTT
38851472 CTTTTTGATG
Statistics
Matches: 188, Mismatches: 31, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
105 9 0.05
106 84 0.45
107 95 0.51
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (107 bp):
TTGAAAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGG
GCACGTTTTCTCGAATTTCCAAATGCGAAATATTGCCTTATT
Found at i:38854459 original size:9 final size:9
Alignment explanation
Indices: 38854439--38854473 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
38854429 ACATCTATGT
38854439 TAAAAAATCA
1 TAAAAAA-CA
38854449 TAAAAAACA
1 TAAAAAACA
*
38854458 TAAAAAACG
1 TAAAAAACA
38854467 TAAAAAA
1 TAAAAAA
38854474 GATGATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (9 bp):
TAAAAAACA
Found at i:38854742 original size:27 final size:27
Alignment explanation
Indices: 38854712--38854798 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
38854702 AAAATCAATC
38854712 TGATGAAGAAAAAACTTCAGCAGATCA
1 TGATGAAGAAAAAACTTCAGCAGATCA
* *
38854739 TGAT--A-TAAAAA-TT-AGTA-ATCAA
1 TGATGAAGAAAAAACTTCAGCAGATC-A
*
38854761 TCTGATGAAGAAAAAACTTCAACAGATCA
1 --TGATGAAGAAAAAACTTCAGCAGATCA
*
38854790 GGATGAAGA
1 TGATGAAGA
38854799 CATAAAAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
21 3 0.07
22 4 0.09
23 2 0.04
24 9 0.20
25 1 0.02
26 1 0.02
27 17 0.38
28 2 0.04
29 3 0.07
30 3 0.07
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.22
Consensus pattern (27 bp):
TGATGAAGAAAAAACTTCAGCAGATCA
Found at i:38858469 original size:21 final size:21
Alignment explanation
Indices: 38858428--38858469 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
38858418 GCCTGCTCAA
* *
38858428 AAATCAACAAATATTAGTAAT
1 AAATCAACAAATATAACTAAT
38858449 AAATC-ACAAATAGTAACTAAT
1 AAATCAACAAATA-TAACTAAT
38858470 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.26
Consensus pattern (21 bp):
AAATCAACAAATATAACTAAT
Found at i:38860719 original size:3 final size:3
Alignment explanation
Indices: 38860711--38860742 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
38860701 AAAATGAGTA
38860711 AAT AAT AAT AAT AAT AAT CAAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
38860743 CAAGATTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38861593 original size:15 final size:16
Alignment explanation
Indices: 38861561--38861599 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
38861551 ACTTTGAAAT
*
38861561 AAAAAAATGAAAATAA
1 AAAAAAATGAAAACAA
38861577 AAAAAAATG-AAACAA
1 AAAAAAATGAAAACAA
38861592 AAATAAAA
1 AAA-AAAA
38861600 AGAAGAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAAAATGAAAACAA
Found at i:38862467 original size:95 final size:95
Alignment explanation
Indices: 38862312--38862702 Score: 586
Period size: 95 Copynumber: 4.1 Consensus size: 95
38862302 GGGGGACAGA
* *** *
38862312 ATCTGCAATCTTCAATCTATTCCACTGCTGTCCAGGGAGATAGAATTATTGGCTTCAATGTACTC
1 ATCTTCAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTC
38862377 CACTGTAGTCACAAGGAGGTAAAATCTGCC
66 CACTGTAGTCACAAGGAGGTAAAATCTGCC
* *
38862407 ATATTCAATCTTCAATCTATTCCACTGCCAACCAAGGAGATAGAATTATCGGCTTCAATGTACTC
1 ATCTTCAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTC
38862472 CACTGTAGTCACAAGGAGGTAAAATCTGCC
66 CACTGTAGTCACAAGGAGGTAAAATCTGCC
* * *
38862502 ATCTTCAATCTGCAATCTATTCCACTGCCAACCAGGGAGATATAATTATCGGTTTCAATGTACTC
1 ATCTTCAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTC
*
38862567 CACTGTAGTCAC-AGAGAGGTAAAATCTGTC
66 CACTGTAGTCACAAG-GAGGTAAAATCTGCC
* * * * *
38862597 ATCTTCGATCTTCAATCTATTCTATTGCCAACTAGGGAGATAGAATTATCGGCTTCAATATACTC
1 ATCTTCAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTC
* *
38862662 CACTGTAGTCATAGGGAGGTAAAATCTGCC
66 CACTGTAGTCACAAGGAGGTAAAATCTGCC
* *
38862692 ATTTTCGATCT
1 ATCTTCAATCT
38862703 GCCCCACTTT
Statistics
Matches: 269, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
94 2 0.01
95 266 0.99
96 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (95 bp):
ATCTTCAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTC
CACTGTAGTCACAAGGAGGTAAAATCTGCC
Found at i:38862981 original size:88 final size:88
Alignment explanation
Indices: 38862840--38863719 Score: 1361
Period size: 88 Copynumber: 10.0 Consensus size: 88
38862830 CAATCTGAAA
* * * **
38862840 TCTTCAACCTGCTCCACTACAACCGAG-GAAGACAAGGCTTGTGTCTTCGATCTGCTTTACTGTC
1 TCTTCAACCAGCTCCACTACAACCGAGAG-AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTC
* * *
38862904 GATGCAGGAAGGCAAGATCTGTTA
65 AAGGCAGGAAGGCAAGATCTGTTG
*
38862928 TCTTCAACCAGCTCCACTGCAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTGT-GCTGTC
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCT-TCGCTGTC
38862992 AAGGCAGGAAGGCAAGATCTGTTG
65 AAGGCAGGAAGGCAAGATCTGTTG
* * *
38863016 TCTTCAACCAGCTCTACTACAACTGAGAGAGGCAAGTTTTGTGTCTTCGATCTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
38863081 AGGCAGGAAGGCAAGATCTGTTG
66 AGGCAGGAAGGCAAGATCTGTTG
* *
38863104 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTTGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
* * *
38863169 AGTCAGGAATGTAAGATCTGTTG
66 AGGCAGGAAGGCAAGATCTGTTG
*
38863192 TCTTCAACCAACTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
* * *
38863257 AAGTAGAAAGGCAAGATCTGTTG
66 AGGCAGGAAGGCAAGATCTGTTG
* *
38863280 TCTTCACCCAGCTCCACTACAACCGAGAAAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
* * * *
38863345 AGGTAAGAAGGCAAGATATATTG
66 AGGCAGGAAGGCAAGATCTGTTG
* * *
38863368 TCTTCAACCAGCTCCATTACAACCGAGAGAGTCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
38863433 AGGCAGGAAGGCAAGATCTGTTG
66 AGGCAGGAAGGCAAGATCTGTTG
38863456 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAA-GTTTGTGTCTTCGATCTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
*
38863520 AGGCAGGAAGGCAAGATTTGTTG
66 AGGCAGGAAGGCAAGATCTGTTG
* *
38863543 TCTTCAACCAGCTCCACTACAACCGAGAGAGACAAGGTTTGTGTCTTCGATTTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
38863608 AGGCAGGAAGGCAAGATCTGTTG
66 AGGCAGGAAGGCAAGATCTGTTG
** * * *
38863631 TCTTCAACCAGCTCCACTACAATTGAGAAATGCAAGGTTTGTATCTTCGATCTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
* *
38863696 AGGCAGGGAGACAAGATCTGTTG
66 AGGCAGGAAGGCAAGATCTGTTG
38863719 T
1 T
38863720 TTTTCATTTA
Statistics
Matches: 726, Mismatches: 62, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
87 85 0.12
88 639 0.88
89 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (88 bp):
TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
AGGCAGGAAGGCAAGATCTGTTG
Found at i:38865796 original size:13 final size:13
Alignment explanation
Indices: 38865778--38865817 Score: 57
Period size: 11 Copynumber: 3.2 Consensus size: 13
38865768 CCTTGACCTC
38865778 TCCTTTTTCTTTT
1 TCCTTTTTCTTTT
38865791 TCC-TTTT-TTTT
1 TCCTTTTTCTTTT
38865802 TCCTTCTTTCTTTT
1 TCCTT-TTTCTTTT
38865816 TC
1 TC
38865818 TCCTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 5 0.21
13 6 0.25
14 6 0.25
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TCCTTTTTCTTTT
Found at i:38865826 original size:27 final size:24
Alignment explanation
Indices: 38865778--38865827 Score: 64
Period size: 27 Copynumber: 2.0 Consensus size: 24
38865768 CCTTGACCTC
*
38865778 TCCTTTTTCTTTTTCCTTTTTTTT
1 TCCTTTTTCTTTTTCCTATTTTTT
38865802 TCCTTCTTTCTTTTTCTCCTATTTTT
1 TCCTT-TTTC-TTTT-TCCTATTTTT
38865828 GACTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 4 0.18
26 4 0.18
27 9 0.41
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (24 bp):
TCCTTTTTCTTTTTCCTATTTTTT
Found at i:38865882 original size:16 final size:15
Alignment explanation
Indices: 38865836--38865886 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
38865826 TTGACTTTAA
38865836 TTTTTTTT-ATTTTT
1 TTTTTTTTGATTTTT
38865850 TTGATTTTTTGATTTTT
1 TT--TTTTTTGATTTTT
38865867 GTTTTTTTTG-TGTTTT
1 -TTTTTTTTGAT-TTTT
38865883 TTTT
1 TTTT
38865887 AGTCTGAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.06
15 5 0.16
16 17 0.53
17 6 0.19
18 2 0.06
ACGTcount: A:0.06, C:0.00, G:0.10, T:0.84
Consensus pattern (15 bp):
TTTTTTTTGATTTTT
Found at i:38866617 original size:4 final size:4
Alignment explanation
Indices: 38866608--38866646 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
38866598 CAGTATGATT
* *
38866608 ATGA ATGA ATGA ATGA ATGA ATGA TTTGA ATGA AAGA AT
1 ATGA ATGA ATGA ATGA ATGA ATGA -ATGA ATGA ATGA AT
38866647 AAAAGAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (4 bp):
ATGA
Found at i:38866654 original size:25 final size:26
Alignment explanation
Indices: 38866602--38866654 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
38866592 TCTGCACAGT
* * *
38866602 ATGATTATGAATGAATGAATGAATGA
1 ATGATTATGAATGAAAGAATAAAAGA
38866628 ATGATT-TGAATGAAAGAATAAAAGA
1 ATGATTATGAATGAAAGAATAAAAGA
38866653 AT
1 AT
38866655 AAAAATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (26 bp):
ATGATTATGAATGAAAGAATAAAAGA
Found at i:38870435 original size:27 final size:28
Alignment explanation
Indices: 38870379--38870435 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
38870369 GCTTGAATTA
* **
38870379 ATGGCTGCTTCCCTCACTTGCTTGTGTC
1 ATGGCTGCTTCCATCACTTGCTTGCATC
38870407 ATGGCTGCTTCCATCA-TTGCTTGCATC
1 ATGGCTGCTTCCATCACTTGCTTGCATC
38870434 AT
1 AT
38870436 CATTGTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.12, C:0.30, G:0.19, T:0.39
