Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 10 of 410
Found at i:2606934 original size:22 final size:20
Alignment explanation
Indices: 2606909--2606948 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2606899 TTTAGAATTT
2606909 ATTTTAATTAATTTTGATATGA
1 ATTTT-ATTAATTTT-ATATGA
*
2606931 ATTTTGTTAATTTTATAT
1 ATTTTATTAATTTTATAT
2606949 TTTATTAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
ATTTTATTAATTTTATATGA
Found at i:2608198 original size:30 final size:30
Alignment explanation
Indices: 2608140--2608198 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2608130 AAGTTATTTT
*
2608140 CTTGTTAAGAGTTAATTGCTGGATTATTCA
1 CTTGTTAAGAGTTAATTGCGGGATTATTCA
*
2608170 CTTGTTAAGGGTTAATTGACGGGA-TATTC
1 CTTGTTAAGAGTTAATTG-CGGGATTATTC
2608199 CCACAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (30 bp):
CTTGTTAAGAGTTAATTGCGGGATTATTCA
Found at i:2609429 original size:22 final size:22
Alignment explanation
Indices: 2609388--2609430 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2609378 ACATAATATT
* *
2609388 AATATTTTAAATTTTTAATTAA
1 AATATTTTAAAATTTAAATTAA
2609410 AATATTTTAAAATTTAAATTA
1 AATATTTTAAAATTTAAATTA
2609431 TAGTTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTTTAAAATTTAAATTAA
Found at i:2611060 original size:16 final size:16
Alignment explanation
Indices: 2611029--2611067 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2611019 TGTTGTTTAG
*
2611029 TAGAATAACTCATGTT
1 TAGAACAACTCATGTT
* *
2611045 TGGAACAACTCGTGTT
1 TAGAACAACTCATGTT
2611061 TAGAACA
1 TAGAACA
2611068 CTCTTTGTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (16 bp):
TAGAACAACTCATGTT
Found at i:2611088 original size:24 final size:24
Alignment explanation
Indices: 2611056--2611103 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2611046 GGAACAACTC
2611056 GTGTTTAGAACACTCTTTGTCAAG
1 GTGTTTAGAACACTCTTTGTCAAG
2611080 GTGTTTAGAACACTCTTTGTCAAG
1 GTGTTTAGAACACTCTTTGTCAAG
2611104 ACTATCTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (24 bp):
GTGTTTAGAACACTCTTTGTCAAG
Found at i:2612759 original size:14 final size:14
Alignment explanation
Indices: 2612740--2612769 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2612730 ATATTCAAAC
2612740 AATAACAATAAAAT
1 AATAACAATAAAAT
*
2612754 AATAACAATATAAT
1 AATAACAATAAAAT
2612768 AA
1 AA
2612770 CGAGTGGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAACAATAAAAT
Found at i:2613259 original size:23 final size:23
Alignment explanation
Indices: 2613233--2613276 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2613223 TAATTAAGCG
* *
2613233 AAAAATT-TATAAAAATTATAAA
1 AAAAATTATAGAAAAATCATAAA
2613255 AAAAATTATAGAAAAATCATAA
1 AAAAATTATAGAAAAATCATAA
2613277 CTAGTAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAAATTATAGAAAAATCATAAA
Found at i:2616101 original size:18 final size:18
Alignment explanation
Indices: 2616080--2616118 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2616070 GCTTTTCTAA
*
2616080 TATACGAAATCAAATGTC
1 TATACGAAATCAAATCTC
2616098 TATACGAAATCAAATCTC
1 TATACGAAATCAAATCTC
2616116 TAT
1 TAT
2616119 GCATTTTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (18 bp):
TATACGAAATCAAATCTC
Found at i:2619256 original size:13 final size:13
Alignment explanation
Indices: 2619238--2619265 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2619228 TTATCAGTTC
2619238 AAAATCTAAGATG
1 AAAATCTAAGATG
2619251 AAAATCTAAGATG
1 AAAATCTAAGATG
2619264 AA
1 AA
2619266 CACCCTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAATCTAAGATG
Found at i:2627237 original size:25 final size:24
Alignment explanation
Indices: 2627209--2627272 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
2627199 CTATTCAAAA
2627209 TTTAATAAAATATTAATATATATTT
1 TTTAAT-AAATATTAATATATATTT
** *
2627234 TTTAATTGATATT-TTATATATTT
1 TTTAATAAATATTAATATATATTT
2627257 TTATAATTAAAT-TTAA
1 TT-TAA-TAAATATTAA
2627273 ATAATAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
23 11 0.37
24 10 0.33
25 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTAATAAATATTAATATATATTT
Found at i:2627270 original size:23 final size:23
Alignment explanation
Indices: 2627225--2627270 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2627215 AAAATATTAA
*
2627225 TATATATTTTTTAATTGATATTT
1 TATATATTTTTTAATTGAAATTT
2627248 TATATATTTTTATAATT-AAATTT
1 TATATATTTTT-TAATTGAAATTT
2627271 AAATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TATATATTTTTTAATTGAAATTT
Found at i:2628647 original size:21 final size:21
Alignment explanation
Indices: 2628622--2628689 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
2628612 CCACTGATTT
* *
2628622 TTTAATAATTATACAAAATTA
1 TTTAAAAATTATAAAAAATTA
2628643 TTTAAAAATTATAAAAAA-TA
1 TTTAAAAATTATAAAAAATTA
* *
2628663 -TT-AACATTATTTAAAAATTA
1 TTTAAAAATTA-TAAAAAATTA
2628683 -TTAAAAA
1 TTTAAAAA
2628690 GAATATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 6 0.15
19 8 0.21
20 6 0.15
21 19 0.49
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAAAAATTATAAAAAATTA
Found at i:2628652 original size:11 final size:10
Alignment explanation
Indices: 2628623--2628689 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
2628613 CACTGATTTT
*
2628623 TTAATAATTA
1 TTAAAAATTA
2628633 -TACAAAATTA
1 TTA-AAAATTA
2628643 TTTAAAAATTA
1 -TTAAAAATTA
*
2628654 -TAAAAAATA
1 TTAAAAATTA
*
2628663 TT-AACATTA
1 TTAAAAATTA
2628672 TTTAAAAATTA
1 -TTAAAAATTA
2628683 TTAAAAA
1 TTAAAAA
2628690 GAATATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
9 15 0.33
10 16 0.35
11 13 0.28
12 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:2630021 original size:44 final size:45
Alignment explanation
Indices: 2629931--2630040 Score: 150
Period size: 44 Copynumber: 2.4 Consensus size: 45
2629921 GACAGAACGA
*
2629931 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
2629977 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* **
2630021 AATAATTCATGTAAGTCCAT
1 AATGAGCCATGTAAGTCCAT
2630041 GTCAAAGACA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.61
46 22 0.39
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:2631449 original size:20 final size:20
Alignment explanation
Indices: 2631424--2631465 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2631414 TATCTATTTG
*
2631424 AATTAT-AAGAAATTGTAAAA
1 AATTATCAAG-AATTATAAAA
2631444 AATTATCAAGAATTATAAAA
1 AATTATCAAGAATTATAAAA
2631464 AA
1 AA
2631466 AAGTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (20 bp):
AATTATCAAGAATTATAAAA
Found at i:2637968 original size:3 final size:3
Alignment explanation
Indices: 2637960--2638071 Score: 95
Period size: 3 Copynumber: 37.7 Consensus size: 3
2637950 AGTATTTTCC
* * * * *
2637960 ATT ATT ATT ATT AAT ATC ACT ACT ATC ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * *
2638007 ACG A-T ACCTT TTT ATT ATT ATT ACT ATT -GT ATT ATT ATT ATT ATT
1 ATT ATT A--TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2638052 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
2638072 ATTTCCCTTT
Statistics
Matches: 87, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
2 4 0.05
3 82 0.94
5 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2638167 original size:20 final size:21
Alignment explanation
Indices: 2638142--2638204 Score: 56
Period size: 26 Copynumber: 2.8 Consensus size: 21
2638132 TATTTTAGCA
2638142 CATTTATTTTATTTATTT-AT
1 CATTTATTTTATTTATTTCAT
2638162 CATTTACTCTCATTATTATTATTTCAT
1 CATTTA-T-T--TTA-T-TTATTTCAT
*
2638189 CATCTATTTTATTTAT
1 CATTTATTTTATTTAT
2638205 AGTTTTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
20 6 0.17
21 5 0.14
22 2 0.06
23 3 0.09
24 3 0.09
25 2 0.06
26 7 0.20
27 7 0.20
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (21 bp):
CATTTATTTTATTTATTTCAT
Found at i:2642601 original size:39 final size:39
Alignment explanation
Indices: 2642515--2642601 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
2642505 TTTAAAATAT
* * *
2642515 ATATATATATATATAATAGTATTTAAGAATATATACATA
1 ATATATATATATATAATAGCATTAAAAAATATATACATA
* * *
2642554 AGAAATATATA-ACTAATGGCATTAAAAAATATATACATA
1 ATATATATATATA-TAATAGCATTAAAAAATATATACATA
2642593 ATATATATA
1 ATATATATA
2642602 AAATACCTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 1 0.03
39 38 0.97
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.36
Consensus pattern (39 bp):
ATATATATATATATAATAGCATTAAAAAATATATACATA
Found at i:2643095 original size:24 final size:24
Alignment explanation
Indices: 2643056--2643104 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2643046 GTTAGGTGGC
*
2643056 TAGGTTTTTTTATTTTTTTATTTT
1 TAGGTTTTTTTATTTTCTTATTTT
*
2643080 TAGGTTTTTCTT-TTTTCTTCTTTT
1 TAGGTTTTT-TTATTTTCTTATTTT
2643104 T
1 T
2643105 TTTTTGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.78
Consensus pattern (24 bp):
TAGGTTTTTTTATTTTCTTATTTT
Found at i:2643095 original size:29 final size:30
Alignment explanation
Indices: 2643060--2643153 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 30
2643050 GGTGGCTAGG
2643060 TTTTTTTATTTTTTTATTT-TTAGGTTTTTC
1 TTTTTTT-TTTTTTTATTTGTTAGGTTTTTC
*
2643090 TTTTTTCTTCTTTTTTTTTTGGGTTAGGTTTTTC
1 TTTTTT-TT-TTTTTTATTT--GTTAGGTTTTTC
*
2643124 TTTTTCTTTTTTTTT-TTGGGTTAGGTTTTT
1 TTTTT-TTTTTTTTTATT-TGTTAGGTTTTT
2643154 TTTGGGGGGC
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
30 7 0.13
31 21 0.38
32 2 0.04
33 6 0.11
34 18 0.33
35 1 0.02
ACGTcount: A:0.05, C:0.05, G:0.13, T:0.77
Consensus pattern (30 bp):
