Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 84 of 284
Found at i:27997112 original size:16 final size:17
Alignment explanation
Indices: 27997088--27997121 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27997078 AATAAAAATT
*
27997088 TTATTTAAGT-TATGTA
1 TTATGTAAGTGTATGTA
27997104 TTATGTAAGTGTATGTA
1 TTATGTAAGTGTATGTA
27997121 T
1 T
27997122 AAGTTATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (17 bp):
TTATGTAAGTGTATGTA
Found at i:27997189 original size:19 final size:19
Alignment explanation
Indices: 27997167--27997208 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
27997157 TGATATGATT
*
27997167 TATAAGTTTTGAAA-AAATA
1 TATAAATTTT-AAATAAATA
*
27997186 TATAAATTTTAAATATATA
1 TATAAATTTTAAATAAATA
27997205 TATA
1 TATA
27997209 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TATAAATTTTAAATAAATA
Found at i:28001330 original size:115 final size:114
Alignment explanation
Indices: 28001119--28001616 Score: 590
Period size: 114 Copynumber: 4.4 Consensus size: 114
28001109 TTAGGTTTTT
* * * * * * *
28001119 GCGGCGCTTTACTT-AAAACGCCGCTAAATAACCCGAAAACTAAGAAAACGGCGTCGTTGCGTTT
1 GCGGCGCTTTA-TTAAAAACGCCGCTAAAT-CCCCGAAAGCTCACAAAACGGCATCGTTGGGCTT
* * * **
28001183 A-GTTTTTTTAGTGGCGCTTT-TGAGCAAACGCCGCTAAAAGGTCTGAGCATTA
64 ATGTTTTTTT-GCGGCGCTTTCTCA-AAAACGCCGCT-AAAGCCCTGAGCATTA
* * *
28001235 GCGGCGCTTTATTAGAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCATTGGGCTTAG
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAT
* * * * *
28001300 GTTTTTTTGCGGCGCTTTATCAAAACCGCCGCCAAAACACTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
28001349 GCGGCGCTTTACTAAAAACGCCGCTAAATTCCCGAAAGCTCACAAAACGACATCGTTGGGCATAT
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAT
*
28001414 GTTTTTTTGCGGCGCTTTCTCAAAAACGCTGCTAAAGCCCTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * * *
28001463 GCGGCGCTTTATAAAAAACGCCGCTAAATCCCC-AAATGCTCAGAGAATGGCATCGTTGGGATTA
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAA-GCTCACAAAACGGCATCGTTGGGCTTA
* *
28001527 TGTTTTTTTGCGGCGCTTGCTTAAAAACGCCGCTAAAGCCCTGAGCATTA
65 TGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
28001577 GCGGCGATTTCTTACAAACGCCGCTAAATCCCCAAAAGCT
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCT
28001617 GAGGGAATGC
Statistics
Matches: 331, Mismatches: 46, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
113 3 0.01
114 244 0.74
115 49 0.15
116 35 0.11
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAT
GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:28003432 original size:42 final size:44
Alignment explanation
Indices: 28003385--28003495 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 44
28003375 GTCTTAAACT
* *
28003385 GTGTAACTCACTGACTTAGTTCACACAACAG-TATGT-CAGGCC
1 GTGTAACTCACTGACTTAGTTCACACAACAGCCATGTCCAGACC
* *
28003427 GTGTAACTCTCTGACTT-GAT-ACAC-ACAGCCATGTCGCAGACC
1 GTGTAACTCACTGACTTAGTTCACACAACAGCCATGTC-CAGACC
* * *
28003469 GTGTAACTCACTAACTTAATACACACA
1 GTGTAACTCACTGACTTAGTTCACACA
28003496 GCCTTGTCGC
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
39 4 0.07
40 8 0.15
41 2 0.04
42 36 0.67
44 4 0.07
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (44 bp):
GTGTAACTCACTGACTTAGTTCACACAACAGCCATGTCCAGACC
Found at i:28003496 original size:42 final size:42
Alignment explanation
Indices: 28003425--28003512 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
28003415 GTATGTCAGG
* * * *
28003425 CCGTGTAACTCTCTGACTTGATACACACAGCCATGTCGCAGA
1 CCGTGTAACTCACTAACTTAATACACACAGCCATGTCGCAAA
*
28003467 CCGTGTAACTCACTAACTTAATACACACAGCCTTGTCGCAAA
1 CCGTGTAACTCACTAACTTAATACACACAGCCATGTCGCAAA
28003509 CCGT
1 CCGT
28003513 ATACGGGCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (42 bp):
CCGTGTAACTCACTAACTTAATACACACAGCCATGTCGCAAA
Found at i:28006295 original size:21 final size:22
Alignment explanation
Indices: 28006271--28006312 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28006261 ATGAGGTCTT
*
28006271 AAAATCGATGGA-AACAAGAAG
1 AAAATCGATGGAGAAAAAGAAG
*
28006292 AAAATTGATGGAGAAAAAGAA
1 AAAATCGATGGAGAAAAAGAA
28006313 TTTAGTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.05, G:0.24, T:0.12
Consensus pattern (22 bp):
AAAATCGATGGAGAAAAAGAAG
Found at i:28007757 original size:10 final size:10
Alignment explanation
Indices: 28007725--28007749 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28007715 CTCAATAAAC
28007725 AAAAAAAGAA
1 AAAAAAAGAA
28007735 AAAAAAAGAA
1 AAAAAAAGAA
28007745 AAAAA
1 AAAAA
28007750 GGGAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:28007998 original size:3 final size:3
Alignment explanation
Indices: 28007990--28008019 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28007980 TCTCTGATTC
28007990 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
28008020 CTCTATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:28041899 original size:56 final size:55
Alignment explanation
Indices: 28041806--28041917 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 55
28041796 ATATGGAGTG
* *
28041806 TCAAAATCAATGCATGAATATGTGTGTTTGAGGACAACATATTGGACTGAACCGC
1 TCAAAATCAATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGAACCGC
*
28041861 NTCAAAATCAATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGACCCGC
1 -TCAAAATCAATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGAACCGC
28041917 T
1 T
28041918 ATGAGTATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 1 0.02
56 52 0.98
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (55 bp):
TCAAAATCAATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGAACCGC
Found at i:28048343 original size:28 final size:27
Alignment explanation
Indices: 28048279--28048430 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
28048269 TTATTAAGTC
* *
28048279 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
28048306 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
28048334 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
28048361 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
28048389 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
28048416 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28048431 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28048363 original size:55 final size:55
Alignment explanation
Indices: 28048279--28048455 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
28048269 TTATTAAGTC
* * *
28048279 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
28048334 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
28048389 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
28048445 CGCACACTTAG
1 CGCACACTTAG
28048456 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:28066750 original size:204 final size:205
Alignment explanation
Indices: 28066474--28066972 Score: 716
Period size: 204 Copynumber: 2.4 Consensus size: 205
28066464 CGGGGAGCAG
* * * * * * * *
28066474 ATCGAAGATATAGCTGATTTTGCTTTCACGTATTTACGATGAAGCAAATCCAAGATGATTTGTCG
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTACTTACGTTAAAGCAAATCTAAGATGATTTGGCA
* * * * *
28066539 TCTCTGTAGTGTCAAAGAACAAATCGAAGTCTGGCATCTCTACTTCAAT-AGAGAGCAGATACAT
66 TCTCTGTATTGTCAGAGAACAAATCCAAGTCTGGCATCTCCACTTCAATGA-AGAGCAGACACAT
* * * *
28066603 AGCAGATCTC-ACCTTCAGATGTTTATGCTGAAGCAGATCCGAGATGGTTTGGTATCCTTGTACT
130 AGCAGATC-CAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTAGCATCCTTGTACT
28066667 TACAAGGAACAA
194 TACAAGGAACAA
*
28066679 ATCGAAGACATAGCTGATTTGGCTTTCACG-GCTTACGTTAAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTACTTACGTTAAAGCAAATCTAAGATGATTTGGCA