Consensus pattern (28 bp):
ATGGCTGCTTCCATCACTTGCTTGCATC
Found at i:38871352 original size:14 final size:14
Alignment explanation
Indices: 38871333--38871360 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38871323 CTATCTAGAT
38871333 TTGTTATATAAACA
1 TTGTTATATAAACA
38871347 TTGTTATATAAACA
1 TTGTTATATAAACA
38871361 GATTCTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTGTTATATAAACA
Found at i:38874085 original size:106 final size:106
Alignment explanation
Indices: 38873894--38874088 Score: 266
Period size: 106 Copynumber: 1.8 Consensus size: 106
38873884 AATTTTTTTA
** * *
38873894 AGGCAATATTTTGCGTTTGGAAAATCGAGAAAGCGTGTTCTAACGTGCTGTGTTTCGATTTCTCT
1 AGGCAATATTTTGCGTTTGGAAAATCGAGAAAGCGTGCCCTAACGTGCTGGGTTTCGATTTCTCG
* * *
38873959 TTTGACCAAATAGTCGAATATCCTTTCGAATTTTCAAAACG
66 TTCGACCAAATAGCCAAATATCCTTTCGAATTTTCAAAACG
* * * *
38874000 AGGCGATATTTTGCGTTTGGACATTCGAGAGAA-CGTGCCCTAATGTGCTGGGTTTCGATTTCTC
1 AGGCAATATTTTGCGTTTGGAAAATCGAGA-AAGCGTGCCCTAACGTGCTGGGTTTCGATTTCTC
*
38874064 GTTCGACTAAATAGCCAAATATCCT
65 GTTCGACCAAATAGCCAAATATCCT
38874089 CTTAAAACTT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
106 74 0.97
107 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (106 bp):
AGGCAATATTTTGCGTTTGGAAAATCGAGAAAGCGTGCCCTAACGTGCTGGGTTTCGATTTCTCG
TTCGACCAAATAGCCAAATATCCTTTCGAATTTTCAAAACG
Found at i:38876621 original size:109 final size:109
Alignment explanation
Indices: 38876417--38876651 Score: 336
Period size: 110 Copynumber: 2.2 Consensus size: 109
38876407 ATTTTGGGGC
38876417 CAAAAGTTACATTATCCCCATTTTTTTCACAGTCATTACAAATGAGCTTAAATGAATAAAGATTT
1 CAAAAGTTACATTATCCCCATTTTTTTCACAGTCATTACAAATGAGCTTAAATGAATAAAGATTT
*
38876482 TCAAGCTTAAGGGTCAAAGTGGACAAAAAAAGTTTAGGGTAGGT
66 TCAAGCTTAAAGGTCAAAGTGGACAAAAAAAGTTTAGGGTAGGT
* * *
38876526 CAAAAGTTACATTATCCCCATTTTTTTCACAGTCATTGCAAAATGAGCTTAAATGAATAACGGTT
1 CAAAAGTTACATTATCCCCATTTTTTTCACAGTCATTAC-AAATGAGCTTAAATGAATAAAGATT
*
38876591 TTCAAG-TTCAAAGGTCAAAGTGG-CTAAAAAAAAGTTCA-GG--GGT
65 TTCAAGCTT-AAAGGTCAAAGTGGAC--AAAAAAAGTTTAGGGTAGGT
* *
38876634 CAAAAGTGACCTTATCCC
1 CAAAAGTTACATTATCCC
38876652 TAATTTTATT
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
108 19 0.17
109 41 0.36
110 44 0.38
111 11 0.10
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (109 bp):
CAAAAGTTACATTATCCCCATTTTTTTCACAGTCATTACAAATGAGCTTAAATGAATAAAGATTT
TCAAGCTTAAAGGTCAAAGTGGACAAAAAAAGTTTAGGGTAGGT
Found at i:38881243 original size:42 final size:42
Alignment explanation
Indices: 38881158--38881255 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
38881148 TGCATTGCCG
* *
38881158 TCTCAGTTCAATGCATCGCCATCAGATGTTGATTCGATGCAA
1 TCTCAGTTCAATGCATCGCCACCAGATGTTGATTCAATGCAA
* * * *
38881200 TCTCAATTCAATGCCTCTCCACCAGATGTTGAGTT-AATTCAA
1 TCTCAGTTCAATGCATCGCCACCAGATGTTGA-TTCAATGCAA
*
38881242 TCTCAGTCCAATGC
1 TCTCAGTTCAATGC
38881256 TTCTTCGACT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 45 0.96
43 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (42 bp):
TCTCAGTTCAATGCATCGCCACCAGATGTTGATTCAATGCAA
Found at i:38890189 original size:17 final size:16
Alignment explanation
Indices: 38890167--38890200 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
38890157 AAATAATTTT
*
38890167 AAAATATAAAATATAAA
1 AAAATACAAAATA-AAA
38890184 AAAATACAAAATAAAA
1 AAAATACAAAATAAAA
38890200 A
1 A
38890201 TATGTGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATACAAAATAAAA
Found at i:38915032 original size:9 final size:9
Alignment explanation
Indices: 38914960--38915042 Score: 53
Period size: 10 Copynumber: 8.9 Consensus size: 9
38914950 TCATTTAAAT
38914960 TTATAAAAAA
1 TTAT-AAAAA
*
38914970 TCATAAAAA
1 TTATAAAAA
*
38914979 TGTAAAAAAA
1 T-TATAAAAA
* *
38914989 TTAATTAAAT
1 TT-ATAAAAA
*
38914999 TTATAAAGA
1 TTATAAAAA
*
38915008 -T-TAAAAT
1 TTATAAAAA
38915015 TTATAAAAAA
1 TTAT-AAAAA
38915025 TTATAAAAA
1 TTATAAAAA
38915034 TATATAAAA
1 T-TATAAAA
38915043 GTTTACGTAG
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
7 4 0.07
8 2 0.04
9 18 0.33
10 31 0.56
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:38944508 original size:30 final size:30
Alignment explanation
Indices: 38944465--38944521 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
38944455 GTATACTTTG
38944465 ACGTAAGTAAAATTGATCTCTCCACTAATT
1 ACGTAAGTAAAATTGATCTCTCCACTAATT
* *
38944495 ACGTATGTCAAATTGATCTCTCCACTA
1 ACGTAAGTAAAATTGATCTCTCCACTA
38944522 GCTCGTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (30 bp):
ACGTAAGTAAAATTGATCTCTCCACTAATT
Found at i:38950899 original size:22 final size:22
Alignment explanation
Indices: 38950871--38950918 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
38950861 GAGTCGGGTT
*
38950871 TAATTTA-TATTGATTTATAAAA
1 TAATTTATTATTCATTTA-AAAA
*
38950893 TAATTTATTTTTCATTTAAAAA
1 TAATTTATTATTCATTTAAAAA
38950915 TAAT
1 TAAT
38950919 AAAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATTTATTATTCATTTAAAAA
Found at i:38953798 original size:56 final size:54
Alignment explanation
Indices: 38953722--38953862 Score: 183
Period size: 54 Copynumber: 2.6 Consensus size: 54
38953712 TTACCTATTT
* *
38953722 GCCAACACAGTTCTCCAGCAAGGTAGGTGCATATATATATATTCGTTTACTTAGCC
1 GCCAACACAGTTCGCCAGCAAGGTAGGTGC--ATATATATATTCGTTTACCTAGCC
*
38953778 GCCAACACAGTTCGCTAGCAAGGTAGGTGCATATATATATTCGTTTACCTAGCC
1 GCCAACACAGTTCGCCAGCAAGGTAGGTGCATATATATATTCGTTTACCTAGCC
** * * **
38953832 ATCAACATAGTTTGCCAATAAGGTAGGTGCA
1 GCCAACACAGTTCGCCAGCAAGGTAGGTGCA
38953863 CCTAATTTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
54 47 0.63
56 28 0.37
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (54 bp):
GCCAACACAGTTCGCCAGCAAGGTAGGTGCATATATATATTCGTTTACCTAGCC
Found at i:38960255 original size:54 final size:54
Alignment explanation
Indices: 38960149--38961092 Score: 404
Period size: 55 Copynumber: 17.4 Consensus size: 54
38960139 CAACAAACTG
* * * * * * *
38960149 CAAGACTCTGAAAATATTGTAAATTAAAAAGTAGAGATCTGAAATC-AGCGAACCC
1 CAAGATTCTGAAAATCTTGTAAGTT-AAAAGTTGCGATATGAAATCGA-CGAACCA
* * *
38960204 CAAAATTTTAAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACGAACCA
1 CAAGATTCTGAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACGAACCA
* * * * * ** ***
38960258 CAAGATTATGAAAATTTTGTAAGTTAAAAGTTTACGATCTAAAATCGGTGAATTG
1 CAAGATTCTGAAAATCTTGTAAGTTAAAAG-TTGCGATATGAAATCGACGAACCA
* * * * ** *
38960313 CGAGATTCTGAAAATATTGTAATTTAAAAGGTTGTGATATGAAATCGGTGAACTA
1 CAAGATTCTGAAAATCTTGTAAGTTAAAA-GTTGCGATATGAAATCGACGAACCA
** * * * * * *
38960368 TGAGATTTTTAAGATCTTGTCAA-TTAAAAAGTTGTGATATGAAATTGACGAACCG
1 CAAGATTCTGAAAATCTTGT-AAGTT-AAAAGTTGCGATATGAAATCGACGAACCA
* * * * * **
38960423 CAAGACTCT-AAAATCTTGTAAGTTAAAA--T-CAATATAAAATCAACAAACTG
1 CAAGATTCTGAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACGAACCA
* * * * * *
38960473 CAAGACTCTGAAAATATTGTAAATTAAAAAGTAGAGATCTGAAATC-AGCGAACC-
1 CAAGATTCTGAAAATCTTGTAAGTT-AAAAGTTGCGATATGAAATCGA-CGAACCA
* * * *
38960527 CAAAATTTTAAAAATCTTGTAAGTTAAAAGTTGCGTTATGAAATCGACGAACCA
1 CAAGATTCTGAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACGAACCA
* * ** * * ** **
38960581 CAAGAATATGAAAAT-TTCGTAAGTTAAAAGTTTATGATCTAAAATCGGTGAATTA
1 CAAGATTCTGAAAATCTT-GTAAGTTAAAAG-TTGCGATATGAAATCGACGAACCA
* * * * * **
38960636 CGAGATTCTGAAAATATTGTAAGTTAAAATGTCGCGATCTGAAATTAGA-GAACTG
1 CAAGATTCTGAAAATCTTGTAAGTTAAAA-GTTGCGATATGAAA-TCGACGAACCA
** * * * * ** *
38960691 TGAGATTATGAAAATATTGTAATTTAAAAGGTTGTGATATGAAATCGGTGAACTA
1 CAAGATTCTGAAAATCTTGTAAGTTAAAA-GTTGCGATATGAAATCGACGAACCA
** * * * * * *
38960746 TGAGATTTTTAAGATCTTGTCAA-TTAAAAAGTTGTGATATGAAATTGACGAACCG
1 CAAGATTCTGAAAATCTTGT-AAGTT-AAAAGTTGCGATATGAAATCGACGAACCA
* * *
38960801 TAAGACTCTG-AAATCTTGTAAGTTAAAATGTTACGATATGAAATC-ATC-AA--A
1 CAAGATTCTGAAAATCTTGTAAGTTAAAA-GTTGCGATATGAAATCGA-CGAACCA
*** * * * * * * * **
38960852 TTGGACTCTGAAAAATATTGTAAGTTAAAAGGTCGCAATTTCAAATCGACGGACTG
1 CAAGATTCTG-AAAATCTTGTAAGTTAAAA-GTTGCGATATGAAATCGACGAACCA
* * * * * *
38960908 CGAGATTTTGAAAATATTGTAAG-TAAAAGGTTGCGATCTGAAATCGATGAACCG
1 CAAGATTCTGAAAATCTTGTAAGTTAAAA-GTTGCGATATGAAATCGACGAACCA
* * * * **
38960962 CGAA-ATTCT-AAGATCTTGTAAG-TAGGAAGTCGCGATCAT-AAATCTACGAATTA
1 C-AAGATTCTGAAAATCTTGTAAGTTA-AAAGTTGCGAT-ATGAAATCGACGAACCA
* * ** * * *
38961015 TAAGATTCTGAAAATTTTGTAAG-TAGATGGTTGCGA-CTGTAAATCGATGAATCA
1 CAAGATTCTGAAAATCTTGTAAGTTA-AAAGTTGCGATATG-AAATCGACGAACCA
* *
38961069 TAAGATTCTTAAAATCTTGTAAGT
1 CAAGATTCTGAAAATCTTGTAAGT
38961093 ATAAGGTAAC
Statistics
Matches: 677, Mismatches: 173, Indels: 78
0.73 0.19 0.08
Matches are distributed among these distances:
50 23 0.03
51 22 0.03
52 7 0.01
53 102 0.15
54 216 0.32
55 284 0.42
56 23 0.03
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (54 bp):
CAAGATTCTGAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACGAACCA
Found at i:38960727 original size:323 final size:324
Alignment explanation
Indices: 38960123--38960735 Score: 1032
Period size: 323 Copynumber: 1.9 Consensus size: 324
38960113 GGTGGATAGC
38960123 AAAATCAATATAAAATCAACAAACTGCAAGACTCTGAAAATATTGTAAATTAAAAAGTAGAGATC
1 AAAATCAATATAAAATCAACAAACTGCAAGACTCTGAAAATATTGTAAATTAAAAAGTAGAGATC
38960188 TGAAATCAGCGAACCCCAAAATTTTAAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACG
66 TGAAATCAGCGAACCCCAAAATTTTAAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACG
* * *
38960253 AACCACAAGATTATGAAAATTTTGTAAGTTAAAAGTTTACGATCTAAAATCGGTGAATTGCGAGA
131 AACCACAAGAATATGAAAATTTCGTAAGTTAAAAGTTTACGATCTAAAATCGGTGAATTACGAGA
* * * * * * * *
38960318 TTCTGAAAATATTGTAATTTAAAAGGTTGTGATATGAAATCGGTGAACTATGAGATTTTTAAGAT
196 TTCTGAAAATATTGTAAGTTAAAAGGTCGCGATATGAAATCAGAGAACTATGAGATTATGAAAAT
*
38960383 CTTGTCAATTAAAAAGTTGTGATATGAAATTGACGAACCGCAAGACTCTAAAATCTTGTAAGTT
261 ATTGTCAATTAAAAAGTTGTGATATGAAATTGACGAACCGCAAGACTCTAAAATCTTGTAAGTT
38960447 AAAATCAATATAAAATCAACAAACTGCAAGACTCTGAAAATATTGTAAATTAAAAAGTAGAGATC
1 AAAATCAATATAAAATCAACAAACTGCAAGACTCTGAAAATATTGTAAATTAAAAAGTAGAGATC
*
38960512 TGAAATCAGCGAA-CCCAAAATTTTAAAAATCTTGTAAGTTAAAAGTTGCGTTATGAAATCGACG
66 TGAAATCAGCGAACCCCAAAATTTTAAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACG
*
38960576 AACCACAAGAATATGAAAATTTCGTAAGTTAAAAGTTTATGATCTAAAATCGGTGAATTACGAGA
131 AACCACAAGAATATGAAAATTTCGTAAGTTAAAAGTTTACGATCTAAAATCGGTGAATTACGAGA
* * * *
38960641 TTCTGAAAATATTGTAAGTTAAAATGTCGCGATCTGAAATTAGAGAACTGTGAGATTATGAAAAT
196 TTCTGAAAATATTGTAAGTTAAAAGGTCGCGATATGAAATCAGAGAACTATGAGATTATGAAAAT
*
38960706 ATTGT-AATTTAAAAGGTTGTGATATGAAAT
261 ATTGTCAA-TTAAAAAGTTGTGATATGAAAT
38960736 CGGTGAACTA
Statistics
Matches: 269, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
322 2 0.01
323 189 0.70
324 78 0.29
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (324 bp):
AAAATCAATATAAAATCAACAAACTGCAAGACTCTGAAAATATTGTAAATTAAAAAGTAGAGATC
TGAAATCAGCGAACCCCAAAATTTTAAAAATCTTGTAAGTTAAAAGTTGCGATATGAAATCGACG
AACCACAAGAATATGAAAATTTCGTAAGTTAAAAGTTTACGATCTAAAATCGGTGAATTACGAGA
TTCTGAAAATATTGTAAGTTAAAAGGTCGCGATATGAAATCAGAGAACTATGAGATTATGAAAAT
ATTGTCAATTAAAAAGTTGTGATATGAAATTGACGAACCGCAAGACTCTAAAATCTTGTAAGTT
Found at i:38961093 original size:54 final size:54
Alignment explanation
Indices: 38960910--38961393 Score: 292
Period size: 54 Copynumber: 8.9 Consensus size: 54
38960900 ACGGACTGCG
* * **
38960910 AGATT-TTGAAAATATTGTAAGTAAAAGGTTGCGATC-TGAAATCGATGAACCGCGA
1 AGATTCTT-AAAATCTTGTAAGTAGAAGGTTGCGATCGT-AAATCGATGAACC-ATA
* * * * * **
38960965 A-ATTC-TAAGATCTTGTAAGTAGGAA-GTCGCGATCATAAATCTACGAATTATA
1 AGATTCTTAAAATCTTGTAAGTA-GAAGGTTGCGATCGTAAATCGATGAACCATA
* * * *
38961017 AGATTCTGAAAATTTTGTAAGTAGATGGTTGCGA-CTGTAAATCGATGAATCATA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTGCGATC-GTAAATCGATGAACCATA
* ** * ** *
38961071 AGATTCTTAAAATCTTGTAAGTATAAGGTAACGATCGTAAATCAACCAACCGTA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTGCGATCGTAAATCGATGAACCATA
* * * * *
38961125 AAATCCTTGAAATCTTGTAAGTAGAAGGTTGCGATTGTAAAT-TA-GCAAACCATA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTGCGATCGTAAATCGATG--AACCATA
* * ** * * * * * **
38961179 AGATTCTTGAAATCTTGTAAGTAAAAGGTCACAATCATAAATGGGTGAATCGCA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTGCGATCGTAAATCGATGAACCATA
* * * *
38961233 ATATTCTTAAAATCTTGTAAGTAGAAGG-TGACAATCGCAAATC-AGTGAACCGTA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTG-CGATCGTAAATCGA-TGAACCATA
* * *
38961287 AAATTCTTAAAATCTTGTAAGTAGGAGGTCGTC-ATCGTAAATC-A-GCAAACCATA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTG-CGATCGTAAATCGATG--AACCATA
* * * * * *
38961341 AGATTCTAAAAATGTTTTAAGTAAGGGAGGTTACGATCGTAAATCGGTGAACC
1 AGATTCTTAAAATCTTGTAAGT-A-GAAGGTTGCGATCGTAAATCGATGAACC
38961394 GCAAAATGCT
Statistics
Matches: 330, Mismatches: 77, Indels: 43
0.73 0.17 0.10
Matches are distributed among these distances:
52 3 0.01
53 38 0.12
54 261 0.79
55 6 0.02
56 21 0.06
58 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (54 bp):
AGATTCTTAAAATCTTGTAAGTAGAAGGTTGCGATCGTAAATCGATGAACCATA
Found at i:38961146 original size:162 final size:162
Alignment explanation
Indices: 38960974--38961347 Score: 398
Period size: 162 Copynumber: 2.3 Consensus size: 162
38960964 AAATTCTAAG
* ** *
38960974 ATCTTGTAAGTAGGAAGTCGCGATCATAAATCTA-CGAATTATAAGATTC-TGAAAATTTTGTAA
1 ATCTTGTAAGTAGGAAGTCGCGATCATAAAT-TAGCAAACCATAAGATTCTTG-AAATCTTGTAA
* * ** * * * *
38961037 GTAGATGGTTGCGA-CTGTAAATCGATGAATCATAAGATTCTTAAAATCTTGTAAGTATAAGGTA
64 GTAAAAGGTCACAATC-ATAAATCGATGAATCACAAGATTCTTAAAATCTTGTAAGTAGAAGGTA
* * *
38961101 ACGATCGTAAATCAACCAACCGTAAAATCCTTGAA
128 ACAATCGCAAATCAACCAACCGTAAAATCCTTAAA
* **
38961136 ATCTTGTAAGTA-GAAGGTTGCGATTGTAAATTAGCAAACCATAAGATTCTTGAAATCTTGTAAG
1 ATCTTGTAAGTAGGAA-GTCGCGATCATAAATTAGCAAACCATAAGATTCTTGAAATCTTGTAAG
* * * * *
38961200 TAAAAGGTCACAATCATAAATGGGTGAATCGCAATATTCTTAAAATCTTGTAAGTAGAAGGTGAC
65 TAAAAGGTCACAATCATAAATCGATGAATCACAAGATTCTTAAAATCTTGTAAGTAGAAGGTAAC
*** *
38961265 AATCGCAAATCAGTGAACCGTAAAATTCTTAAA
130 AATCGCAAATCAACCAACCGTAAAATCCTTAAA
* * *
38961298 ATCTTGTAAGTAGGAGGTCGTC-ATCGTAAATCAGCAAACCATAAGATTCT
1 ATCTTGTAAGTAGGAAGTCG-CGATCATAAATTAGCAAACCATAAGATTCT
38961348 AAAAATGTTT
Statistics
Matches: 175, Mismatches: 31, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
161 5 0.03
162 164 0.94
163 6 0.03
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (162 bp):
ATCTTGTAAGTAGGAAGTCGCGATCATAAATTAGCAAACCATAAGATTCTTGAAATCTTGTAAGT
AAAAGGTCACAATCATAAATCGATGAATCACAAGATTCTTAAAATCTTGTAAGTAGAAGGTAACA
ATCGCAAATCAACCAACCGTAAAATCCTTAAA
Found at i:38961347 original size:108 final size:108
Alignment explanation
Indices: 38960910--38961400 Score: 336
Period size: 108 Copynumber: 4.5 Consensus size: 108
38960900 ACGGACTGCG
* * **
38960910 AGATT-TTGAAAATATTGTAAGTAAAAGGTTGCGATC-TGAAATC-GATGAACCGCGAAATTC-T
1 AGATTCTT-AAAATCTTGTAAGTAGAAGGTTGCGATCGT-AAATCAG-TGAACCGTAAAATTCTT
* * **
38960971 AAGATCTTGTAAGTAGGAA-GTCGCGATCATAAATCTA-CGAATTATA
63 AAAATCTTGTAAGTA-GAAGGTCGCAATCATAAATC-AGCGAACCATA
* * * * * *
38961017 AGATTCTGAAAATTTTGTAAGTAGATGGTTGCGA-CTGTAAATC-GATGAATCATAAGATTCTTA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTGCGATC-GTAAATCAG-TGAACCGTAAAATTCTTA
* ** * * * * *
38961080 AAATCTTGTAAGTATAAGGTAACGATCGTAAATCAACCAACCGTA
64 AAATCTTGTAAGTAGAAGGTCGCAATCATAAATCAGCGAACCATA
* * * * * ** * * *
38961125 AAATCCTTGAAATCTTGTAAGTAGAAGGTTGCGATTGTAAATTAGCAAACCATAAGATTCTTGAA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTGCGATCGTAAATCAGTGAACCGTAAAATTCTTAAA
* * ** * * **
38961190 ATCTTGTAAGTAAAAGGTCACAATCATAAATGGGTGAATCGCA
66 ATCTTGTAAGTAGAAGGTCGCAATCATAAATCAGCGAACCATA
* * *
38961233 ATATTCTTAAAATCTTGTAAGTAGAAGG-TGACAATCGCAAATCAGTGAACCGTAAAATTCTTAA
1 AGATTCTTAAAATCTTGTAAGTAGAAGGTTG-CGATCGTAAATCAGTGAACCGTAAAATTCTTAA
* * *
38961297 AATCTTGTAAGTAGGAGGTCGTC-ATCGTAAATCAGCAAACCATA
65 AATCTTGTAAGTAGAAGGTCG-CAATCATAAATCAGCGAACCATA
* * * * * * *
38961341 AGATTCTAAAAATGTTTTAAGTAAGGGAGGTTACGATCGTAAATCGGTGAACCGCAAAAT
1 AGATTCTTAAAATCTTGTAAGT-A-GAAGGTTGCGATCGTAAATCAGTGAACCGTAAAAT
38961401 GCTAGTTGTA
Statistics
Matches: 297, Mismatches: 74, Indels: 23
0.75 0.19 0.06
Matches are distributed among these distances:
106 1 0.00
107 50 0.17
108 215 0.72
109 3 0.01
110 27 0.09
111 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (108 bp):
AGATTCTTAAAATCTTGTAAGTAGAAGGTTGCGATCGTAAATCAGTGAACCGTAAAATTCTTAAA
ATCTTGTAAGTAGAAGGTCGCAATCATAAATCAGCGAACCATA
Found at i:38961364 original size:162 final size:162
Alignment explanation
Indices: 38961073--38961364 Score: 415
Period size: 162 Copynumber: 1.8 Consensus size: 162
38961063 GAATCATAAG
* * * *
38961073 ATTCTTAAAATCTTGTAAGTATAAGGTAACGATCGTAAATCAACCAACCGTAAAATCCTTGAAAT
1 ATTCTTAAAATCTTGTAAGTAGAAGGTAACAATCGCAAATCAACCAACCGTAAAATCCTTAAAAT
* * * **
38961138 CTTGTAAGTAGAAGGTTGCGATTGTAAATTAGCAAACCATAAGATTCTTGAAATCTTGTAAGTAA
66 CTTGTAAGTAGAAGGTCGCGATCGTAAATCAGCAAACCATAAGATTCTAAAAATCTTGTAAGTAA
38961203 AAGGTCACAATCATAAATGGGTGAATCGCAAT
131 AAGGTCACAATCATAAATGGGTGAATCGCAAT
* *** *
38961235 ATTCTTAAAATCTTGTAAGTAGAAGGTGACAATCGCAAATCAGTGAACCGTAAAATTCTTAAAAT
1 ATTCTTAAAATCTTGTAAGTAGAAGGTAACAATCGCAAATCAACCAACCGTAAAATCCTTAAAAT
* * *
38961300 CTTGTAAGTAGGAGGTCGTC-ATCGTAAATCAGCAAACCATAAGATTCTAAAAATGTTTTAAGTA
66 CTTGTAAGTAGAAGGTCG-CGATCGTAAATCAGCAAACCATAAGATTCTAAAAATCTTGTAAGTA
38961364 A
130 A
38961365 GGGAGGTTAC
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
162 111 0.99
163 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (162 bp):
ATTCTTAAAATCTTGTAAGTAGAAGGTAACAATCGCAAATCAACCAACCGTAAAATCCTTAAAAT
CTTGTAAGTAGAAGGTCGCGATCGTAAATCAGCAAACCATAAGATTCTAAAAATCTTGTAAGTAA
AAGGTCACAATCATAAATGGGTGAATCGCAAT
Found at i:38961756 original size:13 final size:15
Alignment explanation
Indices: 38961738--38961769 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
38961728 AATCAAAACC
38961738 AAAACCA-ACAGT-T
1 AAAACCATACAGTCT
38961751 AAAACCATACAGTCT
1 AAAACCATACAGTCT
38961766 AAAA
1 AAAA
38961770 AGCCCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.56, C:0.22, G:0.06, T:0.16
Consensus pattern (15 bp):
AAAACCATACAGTCT
Found at i:38965329 original size:31 final size:30
Alignment explanation
Indices: 38965294--38965639 Score: 230
Period size: 31 Copynumber: 11.2 Consensus size: 30
38965284 TTGTGAGGTT
* *
38965294 GTGAGGTGTGACAGGATCACTTAGGTAGATG
1 GTGAGGCGTGATAGGATCACTTAGG-AGATG
* * **
38965325 GTGAGGCATGATGGGATCACTTCACAAGATG
1 GTGAGGCGTGATAGGATCACTT-AGGAGATG
* * * *
38965356 GTGAGGCGTGA-CGAGATAACTTCATGAGGTG
1 GTGAGGCGTGATAG-GATCACTT-AGGAGATG