TTTTTTTTTTTTTTATTTGTTAGGTTTTTC
Found at i:2643139 original size:31 final size:34
Alignment explanation
Indices: 2643079--2643153 Score: 129
Period size: 31 Copynumber: 2.3 Consensus size: 34
2643069 TTTTTTATTT
2643079 TTAGGTTTTTCTTTTTTCTTCTTTTTTTTTTGGG
1 TTAGGTTTTTCTTTTTTCTTCTTTTTTTTTTGGG
2643113 TTAGGTTTTTC-TTTTTC-T-TTTTTTTTTTGGG
1 TTAGGTTTTTCTTTTTTCTTCTTTTTTTTTTGGG
2643144 TTAGGTTTTT
1 TTAGGTTTTT
2643154 TTTGGGGGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
31 23 0.56
32 1 0.02
33 6 0.15
34 11 0.27
ACGTcount: A:0.04, C:0.07, G:0.16, T:0.73
Consensus pattern (34 bp):
TTAGGTTTTTCTTTTTTCTTCTTTTTTTTTTGGG
Found at i:2644015 original size:30 final size:30
Alignment explanation
Indices: 2643979--2644036 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
2643969 TTTTGAAAAA
2643979 CAGAAATT-AAAAGACTCAACTCAACTCTAG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTAG
*
2644009 CAGAAATTAAAAAGCTCAACTCACCTCT
1 CAGAAATTAAAAAGCTCAACTCAACTCT
2644037 CGCAATATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.45, C:0.26, G:0.09, T:0.21
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTAG
Found at i:2644274 original size:79 final size:77
Alignment explanation
Indices: 2644145--2644740 Score: 330
Period size: 79 Copynumber: 7.7 Consensus size: 77
2644135 AAACAGAATC
** * * * * * * *
2644145 TGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTG
1 TGAAAAACAGAAATTGAAAATACCTCAACGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATG
2644210 AGTTGATTTTTT
66 AGTTGATTTTTT
* *
2644222 TGAAAAACATAAATTGAAAAAATACCTCAATGTGTGATCTGAAGCTCAACTCACCTCTCGCAATA
1 TGAAAAACAGAAATTG--AAAATACCTCAACGTGTGATCTGAAGCTCAACTCACCTCTCGCAATA
2644287 TGAGTTGATTTTTT
64 TGAGTTGATTTTTT
* * * ** * *
2644301 TGAAAGACAGAAATTGAAAATAGCTCAGCGCATGAGC-CAAGGCTCAACTCACCTCTCGCAATAT
1 TGAAAAACAGAAATTGAAAATACCTCAACGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATAT
2644365 GAGTTGATTTTTTTTT
65 GAGTTGA---TTTTTT
** * * ** * * * * *
2644381 TGAAAGGCAGAAATTGAAAA-ACGGAAATTGAAAATGCCTCG-GCGTGTGACCTGAGACTTAACT
1 TGAAAAACAGAAATTGAAAATAC-----CTCAACGTG--T-GATC-TG-AAGCTCA-AC-TCAC-
* * ** *
2644444 CACCTCTCACAAT-A--CGAGTTGATTTT
53 C-TCTCGCAATATGAGTTGA-TT--TTTT
* * * * *
2644470 TTTG-ACAACAGAAATTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATA
1 --TGAAAAACAGAAATTGAAAATACCTCAACGTGTGATCTGAAGCTCAACTCACCTCTCGCAATA
2644532 TGAGTTGA-TTTTT
64 TGAGTTGATTTTTT
* *
2644545 TGAAAAACAGAAATTGAAAATACCTCAACGTGT-CTC-GAGGCTCAACTCACCTCTCGCAATATG
1 TGAAAAACAGAAATTGAAAATACCTCAACGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATG
*
2644608 AGTTGATTTCTT
66 AGTTGATTTTTT
* * * * * * * **
2644620 TGAAAAACAAAAATTGAAAATATCTCAGCATGT-CT-TGAGGCCCAACTCATTTCTCGCAATATG
1 TGAAAAACAGAAATTGAAAATACCTCAACGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATG
*
2644683 AGTTGA--ATTT
66 AGTTGATTTTTT
* * * *
2644693 TG-AAAACAGAAATTGAAATTACCTCAGCGTGT-CT-TGAGGCTCAACTCA
1 TGAAAAACAGAAATTGAAAATACCTCAACGTGTGATCTGAAGCTCAACTCA
2644741 TTTTGAACAG
Statistics
Matches: 407, Mismatches: 79, Indels: 71
0.73 0.14 0.13
Matches are distributed among these distances:
72 41 0.10
73 6 0.01
74 60 0.15
75 70 0.17
76 9 0.02
77 61 0.15
78 3 0.01
79 72 0.18
80 28 0.07
81 2 0.00
82 1 0.00
84 3 0.01
86 7 0.02
87 3 0.01
88 3 0.01
89 9 0.02
90 16 0.04
91 6 0.01
92 7 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (77 bp):
TGAAAAACAGAAATTGAAAATACCTCAACGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTT
Found at i:2644357 original size:77 final size:78
Alignment explanation
Indices: 2644184--2644718 Score: 359
Period size: 74 Copynumber: 6.8 Consensus size: 78
2644174 ATGTGACCCG
* * * *
2644184 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAACATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG--AAAATACCT
* ** * *
2644249 CAATGTGTGATCTGA
64 CAACGCATGAGCTCA
*
2644264 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
*
2644328 GCGCATGAGC-CA
66 ACGCATGAGCTCA
* *
2644340 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAGGCAGAAATTGAAAA-ACG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTGAAAGACAGAAATTGAAAATACC
** * * * *
2644404 GAAATTGAAAATG-CCTCGGCG
63 TCAA-CG--CATGAGCT---CA
* * * * * *
2644425 TGTGACCTGAGACTTAACTCACCTCTCACAATACGAGTTGATTTTTTTGACA-ACAGAAATTGAA
1 AG-G--CTCA-AC-T--CAC-C-TCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAA
* * ** *
2644489 ATTACCTC-A-GCGTGTCCT-G
57 AATACCTCAACGCATGAGCTCA
*
2644508 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
* *
2644572 ACG--TG-TCTCG
66 ACGCATGAGCTCA
* * * *
2644582 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTCTTTGAAAAACAAAAATTGAAAATATCTC-
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
* **
2644646 A-GCATG-TCTTG
66 ACGCATGAGCTCA
* ** * *
2644657 AGGCCCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
2644719 GCGTGTCTTG
Statistics
Matches: 371, Mismatches: 54, Indels: 67
0.75 0.11 0.14
Matches are distributed among these distances:
72 17 0.05
73 19 0.05
74 71 0.19
75 65 0.18
76 5 0.01
77 45 0.12
78 1 0.00
79 52 0.14
80 30 0.08
81 1 0.00
82 4 0.01
83 2 0.01
85 2 0.01
86 3 0.01
87 3 0.01
88 4 0.01
89 2 0.01
90 14 0.04
91 12 0.03
92 2 0.01
93 1 0.00
94 16 0.04
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
ACGCATGAGCTCA
Found at i:2644373 original size:244 final size:244
Alignment explanation
Indices: 2643813--2644625 Score: 948
Period size: 244 Copynumber: 3.3 Consensus size: 244
2643803 ACAGACATTA
2643813 AAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
** * *
2643878 TGA-TTTTTG-AAACTTAA-CTTGAAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGAAGG
66 TGATTTTTTGAAAACAGAATC-TGAAAAACAGATTTTGAAAATACCTCGACATGTGACCTG-AGG
* * *
2643939 TTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATT-AAAAGACTCAACTC
129 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA-AAT-ACCTC
* * *
2644001 AACTCTAGCAGAAAT-TAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTG
192 AA-TGT-G-TG--ATCT--GAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTG
* *
2644061 AAAA-AAAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
*
2644125 TGA-TTTTTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCT
66 TGATTTTTTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCTGAGGCT
* * *
2644189 CAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAACATAAATTGAAAAAATACCTCAATG
131 CAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACCTCAATG
2644254 TGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
196 TGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* *
2644303 AAAGACAGAAATTGAAAATAGCTCAGCGCATGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAA-ACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * ** * * *
2644368 TTGATTTTTTTTTTGAAAGGCAGAAAT-TGAAAAACGGAAATTGAAAATGCCTCGGCGTGTGACC
65 TTGA----TTTTTTGAAA-ACAG-AATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACC
* * * * * *
2644432 TGAGACTTAACTCACCTCTCACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG--AAATTAC
124 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATAC
* *
2644494 CTC-A-GCGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG
189 CTCAATGTGTGAT-CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * *
2644547 AAAAACAGAAATTGAAAATACCTCA--ACGTG-TCTCGAGGCTCAACTCACCTCTCGCAATATGA
1 -AAAACAGAAATTGAAAATAGCTCAGCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
2644609 GTTGATTTCTTTGAAAA
64 GTTGATTT-TTTGAAAA
2644626 ACAAAAATTG
Statistics
Matches: 500, Mismatches: 45, Indels: 50
0.84 0.08 0.08
Matches are distributed among these distances:
238 3 0.01
239 7 0.01
241 1 0.00
242 48 0.10
243 32 0.06
244 89 0.18
245 42 0.08
246 2 0.00
247 77 0.15
248 74 0.15
249 29 0.06
250 89 0.18
251 7 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (244 bp):
AAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCTGAGGCT
CAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACCTCAATG
TGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:2644531 original size:74 final size:74
Alignment explanation
Indices: 2644394--2644740 Score: 441
Period size: 74 Copynumber: 4.7 Consensus size: 74
2644384 AAGGCAGAAA
* * * * * * *
2644394 TTGAAAAACGGAAATTGAAAATGCCTCGGCGTGTGACCTGAGACTTAACTCACCTCTCACAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATAT
2644459 GAGTTGATTTTT
64 GAGTTGA-TTTT
* *
2644471 TTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
2644535 GTTGATTTT
66 GTTGATTTT
*
2644544 TTGAAAAACAGAAATTGAAAATACCTCAACGTGT-CTCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCT-GAGGCTCAACTCACCTCTCGCAATATG
2644608 AGTTGATTTCT
65 AGTTGATTT-T
* * * * * **
2644619 TTGAAAAACAAAAATTGAAAATATCTCAGCATGTCTTGAGGCCCAACTCATTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
2644684 GTTGA-ATT
66 GTTGATTTT
* *
2644692 TTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA
2644741 TTTTGAACAG
Statistics
Matches: 240, Mismatches: 26, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
72 41 0.17
73 13 0.05
74 96 0.40
75 61 0.25
76 26 0.11
77 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTT
Found at i:2644675 original size:149 final size:147
Alignment explanation
Indices: 2644394--2644740 Score: 446
Period size: 149 Copynumber: 2.3 Consensus size: 147
2644384 AAGGCAGAAA
* * * * *
2644394 TTGAAAAACGGAAATTGAAAATGCCTCGGCGTGTGAC-CTGAGACTTAACTCACCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--CTC-GAGGCTCAACTCACCTCTCACAATA
* * * * * *