* * *
28066743 TCTCTGTATTGTCAGAGAACAAATCCAAGTCTGGCATCTCCACTTCGATGAAGGGTAGACACATA
66 TCTCTGTATTGTCAGAGAACAAATCCAAGTCTGGCATCTCCACTTCAATGAAGAGCAGACACATA
* *
28066808 GTAGATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTAGCATCCTTGTGCTTA
131 GCAGATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTAGCATCCTTGTACTTA
*
28066873 CAAGGAGCAA
196 CAAGGAACAA
* *
28066883 ATCGAAGACGTAGCTGATTTGGCTTTCACGTACTTAAGTTAAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTACTTACGTTAAAGCAAATCTAAGATGATTTGGCA
*
28066948 TCTCTGTATTGTCAGGGAACAAATC
66 TCTCTGTATTGTCAGAGAACAAATC
28066973 AAAGAAGCAG
Statistics
Matches: 263, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
203 1 0.00
204 177 0.67
205 85 0.32
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (205 bp):
ATCGAAGACATAGCTGATTTGGCTTTCACGTACTTACGTTAAAGCAAATCTAAGATGATTTGGCA
TCTCTGTATTGTCAGAGAACAAATCCAAGTCTGGCATCTCCACTTCAATGAAGAGCAGACACATA
GCAGATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTAGCATCCTTGTACTTA
CAAGGAACAA
Found at i:28067127 original size:45 final size:45
Alignment explanation
Indices: 28067070--28067155 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
28067060 GAAGAAGCAA
* *
28067070 ATTTGGCATCTCTATATTAGACGAGGAGCAGATCGAAGATAACAG
1 ATTTGGCATCTCTATATTAGACGAGGAGCACATCAAAGATAACAG
* * *
28067115 ATTTGGCGTCTCTGTATTAGACGGGGAGCACATCAAAGATA
1 ATTTGGCATCTCTATATTAGACGAGGAGCACATCAAAGATA
28067156 GTAGATATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (45 bp):
ATTTGGCATCTCTATATTAGACGAGGAGCACATCAAAGATAACAG
Found at i:28068100 original size:28 final size:29
Alignment explanation
Indices: 28068062--28068127 Score: 125
Period size: 28 Copynumber: 2.3 Consensus size: 29
28068052 AGGGGTTAGT
28068062 TTTTTTTTTATGAAATGGGGAAAATGA-G
1 TTTTTTTTTATGAAATGGGGAAAATGAGG
28068090 TTTTTTTTTATGAAATGGGGAAAATGAGG
1 TTTTTTTTTATGAAATGGGGAAAATGAGG
28068119 TTTTTTTTT
1 TTTTTTTTT
28068128 TACGGAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (29 bp):
TTTTTTTTTATGAAATGGGGAAAATGAGG
Found at i:28068566 original size:88 final size:90
Alignment explanation
Indices: 28068463--28068654 Score: 343
Period size: 88 Copynumber: 2.2 Consensus size: 90
28068453 ATAAGCCCCT
28068463 TTTTTATTTTTAATTTGCCCCAAAACTTCGTTTTTAATTTGAATTTAGTCTTTTTTTTAATTTAA
1 TTTTTATTTTTAATTTGCCCCAAAACTTCGTTTTTAATTTGAATTTAGTCTTTTTTTTAATTTAA
28068528 GTTGATTTTTATATTATCTTTG-C-
66 GTTGATTTTTATATTATCTTTGCCA
*
28068551 TTTTTATTTTTAATTTGCCCCAAAACTTTGTTTTTAATTTGAATTTAGTCTTTTTTTTAATTTAA
1 TTTTTATTTTTAATTTGCCCCAAAACTTCGTTTTTAATTTGAATTTAGTCTTTTTTTTAATTTAA
*
28068616 GTTGATTTTTATATTATTTTTGCCA
66 GTTGATTTTTATATTATCTTTGCCA
*
28068641 TTTTAATTTTTAAT
1 TTTTTATTTTTAAT
28068655 ATTAGTTCCA
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
88 85 0.86
89 1 0.01
90 13 0.13
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (90 bp):
TTTTTATTTTTAATTTGCCCCAAAACTTCGTTTTTAATTTGAATTTAGTCTTTTTTTTAATTTAA
GTTGATTTTTATATTATCTTTGCCA
Found at i:28077183 original size:3 final size:3
Alignment explanation
Indices: 28077163--28077353 Score: 78
Period size: 3 Copynumber: 64.3 Consensus size: 3
28077153 GGGAGAGTGC
* * * *
28077163 TAT TTT TAT TAT TGT TAT TA- TAT TAG TAT TAT TAT TAT T-T TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
28077209 TAT TAT TAT TAT TATT TAT TA- CATT TAC TAT TAT T-C TAT ATAA TAT
1 TAT TAT TAT TAT TA-T TAT TAT TA-T TAT TAT TAT TAT TAT -TAT TAT
* * * * * * * *
28077255 TAC TGT T-T TCT T-T TAT TAT TAT TAT TAG TAG TAGT GACG TAA TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TA-T
**
28077301 GCT T-T T-T TAT T-T TAT TAT TAT T-T TACCT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT
28077344 TAT TAT TAT T
1 TAT TAT TAT T
28077354 TTAAAACCAT
Statistics
Matches: 142, Mismatches: 30, Indels: 32
0.70 0.15 0.16
Matches are distributed among these distances:
2 18 0.13
3 113 0.80
4 8 0.06
5 3 0.02
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:28077192 original size:20 final size:20
Alignment explanation
Indices: 28077169--28077223 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
28077159 GTGCTATTTT
* *
28077169 TATTATTGTTATTATATTAG
1 TATTATTATTATTATATTAC
*
28077189 TATTATTATTATTTTATTAC
1 TATTATTATTATTATATTAC
28077209 TATTATTATTATTAT
1 TATTATTATTATTAT
28077224 TTATTACATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (20 bp):
TATTATTATTATTATATTAC
Found at i:28077710 original size:3 final size:3
Alignment explanation
Indices: 28077673--28077724 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
28077663 TAAGCTTTAG
* * *
28077673 ATT ACTT ATT ATT -TAT ATT AAT ATT ATC ATC ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28077719 ATT ATT
1 ATT ATT
28077725 TAGACTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 1 0.02
3 37 0.88
4 4 0.10
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:28079669 original size:19 final size:19
Alignment explanation
Indices: 28079645--28079690 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
28079635 CTCTTTTTCT
28079645 TTTGCATT-CATTCCATGCA
1 TTTGCATTGCATTCCAT-CA
*
28079664 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTCCATCA
28079683 TTTGCATT
1 TTTGCATT
28079691 AGATTTTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.46
Consensus pattern (19 bp):
TTTGCATTGCATTCCATCA
Found at i:28084119 original size:44 final size:44
Alignment explanation
Indices: 28083952--28084532 Score: 209
Period size: 44 Copynumber: 13.2 Consensus size: 44
28083942 TTCGACTAGC
*
28083952 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCGC-GAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGCAG-AT
* * * * * ** *
28083996 CTTATCTCCATGTAGCAGCAATGGAGTAGATTTAAGCCACT--AG-C
1 CTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAG--ACTGCAGAT
* * * *
28084040 CTTATCTCCCTAAGCAGTAGTGAAACAG-GCTGAAGATTGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGACTGCAGAT
* *
28084084 CTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGGC-GAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGCAG-AT
* * * * ** *
28084128 CTTATCTCCATATAACAGCAATGGAGCAGATTTAAGCCACT--AG-C
1 CTTATCTCCCTA-AGCAGTAGTGGAGCAGATCGAAG--ACTGCAGAT
* * ** * * *
28084172 CTTATCTCTCTAAGCAGTAGTGGAAC-GGGCTGATGATTGCAGTT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGACTGCAGAT
* * *
28084216 TTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGC-GAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGCAG-AT
* **
28084260 CTTATCTCCATGTAACGACA--A-TGGAGCAGATTTAAGCCACT--AG-T
1 CTTATCTCC--CTAA-G-CAGTAGTGGAGCAGATCGAAG--ACTGCAGAT
* * * ** * *
28084304 TTTATCTCCCCAAGCAGTAGTGGAAC-GGGCTGAAAATTGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGACTGCAGAT
* *
28084348 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGC-GAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGCAG-AT
* * * * * ** * *
28084392 CTTATCTCCATGTAGCAGCAATAGAGCAGATTTAAGTC-GCTAG-C
1 CTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGACTGC-AGAT
* ** * * *
28084436 CTTATCTCCCTAAGCAGTAGTGGAAC-GGGCTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGACTGCAGAT
* * * ** *
28084480 CTTATCTTCCTAAGCAGCAGTGGAGTAGATTAAAGAC-GAAGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGCAG-AT
28084524 CTTATCTCC
1 CTTATCTCC
28084533 ATGTACCGAC
Statistics
Matches: 374, Mismatches: 119, Indels: 88
0.64 0.20 0.15
Matches are distributed among these distances:
40 2 0.01
41 7 0.02
42 6 0.02
43 58 0.16
44 210 0.56
45 74 0.20
46 8 0.02
47 7 0.02