* * *
38965387 GTGAGGTGTAATGGGATCACTTAGTGAGATG
1 GTGAGGCGTGATAGGATCACTTAG-GAGATG
* * *
38965418 GTGAGGCGTGA-CGG-TCACTTCGCGAGTTG
1 GTGAGGCGTGATAGGATCACTTAG-GAGATG
** * *
38965447 GTGAGGTATGATGGGATCACTTAGCGAGATA
1 GTGAGGCGTGATAGGATCACTTAG-GAGATG
* * * *
38965478 GTGAGACGTGATAAGATCAGTTAGTGAGATA
1 GTGAGGCGTGATAGGATCACTTAG-GAGATG
* * * *
38965509 GTGAGGCGTGATGGGATCACCTCGTGAAATG
1 GTGAGGCGTGATAGGATCACTTAG-GAGATG
* * * *
38965540 ATGAGGCGTGACATGATCACTTTGCGAGATG
1 GTGAGGCGTGATAGGATCACTTAG-GAGATG
* * *
38965571 GTGAGGTGTGATAGAATCACTTCGCGAGATG
1 GTGAGGCGTGATAGGATCACTTAG-GAGATG
* *
38965602 GTGAGGCGTGATAGAATCACTTCGCGAGATG
1 GTGAGGCGTGATAGGATCACTTAG-GAGATG
38965633 GTGAGGC
1 GTGAGGC
38965640 ATCCCACAAG
Statistics
Matches: 249, Mismatches: 60, Indels: 12
0.78 0.19 0.04
Matches are distributed among these distances:
29 21 0.08
30 6 0.02
31 220 0.88
32 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.25
Consensus pattern (30 bp):
GTGAGGCGTGATAGGATCACTTAGGAGATG
Found at i:38965401 original size:62 final size:60
Alignment explanation
Indices: 38965323--38965488 Score: 181
Period size: 60 Copynumber: 2.7 Consensus size: 60
38965313 CTTAGGTAGA
* * *
38965323 TGGTGAGGCATGATGGGATCACTTCA-CAAGATGGTGAGGCGTGACGAGATAACTTCATGAGG
1 TGGTGAGGTATAATGGGATCACTT-AGCAAGATGGTGAGGCGTGACG-G-TAACTTCACGAGG
* ** * * *
38965385 TGGTGAGGTGTAATGGGATCACTTAGTGAGATGGTGAGGCGTGACGGTCACTTCGCGAGT
1 TGGTGAGGTATAATGGGATCACTTAGCAAGATGGTGAGGCGTGACGGTAACTTCACGAGG
* * * *
38965445 TGGTGAGGTATGATGGGATCACTTAGCGAGATAGTGAGACGTGA
1 TGGTGAGGTATAATGGGATCACTTAGCAAGATGGTGAGGCGTGA
38965489 TAAGATCAGT
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
60 48 0.54
61 2 0.02
62 39 0.44
ACGTcount: A:0.25, C:0.13, G:0.38, T:0.25
Consensus pattern (60 bp):
TGGTGAGGTATAATGGGATCACTTAGCAAGATGGTGAGGCGTGACGGTAACTTCACGAGG
Found at i:38967353 original size:24 final size:24
Alignment explanation
Indices: 38967337--38967388 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38967327 AATCAAAGTC
38967337 AAATATATTATATTAATAAATGCT
1 AAATATATTATATTAATAAATGCT
* * *
38967361 AAATATATTATACTCATAAATACT
1 AAATATATTATATTAATAAATGCT
38967385 AAAT
1 AAAT
38967389 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATATTATATTAATAAATGCT
Found at i:38976516 original size:105 final size:105
Alignment explanation
Indices: 38976334--38976522 Score: 333
Period size: 105 Copynumber: 1.8 Consensus size: 105
38976324 AAATTATTAT
* *
38976334 GGAAATAATTTTGGTCAAAATTGTTTTGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
1 GGAAATAATTTTGGTCAAAATTATTTTGGGGGTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
38976399 GTGTGCTGATGGCTATAATGGTTTTTTGGAACAACGTGCA
66 GTGTGCTGATGGCTATAATGGTTTTTTGGAACAACGTGCA
* *
38976439 GGAAATAATTTTGGTCAAAATTATTTTGGGGGTGGTCAAACTAATTGTGTTTCTGGTCAAAATGT
1 GGAAATAATTTTGGTCAAAATTATTTTGGGGGTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
*
38976504 GTGTGTTGATGGCTATAAT
66 GTGTGCTGATGGCTATAAT
38976523 TGTGCAGGAC
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 79 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (105 bp):
GGAAATAATTTTGGTCAAAATTATTTTGGGGGTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
GTGTGCTGATGGCTATAATGGTTTTTTGGAACAACGTGCA
Found at i:38976682 original size:18 final size:18
Alignment explanation
Indices: 38976661--38976721 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
38976651 TATTGGGCCA
38976661 AATGCTCCCCTTGGACCG
1 AATGCTCCCCTTGGACCG
38976679 AATGCTCCCCTTGGACCG
1 AATGCTCCCCTTGGACCG
38976697 AATGCTCCCCTTGGACCG
1 AATGCTCCCCTTGGACCG
*
38976715 ATTGCTC
1 AATGCTC
38976722 TTATTAGGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.16, C:0.38, G:0.21, T:0.25
Consensus pattern (18 bp):
AATGCTCCCCTTGGACCG
Found at i:38980038 original size:9 final size:9
Alignment explanation
Indices: 38980024--38980054 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
38980014 GTTAAACGAA
38980024 TCGAGTTAT
1 TCGAGTTAT
*
38980033 TCGAGTTAA
1 TCGAGTTAT
38980042 TCGAGTTAT
1 TCGAGTTAT
38980051 TCGA
1 TCGA
38980055 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:38980136 original size:9 final size:9
Alignment explanation
Indices: 38980107--38980136 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
38980097 TGAGTTTTCG
38980107 AATTCGAAT
1 AATTCGAAT
*
38980116 AACTCGAAT
1 AATTCGAAT
38980125 AATTCGAAT
1 AATTCGAAT
38980134 AAT
1 AAT
38980137 NNNNNNNNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:38980895 original size:5 final size:5
Alignment explanation
Indices: 38980885--38980910 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38980875 CTCGAAAATT
38980885 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
38980911 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:38992454 original size:3 final size:3
Alignment explanation
Indices: 38992448--38992473 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38992438 ATGATAATGA
38992448 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
38992474 ATACAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:38995618 original size:29 final size:29
Alignment explanation
Indices: 38995560--38995619 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
38995550 TTTTTTTTTT
**
38995560 AATTTATAGAAATAGGTCGATTTTTTTAA
1 AATTTATAGAAATAGGTCGATTTTGGTAA
* *
38995589 AATTTAT-GAGAATGGGTTGATTTTGGTAA
1 AATTTATAGA-AATAGGTCGATTTTGGTAA
38995618 AA
1 AA
38995620 CGTTTTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.42
Consensus pattern (29 bp):
AATTTATAGAAATAGGTCGATTTTGGTAA
Found at i:39000828 original size:18 final size:18
Alignment explanation
Indices: 39000795--39000829 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39000785 TATGCAGAAG
**
39000795 GTGGAGGATATGTGGATA
1 GTGGAGGATACATGGATA
39000813 GTGGAGGATACATGGAT
1 GTGGAGGATACATGGAT
39000830 GACGGGTATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.43, T:0.26
Consensus pattern (18 bp):
GTGGAGGATACATGGATA
Found at i:39004294 original size:2 final size:2
Alignment explanation
Indices: 39004289--39004323 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
39004279 AACTGTGATA
*
39004289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39004324 AAACTATGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:39007679 original size:27 final size:28
Alignment explanation
Indices: 39007645--39007715 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
39007635 AAAAATAAAA
*
39007645 ATTTACCAAAATACTA-CAA-GTTTTTTT
1 ATTTACCAAAATA-TATAAACGTTTTTTT
*
39007672 ATTTACCAAAATATATAAACTTTTTTTT
1 ATTTACCAAAATATATAAACGTTTTTTT
39007700 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
39007716 CAAAAAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.05
27 15 0.38
28 23 0.57
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.45
Consensus pattern (28 bp):
ATTTACCAAAATATATAAACGTTTTTTT
Found at i:39007873 original size:27 final size:27
Alignment explanation
Indices: 39007787--39007877 Score: 137
Period size: 27 Copynumber: 3.4 Consensus size: 27
39007777 CACTGGTCAC
** *
39007787 GCCAATGGTATTGGCGGCACCAAAGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
**
39007814 GCCAAAACCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
39007841 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
39007868 GCCAATGCCA
1 GCCAATGCCA
39007878 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:39014100 original size:3 final size:3
Alignment explanation
Indices: 39014094--39014134 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
39014084 CAACAACAAC
*
39014094 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
39014135 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39014504 original size:27 final size:27
Alignment explanation
Indices: 39014474--39014526 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
39014464 TTTGGTTTTT
39014474 TTTATATATTTTGGTAAATAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAG
39014501 TTTATATATTTTGGTAAATAAAAAAA
1 TTTATATATTTTGGTAAATAAAAAAA
39014527 AACTTGTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (27 bp):
TTTATATATTTTGGTAAATAAAAAAAG
Found at i:39014527 original size:29 final size:27
Alignment explanation
Indices: 39014474--39014548 Score: 98
Period size: 29 Copynumber: 2.7 Consensus size: 27
39014464 TTTGGTTTTT
*
39014474 TTTATATATTTTGGTAAATAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAC
39014501 TTTATATATTTTGGTAAATAAAAAAAAAC
1 TTTATATATTTTGGTAAAT--AAAAAAAC
*
39014530 TTGTA-GTATTTTGGTAAAT
1 TT-TATATATTTTGGTAAAT
39014549 TTTTATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.44
29 22 0.51
30 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.43
Consensus pattern (27 bp):
TTTATATATTTTGGTAAATAAAAAAAC
Found at i:39022397 original size:17 final size:17
Alignment explanation
Indices: 39022375--39022414 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
39022365 AAATTTTAGC
39022375 GATTAAGGTGAGTTTTG
1 GATTAAGGTGAGTTTTG
39022392 GATTAAGGTGAGTTTTG
1 GATTAAGGTGAGTTTTG
*
39022409 GTTTAA
1 GATTAA
39022415 ATTTCTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (17 bp):
GATTAAGGTGAGTTTTG
Found at i:39023025 original size:2 final size:2
Alignment explanation