2644458 CGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
63 CGAGTTGATTTCTTTGAAAACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCCCAACTCACCT
*
2644523 CTCGCAATATGAGTTGATTTT
128 CTCGCAATATGAGTTGA-ATT
* * *
2644544 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCACAATACGA
* * **
2644609 GTTGATTTCTTTGAAAAACAAAAATTGAAAATATCTCAGCATGTCTTGAGGCCCAACTCATTTCT
66 GTTGATTTCTTTG-AAAACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCCCAACTCACCTCT
2644674 CGCAATATGAGTTGAATT
130 CGCAATATGAGTTGAATT
* *
2644692 TTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCA
2644741 TTTTGAACAG
Statistics
Matches: 173, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
147 43 0.25
148 42 0.24
149 58 0.34
150 30 0.17
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (147 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCACAATACGA
GTTGATTTCTTTGAAAACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCCCAACTCACCTCTC
GCAATATGAGTTGAATT
Found at i:2644773 original size:49 final size:49
Alignment explanation
Indices: 2644697--2644792 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
2644687 GAATTTTGAA
* *
2644697 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTTTG
2644746 AACAGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTT
2644793 ATCGCAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:2644790 original size:121 final size:121
Alignment explanation
Indices: 2644625--2644864 Score: 399
Period size: 121 Copynumber: 2.0 Consensus size: 121
2644615 TTCTTTGAAA
* * *
2644625 AACAAAAATTGAAAATATCTCAGCATGTCTTGAGGCCCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAAAAATTGAAAATAACTCAACATGTCTTGAGGCCCAACTCATTTATCGCAATATGAGTTGAA
*
2644690 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
* * * *
2644746 AACAGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTTATCGCAATATGAGTTGAA
1 AACAAAAATTGAAAATAACTCAACATGTCTTGAGGCCCAACTCATTTATCGCAATATGAGTTGAA
*
2644811 TTTTGAAAATAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
2644865 CTCGCAATAT
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 110 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (121 bp):
AACAAAAATTGAAAATAACTCAACATGTCTTGAGGCCCAACTCATTTATCGCAATATGAGTTGAA
TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:2644855 original size:72 final size:72
Alignment explanation
Indices: 2644749--2644886 Score: 258
Period size: 72 Copynumber: 1.9 Consensus size: 72
2644739 CATTTTGAAC
2644749 AGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTTATCGCAATATGAGTTGAATTT
1 AGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTTATCGCAATATGAGTTGAATTT
2644814 TGAAAAT
66 TGAAAAT
* *
2644821 AGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTT
1 AGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTTATCGCAATATGAGTTGAATTT
2644886 T
66 T
2644887 TTTTTTGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (72 bp):
AGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTTATCGCAATATGAGTTGAATTT
TGAAAAT
Found at i:2644967 original size:50 final size:48
Alignment explanation
Indices: 2644898--2644993 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 48
2644888 TTTTTGAAAG
2644898 ACAGAAATTGAAAATACCTCAGCATGTGGAC-GAGGCTCAACTCATTTTGA
1 ACAGAAATTGAAAATACCTCA--ATGT-GACTGAGGCTCAACTCATTTTGA
* *
2644948 ACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTT
1 ACAGAAATTGAAAATACCTCAATGTGAC-TGAGGCTCAACTCATTT
2644994 CTCGCAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 2 0.05
48 4 0.10
49 16 0.38
50 20 0.48
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (48 bp):
ACAGAAATTGAAAATACCTCAATGTGACTGAGGCTCAACTCATTTTGA
Found at i:2644987 original size:201 final size:201
Alignment explanation
Indices: 2644550--2645144 Score: 900
Period size: 201 Copynumber: 3.0 Consensus size: 201
2644540 TTTTTTGAAA
* * **
2644550 AACAGAAATTGAAAATACCTCAACGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
* * * * * * *
2644615 TTCTTTGAAAAACAAAAATTGAAAATATCTCAGCATGTCTTGAGGCCCAACTCATTTCTCGCAAT
65 AT-TTTG-AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
* * ***
2644680 ATGAGTTGAA------TTTTGAAA-ACAGAAATTGAAATTACCTCAGCGTGT-CTTGAGGCTCAA
128 ATGAGTTGAATTTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACGAGGCTCAA
2644737 CTCATTTTG
193 CTCATTTTG
* *
2644746 AACAGAAATTGAAATTAACTCAACGTGTCTTGAGGCTCAACTCATTTATCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
*
2644811 TTTTGAAAATAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
*
2644876 AGTTGAATTTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGGACGAGGCTCAACTC
131 AGTTGAATTTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACGAGGCTCAACTC
2644941 ATTTTG
196 ATTTTG
*
2644947 AACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
2645012 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
2645077 AGTTGAATTTTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAAC
131 AGTTGAA-TTTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAA-CGAGGCTCAAC
2645142 TCA
194 TCA
2645145 CCTCTCGCAA
Statistics
Matches: 365, Mismatches: 24, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
193 60 0.16
194 4 0.01
195 1 0.00
196 58 0.16
199 8 0.02
200 25 0.07
201 151 0.41
202 44 0.12
203 14 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (201 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
AGTTGAATTTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACGAGGCTCAACTC
ATTTTG
Found at i:2645034 original size:72 final size:72
Alignment explanation
Indices: 2644947--2645173 Score: 278
Period size: 72 Copynumber: 3.0 Consensus size: 72
2644937 ACTCATTTTG
2644947 AACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
2645012 TTTTGAA
66 TTTTGAA
*
2645019 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
2645084 TTTTTTTTTTTGAA
66 -------TTTTGAA
* * * ** *
2645098 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAATTACCTCA--ATGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
2645162 TG-ATTTTGAA
62 TGAATTTTGAA
2645172 AA
1 AA
2645174 AGTAGAAATT
Statistics
Matches: 136, Mismatches: 8, Indels: 21
0.82 0.05 0.13
Matches are distributed among these distances:
72 64 0.47
73 1 0.01
74 8 0.06
79 8 0.06
80 20 0.15
81 1 0.01
82 33 0.24
83 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:2645108 original size:80 final size:79
Alignment explanation
Indices: 2645012--2645168 Score: 201
Period size: 82 Copynumber: 2.0 Consensus size: 79
2645002 ATGAGTTGAA
* * * **
2645012 TTTTGAAAACAGAAATTGAAATTACCTCA-ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATA
1 TTTTGAAAACAGAAATTGAAAATACCTCACACGTGAAC-CGAGGCTCAACTCACCTCTCGCAATA
*
2645075 TGAGTTGAATTTTTTT
65 TGAGCTG-ATTTTTTT
*
2645091 TTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAAT
1 TTTTGAAA-ACAGAAATTGAAAATACCTCA-CACGTGAACCGAGGCTCAACTCACCTCTCGCAAT
2645156 ATGAGCTGATTTT
64 ATGAGCTGATTTT
2645169 GAAAAAGTAG
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
79 8 0.12
80 20 0.30
81 5 0.07
82 33 0.49
83 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (79 bp):
TTTTGAAAACAGAAATTGAAAATACCTCACACGTGAACCGAGGCTCAACTCACCTCTCGCAATAT
GAGCTGATTTTTTT
Found at i:2645237 original size:54 final size:54
Alignment explanation
Indices: 2645137--2645242 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
2645127 GAACCGAGGC
*
2645137 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
2645191 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAATAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
2645243 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:2645367 original size:72 final size:71
Alignment explanation
Indices: 2645233--2645398 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
2645223 TGAATAACGT
* * * *
2645233 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
2645298 GAGTTG
66 GAGTTG
*
2645304 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
2645369 TGAGTTG
65 TGAGTTG
**
2645376 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
2645399 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:2645493 original size:122 final size:124
Alignment explanation
Indices: 2645273--2645519 Score: 374
Period size: 122 Copynumber: 2.0 Consensus size: 124
2645263 GCGTGACCTG
* *
2645273 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
*
2645338 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAATTTTG-AAAACAAAAATTAAA
* * * *
2645398 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* **
2645460 TGCCCCGAGGCTCAACTCACTTCTCTCAATATGAGTTAATTTTGAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAATTTTGAAAACAAAAATTAAA
2645519 A
1 A
2645520 ATACCTCAAC
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
121 16 0.14
122 61 0.54
123 7 0.06
124 1 0.01
125 27 0.24
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAATTTTGAAAACAAAAATTAAA
Found at i:2645527 original size:71 final size:70
Alignment explanation
Indices: 2645398--2645573 Score: 221
Period size: 71 Copynumber: 2.5 Consensus size: 70
2645388 AAAAATTAAA
* * * * *
2645398 AGGCTTAACTCACCTCTCGCAATATGAGTCAA-TTTAAAACATAAACTAAAAATACCTCAGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTAATTTTAAAACAAAAACTAAAAATACCTCAACGTG
2645462 CCCCG
66 CCCCG
* *
2645467 AGGCTCAACTCACTTCTCTCAATATGAGTTAATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTAATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
2645532 GTCTTG
65 GCCCCG
*
2645538 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTAATTTT
2645574 CCTTGAAAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 28 0.30
70 4 0.04
71 60 0.65
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTAATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:2647437 original size:41 final size:39
Alignment explanation
Indices: 2647372--2647451 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 39
2647362 ACATGAATTT
*
2647372 TATCGCCGTATTTGAATTTGTGGCATTTTCTGGCAAAAC
1 TATCGCCGTAATTGAATTTGTGGCATTTTCTGGCAAAAC
2647411 TATCGCCGTAGATTGACATTTGTGGCATTTTCTGGCAAAAC
1 TATCGCCGTA-ATTGA-ATTTGTGGCATTTTCTGGCAAAAC
2647452 AATGCAGTCG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 10 0.26
40 4 0.11
41 24 0.63
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (39 bp):
TATCGCCGTAATTGAATTTGTGGCATTTTCTGGCAAAAC
Found at i:2648662 original size:31 final size:31
Alignment explanation
Indices: 2648614--2648708 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
2648604 CATTTATATT
* **
2648614 TTATATATTATTATATTAAATTATTTGAATA
1 TTATTTATTATTATATTAAATTATTCAAATA
* *
2648645 -TAGTTTATTTTTATATTAAATTACTCAAATA
1 TTA-TTTATTATTATATTAAATTATTCAAATA
* *
2648676 TTATTTATTATTATATTTAATTATTAAAATA
1 TTATTTATTATTATATTAAATTATTCAAATA
2648707 TT
1 TT
2648709 TTTGTAAATT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 2 0.04
31 49 0.92
32 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
TTATTTATTATTATATTAAATTATTCAAATA
Found at i:2651167 original size:15 final size:16
Alignment explanation
Indices: 2651149--2651181 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2651139 TATTTATTAA
*
2651149 ATTTATAAT-TATTTT
1 ATTTAAAATGTATTTT
2651164 ATTTAAAATGTATTTT
1 ATTTAAAATGTATTTT
2651180 AT
1 AT
2651182 GACACTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTAAAATGTATTTT
Found at i:2653568 original size:25 final size:27
Alignment explanation
Indices: 2653540--2653603 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 27
2653530 TAAGAAAGGA
2653540 ACAAGTAA-G-AGTTCCAAGTTGGTTG
1 ACAAGTAAGGAAGTTCCAAGTTGGTTG
2653565 ACAAGTAATAGTGTAAGTTCCAAGTTGGTTG
1 ACAAGT-A-AG-G-AAGTTCCAAGTTGGTTG
2653596 ACAAGTAA
1 ACAAGTAA
2653604 TAGTGTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
25 6 0.18
26 1 0.03
27 1 0.03
29 2 0.06
30 1 0.03
31 22 0.67
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (27 bp):
ACAAGTAAGGAAGTTCCAAGTTGGTTG
Found at i:2653584 original size:31 final size:31
Alignment explanation
Indices: 2653549--2653611 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2653539 AACAAGTAAG
2653549 AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
1 AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
2653580 AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
1 AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
2653611 A
1 A
2653612 TTACAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (31 bp):
AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
Found at i:2655122 original size:16 final size:16
Alignment explanation
Indices: 2655096--2655165 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 16
2655086 TGAATTACTA
* *
2655096 ATTACAGCTCTATTCT
1 ATTACAACTCTATTCC
*
2655112 ATTATAACTCTATTCC
1 ATTACAACTCTATTCC
* *
2655128 ATTACAACTCGATACC
1 ATTACAACTCTATTCC
** *
2655144 ATTACAGTTCTATTTC
1 ATTACAACTCTATTCC
2655160 ATTACA
1 ATTACA
2655166 GCGAACCAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:2657101 original size:18 final size:18
Alignment explanation
Indices: 2657078--2657114 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2657068 TATCTCGTAA
2657078 ATTATTTGTTATTTTTAT
1 ATTATTTGTTATTTTTAT
* *
2657096 ATTATTTTTTGTTTTTAT
1 ATTATTTGTTATTTTTAT
2657114 A
1 A
2657115 CATTTGCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
ATTATTTGTTATTTTTAT
Found at i:2660797 original size:74 final size:74
Alignment explanation
Indices: 2660513--2660783 Score: 353
Period size: 74 Copynumber: 3.7 Consensus size: 74
2660503 TTGTGCTCAA
* * * * * * * * *
2660513 TGCTAGTTGGATTAACCGACAATAATGAATGTGAGCCTAGATCTAGTTGGAAAAGCCAATGATAT
1 TGCTAGTCGGATAAATCGAAAATAATGAATGTGAGCCCAGCTCTAGTTGGACAAGACAACGATAT
2660578 TGCACCTAG
66 TGCACCTAG
*
2660587 TGCTAGTCGGATAAATTGAAAATAATGAATGTGAGCCCAGCTCTAGTTGGACAAGACAACGATAT
1 TGCTAGTCGGATAAATCGAAAATAATGAATGTGAGCCCAGCTCTAGTTGGACAAGACAACGATAT
*
2660652 TGCACCCAG
66 TGCACCTAG
* * * *
2660661 TGCTAGTCGGATAAACCGACAATAATGAATGTGAGCACAGCTCTAGTTGGATAAGACAACGATAT
1 TGCTAGTCGGATAAATCGAAAATAATGAATGTGAGCCCAGCTCTAGTTGGACAAGACAACGATAT
2660726 TGCACCTAG
66 TGCACCTAG
* ** * * *
2660735 TGCTAGTCAGATAAATCGATGATGATAAATGTGAGCCCAGCTCAAGTTG
1 TGCTAGTCGGATAAATCGAAAATAATGAATGTGAGCCCAGCTCTAGTTG
2660784 AACGTATCAA
Statistics
Matches: 172, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 172 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (74 bp):
TGCTAGTCGGATAAATCGAAAATAATGAATGTGAGCCCAGCTCTAGTTGGACAAGACAACGATAT
TGCACCTAG
Found at i:2660797 original size:148 final size:148
Alignment explanation
Indices: 2660513--2660783 Score: 409
Period size: 148 Copynumber: 1.8 Consensus size: 148
2660503 TTGTGCTCAA
* * * *
2660513 TGCTAGTTGGATTAACCGACAATAATGAATGTGAGCCTAGATCTAGTTGGAAAAGCCAATGATAT
1 TGCTAGTCGGATAAACCGACAATAATGAATGTGAGCCTAGATCTAGTTGGAAAAGACAACGATAT
* * * *
2660578 TGCACCTAGTGCTAGTCGGATAAATTGAAAATAATGAATGTGAGCCCAGCTCTAGTTGGACAAGA
66 TGCACCTAGTGCTAGTCAGATAAATCGAAAATAATAAATGTGAGCCCAGCTCAAGTTGGACAAGA
2660643 CAACGATATTGCACCCAG
131 CAACGATATTGCACCCAG
* *
2660661 TGCTAGTCGGATAAACCGACAATAATGAATGTGAGCAC-AGCTCTAGTTGGATAAGACAACGATA
1 TGCTAGTCGGATAAACCGACAATAATGAATGTGAGC-CTAGATCTAGTTGGAAAAGACAACGATA
** *
2660725 TTGCACCTAGTGCTAGTCAGATAAATCGATGATGATAAATGTGAGCCCAGCTCAAGTTG
65 TTGCACCTAGTGCTAGTCAGATAAATCGAAAATAATAAATGTGAGCCCAGCTCAAGTTG
2660784 AACGTATCAA
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
148 108 0.99
149 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (148 bp):
TGCTAGTCGGATAAACCGACAATAATGAATGTGAGCCTAGATCTAGTTGGAAAAGACAACGATAT
TGCACCTAGTGCTAGTCAGATAAATCGAAAATAATAAATGTGAGCCCAGCTCAAGTTGGACAAGA
CAACGATATTGCACCCAG
Found at i:2662892 original size:29 final size:30
Alignment explanation
Indices: 2662860--2662921 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2662850 ACTTAACAAG
*
2662860 CAAATG-CTTCTAAAATTATAA-AAAAATAA
1 CAAATGCCTT-TAAAATAATAAGAAAAATAA
*
2662889 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAAATAA
2662919 CAA
1 CAA
2662922 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAGAAAAATAA
Found at i:2663792 original size:44 final size:46
Alignment explanation
Indices: 2663723--2663810 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 46
2663713 TTACAACATC
*
2663723 ATTCCATTCAACCAAACACAAGAATT-C-TATTACAGTTCTATTTT
1 ATTCCATCCAACCAAACACAAGAATTACTTATTACAGTTCTATTTT
***
2663767 ATTCCATCCAACCAAACAGTTGAATTACTTATTACAGTTCTATT
1 ATTCCATCCAACCAAACACAAGAATTACTTATTACAGTTCTATT
2663811 CCATTACAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 22 0.58
45 1 0.03
46 15 0.39
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (46 bp):
ATTCCATCCAACCAAACACAAGAATTACTTATTACAGTTCTATTTT
Found at i:2663818 original size:16 final size:16
Alignment explanation
Indices: 2663797--2663836 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2663787 TGAATTACTT
2663797 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
*
2663813 ATTACAGCTCTATTCC
1 ATTACAGTTCTATTCC
2663829 ATTACAGT
1 ATTACAGT
2663837 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:2667455 original size:35 final size:35
Alignment explanation
Indices: 2667416--2667486 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
2667406 CACTTGCCTC
*
2667416 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
*
2667451 TTCCCATTCTCCCATGCTGTCTGCCACCAACACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
2667486 T
1 T
2667487 CACACACTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.18, C:0.46, G:0.10, T:0.25
Consensus pattern (35 bp):
TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
Found at i:2667892 original size:12 final size:12
Alignment explanation
Indices: 2667871--2667917 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
2667861 TTAAAACATA
2667871 AAAAAAATATAC
1 AAAAAAATATAC
*
2667883 AAAAAGATATAC
1 AAAAAAATATAC
2667895 AAAAAAATATAC
1 AAAAAAATATAC
2667907 AAAAAAATATA
1 AAAAAAATATA
2667918 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.17
Consensus pattern (12 bp):
AAAAAAATATAC
Found at i:2668517 original size:3 final size:3
Alignment explanation
Indices: 2668509--2668542 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2668499 TGCATTTCAA
2668509 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2668543 GAAATACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2668652 original size:3 final size:3
Alignment explanation
Indices: 2668644--2668679 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2668634 TGTGTTTCAA
2668644 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2668680 ATATCCTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2668953 original size:33 final size:30
Alignment explanation
Indices: 2668895--2668964 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
2668885 TAATATTATG
*
2668895 TATATATTTTAATATTATCAGTTATATATA
1 TATATATTTTAATACTATCAGTTATATATA
* *
2668925 CTATATGATTTCTAATACTATTATTTATATATA
1 -TATAT-ATTT-TAATACTATCAGTTATATATA
2668958 TATATAT
1 TATATAT
2668965 ATTTTCTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 9 0.26
33 18 0.53
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (30 bp):