48 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGCAGAT
Found at i:28084754 original size:132 final size:132
Alignment explanation
Indices: 28083952--28084708 Score: 1113
Period size: 132 Copynumber: 5.7 Consensus size: 132
28083942 TTCGACTAGC
*
28083952 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCGCGAATCTTATCTCCATGTAGCAGCAA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAGCAA
* * * * *
28084017 TGGAGTAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGAAACAGGCTGAAGATTGCAG
66 TGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTACAG
28084082 AT
131 AT
* * *
28084084 CTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATATAACAGCAA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAGCAA
* ** *
28084149 TGGAGCAGATTTAAGCCACTAGCCTTATCTCTCTAAGCAGTAGTGGAACGGGCTGATGATTGCAG
66 TGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTACAG
*
28084214 TT
131 AT
* * * *
28084216 TTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTCCATGTAAC-GACA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAG-CA
** * *
28084280 ATGGAGCAGATTTAAGCCACTAGTTTTATCTCCCCAAGCAGTAGTGGAACGGGCTGAAAATTGCA
65 ATGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTACA
28084345 GAT
130 GAT
*
28084348 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAGCAA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAGCAA
* * *
28084413 TAGAGCAGATTTAAGTCGCTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTACAG
66 TGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTACAG
28084478 AT
131 AT
* * * ** ** *
28084480 CTTATCTTCCTAAGCAGCAGTGGAGTAGATTAAAGACGAAGAATCTTATCTCCATGTA-CCGACA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAG-CA
* * *
28084544 ATGGAGCAGATTTAAGCCATTAGCCTTATCTCCGTAAGCAGTAGTGGAACGGGCTAAAAATTACA
65 ATGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTACA
28084609 GAT
130 GAT
* * *
28084612 CTTATCTCCCTAAGCCGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTCCATGTAGCGGCAA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAGCAA
*
28084677 TGGAGCAGATTTAAGCCACCAGCCTTATCTCC
66 TGGAGCAGATTTAAGCCACTAGCCTTATCTCC
28084709 TTGAAGTTGC
Statistics
Matches: 564, Mismatches: 57, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
131 3 0.01
132 558 0.99
133 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (132 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAGCAA
TGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTACAG
AT
Found at i:28084817 original size:396 final size:396
Alignment explanation
Indices: 28083952--28084818 Score: 945
Period size: 396 Copynumber: 2.2 Consensus size: 396
28083942 TTCGACTAGC
* * * * * * * * * * *
28083952 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCGCGAATCTTATCTCCATGTAGCAGCAA
1 CTTATCTCCCTAAACAGCAGTGAAGCAGACCAAAAACGGAGAATATTATCTCCATGAAACAGCAA
* * * *
28084017 TGGAGTAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGAAACAGGCTGAAGATTGCAG
66 CGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGAAACAGGCTGAAAATTACAG
* * **
28084082 ATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATATAACAGC
131 ATCTTATCTCCCTAAACAGCAGTGGAGCAGATCAAAGACGAAGAATCTTATCTCCATATAACAGC
* ** *
28084147 AATGGAGCAGATTTAAGCCACTAGCCTTATCTCTCTAAGCAGTAGTGGAACGGGCTGATGATTGC
196 AATGGAGCAGATTTAAGCCACTAGCCTTATCTCTCTAAGCAGTAGTGGAACGGGCTAAAAATTAC
* * *
28084212 AGTTTTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTCCATGTAACG
261 AGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGACAGCGAATCTTATCTCCATGTAACG
* ** * * *
28084277 ACAATGGAGCAGATTTAAGCCACTAGTTTTATCTCCCCAAGCAGTAGTGGAACGGGCTGAAAATT
326 ACAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCCAAGCAGCAGTGGAACAGGCTCAAAATT
*
28084342 GCAGAT
391 ACAGAT
* * * * * * * * * * *
28084348 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTCCATGTAGCAGCAA
1 CTTATCTCCCTAAACAGCAGTGAAGCAGACCAAAAACGGAGAATATTATCTCCATGAAACAGCAA
** * * * *
28084413 TAGAGCAGATTTAAGTCGCTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTACAG
66 CGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGAAACAGGCTGAAAATTACAG
* * * * * *
28084478 ATCTTATCTTCCTAAGCAGCAGTGGAGTAGATTAAAGACGAAGAATCTTATCTCCATGT-ACCGA
131 ATCTTATCTCCCTAAACAGCAGTGGAGCAGATCAAAGACGAAGAATCTTATCTCCATATAACAG-
*
28084542 CAATGGAGCAGATTTAAGCCATTAGCCTTATCTC-CGTAAGCAGTAGTGGAACGGGCTAAAAATT
195 CAATGGAGCAGATTTAAGCCACTAGCCTTATCTCTC-TAAGCAGTAGTGGAACGGGCTAAAAATT
** * *
28084606 ACAGATCTTATCTCCCTAAGCCGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTCCATGTAG
259 ACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGACAGCGAATCTTATCTCCATGTAA
* ** ** * * *
28084671 CGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTCAAG
324 CGACAATGGAGCAGATTTAAGCCACCAGCCTTATCTCC-CCAAGCAGCAGTGGAACAGGCTCAAA
28084736 A-TACA-AGT
388 ATTACAGA-T
** * * * * *
28084744 CTTATCTCCCTGAAATTGCAGTGAAGCGGACCAAAAATTGTAG-ATATTATCTCCCT-AAACAGT
1 CTTATCTCCCT-AAACAGCAGTGAAGCAGACCAAAAA-CGGAGAATATTATCTCCATGAAACAGC
*
28084807 AGCGGAGCAGAT
64 AACGGAGCAGAT
28084819 CGAAAACGAT
Statistics
Matches: 397, Mismatches: 68, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
395 5 0.01
396 347 0.87
397 43 0.11
398 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (396 bp):
CTTATCTCCCTAAACAGCAGTGAAGCAGACCAAAAACGGAGAATATTATCTCCATGAAACAGCAA
CGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGAAACAGGCTGAAAATTACAG
ATCTTATCTCCCTAAACAGCAGTGGAGCAGATCAAAGACGAAGAATCTTATCTCCATATAACAGC
AATGGAGCAGATTTAAGCCACTAGCCTTATCTCTCTAAGCAGTAGTGGAACGGGCTAAAAATTAC
AGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGACAGCGAATCTTATCTCCATGTAACG
ACAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCCAAGCAGCAGTGGAACAGGCTCAAAATT
ACAGAT
Found at i:28084818 original size:264 final size:261
Alignment explanation
Indices: 28084014--28084803 Score: 919
Period size: 264 Copynumber: 3.0 Consensus size: 261
28084004 CATGTAGCAG
* * * *
28084014 CAATGGAGTAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGAAACAGGCTGAAGATTG
1 CAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTG
* * *
28084079 CAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATATAAC
66 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGC
*
28084144 AGCAATGGAGCAGATTTAAGCCACTAGCCTTATCT-CTCTAAGCAGTAGTGGAACGGGCTGATGA
131 AGCAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCT-TAAGCAGTAGTGGAACGGGCTGAAGA
* * * * *
28084208 TTGCAGTTTTTATCTCCCTAAGCAAT--AGTGGAGCAGATCGAAGACAGCGA-ATCTTATCTCCA
195 TTACAGATCTTATCTCCCTAA--AATGCAGTGGAGCAGA-CCAA-A-AACGAGATCTTATCTCCA
*
28084270 TGTAACGA
255 T-AAACGA
** *
28084278 CAATGGAGCAGATTTAAGCCACTAGTTTTATCTCCCCAAGCAGTAGTGGAACGGGCTGAAAATTG
1 CAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTG
*
28084343 CAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTCCATGTAGC
66 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGC
* * * * *
28084408 AGCAATAGAGCAGATTTAAGTCGCTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAAT
131 AGCAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCTTAAGCAGTAGTGGAACGGGCTGAAGAT
* * * ** * *
28084473 TACAGATCTTATCTTCCTAAGCA-GCAGTGGAGTAGATTAAAGACGAAGAATCTTATCTCCATGT
196 TACAGATCTTATCTCCCTAA-AATGCAGTGGAGCAGACCAAAAACG-AG-ATCTTATCTCCAT-A
*
28084537 ACCGA
257 AACGA
* * * *
28084542 CAATGGAGCAGATTTAAGCCATTAGCCTTATCTCCGTAAGCAGTAGTGGAACGGGCTAAAAATTA
1 CAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTG
* *
28084607 CAGATCTTATCTCCCTAAGCCGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTCCATGTAGC
66 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGC
* * ** * * * * *
28084672 GGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTCAAGA
131 AGCAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCTT-AAGCAGTAGTGGAACGGGCTGAAGA
* * * * * *
28084737 -TACA-AGTCTTATCTCCCTGAAATTGCAGTGAAGCGGACCAAAAATTGTAGATATTATCTCCCT
195 TTACAGA-TCTTATCTCCCT-AAAATGCAGTGGAGCAGACCAAAAA-CG-AGATCTTATCTCCAT
28084800 AAAC
256 AAAC
28084804 AGTAGCGGAG
Statistics
Matches: 447, Mismatches: 68, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
261 2 0.00
262 2 0.00
263 4 0.01
264 391 0.87
265 45 0.10
266 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (261 bp):
CAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTAAGCAGTAGTGGAACGGGCTGAAAATTG
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTCCATGTAGC
AGCAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCTTAAGCAGTAGTGGAACGGGCTGAAGAT
TACAGATCTTATCTCCCTAAAATGCAGTGGAGCAGACCAAAAACGAGATCTTATCTCCATAAACG
A
Found at i:28084835 original size:177 final size:177
Alignment explanation
Indices: 28084599--28084943 Score: 534
Period size: 177 Copynumber: 1.9 Consensus size: 177
28084589 GGAACGGGCT
* * * * *
28084599 AAAAATTACAGATCTTATCTCCCTAAGCCGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTC
1 AAAAATTACAGATATTATCTCCCTAAACAGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTC
* *
28084664 CATGTAGCGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTC-CTTGAAGTTGCAGTGGAGCA
66 CATGTAGCGGCAATGGAGCAGATTTAAACCACCAGCCTTATCTCTC-TGAAGTTGCAGTAGAGCA
28084728 GGTTCAAGATACAAGTCTTATCTCCCTGAAA-TTGCAGTGAAGCGGACC
130 GGTTCAAGATACAAGTCTTATCTCCCT-AAAGTTGCAGTGAAGCGGACC
** *
28084776 AAAAATTGTAGATATTATCTCCCTAAACAGTAGCGGAGCAGATCGAAA-ACGATGAATCTTATCT
1 AAAAATTACAGATATTATCTCCCTAAACAGTAGCGGAGCAGATC-AAAGACGACGAATCTTATCT
* *
28084840 CCATGTAGCGGCAATGGAGCAGATTTAAATCACCAGCCTTATCTCTCTGAGGTTGCAGTAGAGCA
65 CCATGTAGCGGCAATGGAGCAGATTTAAACCACCAGCCTTATCTCTCTGAAGTTGCAGTAGAGCA
28084905 GGTTCAAGATACAAGTCTTATCTCCCTAAAGTTGCAGTG
130 GGTTCAAGATACAAGTCTTATCTCCCTAAAGTTGCAGTG
28084944 GAGCAGCCTG
Statistics
Matches: 153, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
176 3 0.02
177 146 0.95
178 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (177 bp):
AAAAATTACAGATATTATCTCCCTAAACAGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTC
CATGTAGCGGCAATGGAGCAGATTTAAACCACCAGCCTTATCTCTCTGAAGTTGCAGTAGAGCAG
GTTCAAGATACAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCGGACC
Found at i:28085001 original size:45 final size:44
Alignment explanation
Indices: 28084677--28085001 Score: 156
Period size: 44 Copynumber: 7.3 Consensus size: 44
28084667 GTAGCGGCAA
* ** * * *
28084677 TGGAGCAGATTTAAGCCACCAGCCTTATCTCCTTGAAGTTGCAG
1 TGGAGCAGATTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
* * *
28084721 TGGAGCAGGTTCAAGATACAAGTCTTATCTCCCTGAAATTGCAG
1 TGGAGCAGATTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
* * *** * *** * *** *
28084765 TGAAGCGGACCAAAAATTGTAGATATTATCTCCCT-AAACAGTAG
1 TGGAGCAGATTGAAGATACAAG-TCTTATCTCCCTGAAGTTGCAG
* * * * * ** *
28084809 CGGAGCAGATCGAA-A-ACGATGAATCTTATCTCCATGTAGCGGCAA
1 TGGAGCAGATTGAAGATAC-A--AGTCTTATCTCCCTGAAGTTGCAG
* * * * *
28084854 TGGAGCAGATTTAA-ATCACCAGCCTTATCTCTCTGAGGTTGCAG
1 TGGAGCAGATTGAAGAT-ACAAGTCTTATCTCCCTGAAGTTGCAG
* * * *
28084898 TAGAGCAGGTTCAAGATACAAGTCTTATCTCCCTAAAGTTGCAG
1 TGGAGCAGATTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
**
28084942 TGGAGCAGCCTGAAGATAGC-AGATCTTATCTCCCTGAAGTTGCAG
1 TGGAGCAGATTGAAGATA-CAAG-TCTTATCTCCCTGAAGTTGCAG
* *
28084987 CGGAGTAGATTGAAG
1 TGGAGCAGATTGAAG
28085002 CTATAAATCT
Statistics
Matches: 203, Mismatches: 68, Indels: 19
0.70 0.23 0.07
Matches are distributed among these distances:
43 1 0.00
44 137 0.67
45 63 0.31
47 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
TGGAGCAGATTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
Found at i:28085985 original size:29 final size:30
Alignment explanation
Indices: 28085953--28086031 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
28085943 TCTAAAACTA
** *
28085953 TTATTATTTATCTATTTTTTAT-TTTTTAT
1 TTATTATTTATCTATTTACTATATTTCTAT
28085982 TTA-TATTTATACTA-TTACTATATTTCTAT
1 TTATTATTTAT-CTATTTACTATATTTCTAT
28086011 TTATTATATT-TCTATTT-CTAT
1 TTATTAT-TTATCTATTTACTAT
28086032 TTATATACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
28 12 0.29
29 22 0.52
30 6 0.14
31 2 0.05
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (30 bp):
TTATTATTTATCTATTTACTATATTTCTAT
Found at i:28085996 original size:43 final size:45
Alignment explanation
Indices: 28085949--28086066 Score: 129
Period size: 43 Copynumber: 2.7 Consensus size: 45
28085939 TTATTCTAAA
* *
28085949 ACTATTATTATTTATCTATTTTTTAT-TTTTTATTTATA-TT-TAT
1 ACTATTATTATTT-TCTATTTATTATATTTCTATTTATATTTATAT
* *
28085992 ACTATTACTATATTTCTATTTATTATATTTCTATTTCTATTTATAT
1 ACTATTATTAT-TTTCTATTTATTATATTTCTATTTATATTTATAT
* *
28086038 ACTAATATTATTTTC-A-TTATTATTTTTCT
1 ACTATTATTATTTTCTATTTATTATATTTCT
28086067 TATATATGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
43 33 0.52
44 13 0.20
45 6 0.09
46 12 0.19
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.64
Consensus pattern (45 bp):
ACTATTATTATTTTCTATTTATTATATTTCTATTTATATTTATAT
Found at i:28086011 original size:23 final size:20
Alignment explanation
Indices: 28085979--28086038 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 20
28085969 TTTTATTTTT
*
28085979 TATTTATATTTATACTATTACTA
1 TATTTCTATTTATA-TATT--TA
*
28086002 TATTTCTATTTATTATATTTC
1 TATTTCTATTTA-TATATTTA
28086023 TATTTCTATTTATATA
1 TATTTCTATTTATATA
28086039 CTAATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 4 0.12
21 13 0.38
23 15 0.44
24 2 0.06
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTCTATTTATATATTTA
Found at i:28086020 original size:15 final size:14
Alignment explanation
Indices: 28085953--28086027 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 14
28085943 TCTAAAACTA
28085953 TTATTATTTATCTAT
1 TTATTATTT-TCTAT
* *
28085968 TTTTTATTTTTTAT
1 TTATTATTTTCTAT
28085982 TTA-TATTTATACTA-
1 TTATTATTT-T-CTAT
*
28085996 TTACTATATTTCTAT
1 TTATTAT-TTTCTAT
28086011 TTATTATATTTCTAT
1 TTATTAT-TTTCTAT
28086026 TT
1 TT
28086028 CTATTTATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.10
14 13 0.26
15 30 0.60
16 2 0.04
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATTTTCTAT
Found at i:28086170 original size:3 final size:3
Alignment explanation
Indices: 28086162--28086368 Score: 158
Period size: 3 Copynumber: 68.7 Consensus size: 3
28086152 TTTAAAACTT
*
28086162 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA ATA TT- TCTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA
* * * *
28086207 TTA -TA TT- TCTA TT- TCTA TTTA TGTA TTA ATA TCA TTA TTT TTT TTA
1 TTA TTA TTA T-TA TTA T-TA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
28086253 TTC TT- TTA -TA ATA TTA TTA TTA TCA TTA TTA TTA CTA TTA GTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
28086299 TTA TTTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA CTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
28086345 TTA TTA TTTA TAA TTA TCA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TT
28086369 TTTAAAAGCA
Statistics
Matches: 165, Mismatches: 25, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
2 11 0.07
3 137 0.83
4 16 0.10
5 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28086527 original size:4 final size:4
Alignment explanation
Indices: 28086513--28086542 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