Indices: 39023018--39023042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39023008 TGAGACTTAC
39023018 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
39023043 TTTGCTTATG
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:39024944 original size:25 final size:25
Alignment explanation
Indices: 39024904--39024960 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
39024894 GGGCACACCT
39024904 TAGCTCTTTTGAGCTTCCTGA-TAA
1 TAGCTCTTTTGAGCTTCCTGATTAA
* *
39024928 TTGCTCTTTGTGAGCTTTCTGATTAA
1 TAGCTCTTT-TGAGCTTCCTGATTAA
39024954 TAGCTCT
1 TAGCTCT
39024961 CCGAAGCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 8 0.29
25 11 0.39
26 9 0.32
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.46
Consensus pattern (25 bp):
TAGCTCTTTTGAGCTTCCTGATTAA
Found at i:39027415 original size:110 final size:107
Alignment explanation
Indices: 39027278--39027481 Score: 293
Period size: 110 Copynumber: 1.9 Consensus size: 107
39027268 AAAAATAATA
* * * *
39027278 AAGGCAATATTTTGCATTTGTGGATTCGAGAAAGCGTGCCTTAATGTGTTGGGTTTCGATTTTTT
1 AAGGCAATATTTTGCATTTGTGAATTCGAGAAAACGTGCCTTAATGTGCTGGGCTTCGA---TTT
*
39027343 TTCGTTCGACAAAATAGCCAAATATCCTCTTAAAAGTTTCAAAAT
63 CTCGTTCGACAAAATAGCCAAATATCCTCTTAAAAGTTTCAAAAT
*
39027388 AAGGCAATGTTTTGCATTTG-GAAATTCGAGAAAACGTGCCTTAATGTGCTGGGCTTCGATTTCT
1 AAGGCAATATTTTGCATTTGTG-AATTCGAGAAAACGTGCCTTAATGTGCTGGGCTTCGATTTCT
* *
39027452 CGTTGGACCAAATAGCCAAATATCCTCTTA
65 CGTTCGACAAAATAGCCAAATATCCTCTTA
39027482 TATCTTAATC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 32 0.38
109 1 0.01
110 52 0.61
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (107 bp):
AAGGCAATATTTTGCATTTGTGAATTCGAGAAAACGTGCCTTAATGTGCTGGGCTTCGATTTCTC
GTTCGACAAAATAGCCAAATATCCTCTTAAAAGTTTCAAAAT
Found at i:39027672 original size:30 final size:29
Alignment explanation
Indices: 39027625--39027684 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
39027615 TCCTCATACG
* * *
39027625 TAACCGACTCCCGAACCCAATAGGCCCAA
1 TAACCAACTCCCAAACCCAATAGGCACAA
39027654 TAACCAACTACCCAAACCCAATAGGCACAA
1 TAACCAACT-CCCAAACCCAATAGGCACAA
39027684 T
1 T
39027685 CTACCTAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.12
Consensus pattern (29 bp):
TAACCAACTCCCAAACCCAATAGGCACAA
Found at i:39029689 original size:111 final size:107
Alignment explanation
Indices: 39029538--39029742 Score: 259
Period size: 111 Copynumber: 1.9 Consensus size: 107
39029528 AAAAATAATA
* * * * *
39029538 AAGGCAATATTTTGCATTTGTGAATTCGAGAAAGCATGCCCTAATGTGTTGGGTTTCGATTTTTT
1 AAGGCAATATTTTACATTTGTGAATTCGAGAAAACATGCCCTAATGTGCTAGGCTTCGA---TTT
* * *
39029603 TTCGTTCGACTAAATAGCCAAAATATCCTCTTAAAAGTTTCAAAAT
63 CTCGTTAGACCAAATAGCC-AAATATCCTCTTAAAAGTTTCAAAAT
* * *
39029649 AAGGCAATGTTTTACGTTTG-GAAATTCGAGAAAACGTGCCCTAATGTGCTAGGCTTCGATTTCT
1 AAGGCAATATTTTACATTTGTG-AATTCGAGAAAACATGCCCTAATGTGCTAGGCTTCGATTTCT
39029713 CGTTAGACCAAATAGCCAAATATCCTCTTA
65 CGTTAGACCAAATAGCCAAATATCCTCTTA
39029743 TATCTTAATC
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 13 0.16
108 19 0.23
110 1 0.01
111 49 0.60
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (107 bp):
AAGGCAATATTTTACATTTGTGAATTCGAGAAAACATGCCCTAATGTGCTAGGCTTCGATTTCTC
GTTAGACCAAATAGCCAAATATCCTCTTAAAAGTTTCAAAAT
Found at i:39030163 original size:9 final size:8
Alignment explanation
Indices: 39030142--39030166 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39030132 GTGTTGATGA
39030142 CTTTTTGT
1 CTTTTTGT
39030150 CTTTTTGT
1 CTTTTTGT
39030158 CTTTTTGT
1 CTTTTTGT
39030166 C
1 C
39030167 GAAAATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (8 bp):
CTTTTTGT
Found at i:39034432 original size:24 final size:24
Alignment explanation
Indices: 39034388--39034434 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
39034378 TGTCCCAAAA
*
39034388 TTACAGTGGACTTAACCTTGAAGG
1 TTACAGCGGACTTAACCTTGAAGG
*
39034412 TTACAGCGGA-TTGAACTTTGAAG
1 TTACAGCGGACTT-AACCTTGAAG
39034435 ATTTCAGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (24 bp):
TTACAGCGGACTTAACCTTGAAGG
Found at i:39035933 original size:132 final size:132
Alignment explanation
Indices: 39034752--39035912 Score: 1822
Period size: 132 Copynumber: 8.8 Consensus size: 132
39034742 CGAAACCACC
* * * *
39034752 AGTCCTATCTCCCTAAACAGTAGTGGAGTAGGTTGAAAATTACAGATTCTGTCTCCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * **
39034817 AGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGATAGCAGAGAAGCAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAAGCCA
39034882 TT
131 TT
** * * * *
39034884 AGTTTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGCTTGTAGATTCTATCACACTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * * * *
39034949 AGTGGAACAGATCGAATATGGTGAATCTTATCTTCCCAAGATAGCGGAGAAGTAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAAGCCA
39035014 TT
131 TT
* * *
39035016 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTATCACCCTAAGTAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
39035081 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGCGGAGAAGC-GAATTTAAGCC
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAG-ATTTAAGCC
39035145 ATT
130 ATT
* *
39035148 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTATCACCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * *
39035213 ACTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGCGGAGAAGCATATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAAGCCA
39035278 TT
131 TT
* *
39035280 AGTCTTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
39035345 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGAAGAAGCAAATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAAGCCA
39035410 TT
131 TT
* * *
39035412 AGTCCTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAAATTGCAGATTCTGTCACCCTAAGTAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
39035477 AGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGTAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAAGCCA
39035542 TT
131 TT
* *
39035544 AGTCCTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAAATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
39035609 AGTGGAGCAGATTGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAATCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAAGCCA
39035674 TT
131 TT
*
39035676 AGTCCTATCTCTCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
39035741 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGT-GAGGAAGCAGATTTAAGCC
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGA-GAAGCAGATTTAAGCC
39035805 ATT
130 ATT
* * * * * *
39035808 AGTCCAATCTCCCCAAGCAGTAGTCGAGTAGGTTGAAGACTGCAGATTCTGTCTCCTTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * *
39035873 AGTGGAGCAGATCAAAGATGGTGAATCTTATATTCCCAAG
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAG
39035913 GTAATAGGGA
Statistics
Matches: 960, Mismatches: 66, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
131 3 0.00
132 957 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (132 bp):
AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAAGCCA
TT
Found at i:39037292 original size:3 final size:3
Alignment explanation
Indices: 39037280--39037311 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
39037270 AAAGTAATAA
39037280 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39037312 GCTATGTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39038138 original size:110 final size:107
Alignment explanation
Indices: 39038012--39038215 Score: 293
Period size: 110 Copynumber: 1.9 Consensus size: 107
39038002 AAAAATAATA
* * * *
39038012 AAGGCAATATTTTGCATTTGTG-GATTCGAGAAAGCGTGCCTTAATGTGTTGGGTTTCGATTTTT
1 AAGGCAATATTTTGCATTTG-GAAATTCGAGAAAACGTGCCTTAATGTGCTGGGCTTCGA---TT
*
39038076 TTTCGTTCGACAAAATAGCCAAATATCCTCTTAAAAGTTTCAAAAT
62 TCTCGTTCGACAAAATAGCCAAATATCCTCTTAAAAGTTTCAAAAT
*
39038122 AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGCTTCGATTTCTC
1 AAGGCAATATTTTGCATTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGCTTCGATTTCTC
* *
39038187 GTTGGACCAAATAGCCAAATATCCTCTTA
66 GTTCGACAAAATAGCCAAATATCCTCTTA
39038216 TATCTTAATC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 32 0.38
109 1 0.01
110 52 0.61
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (107 bp):
AAGGCAATATTTTGCATTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGCTTCGATTTCTC
GTTCGACAAAATAGCCAAATATCCTCTTAAAAGTTTCAAAAT
Found at i:39050372 original size:15 final size:17
Alignment explanation
Indices: 39050341--39050372 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
39050331 AGCCCCGGCA
39050341 ATAGCTGTCCAAATGAC
1 ATAGCTGTCCAAATGAC
39050358 ATAGCT-TCC-AATGAC
1 ATAGCTGTCCAAATGAC
39050373 GAAAGCATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (17 bp):
ATAGCTGTCCAAATGAC
Found at i:39079527 original size:16 final size:16
Alignment explanation
Indices: 39079502--39079535 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
39079492 ATTTATATTA
39079502 TAAAATTATTATTAAAT
1 TAAAATTATTA-TAAAT
39079519 TAAAA-TATTATAAAT
1 TAAAATTATTATAAAT
39079534 TA
1 TA
39079536 TATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTATTATAAAT
Found at i:39079556 original size:25 final size:24
Alignment explanation