TATATATTTTAATACTATCAGTTATATATA
Found at i:2671066 original size:19 final size:17
Alignment explanation
Indices: 2671020--2671067 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
2671010 AATTTAGTCC
*
2671020 TATATTTATTCTATATA
1 TATATTTATTTTATATA
*
2671037 TATATATATTTTATATA
1 TATATTTATTTTATATA
2671054 TTGATATTTATTTT
1 -T-ATATTTATTTT
2671068 TATCCTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 15 0.58
18 1 0.04
19 10 0.38
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TATATTTATTTTATATA
Found at i:2671537 original size:14 final size:14
Alignment explanation
Indices: 2671470--2671539 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 14
2671460 TACCTACTTT
2671470 TATTTTATATA-TA
1 TATTTTATATATTA
2671483 T-TTTTATATAATTA
1 TATTTTATAT-ATTA
*
2671497 TTATTCTCT-TATA-AA
1 -TATT-T-TATATATTA
*
2671512 TATTTTGT-TATTA
1 TATTTTATATATTA
2671525 TATTTTATATATTA
1 TATTTTATATATTA
2671539 T
1 T
2671540 GTAGCAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 17
0.69 0.05 0.26
Matches are distributed among these distances:
12 11 0.24
13 12 0.27
14 12 0.27
15 2 0.04
16 3 0.07
17 4 0.09
18 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (14 bp):
TATTTTATATATTA
Found at i:2673506 original size:21 final size:19
Alignment explanation
Indices: 2673432--2673513 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 19
2673422 ATGATTTTTT
*
2673432 AATTCATATAATAATTATTT
1 AATT-ATATAATAATTATTA
* * *
2673452 TATTA-AGAAT-GTTATTA
1 AATTATATAATAATTATTA
*
2673469 AATTATATAATATTTATTA
1 AATTATATAATAATTATTA
*
2673488 AATTGTATTTAATAATTATTA
1 AA-T-TATATAATAATTATTA
*
2673509 TATTA
1 AATTA
2673514 AAAATGATTA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
17 9 0.19
18 8 0.17
19 11 0.23
20 5 0.10
21 15 0.31
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (19 bp):
AATTATATAATAATTATTA
Found at i:2673569 original size:26 final size:25
Alignment explanation
Indices: 2673538--2673589 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
2673528 ATTTATTTTT
*
2673538 ATTTTATTAAAATATATTTAACAATA
1 ATTTTATTAAAATATA-ATAACAATA
*
2673564 ATTTTATTAAAATTTAATAACAATA
1 ATTTTATTAAAATATAATAACAATA
2673589 A
1 A
2673590 CAATAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTTTATTAAAATATAATAACAATA
Found at i:2674643 original size:44 final size:46
Alignment explanation
Indices: 2674573--2674666 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
2674563 ATTACAACAT
*
2674573 CATTCCATTCAACCAAACACAAGAATT-C-TATTACAGTTCTATTC
1 CATTCCATCCAACCAAACACAAGAATTACTTATTACAGTTCTATTC
*** *
2674617 CATTCCATCCAACCAAACAGTTGAATTACTTATTACGGTTCTATTC
1 CATTCCATCCAACCAAACACAAGAATTACTTATTACAGTTCTATTC
2674663 CATT
1 CATT
2674667 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 23 0.53
45 1 0.02
46 19 0.44
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (46 bp):
CATTCCATCCAACCAAACACAAGAATTACTTATTACAGTTCTATTC
Found at i:2674675 original size:16 final size:16
Alignment explanation
Indices: 2674656--2674718 Score: 110
Period size: 16 Copynumber: 3.9 Consensus size: 16
2674646 TTATTACGGT
2674656 TCTATTCCATTACAGC
1 TCTATTCCATTACAGC
2674672 TCTATTCCATTACAGC
1 TCTATTCCATTACAGC
2674688 TCTATT-CAGTTACAGC
1 TCTATTCCA-TTACAGC
2674704 TCTATTCCATTACAG
1 TCTATTCCATTACAG
2674719 TGAACCAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
15 2 0.04
16 41 0.91
17 2 0.04
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (16 bp):
TCTATTCCATTACAGC
Found at i:2674925 original size:41 final size:42
Alignment explanation
Indices: 2674874--2674961 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
2674864 TATATTAGCT
*
2674874 ATTTATATTTTA-AAAGGTA-TATAAAAAATTATTTGAATATC
1 ATTTACATTTTATAAA-GTATTATAAAAAATTATTTGAATATC
* * **
2674915 ATTTACATTTTATATATTATTATATTAAATTATTTGAATATC
1 ATTTACATTTTATAAAGTATTATAAAAAATTATTTGAATATC
2674957 ATTTA
1 ATTTA
2674962 TTATTGTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
41 13 0.32
42 27 0.68
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (42 bp):
ATTTACATTTTATAAAGTATTATAAAAAATTATTTGAATATC
Found at i:2675000 original size:31 final size:31
Alignment explanation
Indices: 2674937--2675000 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
2674927 TATATTATTA
** *
2674937 TATTAAATTATTTGAATATCATTTATTATTG
1 TATTAAATTATTAAAATATCATTTATAATTG
*
2674968 TATTAAATTATTAAAATAT-TTTTATAACTTG
1 TATTAAATTATTAAAATATCATTTATAA-TTG
2674999 TA
1 TA
2675001 CAAATAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (31 bp):
TATTAAATTATTAAAATATCATTTATAATTG
Found at i:2677119 original size:29 final size:29
Alignment explanation
Indices: 2677046--2677122 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
2677036 AAAAAATTTC
*
2677046 AATAAATAAAAAT-ATATAAAATTATTAA
1 AATAAATTAAAATAATATAAAATTATTAA
* * *
2677074 ATATTAAAATAATATAATATAAATATT-TTTA
1 A-A-TAAATTAAAATAATATAAA-ATTATTAA
2677105 AATAAATTAAAATAATAT
1 AATAAATTAAAATAATAT
2677123 GGATGAGCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.03
29 15 0.38
30 9 0.23
31 11 0.28
32 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AATAAATTAAAATAATATAAAATTATTAA
Found at i:2682433 original size:17 final size:17
Alignment explanation
Indices: 2682411--2682521 Score: 69
Period size: 17 Copynumber: 6.7 Consensus size: 17
2682401 TTAAAGTTTT
2682411 TTAAAATTTTAAATATA
1 TTAAAATTTTAAATATA
*
2682428 TTAAAAAATATTAAATATA
1 TT--AAAATTTTAAATATA
* *
2682447 --ACCAATTTTAAA-ATT
1 TTA-AAATTTTAAATATA
2682462 TTAATACA-TTT-AATATA
1 TTAA-A-ATTTTAAATATA
*
2682479 TT----TTTAAAAATATA
1 TTAAAATTTTAA-ATATA
2682493 TTAAAATTTTAAATATA
1 TTAAAATTTTAAATATA
2682510 TTAAAATTTTAA
1 TTAAAATTTTAA
2682522 TATTCTTAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 30
0.65 0.07 0.28
Matches are distributed among these distances:
12 2 0.03
13 1 0.01
14 7 0.10
15 3 0.04
16 10 0.14
17 28 0.39
18 6 0.08
19 14 0.20
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAAATTTTAAATATA
Found at i:2682504 original size:19 final size:19
Alignment explanation
Indices: 2682480--2682521 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
2682470 TTTAATATAT
2682480 TTTTAAAAATATATTAAAA
1 TTTTAAAAATATATTAAAA
2682499 TTTT--AAATATATTAAAA
1 TTTTAAAAATATATTAAAA
2682516 TTTTAA
1 TTTTAA
2682522 TATTCTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 17 0.81
19 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTTAAAAATATATTAAAA
Found at i:2682530 original size:17 final size:17
Alignment explanation
Indices: 2682486--2682521 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2682476 ATATTTTTAA
2682486 AAATATATTAAAATTTT
1 AAATATATTAAAATTTT
2682503 AAATATATTAAAATTTT
1 AAATATATTAAAATTTT
2682520 AA
1 AA
2682522 TATTCTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATATTAAAATTTT
Found at i:2682617 original size:17 final size:17
Alignment explanation
Indices: 2682595--2682637 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2682585 TTAAAAAACT
2682595 TTAAAAAATTAAATATA
1 TTAAAAAATTAAATATA
**
2682612 TTAAAATTTTAAATATA
1 TTAAAAAATTAAATATA
2682629 TTAAAAAAT
1 TTAAAAAAT
2682638 GTTAAGTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAAATTAAATATA
Found at i:2682636 original size:19 final size:18
Alignment explanation
Indices: 2682595--2682647 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
2682585 TTAAAAAACT
2682595 TTAAAAAA-TTAAATATA
1 TTAAAAAATTTAAATATA
*
2682612 TT-AAAATTTTAAATATA
1 TTAAAAAATTTAAATATA
*
2682629 TTAAAAAATGTTAAGTATA
1 TTAAAAAAT-TTAAATATA
2682648 ACCAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 4 0.13
17 13 0.43
18 5 0.17
19 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TTAAAAAATTTAAATATA
Found at i:2682737 original size:26 final size:27
Alignment explanation
Indices: 2682707--2682765 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
2682697 AAGGATTTTT
2682707 AATATATTTAAAA-TTTAAAAAAATTA
1 AATATATTTAAAATTTTAAAAAAATTA
* *
2682733 AATATA-TTAAAATTTTAAATATATTA
1 AATATATTTAAAATTTTAAAAAAATTA
*
2682759 AAAATAT
1 AATATAT
2682766 GTGAAGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATATTTAAAATTTTAAAAAAATTA
Found at i:2682744 original size:15 final size:16
Alignment explanation
Indices: 2682725--2682761 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
2682715 TAAAATTTAA
*
2682725 AAAAATTAAATATATT
1 AAAATTTAAATATATT
2682741 AAAATTTTAAATATATT
1 AAAA-TTTAAATATATT
2682758 AAAA
1 AAAA
2682762 ATATGTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTTAAATATATT
Found at i:2682753 original size:127 final size:130
Alignment explanation
Indices: 2682589--2682866 Score: 415
Period size: 127 Copynumber: 2.1 Consensus size: 130
2682579 AAGATTTTAA
*
2682589 AAAACTTTAAAAAATTAAATATATTAAAATTTTAAATATATTAAAAA-ATGTTAAGTATAACCAA
1 AAAA-TTTAAAAAATTAAATATATTAAAATTTTAAATATATTAAAAATATGTGAAGTAT-ACCAA
2682653 TTTTAAAAATTTAATATATTCAATATA-TTTTT-TA-AT-AGGTAAAAAAGGA-TTTTTAATATA
64 TTTTAAAAATTTAATATATTCAATATATTTTTTATAGATAAGGTAAAAAA-GATTTTTTAATATA
2682713 TTT
128 TTT
2682716 AAAATTTAAAAAAATTAAATATATTAAAATTTTAAATATATTAAAAATATGTGAAGTATACCAAT
1 AAAATTT-AAAAAATTAAATATATTAAAATTTTAAATATATTAAAAATATGTGAAGTATACCAAT
*
2682781 TTTAAAAATTTAATATATTTAATATATTTTTTAATAGATAAAGGTAAAAAAGATTTTTTTAATAT
65 TTTAAAAATTTAATATATTCAATATATTTTTT-ATAGAT-AAGGTAAAAAAGA-TTTTTTAATAT
2682846 ATTT
127 ATTT
2682850 AAAATTTCCAAAAAATT
1 AAAATTT--AAAAAATT
2682867 TAAAGAAAAA
Statistics
Matches: 137, Mismatches: 3, Indels: 14
0.89 0.02 0.09
Matches are distributed among these distances:
126 3 0.02
127 74 0.54
128 15 0.11
130 2 0.01
131 2 0.01
132 2 0.01
133 10 0.07
134 21 0.15
135 8 0.06
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (130 bp):
AAAATTTAAAAAATTAAATATATTAAAATTTTAAATATATTAAAAATATGTGAAGTATACCAATT
TTAAAAATTTAATATATTCAATATATTTTTTATAGATAAGGTAAAAAAGATTTTTTAATATATTT
Found at i:2682759 original size:9 final size:9
Alignment explanation
Indices: 2682707--2682765 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
2682697 AAGGATTTTT
2682707 AATATATTTA
1 AATATA-TTA
2682717 AA-AT-TTA
1 AATATATTA
* *
2682724 AAAAAATTA
1 AATATATTA
2682733 AATATATTA
1 AATATATTA
*
2682742 AA-ATTTTA
1 AATATATTA
2682750 AATATATTA
1 AATATATTA
*
2682759 AAAATAT
1 AATATAT
2682766 GTGAAGTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
7 5 0.12
8 8 0.20
9 25 0.62
10 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATATATTA
Found at i:2683387 original size:40 final size:39
Alignment explanation
Indices: 2683316--2683456 Score: 99
Period size: 40 Copynumber: 3.6 Consensus size: 39
2683306 AAATGACTAC
* ** *
2683316 TTTTATATATTTTTAGCTTTTTATTATGTTTTTTAATAAT
1 TTTTATATATTTATAAATTTTTA-TAAGTTTTTTAATAAT
*
2683356 TTTTATATTATTTATAAATTTTTATAAGTTTTTATAAAAAT
1 TTTTATA-TATTTATAAATTTTTATAAGTTTTT-TAATAAT
*** * * * *
2683397 TCAAATATATTT-TATTACTTTTATAA-TTTTATAAT-TT
1 TTTTATATATTTATA-AATTTTTATAAGTTTTTTAATAAT
*
2683434 TTTTATAATATTTATAAGTTTTT
1 TTTTAT-ATATTTATAAATTTTT
2683457 TTTTATGATT
Statistics
Matches: 77, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
37 4 0.05
38 13 0.17
39 8 0.10
40 29 0.38
41 23 0.30
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (39 bp):
TTTTATATATTTATAAATTTTTATAAGTTTTTTAATAAT
Found at i:2683435 original size:9 final size:9
Alignment explanation
Indices: 2683345--2683761 Score: 93
Period size: 9 Copynumber: 43.8 Consensus size: 9
2683335 TTTATTATGT
2683345 TTTTTAATAA
1 TTTTT-ATAA
2683355 TTTTTAT-A
1 TTTTTATAA
2683363 TTATTTATAAA
1 TT-TTTAT-AA
2683374 TTTTTATAA
1 TTTTTATAA
2683383 GTTTTTATAAA
1 -TTTTTAT-AA
** * *
2683394 AATTCAAATA
1 TTTTTATA-A
*
2683404 TATTTTATTA
1 T-TTTTATAA
*
2683414 CTTTTATAA
1 TTTTTATAA
2683423 -TTTTATAA
1 TTTTTATAA
2683431 TTTTTTTATAA
1 --TTTTTATAA
*
2683442 TATTTATAA
1 TTTTTATAA
*
2683451 -GTTT-T--
1 TTTTTATAA
*
2683456 TTTTTATGAT
1 TTTTTAT-AA
2683466 TTTTTATAA
1 TTTTTATAA
*
2683475 TTATTATAA
1 TTTTTATAA
*
2683484 GTTTATATAA
1 -TTTTTATAA
** *
2683494 TTTCAATAT
1 TTTTTATAA
2683503 TTTTTA-AA
1 TTTTTATAA
*
2683511 TTGTTAATGATA
1 TT-TTTAT-A-A
* *
2683523 TTTTTCTTA
1 TTTTTATAA
*
2683532 TTTTTAATGATT
1 TTTTT-AT-A-A
2683544 TTTTTATATA
1 TTTTTATA-A
*
2683554 TTTTTATATG
1 TTTTTATA-A
2683564 TTTTTATAAA
1 TTTTTAT-AA
*
2683574 ATTTTA-AA
1 TTTTTATAA
*
2683582 TATTTTAAATA
1 T-TTTTATA-A
*
2683593 TGTTTTATTCA
1 T-TTTTA-TAA
**
2683604 TTTTATATTT
1 TTTT-TATAA
2683614 TTTTTATAA
1 TTTTTATAA
* *
2683623 TTTATTAGAT
1 TTT-TTATAA
2683633 TTTTTA-AA
1 TTTTTATAA
* *
2683641 TATTTAAGTTA
1 T-TTTTA-TAA
2683652 TTTTTATAA
1 TTTTTATAA
*
2683661 TATTTATAA
1 TTTTTATAA
*
2683670 GTTTCTATAA
1 -TTTTTATAA
*
2683680 ATTTTA-ATA
1 TTTTTATA-A
*
2683689 TTTTTATTA
1 TTTTTATAA
*
2683698 -TTTAATAA
1 TTTTTATAA
*
2683706 -TTTAATAA
1 TTTTTATAA
* *
2683714 TTTTAATGAT
1 TTTTTAT-AA
2683724 TTTTTAATAAA
1 TTTTT-AT-AA
*
2683735 TTTTTTATGA
1 -TTTTTATAA
*
2683745 TTTTTAATAG
1 TTTTT-ATAA
2683755 TTTTTAT
1 TTTTTAT
2683762 GAGAAAATAT
Statistics
Matches: 300, Mismatches: 66, Indels: 83
0.67 0.15 0.18
Matches are distributed among these distances:
6 3 0.01
7 2 0.01
8 36 0.12
9 105 0.35
10 100 0.33
11 41 0.14
12 13 0.04
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:2683439 original size:19 final size:21
Alignment explanation
Indices: 2683415--2683458 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
2683405 ATTTTATTAC
2683415 TTTTATAAT-TTTATAA-TTT
1 TTTTATAATATTTATAAGTTT
2683434 TTTTATAATATTTATAAGTTT
1 TTTTATAATATTTATAAGTTT
2683455 TTTT
1 TTTT
2683459 TTATGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.39
20 7 0.30
21 7 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTATAATATTTATAAGTTT
Found at i:2683467 original size:21 final size:19
Alignment explanation
Indices: 2683424--2683467 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2683414 CTTTTATAAT
*
2683424 TTTATAATTTTTTTATAATA
1 TTTATAATTTTTTT-TTATA
2683444 TTTATAAGTTTTTTTTTATGA
1 TTTATAA-TTTTTTTTTAT-A
2683465 TTT
1 TTT
2683468 TTTATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTATAATTTTTTTTTATA
Found at i:2683474 original size:33 final size:34
Alignment explanation
Indices: 2683423--2683487 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
2683413 ACTTTTATAA
2683423 TTTTATAATTTTTTTATAA-TATTTATAAGTTTTT
1 TTTTATAATTTTTTTATAATTA-TTATAAGTTTTT
*
2683457 TTTTATGA-TTTTTTATAATTATTATAAGTTT
1 TTTTATAATTTTTTTATAATTATTATAAGTTT
2683488 ATATAATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (34 bp):
TTTTATAATTTTTTTATAATTATTATAAGTTTTT
Found at i:2683557 original size:21 final size:20
Alignment explanation
Indices: 2683485--2683587 Score: 63
Period size: 21 Copynumber: 5.0 Consensus size: 20
2683475 TTATTATAAG
*
2683485 TTTATATAATTTCAATA-TTT
1 TTTATAT-ATTTTAATATTTT
2683505 TTTA-A-ATTGTTAATGATATTT
1 TTTATATATT-TTAAT-AT-TTT
2683526 TTCT-TAT-TTTTAATGATTTT
1 TT-TATATATTTTAAT-ATTTT
* *
2683546 TTTATATATTTTTATATGTT
1 TTTATATATTTTAATATTTT
*
2683566 TTTATAAAATTTTAAATATTTT
1 TTTAT-ATATTTT-AATATTTT
2683588 AAATATGTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
17 3 0.05
18 4 0.06
19 3 0.05
20 21 0.32
21 25 0.38
22 10 0.15
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTATATATTTTAATATTTT
Found at i:2683587 original size:20 final size:20
Alignment explanation
Indices: 2683544--2683587 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2683534 TTTAATGATT
* * * *
2683544 TTTTTATATATTTTTATATG
1 TTTTTATAAAATTTTAAATA
2683564 TTTTTATAAAATTTTAAATA
1 TTTTTATAAAATTTTAAATA
2683584 TTTT
1 TTTT
2683588 AAATATGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTATAAAATTTTAAATA
Found at i:2683703 original size:16 final size:17
Alignment explanation
Indices: 2683614--2683761 Score: 69
Period size: 19 Copynumber: 8.4 Consensus size: 17
2683604 TTTTATATTT
2683614 TTTTTATAATTTATTAGAT-
1 TTTTTATAA-TT-TTA-ATA
2683633 TTTTTA-AATATTTAAGTTA
1 TTTTTATAAT-TTTAA--TA
2683652 TTTTTATAATATTT-ATAA
1 TTTTTATAAT-TTTAAT-A
*
2683670 GTTTCTATAAATTTTAATA
1 -TTTTTAT-AATTTTAATA
*
2683689 TTTTTATTA-TTTAATA
1 TTTTTATAATTTTAATA
* *
2683705 ATTTAATAATTTTAATGA
1 TTTTTATAATTTTAAT-A
*
2683723 TTTTT-TAA--TAAAT-
1 TTTTTATAATTTTAATA
*
2683736 TTTTTATGATTTTTAATA
1 TTTTTAT-AATTTTAATA
2683754 GTTTTTAT
1 -TTTTTAT
2683762 GAGAAAATAT
Statistics
Matches: 101, Mismatches: 11, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
13 5 0.05
14 1 0.01
15 5 0.05
16 14 0.14
17 19 0.19
18 15 0.15
19 30 0.30
20 12 0.12
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (17 bp):
TTTTTATAATTTTAATA
Found at i:2683759 original size:21 final size:22
Alignment explanation
Indices: 2683706--2683753 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2683696 TATTTAATAA
2683706 TTTAAT-AA-TTTTAATGATTT
1 TTTAATAAATTTTTAATGATTT
*
2683726 TTTAATAAATTTTTTATGA-TT
1 TTTAATAAATTTTTAATGATTT
2683747 TTTAATA
1 TTTAATA
2683754 GTTTTTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 11 0.44
22 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTAATAAATTTTTAATGATTT
Found at i:2685691 original size:43 final size:44
Alignment explanation
Indices: 2685644--2685795 Score: 168
Period size: 43 Copynumber: 3.5 Consensus size: 44
2685634 TATATGGCAA
2685644 CTTGTCTG-CAAAATTGGTGGTTTATCCACAACCTACATGATAG
1 CTTGTCTGTCAAAATTGGTGGTTTATCCACAACCTACATGATAG
* * * **
2685687 CTTGTCTGTGAATATTGGTTGCTTCGTCCACAACCTACATGATAG
1 CTTGTCTGTCAAAATTGG-TGGTTTATCCACAACCTACATGATAG
* * *
2685732 CTTGTTTGTC-AATTTGGTGGTTTATCCACAACCTACATGGTAG
1 CTTGTCTGTCAAAATTGGTGGTTTATCCACAACCTACATGATAG
*
2685775 TTTG-CT-TACAAATATTGGTGG
1 CTTGTCTGT-CAAA-ATTGGTGG
2685796 CTTCAACCAC
Statistics
Matches: 88, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 35 0.40
44 19 0.22
45 31 0.35
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (44 bp):
CTTGTCTGTCAAAATTGGTGGTTTATCCACAACCTACATGATAG
Found at i:2685721 original size:45 final size:43
Alignment explanation
Indices: 2685644--2685770 Score: 148
Period size: 45 Copynumber: 2.9 Consensus size: 43
2685634 TATATGGCAA
* * *
2685644 CTTGTCTG-CAAAATTGGTGGTTTATCCACAACCTACATGATAG
1 CTTGTCTGTC-AATTTGGTGCTTCATCCACAACCTACATGATAG
* *
2685687 CTTGTCTGTGAATATTGGTTGCTTCGTCCACAACCTACATGATAG
1 CTTGTCTGTCAAT-TTGG-TGCTTCATCCACAACCTACATGATAG
* * *
2685732 CTTGTTTGTCAATTTGGTGGTTTATCCACAACCTACATG
1 CTTGTCTGTCAATTTGGTGCTTCATCCACAACCTACATG
2685771 GTAGTTTGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 29 0.41
44 8 0.11
45 34 0.48
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (43 bp):
CTTGTCTGTCAATTTGGTGCTTCATCCACAACCTACATGATAG
Found at i:2685723 original size:88 final size:89
Alignment explanation
Indices: 2685607--2685770 Score: 224
Period size: 88 Copynumber: 1.9 Consensus size: 89
2685597 TTGCAAGGAG
* * *
2685607 GAATAATTGGTGGCTTCGCCCATAACCTATATGGCAACTTGTCTG-CAAAATTGGTGGTTTATCC
1 GAATAATTGGTGGCTTCGCCCACAACCTACATGACAACTTGTCTGTC-AAATTGGTGGTTTATCC
2685671 ACAACCTACATGATAGCTTGTCTGT
65 ACAACCTACATGATAGCTTGTCTGT
* * * * * *
2685696 GAAT-ATTGGTTGCTTCGTCCACAACCTACATGATAGCTTGTTTGTCAATTTGGTGGTTTATCCA