28086503 TATTATTCCG
*
28086513 TTAT ATAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
28086543 TTAATACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:28092156 original size:32 final size:33
Alignment explanation
Indices: 28092110--28092172 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
28092100 TGTGATGGCT
*
28092110 CAAGTGTGGCTGTGT-GAGCTATACGGGCATGAC
1 CAAGTGTGGCTGTGTAG-GCTACACGGGCATGAC
*
28092143 CAAGT-TGGGTGTGTAGGCTACACGGGCATG
1 CAAGTGTGGCTGTGTAGGCTACACGGGCATG
28092173 TTACACGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (33 bp):
CAAGTGTGGCTGTGTAGGCTACACGGGCATGAC
Found at i:28095890 original size:28 final size:29
Alignment explanation
Indices: 28095870--28095926 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
28095860 CACCAATATC
28095870 ATATAATCC-TCCT-AAACACACCAGAATA
1 ATATAATCCAT-CTAAAACACACCAGAATA
28095898 ATATAATCCATCTAAAACACACCAGAATA
1 ATATAATCCATCTAAAACACACCAGAATA
28095927 GCACAGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.49, C:0.26, G:0.04, T:0.21
Consensus pattern (29 bp):
ATATAATCCATCTAAAACACACCAGAATA
Found at i:28096101 original size:17 final size:17
Alignment explanation
Indices: 28096079--28096117 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28096069 TTTTTTTATT
*
28096079 TCAATTTCATTTCCATA
1 TCAATTTCAATTCCATA
*
28096096 TCAATTTCAATTCCATT
1 TCAATTTCAATTCCATA
28096113 TCAAT
1 TCAAT
28096118 ATACAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (17 bp):
TCAATTTCAATTCCATA
Found at i:28096106 original size:23 final size:24
Alignment explanation
Indices: 28096076--28096124 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
28096066 ACTTTTTTTT
* *
28096076 ATTTCAATTTCATTTCCATAT-CA
1 ATTTCAATTCCATTTCAATATACA
28096099 ATTTCAATTCCATTTCAATATACA
1 ATTTCAATTCCATTTCAATATACA
28096123 AT
1 AT
28096125 CAATTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTCAATTCCATTTCAATATACA
Found at i:28100664 original size:13 final size:14
Alignment explanation
Indices: 28100641--28100674 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
28100631 CATATTAATT
28100641 TGATATTCTGTATC
1 TGATATTCTGTATC
28100655 TGAT-TTCTGTATC
1 TGATATTCTGTATC
*
28100668 TGTTATT
1 TGATATT
28100675 GGGGTGCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.56
Consensus pattern (14 bp):
TGATATTCTGTATC
Found at i:28102866 original size:14 final size:13
Alignment explanation
Indices: 28102837--28102878 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
28102827 GAAACCCTAA
*
28102837 TTTTTC-TCTTTA
1 TTTTTCTTCTTTC
28102849 TTTTTCTTTCTTTC
1 TTTTTC-TTCTTTC
28102863 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
28102876 TTT
1 TTT
28102879 CCCCTGTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 6 0.22
13 10 0.37
14 11 0.41
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:28104615 original size:41 final size:40
Alignment explanation
Indices: 28104569--28104681 Score: 106
Period size: 41 Copynumber: 2.9 Consensus size: 40
28104559 TCGACCTCAA
*
28104569 GTCGATGAGATACTGGGTGTCACTATATTTCTTCGGATAG
1 GTCGATGAGATACTGGGTGTCACTATATTACTTCGGATAG
* * * ** *
28104609 ATTCGATAAGGTACTGGGTACCAC--T-TTACTTCGGCTAG
1 -GTCGATGAGATACTGGGTGTCACTATATTACTTCGGATAG
* * *
28104647 GCCGATGAGACACTGGGTGTCACTATATTGCTTCG
1 GTCGATGAGATACTGGGTGTCACTATATTACTTCG
28104682 AACTATCCGA
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
37 16 0.30
38 11 0.20
39 2 0.04
40 7 0.13
41 18 0.33
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (40 bp):
GTCGATGAGATACTGGGTGTCACTATATTACTTCGGATAG
Found at i:28115400 original size:17 final size:17
Alignment explanation
Indices: 28115378--28115410 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28115368 ATAAGTATAC
*
28115378 ATTGTCATTGCATTTTT
1 ATTGTCATTACATTTTT
28115395 ATTGTCATTACATTTT
1 ATTGTCATTACATTTT
28115411 AGCATTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:28118181 original size:47 final size:47
Alignment explanation
Indices: 28118129--28118225 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
28118119 CATGCCATAA
28118129 GATCGAGTTCAAATATTTAACAAAATACCAAAAGAAGTCGATAGTGT
1 GATCGAGTTCAAATATTTAACAAAATACCAAAAGAAGTCGATAGTGT
*
28118176 GATCGAGTTCAATTATTTAACAAAATACCAAAAGAAGTCGATAGTGT
1 GATCGAGTTCAAATATTTAACAAAATACCAAAAGAAGTCGATAGTGT
28118223 GAT
1 GAT
28118226 GGACTGTGCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (47 bp):
GATCGAGTTCAAATATTTAACAAAATACCAAAAGAAGTCGATAGTGT
Found at i:28119015 original size:41 final size:41
Alignment explanation
Indices: 28118970--28119166 Score: 283
Period size: 41 Copynumber: 4.8 Consensus size: 41
28118960 TGATTCAGTA
*
28118970 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAATGTAT
*
28119011 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTAT
* *
28119052 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTAAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTAT
*
28119093 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TACTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTA--T
* *
28119134 CACCGGCATTAAGCCTGCTAGACGTAACGTCTG
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTG
28119167 TATTACATTC
Statistics
Matches: 147, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 140 0.95
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTAT
Found at i:28119172 original size:41 final size:40
Alignment explanation
Indices: 28118928--28119166 Score: 268
Period size: 41 Copynumber: 5.8 Consensus size: 40
28118918 TTAAACAGAT
** * ** *
28118928 TCACCGGCATTTTGCCTGCTAGGCTTAAAACCTGATTCAGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAT--GTA
* *
28118970 -CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTG-AATGTA
* *
28119010 TCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AATGTA
*
28119051 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTAAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCT-GAATGTA
28119092 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAT-TA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATGTA
* *
28119131 CTTCACCGGCATTAAGCCTGCTAGACGTAACGTCTG
1 --TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG
28119167 TATTACATTC
Statistics
Matches: 177, Mismatches: 13, Indels: 15
0.86 0.06 0.07
Matches are distributed among these distances:
39 2 0.01
40 8 0.05
41 163 0.92
42 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (40 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATGTA
Found at i:28121956 original size:28 final size:27
Alignment explanation
Indices: 28121924--28121981 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 27
28121914 TTAGATGTGA
28121924 ACAAAGAATAAGTAAATTAGTATTATTC
1 ACAAAGAATAAGTAAATTA-TATTATTC
28121952 ACAAAGAATAAGTAAATTATATTATTC
1 ACAAAGAATAAGTAAATTATATTATTC
28121979 ACA
1 ACA
28121982 TGATATACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.31
Consensus pattern (27 bp):
ACAAAGAATAAGTAAATTATATTATTC
Found at i:28128600 original size:22 final size:22
Alignment explanation
Indices: 28128557--28128600 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28128547 GGATATTTGA
*
28128557 GAATATTTAATTTTTTAAATTT
1 GAATATTTAATTTCTTAAATTT
*
28128579 GAATATTT-ATTTACTTATATTT
1 GAATATTTAATTT-CTTAAATTT
28128601 ATGTTCGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (22 bp):
GAATATTTAATTTCTTAAATTT
Found at i:28129620 original size:37 final size:37
Alignment explanation
Indices: 28129557--28129632 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
28129547 TTACAAGCCA