Indices: 39079504--39079563 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
39079494 TTATATTATA
**
39079504 AAATTATTATTAAATTAAAATATTAT
1 AAATTA-TATT-AATTAAAATAAGAT
39079530 AAATTATATTAATTAAAATTAAGAT
1 AAATTATATTAATTAAAA-TAAGAT
39079555 -AA-TATATTA
1 AAATTATATTA
39079564 TAGGAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 7 0.23
24 10 0.32
25 8 0.26
26 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATTATATTAATTAAAATAAGAT
Found at i:39084669 original size:37 final size:37
Alignment explanation
Indices: 39084628--39084706 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
39084618 TGTTTGTGAT
39084628 GAAGTAACTCATAAGGCATGTGGGTGTGGAAGATGTG
1 GAAGTAACTCATAAGGCATGTGGGTGTGGAAGATGTG
*
39084665 GAAGTAACTCATAAGGGATGTGGGTGTGGAAGATGTG
1 GAAGTAACTCATAAGGCATGTGGGTGTGGAAGATGTG
39084702 GAAGT
1 GAAGT
39084707 GCAAACCTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.30, C:0.06, G:0.39, T:0.24
Consensus pattern (37 bp):
GAAGTAACTCATAAGGCATGTGGGTGTGGAAGATGTG
Found at i:39087140 original size:7 final size:7
Alignment explanation
Indices: 39087130--39087164 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
39087120 GGCTCCAGGC
39087130 TCCTGTA
1 TCCTGTA
39087137 TCCTGTA
1 TCCTGTA
39087144 TCCTGTA
1 TCCTGTA
39087151 TCCTGTA
1 TCCTGTA
39087158 TCCTGTA
1 TCCTGTA
39087165 AGGATTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (7 bp):
TCCTGTA
Found at i:39090937 original size:16 final size:16
Alignment explanation
Indices: 39090916--39090965 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
39090906 NNNNAAAATC
39090916 TAAAATTATATTTTAT
1 TAAAATTATATTTTAT
39090932 TAAAATT-TATTATTAT
1 TAAAATTATATT-TTAT
**
39090948 TATTATTATTATTTTAT
1 TAAAATTA-TATTTTAT
39090965 T
1 T
39090966 CATTGGCGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 16 0.55
17 5 0.17
18 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAAAATTATATTTTAT
Found at i:39096839 original size:16 final size:16
Alignment explanation
Indices: 39096818--39096849 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39096808 ACAGATATAC
39096818 GAAAAAGGAAAAAAAT
1 GAAAAAGGAAAAAAAT
*
39096834 GAAAAATGAAAAAAAT
1 GAAAAAGGAAAAAAAT
39096850 AAATTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (16 bp):
GAAAAAGGAAAAAAAT
Found at i:39097097 original size:210 final size:208
Alignment explanation
Indices: 39096843--39097380 Score: 620
Period size: 210 Copynumber: 2.5 Consensus size: 208
39096833 TGAAAAATGA
* *
39096843 AAAAAATAAATTTTTTGGGTGCTGGCCTGTCAATGGCTGGCACCCAGTACAAATTTTAAAAAAAA
1 AAAAAA-AATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAC-AATTTTAAAAAAAA
*
39096908 ATTTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAATTTTAAAAAAAATTTTGAGTG
64 ATTTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAA--GTAAAAAAAATTTTG-GTG
***
39096973 ATGGCCTGTCAATGGCC-G-GTACAAATTAAAAAAAAATCTTTTTTTT-GTTTCAAAATCAGATA
126 ATGGCCTGTCAATGGCCGGCGTACAAATTAAAAAAAAATCTTTTTTTTAACGTCAAAATCAGATA
39097035 TCAGTATACGAAAAAAAATT
191 TCAGTATACG--AAAAAATT
* ** * * * **
39097055 -TAAAATTTTTTTTTTGGTGCTGACCTATCAATGGCCGGCACCCAGTACAA-TTTAAAAAATTTT
1 AAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAA--AA
* * *
39097118 CTTTTTTTTTCGTGTCAGAATCAGATATCGGTATACG-AAAAAAGTAAAAAAAATTTTGGTGTTG
64 ATTTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAAGTAAAAAAAATTTTGGTGATG
* *
39097182 GCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATCTTTTTTTTAACGTCAGAATCAGA
129 GCCTGTCAATGGCCGG----C-GTACAAATTAAAAAAAAATCTTTTTTTTAACGTCAAAATCAGA
39097247 TATCAGTATACGAAAAAATT
189 TATCAGTATACGAAAAAATT
* * *
39097267 CAAAAAAAAATTTTTTTGGGTGCTGGCTTGTCAATAGCCAGCACCCAGTACAATTTATAAAAAAA
1 --AAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTT-T-AAAAAA
* *
39097332 AAATTCTTTTTATTTTCGTGTCAGAATTAGATATCAGTATATGAAAAAA
62 AAA---TTTTT-TTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAA
39097381 TAATATTACG
Statistics
Matches: 271, Mismatches: 34, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
206 19 0.07
207 15 0.06
208 9 0.03
209 8 0.03
210 71 0.26
211 4 0.01
212 8 0.03
213 27 0.10
214 22 0.08
215 41 0.15
216 2 0.01
217 1 0.00
218 6 0.02
219 5 0.02
220 28 0.10
221 5 0.02
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (208 bp):
AAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAAT
TTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAAGTAAAAAAAATTTTGGTGATGGC
CTGTCAATGGCCGGCGTACAAATTAAAAAAAAATCTTTTTTTTAACGTCAAAATCAGATATCAGT
ATACGAAAAAATT
Found at i:39097356 original size:110 final size:104
Alignment explanation
Indices: 39096855--39097380 Score: 332
Period size: 110 Copynumber: 4.9 Consensus size: 104
39096845 AAAATAAATT
* ** * * * **
39096855 TTTTGGGTGCTGGCCTGTCAATGGCTGGCACCCAGTACAAATTTTAAAAAAAAATTTTTTTTTCG
1 TTTT-GGTGCTGGCCTGTCAATAGCCAGCACCCAGTAC-AATTTAAAAAAAAAAATTCTTTTTAA
* *
39096920 TGTCAGAATCAGATATCAGTATACGAAAAAAATTTTAAAAAAAA
64 CGTCAGAATCAGATATCAGTATACG-AAAAAA--GTAAAAAAAA
* * * ** ***
39096964 TTTTGAGTGATGGCCTGTCAAT-G---G---CCGGTACAAATTAAAAAAAAATCTT-TTTTTTGT
1 TTTTG-GTGCTGGCCTGTCAATAGCCAGCACCCAGTACAATTTAAAAAAAAAAATTCTTTTTAAC
* * * ****
39097021 TTCAAAATCAGATATCAGTATACGAAAAAAAATTTAAAATTTTTT
65 GTCAGAATCAGATATCAGTATACG--AAAAAA-GTAAAA--AAAA
* * * * ***** **
39097066 TTTTGGTGCTGACCTATCAATGGCCGGCACCCAGTACAATTTAAAAAATTTTCTT-TTTTTTTCG
1 TTTTGGTGCTGGCCTGTCAATAGCCAGCACCCAGTACAATTTAAAAAAAAAAATTCTTTTTAAC-
*
39097130 TGTCAGAATCAGATATCGGTATACGAAAAAAGTAAAAAAAA
65 -GTCAGAATCAGATATCAGTATACGAAAAAAGTAAAAAAAA
* * * ** *
39097171 TTTTGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATCTTTTTTTTAACG
1 TTTTGGTGCTGGCCTGTCAATAGCCAGCACCCAGTACAATTTAAAAAAAAAAATTCTTTTTAACG
*
39097236 TCAGAATCAGATATCAGTATACGAAAAAATTCAAAAAAAAA
66 TCAGAATCAGATATCAGTATACGAAAAAAGT--AAAAAAAA
*
39097277 TTTTTTTGGGTGCTGGCTTGTCAATAGCCAGCACCCAGTACAATTTATAAAAAAAAAATTCTTTT
1 ---TTTT-GGTGCTGGCCTGTCAATAGCCAGCACCCAGTACAATTTA-AAAAAAAAAATTCTTTT
* * *
39097342 TATTTTCGTGTCAGAATTAGATATCAGTATATGAAAAAA
61 TA---AC--GTCAGAATCAGATATCAGTATACGAAAAAA
39097381 TAATATTACG
Statistics
Matches: 340, Mismatches: 51, Indels: 45
0.78 0.12 0.10
Matches are distributed among these distances:
100 36 0.11
101 34 0.10
102 12 0.04
104 30 0.09
105 51 0.15
106 14 0.04
107 5 0.01
108 34 0.10
109 23 0.07
110 56 0.16
111 16 0.05
114 1 0.00
116 28 0.08
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (104 bp):
TTTTGGTGCTGGCCTGTCAATAGCCAGCACCCAGTACAATTTAAAAAAAAAAATTCTTTTTAACG
TCAGAATCAGATATCAGTATACGAAAAAAGTAAAAAAAA
Found at i:39098145 original size:215 final size:214
Alignment explanation
Indices: 39097575--39098245 Score: 793
Period size: 215 Copynumber: 3.1 Consensus size: 214
39097565 AAAAATTAAA
* *
39097575 ATTGATAGGCTAGCACCCAAAAAAAATTTTTTTAAATTTTTTTCGTATATTGATATCTGATTTTG
1 ATTGACAGGCCAGCACCCAAAAAAAA---TTTTAAATTTTTTTCGTATATTGATATCTGATTTTG
* *
39097640 ACACG-AAAAAAAAGAA--TTTTTTT-ATTTTAATGGGTGCCGGCCATTGACAGGCCAGCACTCA
63 ACACGAAAAAAAAAGAATTTTTTTTTAATTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
* * * *
39097701 AAATTTTTTTTTAATTTTTTTCGTATATTGGTATCTGATTTTGACACG-AAAAAAATAATTTTTT
128 AAA--TTTTTTTAATTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAGAATTTATA
*
39097765 TTTAAAATTATACTGGGTGCCGGCC
191 TTT-AAATTGTACTGGGTGCCGGCC
*** ** * * * * *
39097790 ATTGACAGGCCAGCACCC--AAATTTTTTTTTACTTTTTT-GTATACTGATATCTAATTCTGAAA
1 ATTGACAGGCCAGCACCCAAAAAAAATTTTAAATTTTTTTCGTATATTGATATCTGATTTTGACA
* * *
39097852 AGAGAAAAAAAAGTAAATTTTTTTTAAAAAAATTTTACTGGGTGCCAGCCATTGACAGGCCAGCA
66 CGA-AAAAAAAAG--AATTTTTTTT----TAATTTTACTGGGTGCCGGCCATTGACAGGCCAGCA
* * * * ***
39097917 CCCAAATTTTTTTTAATTTTATTCGTATACTGATATCTAATTTTGACACGAAAAAAAAGAAAAAA
124 CCCAAAATTTTTTTAATTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAGAATTTA
* *
39097982 AATTT-AATTGTACTGGGTGCCTGCC
189 TATTTAAATTGTACTGGGTGCCGGCC
*
39098007 ATTGACAGGCCAGCACCCAAAAAAAATTTTAAATTTTTTTCGTATATTGATATTTGATTTTGACA
1 ATTGACAGGCCAGCACCCAAAAAAAATTTTAAATTTTTTTCGTATATTGATATCTGATTTTGACA
*
39098072 CGAAAAACAAAAGAATTTTCTTTTTAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
66 CGAAAAA-AAAAGAATTTT-TTTTTAATTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
* * *
39098137 AATTTTTTTTATTTTTTTCGTATATTGATATCTGATTCTGACACGAAAAAAAAGAATTTGTATTT
129 AATTTTTTTAATTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAGAATTTATATTT
39098202 AAAATTTGTACTGGGTGCCGGCC
194 -AAA-TTGTACTGGGTGCCGGCC
*
39098225 ATTGACAGGTCAGCACCCAAA
1 ATTGACAGGCCAGCACCCAAA
39098246 TTTTTTTTTT
Statistics
Matches: 377, Mismatches: 59, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
209 21 0.06
210 11 0.03
211 9 0.02
213 5 0.01
215 114 0.30
217 38 0.10
218 82 0.22
219 34 0.09
220 63 0.17
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (214 bp):
ATTGACAGGCCAGCACCCAAAAAAAATTTTAAATTTTTTTCGTATATTGATATCTGATTTTGACA
CGAAAAAAAAAGAATTTTTTTTTAATTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
TTTTTTTAATTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAGAATTTATATTTAA
ATTGTACTGGGTGCCGGCC
Found at i:39098263 original size:108 final size:104
Alignment explanation
Indices: 39097611--39098255 Score: 694
Period size: 108 Copynumber: 6.0 Consensus size: 104
39097601 TTTTTTTAAA
* *
39097611 TTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAGAATTTT-TTT---ATTTTAATG