1 GAATAATTGGTGGCTTCGCCCACAACCTACATGACAACTTGTCTGTCAAATTGGTGGTTTATCCA
2685760 CAACCTACATG
66 CAACCTACATG
2685771 GTAGTTTGCT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
88 60 0.92
89 5 0.08
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (89 bp):
GAATAATTGGTGGCTTCGCCCACAACCTACATGACAACTTGTCTGTCAAATTGGTGGTTTATCCA
CAACCTACATGATAGCTTGTCTGT
Found at i:2687169 original size:10 final size:10
Alignment explanation
Indices: 2687154--2687252 Score: 75
Period size: 10 Copynumber: 10.2 Consensus size: 10
2687144 AAAATAAAAG
2687154 AAATTATAAA
1 AAATTATAAA
2687164 AAATTAT--A
1 AAATTATAAA
*
2687172 AAATTAT-TA
1 AAATTATAAA
2687181 AAATATATAAA
1 AAAT-TATAAA
*
2687192 AAA-TATAATT
1 AAATTATAA-A
*
2687202 AAATTGATAGA
1 AAATT-ATAAA
*
2687213 AAGTTAT-AA
1 AAATTATAAA
2687222 AAATTATAAA
1 AAATTATAAA
*
2687232 AAATAAT-AA
1 AAATTATAAA
*
2687241 ATATTATAAA
1 AAATTATAAA
2687251 AA
1 AA
2687253 TCAAATTAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
8 8 0.11
9 24 0.34
10 26 0.37
11 9 0.13
12 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (10 bp):
AAATTATAAA
Found at i:2687174 original size:9 final size:9
Alignment explanation
Indices: 2687154--2687253 Score: 85
Period size: 9 Copynumber: 10.4 Consensus size: 9
2687144 AAAATAAAAG
2687154 AAATTATAAA
1 AAATTAT-AA
2687164 AAATTAT-A
1 AAATTATAA
*
2687172 AAATTATTA
1 AAATTATAA
2687181 AAATATATAA
1 AAAT-TATAA
*
2687191 AAAATATAA
1 AAATTATAA
2687200 TTAAATTGATAGA
1 --AAATT-ATA-A
*
2687213 AAGTTATAA
1 AAATTATAA
2687222 AAATTATAAA
1 AAATTAT-AA
*
2687232 AAATAATAA
1 AAATTATAA
*
2687241 ATATTATAA
1 AAATTATAA
2687250 AAAT
1 AAAT
2687254 CAAATTAATT
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
8 8 0.11
9 29 0.39
10 25 0.34
11 8 0.11
12 3 0.04
13 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
AAATTATAA
Found at i:2687193 original size:19 final size:19
Alignment explanation
Indices: 2687154--2687253 Score: 50
Period size: 19 Copynumber: 5.2 Consensus size: 19
2687144 AAAATAAAAG
*
2687154 AAATTA-TAAAAAAT-TATA
1 AAATTATTAAAATATATA-A
2687172 AAATTATTAAAATATATAAA
1 AAATTATTAAAATATAT-AA
2687192 AAATATAATT-AAAT-TGATAGA
1 AAAT-T-ATTAAAATAT-ATA-A
* *
2687213 AAGTTATAAAAAT-TATAA
1 AAATTATTAAAATATATAA
* *
2687231 AAAATAAT-AAATATTATAA
1 AAATTATTAAAATA-TATAA
2687250 AAAT
1 AAAT
2687254 CAAATTAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
17 4 0.06
18 11 0.17
19 20 0.31
20 14 0.22
21 12 0.19
22 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATTATTAAAATATATAA
Found at i:2687253 original size:58 final size:58
Alignment explanation
Indices: 2687152--2687261 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 58
2687142 ATAAAATAAA
* *
2687152 AGAAATTATAAAAAATTATAAAATTATTAAAATATATAAAAAAT-ATAATTAAATTGAT
1 AGAAATTATAAAAAATTATAAAAATAATAAAATATATAAAAAATCA-AATTAAATTGAT
2687210 AGAAAGTTAT-AAAAATTATAAAAAATAAT-AAATAT-TATAAAAATCAAATTAA
1 AGAAA-TTATAAAAAATTAT-AAAAATAATAAAATATATA-AAAAATCAAATTAA
2687262 TTCTAATAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
57 2 0.04
58 32 0.70
59 12 0.26
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.32
Consensus pattern (58 bp):
AGAAATTATAAAAAATTATAAAAATAATAAAATATATAAAAAATCAAATTAAATTGAT
Found at i:2687332 original size:21 final size:21
Alignment explanation
Indices: 2687308--2687353 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2687298 AAACATATTT
2687308 AAAA-TCTTATAAAAGCGTATA
1 AAAATTCTT-TAAAAGCGTATA
* *
2687329 AAAATTCTTTAAAATCTTATA
1 AAAATTCTTTAAAAGCGTATA
2687350 AAAA
1 AAAA
2687354 GTTCAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAATTCTTTAAAAGCGTATA
Found at i:2687553 original size:17 final size:18
Alignment explanation
Indices: 2687516--2687553 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2687506 GTTTGAATCG
*
2687516 TTTTTACTTTTTTAGTAT
1 TTTTTACTTTTTTAATAT
*
2687534 TTTTTA-TTTTTTAATGT
1 TTTTTACTTTTTTAATAT
2687551 TTT
1 TTT
2687554 ATTTAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTTACTTTTTTAATAT
Found at i:2688087 original size:43 final size:43
Alignment explanation
Indices: 2688018--2688115 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
2688008 TGCAGGGAAC
* * * *
2688018 ACACGCCCGTATGGTCAGGCCGTGTGGCTCACACGGCCAATAA
1 ACACGCCTGTGTGGTCAAGCCATGTGGCTCACACGGCCAATAA
*
2688061 ACACGCCTGTGTGGTCAAGCCATGTGGCTTACACGGCCAATAA
1 ACACGCCTGTGTGGTCAAGCCATGTGGCTCACACGGCCAATAA
2688104 ACACGCCTGTGT
1 ACACGCCTGTGT
2688116 TTCAGGTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.19
Consensus pattern (43 bp):
ACACGCCTGTGTGGTCAAGCCATGTGGCTCACACGGCCAATAA
Found at i:2691385 original size:20 final size:20
Alignment explanation
Indices: 2691343--2691386 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2691333 TATTATATTA
* * *
2691343 TTTATATGTTTTAATGAATT
1 TTTATAAGTTTTAATAAAAT
*
2691363 TTTATAAGTTTTTATAAAAT
1 TTTATAAGTTTTAATAAAAT
2691383 TTTA
1 TTTA
2691387 AATATATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTATAAGTTTTAATAAAAT
Found at i:2691474 original size:9 final size:9
Alignment explanation
Indices: 2691272--2691476 Score: 60
Period size: 9 Copynumber: 21.0 Consensus size: 9
2691262 ATTTTTAATG
*
2691272 TTTTTATGA
1 TTTTTATAA
*
2691281 TCTTTATAAA
1 TTTTTAT-AA
2691291 TTTTTTAGTAA
1 -TTTTTA-TAA
**
2691302 TTTGGATAA
1 TTTTTATAA
*
2691311 TATCTTATAA
1 T-TTTTATAA
*
2691321 TTTATTAGAA
1 TTT-TTATAA
2691331 TTTATTAT-A
1 TTT-TTATAA
2691340 TTATTTAT-A
1 TT-TTTATAA
2691349 TGTTTTAATGAA
1 T-TTTT-AT-AA
2691361 TTTTTATAA
1 TTTTTATAA
2691370 GTTTTTATAAAA
1 -TTTTTAT--AA
*
2691382 TTTTAAATATA
1 TTTT-TATA-A
2691393 TTTTT-TAA
1 TTTTTATAA
2691401 TATTTT-TAA
1 T-TTTTATAA
* *
2691410 TTTTCAATAG
1 TTTT-TATAA
* *
2691420 TTTTGATGA
1 TTTTTATAA
2691429 TTTATTAT-A
1 TTT-TTATAA
*
2691438 TATTTATAA
1 TTTTTATAA
**
2691447 TTTTTTTTATTT
1 ---TTTTTATAA
2691459 TTTTTATAA
1 TTTTTATAA
2691468 TTTTTATAA
1 TTTTTATAA
2691477 GTTTATACCA
Statistics
Matches: 148, Mismatches: 25, Indels: 46
0.68 0.11 0.21
Matches are distributed among these distances:
8 9 0.06
9 60 0.41
10 46 0.31
11 20 0.14
12 13 0.09
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:2691622 original size:25 final size:24
Alignment explanation
Indices: 2691589--2691659 Score: 63
Period size: 27 Copynumber: 2.8 Consensus size: 24
2691579 TAAAATATAT
*
2691589 TTATT-TATTTATAAATTTATTAGA
1 TTATTATATTTATAAATTTATGA-A
*
2691613 TTTTTATATTTTTATAATATTTATGAA
1 TTATTATA--TTTATAA-ATTTATGAA
* *
2691640 TTATTATTTTTATAATTTTA
1 TTATTATATTTATAAATTTA
2691660 ATATTTAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
24 8 0.21
25 9 0.24
27 14 0.37
28 7 0.18
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (24 bp):
TTATTATATTTATAAATTTATGAA
Found at i:2691623 original size:8 final size:8
Alignment explanation
Indices: 2691584--2691721 Score: 57
Period size: 8 Copynumber: 16.1 Consensus size: 8
2691574 AAATTTAAAA
2691584 TATATTTAT
1 TATATTT-T
*
2691593 T-TATTTA
1 TATATTTT
*
2691600 TAAATTTAT
1 TATATTT-T
*
2691609 TAGATTTT
1 TATATTTT
2691617 TATATTTT
1 TATATTTT
*
2691625 TATAATATT
1 TAT-ATTTT
* *
2691634 TATGAATTA
1 TAT-ATTTT
2691643 T-TATTTT
1 TATATTTT
*
2691650 TATAATTT
1 TATATTTT
2691658 TA-ATATTT
1 TATAT-TTT
*
2691666 AATAATTTGTT
1 TAT-A-TT-TT
2691677 TATATTTT
1 TATATTTT
*
2691685 TTTATTTT
1 TATATTTT
2691693 TATAATTTT
1 TAT-ATTTT
*
2691702 CAATGATTTT
1 -TAT-ATTTT
2691712 TATAATTTT
1 TAT-ATTTT
2691721 T
1 T
2691722 TGTGATTTTT
Statistics
Matches: 96, Mismatches: 22, Indels: 22
0.69 0.16 0.16
Matches are distributed among these distances:
7 6 0.06
8 43 0.45
9 32 0.33
10 10 0.10
11 5 0.05
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (8 bp):
TATATTTT
Found at i:2691727 original size:19 final size:18
Alignment explanation
Indices: 2691675--2691732 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
2691665 TAATAATTTG
2691675 TTTAT-ATTTTTTT-ATT
1 TTTATAATTTTTTTGATT
**
2691691 TTTATAATTTTCAATGATT
1 TTTATAATTTT-TTTGATT
2691710 TTTATAATTTTTTGTGATT
1 TTTATAATTTTTT-TGATT
2691729 TTTA
1 TTTA
2691733 ACGTAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.15
17 5 0.15
18 1 0.03
19 23 0.68
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTATAATTTTTTTGATT
Found at i:2692113 original size:15 final size:15
Alignment explanation
Indices: 2692095--2692130 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
2692085 CTTATATACG
2692095 AAAAAGGCCAAAAAAA
1 AAAAAGG-CAAAAAAA
2692111 AAAAA-GCAAAAAAA
1 AAAAAGGCAAAAAAA
2692125 AAAAAG
1 AAAAAG
2692131 TTTCTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 13 0.68
15 1 0.05
16 5 0.26
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAGGCAAAAAAA
Found at i:2694231 original size:17 final size:17
Alignment explanation
Indices: 2694211--2694252 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2694201 AAAATTTTCA
2694211 AAAAAATAAAATAAAA-T
1 AAAAAATAAAA-AAAATT
*
2694228 AAAAATTAAAAAAAATT
1 AAAAAATAAAAAAAATT
2694245 AAAAAATA
1 AAAAAATA
2694253 GTATGAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAAATAAAAAAAATT
Found at i:2698174 original size:14 final size:14
Alignment explanation
Indices: 2698155--2698188 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2698145 TTGTTTGACT
*
2698155 GAAAATAGTTTCCG
1 GAAAATAATTTCCG
*
2698169 GAAAATAATTTCTG
1 GAAAATAATTTCCG
2698183 GAAAAT
1 GAAAAT
2698189 GACTTACTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (14 bp):
GAAAATAATTTCCG
Found at i:2704024 original size:2 final size:2
Alignment explanation