28129557 AAATCATTATAAGCCACATCTCTTGGCTACAT-ACAAC
1 AAATCATTATAAGCCACATCTCTTGGCTA-ATCACAAC
28129594 AAATCATTATAAGCCA-ATACAT-TTGGCTAATCACAAC
1 AAATCATTATAAGCCACAT-C-TCTTGGCTAATCACAAC
28129631 AA
1 AA
28129633 CATCGAGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
36 4 0.11
37 31 0.86
38 1 0.03
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (37 bp):
AAATCATTATAAGCCACATCTCTTGGCTAATCACAAC
Found at i:28132334 original size:13 final size:13
Alignment explanation
Indices: 28132316--28132341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28132306 GCCCAAACGT
28132316 CGAAATTTTCAAA
1 CGAAATTTTCAAA
28132329 CGAAATTTTCAAA
1 CGAAATTTTCAAA
28132342 AAATCATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
CGAAATTTTCAAA
Found at i:28134113 original size:19 final size:19
Alignment explanation
Indices: 28134065--28134114 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
28134055 CGAGTTTGGA
*
28134065 CGAACAGATCACCTAAGGC
1 CGAACAGATCGCCTAAGGC
*
28134084 CGAACGGATCGCCTAAGGC
1 CGAACAGATCGCCTAAGGC
*
28134103 CGCACAGATCGC
1 CGAACAGATCGC
28134115 GAGACGAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.26, T:0.10
Consensus pattern (19 bp):
CGAACAGATCGCCTAAGGC
Found at i:28134478 original size:59 final size:59
Alignment explanation
Indices: 28134404--28134528 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
28134394 TGATCTTAAA
* *
28134404 TCTAAAAATTAAATAAATTTAGCCCTCAATATGTACAAAAATTGTC-ATTTAATTCTAAT
1 TCTAAAAATTAAATAAATTTA-CCCTCAACATGTACAAAAATTGTCAACTTAATTCTAAT
* * * * * * *
28134463 TCTAAAAATTCAATAAATTTATCTTGAACATTTACAAAATTTTTCAACTTAATTCTAAT
1 TCTAAAAATTAAATAAATTTACCCTCAACATGTACAAAAATTGTCAACTTAATTCTAAT
28134522 TCTAAAA
1 TCTAAAA
28134529 GTTTTAAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 17 0.30
59 39 0.70
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (59 bp):
TCTAAAAATTAAATAAATTTACCCTCAACATGTACAAAAATTGTCAACTTAATTCTAAT
Found at i:28137494 original size:14 final size:15
Alignment explanation
Indices: 28137475--28137503 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28137465 CTTACATCAA
28137475 TAATTTT-TAATTTT
1 TAATTTTATAATTTT
28137489 TAATTTTATAATTTT
1 TAATTTTATAATTTT
28137504 CAACTAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TAATTTTATAATTTT
Found at i:28137547 original size:21 final size:21
Alignment explanation
Indices: 28137521--28137560 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28137511 ATTTGATTTT
*
28137521 TTTAAGATGAAAATGTTAAAA
1 TTTAAGATGAAAATATTAAAA
28137542 TTTAAGATGAAAATATTAA
1 TTTAAGATGAAAATATTAA
28137561 TGTCATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (21 bp):
TTTAAGATGAAAATATTAAAA
Found at i:28140220 original size:47 final size:47
Alignment explanation
Indices: 28140151--28140249 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
28140141 AAGTTCAAAG
* *
28140151 AAATTCATATCCTGGTGAAGTTAGAAATTGTGGATACTATATATACT
1 AAATTCATATCCTAGTGAAGTTAGAAATTGTGGATAATATATATACT
*
28140198 AAATTCATATCCTAGTGAAGTTAGAAATTGTGGATAATATTTATACT
1 AAATTCATATCCTAGTGAAGTTAGAAATTGTGGATAATATATATACT
28140245 AAATT
1 AAATT
28140250 AATGTATTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (47 bp):
AAATTCATATCCTAGTGAAGTTAGAAATTGTGGATAATATATATACT
Found at i:28142143 original size:32 final size:32
Alignment explanation
Indices: 28142104--28142196 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 32
28142094 TTAGATATTG
**
28142104 ATTATGTTTTAAGCTTGTCAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
28142136 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
28142168 ATTATGTTTTAAACTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTGGATATTGAA
28142197 ATGATTGACA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTGGATATTGAATTT
Found at i:28143142 original size:175 final size:176
Alignment explanation
Indices: 28142851--28143202 Score: 670
Period size: 175 Copynumber: 2.0 Consensus size: 176
28142841 TTTTTATGCT
28142851 TTTAAATATATTTGATTTATTATATTTTTAATTTTTTTATTTAATGAAATAAGCAAAAAAATTTT
1 TTTAAATATATTTGATTTATTATATTTTTAATTTTTTTATTTAATGAAATAAGCAAAAAAATTTT
*
28142916 AATATGGGTCGGGTCGAGTCGGGCCAGGCTCGAGCTTAGTAATTTTATTTTGGGCTGAGCTTGGA
66 AATATGGGTCGGGTCGAGTCGGGCCAGGCTCGAGCTTAGTAATTTTATTTTGGGCCGAGCTTGGA
*
28142981 CAATTTTTTAGGCCCATATTTTGGGTCGGGCT-GGCCCGGGCCTAG
131 CAATTTTTTAGGCCCATATTTTGGGCCGGGCTGGGCCCGGGCCTAG
28143026 TTTAAATATATTTGATTTATTATATTTTTAATTTTTTTATTTAATGAAATAAGCAAAAAAATTTT
1 TTTAAATATATTTGATTTATTATATTTTTAATTTTTTTATTTAATGAAATAAGCAAAAAAATTTT
28143091 AATATGGGTCGGGTCGAGTCGGGCCAGGCTCGAGCTTAGTAATTTTATTTTGGGCCGAGCTTGGA
66 AATATGGGTCGGGTCGAGTCGGGCCAGGCTCGAGCTTAGTAATTTTATTTTGGGCCGAGCTTGGA
*
28143156 CAATTTTTTAGGCCCATATTTTGGGCCGGGCTGGGCTCGGGCCTAG
131 CAATTTTTTAGGCCCATATTTTGGGCCGGGCTGGGCCCGGGCCTAG
28143202 T
1 T
28143203 AGACCGGCCT
Statistics
Matches: 173, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
175 160 0.92
176 13 0.08
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (176 bp):
TTTAAATATATTTGATTTATTATATTTTTAATTTTTTTATTTAATGAAATAAGCAAAAAAATTTT
AATATGGGTCGGGTCGAGTCGGGCCAGGCTCGAGCTTAGTAATTTTATTTTGGGCCGAGCTTGGA
CAATTTTTTAGGCCCATATTTTGGGCCGGGCTGGGCCCGGGCCTAG
Found at i:28143909 original size:29 final size:29
Alignment explanation
Indices: 28143870--28143929 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
28143860 TTTTAATGTG
28143870 GTGTAATATTAGTTATGCA-ATTGGACAAT
1 GTGTAATATTAGTTATGCACA-TGGACAAT
28143899 GTGTAATATTAGTTATGCACATGGACAAT
1 GTGTAATATTAGTTATGCACATGGACAAT
28143928 GT
1 GT
28143930 TGTTATTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (29 bp):
GTGTAATATTAGTTATGCACATGGACAAT
Found at i:28145045 original size:13 final size:13
Alignment explanation
Indices: 28145027--28145092 Score: 73
Period size: 13 Copynumber: 5.1 Consensus size: 13
28145017 AGTTTGGCAA
*
28145027 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
*
28145040 TGCTTTTGAAAAT
1 TGCTTTTGAAAAG
*
28145053 TG-TTATGGAAAAG
1 TGCTT-TTGAAAAG
28145066 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
28145079 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
28145092 T
1 T
28145093 TTAATTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
12 4 0.09
13 36 0.82
14 4 0.09
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:28156369 original size:17 final size:18
Alignment explanation
Indices: 28156337--28156370 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28156327 ATTTCCTCAT
28156337 TTTAATTTCTGCAATTTA
1 TTTAATTTCTGCAATTTA
28156355 TTTAATTTC-GCAATTT
1 TTTAATTTCTGCAATTT
28156371 CAATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTCTGCAATTTA
Found at i:28160279 original size:48 final size:48
Alignment explanation
Indices: 28160142--28160407 Score: 250
Period size: 48 Copynumber: 5.7 Consensus size: 48
28160132 TTACACATCT
* *
28160142 TCACATAAT-GATGCCATAGCCCAGCTATGGTCTTACACG--T---AT-
1 TCACAT-ATCGATGCCATAACCCAGCTATGGTCTTACATGTATCACATA
28160184 TCACATATCGATGCCAT-ACCCAGCTATGGTCTTACATGTAATCACATA
1 TCACATATCGATGCCATAACCCAGCTATGGTCTTACATGT-ATCACATA
*
28160232 TCACATATCGATGCCATAACCCAGCTATGGTCTTACATGTATTACATA
1 TCACATATCGATGCCATAACCCAGCTATGGTCTTACATGTATCACATA
* * * * *
28160280 TCACATATCGATGCGATAGCCCAGCTATGATCTTACACGAATCACATA
1 TCACATATCGATGCCATAACCCAGCTATGGTCTTACATGTATCACATA
* * * * * * * *
28160328 TCTCA-CT-GATGCCATATCCCAGATATGGTCTTATACGGTAGCATATA
1 TCACATATCGATGCCATAACCCAGCTATGGTCTTACA-TGTATCACATA
* * *
28160375 T--CATACCGATGCCATATCCCAGATATGGTCTTA
1 TCACATATCGATGCCATAACCCAGCTATGGTCTTA
28160408 TATGAAAATC
Statistics