1 TTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAGAATTTTATTTAAAATTGTACTG
*
39097672 GGTGCCGGCCATTGACAGGCCAGCACTCAAAATTTTTTTTT
66 GGTGCCGGCCATTGACAGGCCAGCAC-CCAAA-TTTTTTTT
* * * *
39097713 AATTTTTTTCGTATATTGGTATCTGATTTTGACACGAAAAAAATA-ATTTTTTTTTAAAATTATA
1 --TTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAA-AGAATTTTATTTAAAATTGTA
39097777 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTT
63 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTT
* * * * * *
39097819 TACTTTTTT-GTATACTGATATCTAATTCTGAAAAGAGAAAAAAAAGTAAATTTTTTTTAAAAAA
1 T--TTTTTTCGTATATTGATATCTGATTTTG-ACA-CGAAAAAAAAG--AATTTTATTT---AAA
* *
39097883 ATTTTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAATTTTTTTT
57 ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTT
* * * ****
39097931 AATTTTATTCGTATACTGATATCTAATTTTGACACGAAAAAAAAGAAAAAAAATTT--AATTGTA
1 --TTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAG-AATTTTATTTAAAATTGTA
* * ***
39097994 CTGGGTGCCTGCCATTGACAGGCCAGCACCCAAAAAAAATTTTAAA
63 CTGGGTGCCGGCCATTGACAGGCCAGCACCC----AAATTTTTTTT
* * **
39098040 TTTTTTTCGTATATTGATATTTGATTTTGACACGAAAAACAAAAGAATTTTCTTTTTAATTGTAC
1 TTTTTTTCGTATATTGATATCTGATTTTGACACG-AAAA-AAAAGAATTTTATTTAAAATTGTAC
39098105 TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTT
64 TGGGTGCCGGCCATTGACAGGCCAGCACCC-AAATTTTTTTT
*
39098147 ATTTTTTTCGTATATTGATATCTGATTCTGACACGAAAAAAAAGAATTTGTATTTAAAATTTGTA
1 -TTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAGAATTT-TATTTAAAA-TTGTA
*
39098212 CTGGGTGCCGGCCATTGACAGGTCAGCACCCAAATTTTTTTT
63 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTT
39098254 TT
1 TT
39098256 CATTTTTCAT
Statistics
Matches: 463, Mismatches: 49, Indels: 56
0.82 0.09 0.10
Matches are distributed among these distances:
104 46 0.10
105 57 0.12
106 29 0.06
107 71 0.15
108 109 0.24
109 21 0.05
110 43 0.09
111 10 0.02
112 56 0.12
113 20 0.04
114 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (104 bp):
TTTTTTTCGTATATTGATATCTGATTTTGACACGAAAAAAAAGAATTTTATTTAAAATTGTACTG
GGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTT
Found at i:39098270 original size:16 final size:16
Alignment explanation
Indices: 39098249--39098279 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39098239 ACCCAAATTT
39098249 TTTTTTTCATTTTTCA
1 TTTTTTTCATTTTTCA
*
39098265 TTTTTTTCCTTTTTC
1 TTTTTTTCATTTTTC
39098280 GTATATCAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTCATTTTTCA
Found at i:39106382 original size:160 final size:161
Alignment explanation
Indices: 39106208--39106530 Score: 639
Period size: 160 Copynumber: 2.0 Consensus size: 161
39106198 GTATTATTAT
39106208 TATTTTAATTTACTCAATTATATTCAATGAATTAAAAGTTTCTTAATATCACTTTTGTTATTATC
1 TATTTTAATTTACTCAATTATATTCAATGAATTAAAAGTTTCTTAATATCACTTTTGTTATTATC
39106273 AAATAATAATTAATTATATATTAATGAATTATTTTAATGTCAATTTAATAATATAATAAATAGTA
66 AAATAATAATTAATTATATATTAATGAATTATTTTAATGTCAATTTAATAATATAATAAATAGTA
39106338 AAAAGTTAATTTGTTAAATT-AATTTTTTTC
131 AAAAGTTAATTTGTTAAATTAAATTTTTTTC
39106368 TATTTTAATTTACTCAATTATATTCAATGAATTAAAAGTTTCTTAATATCACTTTTGTTATTATC
1 TATTTTAATTTACTCAATTATATTCAATGAATTAAAAGTTTCTTAATATCACTTTTGTTATTATC
39106433 AAATAATAATTAATTATATATTAATGAATTATTTTAATGTCAATTTAATAATATAATAAATAGTA
66 AAATAATAATTAATTATATATTAATGAATTATTTTAATGTCAATTTAATAATATAATAAATAGTA
39106498 AAAAGTTAATTTGTTAAATTAAATTTTTTTC
131 AAAAGTTAATTTGTTAAATTAAATTTTTTTC
39106529 TA
1 TA
39106531 AATAAATATT
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 150 0.93
161 12 0.07
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (161 bp):
TATTTTAATTTACTCAATTATATTCAATGAATTAAAAGTTTCTTAATATCACTTTTGTTATTATC
AAATAATAATTAATTATATATTAATGAATTATTTTAATGTCAATTTAATAATATAATAAATAGTA
AAAAGTTAATTTGTTAAATTAAATTTTTTTC
Found at i:39111572 original size:14 final size:14
Alignment explanation
Indices: 39111553--39111591 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
39111543 TGGTATATTG
39111553 TATTTGTATATATA
1 TATTTGTATATATA
* *
39111567 TATTTGTAAATATT
1 TATTTGTATATATA
*
39111581 TATTCGTATAT
1 TATTTGTATAT
39111592 GCTGTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (14 bp):
TATTTGTATATATA
Found at i:39117924 original size:38 final size:39
Alignment explanation
Indices: 39117860--39117966 Score: 141
Period size: 38 Copynumber: 2.8 Consensus size: 39
39117850 TATGACTCGT
*
39117860 ATAACAAACAAACTTACTTTTT-TGACTCATACATCTT-C
1 ATAACAAACAAACTTAATTTTTATGACTCATAC-TCTTAC
* *
39117898 ATAGCAAACAAA-TTAATTTTTATGACTCATACTTTTAC
1 ATAACAAACAAACTTAATTTTTATGACTCATACTCTTAC
*
39117936 ATAACAAACAAACTT-ACTTTTATGACTCATA
1 ATAACAAACAAACTTAATTTTTATGACTCATA
39117967 TAAGATAGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
37 11 0.18
38 48 0.79
39 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (39 bp):
ATAACAAACAAACTTAATTTTTATGACTCATACTCTTAC
Found at i:39117994 original size:10 final size:10
Alignment explanation
Indices: 39117979--39118010 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
39117969 AGATAGTGAA
39117979 ACATCTAATC
1 ACATCTAATC
39117989 ACATCTAATC
1 ACATCTAATC
39117999 ACATCTAATC
1 ACATCTAATC
39118009 AC
1 AC
39118011 TTTCATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (10 bp):
ACATCTAATC
Found at i:39126793 original size:30 final size:27
Alignment explanation
Indices: 39126757--39126818 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 27
39126747 CTTTGCTTTA
39126757 TTGTTAATTTTGTTATTATTTTAGAGGTAT
1 TTGTTAA-TTTGTTATTATTTT--AGGTAT
39126787 TTGTTAATTTGTTATTATTTTAGGTAT
1 TTGTTAATTTGTTATTATTTTAGGTAT
39126814 TTGTT
1 TTGTT
39126819 TGTTAAGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 11 0.34
29 14 0.44
30 7 0.22
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.63
Consensus pattern (27 bp):
TTGTTAATTTGTTATTATTTTAGGTAT
Found at i:39129033 original size:6 final size:6
Alignment explanation
Indices: 39129022--39129048 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39129012 AATTATTCAA
39129022 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
39129049 GTGACGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:39142655 original size:328 final size:329
Alignment explanation
Indices: 39142051--39142709 Score: 1176
Period size: 328 Copynumber: 2.0 Consensus size: 329
39142041 AAGTTCATGT
*
39142051 AACTTAATTGTGTATATTTATATGCTTATATTGAGTATTAAATATGTAAATTGTGTAAATTTCAT
1 AACTTAATTGTGTATATTTATATGCTTATATTGAGTATTAAATATGTAAATTGTGTAAATGTCA-
*
39142116 ATATATATGTATGTAATTGATCTCATAACTGAAAATTCTTGATAAATAAATAAGCCTCATTTGGA
65 ATATATATGTATGTAATTGATCTCATAACTGAAAATCCTTGATAAATAAATAAGCCTCATTTGGA
* * *
39142181 TAATTAGATTTGATGGATACAAGGTTCTGTTTCCTGAAATGGTTGTGTTCCTGCATATGTTGCGG
130 TAATTAGATTCGATGAATACAAGGTTCTGTTTCCTGAAATAGTTGTGTTCCTGCATATGTTGCGG
* *
39142246 ATGTATCGTATCTTGAAAGAGCGTCCCGTTACAAGCCCTCTCAAGTTTCCCGTTATAGTGTTCTT
195 ATGTATCGTAGCTCGAAAGAGCGTCCCGTTACAAGCCCTCTCAAGTTTCCCGTTATAGTGTTCTT
* *
39142311 GCAAGGTTCCCGTTAAATGCTCTTCGGTAGGGGTGTGCAAAATTCGGGTAAAACCGAAAAAATTC
260 ACAAGGTTCCCGTTAAATGCTCTTCGGTAGGGGTGTGCAAAATTCAGGTAAAACCGAAAAAATTC
39142376 GGTTA
325 GGTTA
*
39142381 AACTTAATTGTGTATATTTATATGCTTATATTGAGTGTTAAATATGTAAATTGTGTAAATGTC-A
1 AACTTAATTGTGTATATTTATATGCTTATATTGAGTATTAAATATGTAAATTGTGTAAATGTCAA
* *
39142445 TATATATGTATGTAATTGATCTCATAACTGAAAATCCTTGATAAATAAATAAGTCTCGTTTGGAT
66 TATATATGTATGTAATTGATCTCATAACTGAAAATCCTTGATAAATAAATAAGCCTCATTTGGAT
39142510 AATTAGATTCGATGAATACAAGGTTCTGTTTCCTGAAATAGTTGTGTTCCTGCATATGTTGCGGA
131 AATTAGATTCGATGAATACAAGGTTCTGTTTCCTGAAATAGTTGTGTTCCTGCATATGTTGCGGA
39142575 TGTATCGTAGCTCGAAAGAGCGTCCCGTTACAAGCCCTCTCAAGTTTCCCGTTATAGTGTTCTTA
196 TGTATCGTAGCTCGAAAGAGCGTCCCGTTACAAGCCCTCTCAAGTTTCCCGTTATAGTGTTCTTA
* *
39142640 CGAGGTTCTCGTTAAATGCTCTTCGGTAGGGGTGTGCAAAATTCAGGTAAAACCGAAAAAATTCG
261 CAAGGTTCCCGTTAAATGCTCTTCGGTAGGGGTGTGCAAAATTCAGGTAAAACCGAAAAAATTCG
39142705 GTTA
326 GTTA
39142709 A
1 A
39142710 CCGACCGAAT
Statistics
Matches: 315, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
328 254 0.81
330 61 0.19
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (329 bp):
AACTTAATTGTGTATATTTATATGCTTATATTGAGTATTAAATATGTAAATTGTGTAAATGTCAA
TATATATGTATGTAATTGATCTCATAACTGAAAATCCTTGATAAATAAATAAGCCTCATTTGGAT
AATTAGATTCGATGAATACAAGGTTCTGTTTCCTGAAATAGTTGTGTTCCTGCATATGTTGCGGA
TGTATCGTAGCTCGAAAGAGCGTCCCGTTACAAGCCCTCTCAAGTTTCCCGTTATAGTGTTCTTA
CAAGGTTCCCGTTAAATGCTCTTCGGTAGGGGTGTGCAAAATTCAGGTAAAACCGAAAAAATTCG
GTTA
Found at i:39142954 original size:13 final size:13
Alignment explanation
Indices: 39142932--39142965 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39142922 GTACTTAATT
39142932 CAATCCAATTACC
1 CAATCCAATTACC
*
39142945 CAATCTAATTACC
1 CAATCCAATTACC
*
39142958 CAACCCAA
1 CAATCCAA
39142966 CCCAATCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (13 bp):
CAATCCAATTACC
Found at i:39143093 original size:9 final size:9
Alignment explanation
Indices: 39143081--39143139 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
39143071 TCAATTAGGT
*
39143081 TAATTTGGG
1 TAATTCGGG
39143090 TAATTCGGG
1 TAATTCGGG
39143099 TAATTCGGG
1 TAATTCGGG
*
39143108 TAATTCGGT
1 TAATTCGGG
39143117 TAATTCGGG
1 TAATTCGGG
*
39143126 TAATTCGGT
1 TAATTCGGG
39143135 TAATT
1 TAATT