Indices: 2704017--2704061 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
2704007 ATTAAATTGG
2704017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
2704059 AT A
1 AT A
2704062 CAATTTAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2704532 original size:31 final size:31
Alignment explanation
Indices: 2704473--2704532 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2704463 TATACATGAA
*
2704473 ATATATGGAAATGATGGTACATGATATATTG
1 ATATATGGAAATGATGATACATGATATATTG
* *
2704504 ATATATTGAAATGGATGATATATG-TATAT
1 ATATATGGAAAT-GATGATACATGATATAT
2704533 GATGAAACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (31 bp):
ATATATGGAAATGATGATACATGATATATTG
Found at i:2710934 original size:23 final size:23
Alignment explanation
Indices: 2710891--2710935 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2710881 CACTTAAATA
*
2710891 ACAATAGCTCTAGAAGGAAATTG
1 ACAATAGCTCTAGAAGCAAATTG
*
2710914 ACAATAGCT-TGAGTAGCAAATT
1 ACAATAGCTCT-AGAAGCAAATT
2710936 TGAGTAACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.24
Consensus pattern (23 bp):
ACAATAGCTCTAGAAGCAAATTG
Found at i:2715573 original size:18 final size:18
Alignment explanation
Indices: 2715539--2715573 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2715529 AAATAAACAC
**
2715539 ATAATTATTCATTTAATT
1 ATAATTATTCAAATAATT
2715557 ATAATTATTCAAATAAT
1 ATAATTATTCAAATAAT
2715574 ATTATTTAAA
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:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATTATTCAAATAATT
Found at i:2726084 original size:14 final size:15
Alignment explanation
Indices: 2726065--2726093 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2726055 AACTGTTTTA
2726065 AATTAAACTA-TTTG
1 AATTAAACTACTTTG
2726079 AATTAAACTACTTTG
1 AATTAAACTACTTTG
2726094 TGTTGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (15 bp):
AATTAAACTACTTTG
Found at i:2728502 original size:26 final size:26
Alignment explanation
Indices: 2728466--2728575 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
2728456 TGATACAAAT
2728466 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2728492 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
2728518 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
2728544 TGATAATGGGTTAGGTAAATGCTT-CA
1 TGATAATAGGTTAGGTAAATG-TTCCA
2728570 TGATAA
1 TGATAA
2728576 GAATTTCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:2730235 original size:27 final size:27
Alignment explanation
Indices: 2730194--2730333 Score: 165
Period size: 27 Copynumber: 5.2 Consensus size: 27
2730184 GAGGAAGCGT
*
2730194 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
2730221 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
2730248 TCTGATGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
2730275 TCTGGTGGCCCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
2730303 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
2730329 TCTGG
1 TCTGG
2730334 CAGCCATGCT
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
26 5 0.05
27 79 0.81
28 14 0.14
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:2730281 original size:54 final size:55
Alignment explanation
Indices: 2730194--2730333 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 55
2730184 GAGGAAGCGT
* * * *
2730194 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA
* * *
2730248 TCTGATGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA
* *
2730303 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
2730334 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
54 58 0.77
55 17 0.23
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA
Found at i:2734264 original size:53 final size:53
Alignment explanation
Indices: 2734123--2734273 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
2734113 ACAAGTGTGC
* **
2734123 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
2734176 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
2734229 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
2734274 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:2737029 original size:26 final size:25
Alignment explanation
Indices: 2736990--2737056 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 25
2736980 TGATACAAAT
2736990 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
*
2737016 TGATAATGGATTAGGTAAATGTTTCA
1 TGATAATGG-TTAGGTAAATGTTCCA
2737042 TGATAATGGGTTAGG
1 TGATAAT-GGTTAGG
2737057 AGGAGAGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
25 2 0.05
26 34 0.89
27 2 0.05
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTCCA
Found at i:2737962 original size:9 final size:9
Alignment explanation
Indices: 2737950--2737999 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
2737940 TAAAAATTAA
2737950 AAAAATATT
1 AAAAATATT
2737959 AAAAATA-T
1 AAAAATATT
*
2737967 AAAATTATT
1 AAAAATATT
2737976 -AAAA-ATT
1 AAAAATATT
**
2737983 GGAAATATT
1 AAAAATATT
2737992 AAAAATAT
1 AAAAATAT
2738000 ATATTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
7 3 0.09
8 13 0.39
9 17 0.52
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATATT
Found at i:2737970 original size:17 final size:17
Alignment explanation
Indices: 2737940--2738000 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
2737930 TATTTTCTCG
*
2737940 TAAAAATTAAAAAAATAT
1 TAAAAA-TATAAAAATAT
*
2737958 TAAAAATATAAAATTAT
1 TAAAAATATAAAAATAT
**
2737975 TAAAAAT-TGGAAATAT
1 TAAAAATATAAAAATAT
2737991 TAAAAATATA
1 TAAAAATATA
2738001 TATTAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 13 0.36
17 17 0.47
18 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
TAAAAATATAAAAATAT
Found at i:2737991 original size:16 final size:16
Alignment explanation
Indices: 2737951--2738000 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
2737941 AAAAATTAAA
2737951 AAAATATTAAAAATAT
1 AAAATATTAAAAATAT
2737967 AAAATTATTAAAAAT-T
1 AAAA-TATTAAAAATAT
*
2737983 GGAAATATTAAAAATAT
1 -AAAATATTAAAAATAT
2738000 A
1 A
2738001 TATTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (16 bp):
AAAATATTAAAAATAT
Found at i:2738122 original size:15 final size:16
Alignment explanation
Indices: 2738093--2738125 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2738083 CATGTGTCTC
2738093 TATTTTTTAAGTATTT
1 TATTTTTTAAGTATTT
2738109 TATTTTTTAA-TATTT
1 TATTTTTTAAGTATTT
2738124 TA
1 TA
2738126 CTATATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TATTTTTTAAGTATTT
Found at i:2738250 original size:24 final size:24
Alignment explanation
Indices: 2738215--2738269 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
2738205 TTTTCTTTTG
2738215 ATATAAACTTATAAAAATTATTAAAA
1 ATAT-AACTTATAAAAATTA-TAAAA
*
2738241 A-ATAACTTATAAATATTATAAAA
1 ATATAACTTATAAAAATTATAAAA
2738264 ATATAA
1 ATATAA
2738270 AAATTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 6 0.22
24 18 0.67
25 2 0.07
26 1 0.04
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATAACTTATAAAAATTATAAAA
Found at i:2738270 original size:17 final size:18
Alignment explanation
Indices: 2738248--2738291 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
2738238 AAAAATAACT
*
2738248 TATAAATATT-ATAAAAA
1 TATAAAAATTAATAAAAA
*
2738265 TATAAAAATTAATAAAAT
1 TATAAAAATTAATAAAAA
2738283 TAATAAAAA
1 T-ATAAAAA
2738292 CATACTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 7 0.30
19 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TATAAAAATTAATAAAAA
Found at i:2741075 original size:14 final size:13
Alignment explanation
Indices: 2741058--2741106 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
2741048 GAAATTATTA
2741058 TATTATATCATTTT
1 TATTATATCA-TTT
*
2741072 TATTACTTATTATTT
1 TATTA--TATCATTT
2741087 TATTTATATCATTT
1 TA-TTATATCATTT
2741101 TATTAT
1 TATTAT
2741107 TAACTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 4 0.13
14 14 0.47
15 5 0.17
16 7 0.23
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATATCATTT
Found at i:2741114 original size:29 final size:31
Alignment explanation
Indices: 2741055--2741115 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 31
2741045 ATGGAAATTA
*
2741055 TTATATTATATCATTTTTATTACTTATTATT
1 TTATATTATATCATTTTTATTACTTACTATT
2741086 TTAT-TTATATCA-TTTTATTA-TTAACTATT
1 TTATATTATATCATTTTTATTACTT-ACTATT
2741115 T
1 T
2741116 ATTATGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 14 0.50
30 8 0.29
31 4 0.14
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (31 bp):
TTATATTATATCATTTTTATTACTTACTATT
Found at i:2742931 original size:29 final size:29
Alignment explanation
Indices: 2742899--2742970 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
2742889 TATCCTTATA
** * * *
2742899 AGCGAACATGTATGTGCGAACCTTACGTG
1 AGCGAACACCTATGGGCGAACCCTAAGTG
*
2742928 AGCGAACCCCTATGGGCGAACCCTAAGTG
1 AGCGAACACCTATGGGCGAACCCTAAGTG
*
2742957 AGCGAACCCCTATG
1 AGCGAACACCTATG
2742971 TGTGAACCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (29 bp):
AGCGAACACCTATGGGCGAACCCTAAGTG
Found at i:2742948 original size:14 final size:14
Alignment explanation
Indices: 2742926--2742970 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2742916 GAACCTTACG
2742926 TGAGCGAACCCCTA
1 TGAGCGAACCCCTA
*
2742940 TGGGCGAA-CCCTAA
1 TGAGCGAACCCCT-A
2742954 GTGAGCGAACCCCTA
1 -TGAGCGAACCCCTA
2742969 TG
1 TG
2742971 TGTGAACCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 4 0.15
14 10 0.38
15 8 0.31
16 4 0.15
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.16
Consensus pattern (14 bp):
TGAGCGAACCCCTA
Done.