Matches: 190, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
41 21 0.11
42 14 0.07
44 1 0.01
45 2 0.01
46 23 0.12
47 37 0.19
48 70 0.37
49 22 0.12
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (48 bp):
TCACATATCGATGCCATAACCCAGCTATGGTCTTACATGTATCACATA
Found at i:28160464 original size:31 final size:31
Alignment explanation
Indices: 28160429--28160604 Score: 280
Period size: 31 Copynumber: 5.7 Consensus size: 31
28160419 CTTGTCACTT
* *
28160429 GTAGCCGAAGCTATCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
28160460 GTAGCCGGAGCTGCCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
28160491 GTAGCCGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
28160522 GTAGTCGAAGCTACCACTTTTTACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
28160553 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
28160584 GTAGCCGAAGCTACCACTTTT
1 GTAGCCGAAGCTACCACTTTT
28160605 TACTTGTCAT
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 131 1.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:28160682 original size:50 final size:50
Alignment explanation
Indices: 28160584--28160759 Score: 280
Period size: 50 Copynumber: 3.5 Consensus size: 50
28160574 CACTGATCAG
* * * *
28160584 GTAGCCGAAGCTACCACTTTTTACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCCTTGATCAGATAAGT
* *
28160635 TTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATTAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
*
28160685 GTAGCCGAAGCTATCACTTATCACTTTCACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
28160735 GTAGCCGAAGCTATCACTTATCACT
1 GTAGCCGAAGCTATCACTTATCACT
28160760 GGTTGCCATA
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 94 0.81
51 22 0.19
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
Found at i:28165405 original size:27 final size:27
Alignment explanation
Indices: 28165354--28165414 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
28165344 TTGCATTTTC
*
28165354 TTTATTTATTTATGTTTTGAATCAT-T
1 TTTATTTATTTATGTCTTGAATCATAT
28165380 ATTTATTT-TTTAT-TCTTGAATTTCATAT
1 -TTTATTTATTTATGTCTTGAA--TCATAT
28165408 TTTATTT
1 TTTATTT
28165415 GTTTTCGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 6 0.20
26 5 0.17
27 18 0.60
28 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTATTTATTTATGTCTTGAATCATAT
Found at i:28166478 original size:32 final size:32
Alignment explanation
Indices: 28166442--28166506 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
28166432 TGTATGCATT
*
28166442 TTAGCATTTTAATATTTAATGGATGATAGGCA
1 TTAGCATTTTAATAGTTAATGGATGATAGGCA
*
28166474 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATAGGCA
28166506 T
1 T
28166507 GGTAAGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATAGGCA
Found at i:28169662 original size:12 final size:12
Alignment explanation
Indices: 28169645--28169687 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
28169635 ACTCGGGGAA
*
28169645 GAGGCCGTGTTC
1 GAGGCCGTGGTC
28169657 GAGGCCGTGGTC
1 GAGGCCGTGGTC
*
28169669 AAGGCCGTGGTC
1 GAGGCCGTGGTC
28169681 GAGGCCG
1 GAGGCCG
28169688 AGGTAGTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.12, C:0.26, G:0.47, T:0.16
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:28175925 original size:15 final size:15
Alignment explanation
Indices: 28175905--28175936 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28175895 AACCTATTTG
28175905 TTTCTTTTATTTTAT
1 TTTCTTTTATTTTAT
28175920 TTTCTTTTATTTTAT
1 TTTCTTTTATTTTAT
28175935 TT
1 TT
28175937 AAACATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTATTTTAT
Found at i:28177882 original size:19 final size:19
Alignment explanation
Indices: 28177860--28177911 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
28177850 GCGTAAAAAA
*
28177860 CTTTATGGTAATAAGTTTT
1 CTTTTTGGTAATAAGTTTT
* *
28177879 CTTTTTGGAAATACGTTTT
1 CTTTTTGGTAATAAGTTTT
*
28177898 ATTTTTGGTAATAA
1 CTTTTTGGTAATAA
28177912 ATTTGTATGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (19 bp):
CTTTTTGGTAATAAGTTTT
Found at i:28177947 original size:16 final size:16
Alignment explanation
Indices: 28177899--28177950 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
28177889 ATACGTTTTA
28177899 TTTT-TGGTAATAAAT
1 TTTTATGGTAATAAAT
* * * *
28177914 TTGTAT-GCATTTAAT
1 TTTTATGGTAATAAAT
28177929 TTTTATGGTAATAAAT
1 TTTTATGGTAATAAAT
28177945 TTTTAT
1 TTTTAT
28177951 TTTGTTGAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.56
Consensus pattern (16 bp):
TTTTATGGTAATAAAT
Found at i:28177989 original size:21 final size:22
Alignment explanation
Indices: 28177927--28177989 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
28177917 TATGCATTTA
* *
28177927 ATTTTTATGGTAATAAATTTTT
1 ATTTTTTTGGTAATAAGTTTTT
* ** **
28177949 ATTTTGTTGAAAATCCGTTTTT
1 ATTTTTTTGGTAATAAGTTTTT
28177971 -TTTTTTTGGTAATAAGTTT
1 ATTTTTTTGGTAATAAGTTT
28177990 GTAGGTATTT
Statistics
Matches: 29, Mismatches: 12, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.59
Consensus pattern (22 bp):
ATTTTTTTGGTAATAAGTTTTT
Found at i:28179845 original size:29 final size:29
Alignment explanation
Indices: 28179790--28179846 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
28179780 TTTATATTAG
*
28179790 ATAAATATAATTATTTATGTATACAATAT
1 ATAAATATAATTATGTATGTATACAATAT
28179819 ATAAATATAAATTGATGT-TGTAT-CAATA
1 ATAAATAT-AATT-ATGTATGTATACAATA
28179847 ATTACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 13 0.52
30 9 0.36
31 3 0.12
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (29 bp):
ATAAATATAATTATGTATGTATACAATAT
Found at i:28185060 original size:15 final size:15
Alignment explanation
Indices: 28185040--28185068 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28185030 TTTTTGAAAC
28185040 ACAGAAATTAAAAAA
1 ACAGAAATTAAAAAA
28185055 ACAGAAATTAAAAA
1 ACAGAAATTAAAAA
28185069 CAGAATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
ACAGAAATTAAAAAA
Found at i:28185069 original size:13 final size:14
Alignment explanation
Indices: 28185040--28185073 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
28185030 TTTTTGAAAC
28185040 ACAGAAATTAAAAAA
1 ACAGAAATT-AAAAA
28185055 ACAGAAATT-AAAA
1 ACAGAAATTAAAAA
28185068 ACAGAA
1 ACAGAA
28185074 TTTGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
15 9 0.47
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.12
Consensus pattern (14 bp):
ACAGAAATTAAAAA
Found at i:28185350 original size:72 final size:72
Alignment explanation
Indices: 28185157--28186178 Score: 1485
Period size: 72 Copynumber: 14.1 Consensus size: 72
28185147 ATTAGTAAAG
* * * *
28185157 CAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTT-AAGT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-T
28185221 TTTGAAAA
65 TTTGAAAA
* *
28185229 GCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 -CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
28185294 TTTGAAAA
65 TTTGAAAA
* ** *
28185302 CAGAAATTGAAATTACCTCATCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAACT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
28185367 TTGAGAAG
66 TTGA-AAA
* * ** *
28185375 CAGAAATTGAAAATACCTCAACGTGTTTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAACT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
28185440 TTGAGAAG
66 TTGA-AAA
* *
28185448 CAGAAATTGAAAATACCTCAACGTGTCTTGACGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
28185513 TTGAAAA
66 TTGAAAA
* *
28185520 CAGAAATTGAAATTACCTCATCGTGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
28185585 TTGAAAA
66 TTGAAAA