39143140 TTTAACGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:39143102 original size:18 final size:18
Alignment explanation
Indices: 39143073--39143139 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
39143063 TGTATGATTC
* *
39143073 AATTAGGTTAATTTGGGT
1 AATTCGGTTAATTCGGGT
*
39143091 AATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCGGGT
39143109 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
39143127 AATTCGGTTAATT
1 AATTCGGTTAATT
39143140 TTTAACGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.40
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:39143429 original size:26 final size:24
Alignment explanation
Indices: 39143392--39143464 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 24
39143382 GCACAGCGCA
* *
39143392 GCTCTTATGAGCGTCCCGTTACATG
1 GCTCTTATGAGCTTCCCGTTA-AAG
39143417 GCTCTTCATGAGCTTCCCGATTAAAG
1 GCTCTT-ATGAGCTTCCCG-TTAAAG
*
39143443 GCTCTTTGTGAGCTTCCCGTTA
1 GCTC-TTATGAGCTTCCCGTTA
39143465 GTGCTCACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.21
26 28 0.67
27 5 0.12
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.34
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGTTAAAG
Found at i:39157455 original size:2 final size:2
Alignment explanation
Indices: 39157448--39157477 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39157438 TCTTATACAC
39157448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39157478 AATCTGCTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39160609 original size:3 final size:3
Alignment explanation
Indices: 39160601--39160633 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
39160591 ATACTTGTGA
*
39160601 ATG ATG ATG ATG ATG ATG ATG ATG ATA ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
39160634 TCTATGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:39162291 original size:11 final size:11
Alignment explanation
Indices: 39162275--39162299 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39162265 AGTAGCAATG
39162275 TAATAACAAAA
1 TAATAACAAAA
39162286 TAATAACAAAA
1 TAATAACAAAA
39162297 TAA
1 TAA
39162300 CATCAAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (11 bp):
TAATAACAAAA
Found at i:39163801 original size:20 final size:20
Alignment explanation
Indices: 39163776--39163815 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39163766 AAAACCTATT
39163776 CTCATCACAATTGGACATCC
1 CTCATCACAATTGGACATCC
39163796 CTCATCACAATTGGACATCC
1 CTCATCACAATTGGACATCC
39163816 AAGTCAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.35, G:0.10, T:0.25
Consensus pattern (20 bp):
CTCATCACAATTGGACATCC
Found at i:39179486 original size:31 final size:31
Alignment explanation
Indices: 39179451--39179512 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
39179441 CATCCAATTT
39179451 TATACTTAGTCATTTTATTATTTTCAACAAA
1 TATACTTAGTCATTTTATTATTTTCAACAAA
39179482 TATACTTAGTCATTTTATTATTTTCAACAAA
1 TATACTTAGTCATTTTATTATTTTCAACAAA
39179513 ACCCAGATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.48
Consensus pattern (31 bp):
TATACTTAGTCATTTTATTATTTTCAACAAA
Found at i:39190112 original size:16 final size:15
Alignment explanation
Indices: 39190081--39190114 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39190071 ATATTTAAAA
*
39190081 TTCAGTACTTAATTT
1 TTCAGCACTTAATTT
*
39190096 TTCAGCACTTAAATT
1 TTCAGCACTTAATTT
39190111 TTCA
1 TTCA
39190115 ATTTATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (15 bp):
TTCAGCACTTAATTT
Found at i:39190526 original size:25 final size:25
Alignment explanation
Indices: 39190490--39190540 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
39190480 AAGAAGTGTA
*
39190490 TTAGTCTACTTCTGATAGCACGTTT
1 TTAGTCTACTTCTAATAGCACGTTT
* *
39190515 TTAGTCTGCTTCTAATAGCATGTTT
1 TTAGTCTACTTCTAATAGCACGTTT
39190540 T
1 T
39190541 GAATCTAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.47
Consensus pattern (25 bp):
TTAGTCTACTTCTAATAGCACGTTT
Found at i:39197626 original size:35 final size:36
Alignment explanation
Indices: 39197571--39197648 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 36
39197561 AATTGTCATT
* *
39197571 ATCAATCATTTCAATATCCAACAAACTTAAAACATA
1 ATCAATAAATTCAATATCCAACAAACTTAAAACATA
**
39197607 AT-AATAAATTCAATATCCAACAAGGTTAAAACATA
1 ATCAATAAATTCAATATCCAACAAACTTAAAACATA
39197642 ATCAATA
1 ATCAATA
39197649 TCTAACAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 31 0.84
36 6 0.16
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.27
Consensus pattern (36 bp):
ATCAATAAATTCAATATCCAACAAACTTAAAACATA
Found at i:39197646 original size:27 final size:28
Alignment explanation
Indices: 39197616--39197685 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
39197606 AATAATAAAT
*
39197616 TCAATATCCAACAAGGTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
39197643 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
39197671 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
39197686 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:39198061 original size:26 final size:26
Alignment explanation
Indices: 39198025--39198076 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
39198015 AAATTCCAAA
*
39198025 ATGGTTCAGCATCTAGTACACGAAAC
1 ATGGTTCAGCATCTAATACACGAAAC
*
39198051 ATGGTTTAGCATCTAATACACGAAAC
1 ATGGTTCAGCATCTAATACACGAAAC
39198077 CGTTTCTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (26 bp):
ATGGTTCAGCATCTAATACACGAAAC
Found at i:39198836 original size:15 final size:15
Alignment explanation
Indices: 39198816--39198845 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39198806 AAATTATTCG
39198816 TACTAAGAATATCAC
1 TACTAAGAATATCAC
39198831 TACTAAGAATATCAC
1 TACTAAGAATATCAC
39198846 ATAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
TACTAAGAATATCAC
Found at i:39199094 original size:15 final size:17
Alignment explanation
Indices: 39199074--39199113 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
39199064 CGATCCATCT
39199074 ACACAAAAT-TATG-CC
1 ACACAAAATATATGACC
39199089 ACAC-AAATATATGACC
1 ACACAAAATATATGACC
39199105 ACTACAAAA
1 AC-ACAAAA
39199114 AAGATGCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 8 0.38
16 4 0.19
17 2 0.10
18 3 0.14
ACGTcount: A:0.53, C:0.25, G:0.05, T:0.17
Consensus pattern (17 bp):
ACACAAAATATATGACC
Found at i:39199992 original size:10 final size:10
Alignment explanation
Indices: 39199977--39200002 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39199967 TCATTAAGTG
39199977 CTAACAAATA
1 CTAACAAATA
39199987 CTAACAAATA
1 CTAACAAATA
39199997 CTAACA
1 CTAACA
39200003 GATCAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (10 bp):
CTAACAAATA
Found at i:39215872 original size:35 final size:33
Alignment explanation
Indices: 39215754--39215872 Score: 89
Period size: 35 Copynumber: 3.4 Consensus size: 33
39215744 CCGACGACCT
*
39215754 GCTCGAAATATGGGACGGTTCGGTTAAAAATATAG
1 GCTCGAAATAT-GGA-GGTTCGGGTAAAAATATAG
* * *
39215789 GCTCGAAATAT-GA-GTTTGGGCAAAAAAATGAG
1 GCTCGAAATATGGAGGTTCGGGTAAAAATAT-AG
*
39215821 GTCCCGCCTGAAATATGGAAGGGTTCGGGTAAAAATATAG
1 G---C-TC-GAAATATGG-A-GGTTCGGGTAAAAATATAG
39215861 GCTCGAAATATG
1 GCTCGAAATATG
39215873 TGTTTGGACA
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
31 12 0.18
32 3 0.05
33 2 0.03
35 20 0.31
36 2 0.03
37 8 0.12
38 1 0.02
39 1 0.02
40 3 0.05
41 13 0.20
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.24
Consensus pattern (33 bp):
GCTCGAAATATGGAGGTTCGGGTAAAAATATAG
Found at i:39216024 original size:22 final size:21
Alignment explanation
Indices: 39215985--39216025 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39215975 AATTTTAAAA
*
39215985 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATAATTTTTTT
*
39216006 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAATAATTTTTT
39216026 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTTT
Found at i:39225812 original size:16 final size:16
Alignment explanation
Indices: 39225791--39225859 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
39225781 TTGGTTCGCT
39225791 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
39225807 GTAATGGAATAGAGAC
1 GTAATGGAATAGAGGC
*
39225823 GTAATGGATTAGAGGC
1 GTAATGGAATAGAGGC
*
39225839 GTAATGGATTAGAGGC
1 GTAATGGAATAGAGGC
*
39225855 ATAAT
1 GTAAT
39225860 AGCAATTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:39235928 original size:24 final size:24
Alignment explanation
Indices: 39235896--39235956 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
39235886 GTAGGATATG
* *
39235896 ATTTTGTATTTGATTATGCATCTA
1 ATTTTGTATCTGATCATGCATCTA
*
39235920 ATTTTGTATCTGATCATGCATCTG
1 ATTTTGTATCTGATCATGCATCTA
* *
39235944 ATTCTGTACCTGA
1 ATTTTGTATCTGA
39235957 ACTACAATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (24 bp):
ATTTTGTATCTGATCATGCATCTA
Found at i:39238578 original size:23 final size:23
Alignment explanation
Indices: 39238548--39238596 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
39238538 CTGCATTTTA
39238548 TCATGAGAATCAGATTGCTATGT
1 TCATGAGAATCAGATTGCTATGT
39238571 TCATGAGAATCAGATTGCTATGT
1 TCATGAGAATCAGATTGCTATGT
39238594 TCA
1 TCA
39238597 ACTCCTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (23 bp):
TCATGAGAATCAGATTGCTATGT
Done.