28185592 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
**
28185657 TTGCCAA
66 TTGAAAA
* **
28185664 CAGAAATTGAAATTACCTCATCGTGTCTTGAGGCTCAACTCATTTCTCGCAACCTGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
28185729 TTGAAAA
66 TTGAAAA
* *
28185736 CAGAAATTGAGGA-TACCTCAACGTGTCTTGAGGCTCAACGCATTTCTCGCAATATGAGTTGAAT
1 CAGAAATTGA-AATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
**
28185800 TTTGCCAA
65 TTTGAAAA
*
28185808 CAGAAATTGAAATTACCTCATCGTGTCTTGAGGCTCAACTCATTTCT-GACAATATGAGTTGAAT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCG-CAATATGAGTTGAAT
28185872 TTTGAAAA
65 TTTGAAAA
*
28185880 CAGCAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
28185945 TTAAAAA
66 TTGAAAA
* * * *
28185952 GCAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAAT
1 -CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
28186017 TTTGAAAA
65 TTTGAAAA
* * *
28186025 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-AT
*
28186090 TTTTAACAA
65 TTTGAA-AA
* * * ** * *
28186099 CAGAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAATTG-ATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
28186163 TTGAAAAA
66 TTG-AAAA
*
28186171 CATAAATT
1 CAGAAATT
28186179 AAAAGGCTTA
Statistics
Matches: 873, Mismatches: 66, Indels: 21
0.91 0.07 0.02
Matches are distributed among these distances:
71 2 0.00
72 534 0.61
73 277 0.32
74 60 0.07
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (72 bp):
CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
TTGAAAA
Found at i:28201190 original size:3 final size:3
Alignment explanation
Indices: 28201184--28201229 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
28201174 TTTTCTTTCT
*
28201184 TTC TTC TTC CTC TT- TTC TTC TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TT-C TTC TTC TTC TTC
28201230 AAAGTCTAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:28201213 original size:10 final size:10
Alignment explanation
Indices: 28201198--28201226 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
28201188 TCTTCCTCTT
28201198 TTCTTCTTCC
1 TTCTTCTTCC
28201208 TTCTTCTTCC
1 TTCTTCTTCC
28201218 TTCTTCTTC
1 TTCTTCTTC
28201227 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:28201214 original size:13 final size:13
Alignment explanation
Indices: 28201184--28201229 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
28201174 TTTTCTTTCT
28201184 TTCTTCTTCC-TC
1 TTCTTCTTCCTTC
28201196 TT-TTCTT-CTTCC
1 TTCTTCTTCCTT-C
28201208 TTCTTCTTCCTTC
1 TTCTTCTTCCTTC
28201221 TTCTTCTTC
1 TTCTTCTTC
28201230 AAAGTCTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.20
12 5 0.17
13 15 0.50
14 3 0.10
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TTCTTCTTCCTTC
Found at i:28201320 original size:10 final size:10
Alignment explanation
Indices: 28201285--28201334 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
28201275 ACGCCGGTAC
28201285 TCTT-TCTTT
1 TCTTCTCTTT
* *
28201294 TCTTCTCCTC
1 TCTTCTCTTT
28201304 T-TTCTCTTT
1 TCTTCTCTTT
28201313 TCTTCTCTTT
1 TCTTCTCTTT
*
28201323 TCTTCTTTTT
1 TCTTCTCTTT
28201333 TC
1 TC
28201335 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:28201332 original size:19 final size:19
Alignment explanation
Indices: 28201289--28201331 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
28201279 CGGTACTCTT
28201289 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
28201308 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
28201325 TTCTTTT
1 -TCTTTT
28201332 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:28201613 original size:29 final size:29
Alignment explanation
Indices: 28201580--28201696 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
28201570 TGTAATTTTT
*
28201580 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
28201609 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
28201639 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
28201668 GGAAAAGTTTAGGTGTCAAAATGCAATTT
1 AGAAAA-TTTAGG-GTTAAAATGAAATTT
28201697 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 16 0.22
30 54 0.75
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:28201635 original size:30 final size:30
Alignment explanation
Indices: 28201595--28201696 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
28201585 ATTTAGGATT
*
28201595 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
28201625 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
28201655 AAAATGAAATTT-AGGAAAAGTTTAGGTGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
28201685 AAAATGCAATTT
1 AAAATGAAATTT
28201697 TTATTTTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:28201719 original size:16 final size:17
Alignment explanation
Indices: 28201694--28201729 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
28201684 CAAAATGCAA
28201694 TTTTTATTTTTT-AAAT
1 TTTTTATTTTTTGAAAT
*
28201710 TTTTTTTTTTTTGAAAT
1 TTTTTATTTTTTGAAAT
28201727 TTT
1 TTT
28201730 GAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTTGAAAT
Found at i:28201720 original size:17 final size:17
Alignment explanation
Indices: 28201694--28201729 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28201684 CAAAATGCAA
*
28201694 TTTTTATTTTTTAAATT
1 TTTTTATTTTTGAAATT
*
28201711 TTTTTTTTTTTGAAATT
1 TTTTTATTTTTGAAATT
28201728 TT
1 TT
28201730 GAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTGAAATT
Found at i:28206080 original size:26 final size:26
Alignment explanation
Indices: 28206049--28206104 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
28206039 TGAAATGCCC
28206049 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
28206075 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
28206101 ATCA
1 ATCA
28206105 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:28208318 original size:37 final size:36
Alignment explanation
Indices: 28208267--28208337 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 36
28208257 GACTAAATCC
* *
28208267 AGTTCTCTATGAATTTTTAAGAAATATGAAAATTTCG
1 AGTTCTCTACGAATTTTTAAGAAACAT-AAAATTTCG
28208304 AGTTCTCTACGAATTTTTAAGAAACATAAAATTT
1 AGTTCTCTACGAATTTTTAAGAAACATAAAATTT
28208338 TCTTTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (36 bp):
AGTTCTCTACGAATTTTTAAGAAACATAAAATTTCG
Found at i:28209749 original size:25 final size:25
Alignment explanation
Indices: 28209721--28209773 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
28209711 CTCATCCCAA
* *
28209721 CTGAAAATCGGTAAGCTCTTACGAG
1 CTGAAAATCGATAAGCTCATACGAG
* *
28209746 CTGAGAATCGATAAGCTCATATGAG
1 CTGAAAATCGATAAGCTCATACGAG
28209771 CTG
1 CTG
28209774 TGGTGAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (25 bp):
CTGAAAATCGATAAGCTCATACGAG
Found at i:28221009 original size:17 final size:17
Alignment explanation
Indices: 28220984--28221069 Score: 57
Period size: 17 Copynumber: 5.6 Consensus size: 17
28220974 ACCCTACTAA
*
28220984 ATCATCCCACTAACTCC
1 ATCACCCCACTAACTCC
*
28221001 ATCACCCCACTAA-ACC
1 ATCACCCCACTAACTCC
*
28221017 AT----CCACTATCTCC
1 ATCACCCCACTAACTCC
*
28221030 ATCACCCCACTAA-ACC
1 ATCACCCCACTAACTCC
*
28221046 AT----CCACTATCTCC
1 ATCACCCCACTAACTCC
28221059 ATCACCCCACT
1 ATCACCCCACT
28221070 TGCCTACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
12 12 0.24
13 8 0.16
16 8 0.16
17 23 0.45
ACGTcount: A:0.30, C:0.49, G:0.00, T:0.21
Consensus pattern (17 bp):
ATCACCCCACTAACTCC
Found at i:28221032 original size:29 final size:29
Alignment explanation
Indices: 28220973--28221069 Score: 158
Period size: 29 Copynumber: 3.3 Consensus size: 29
28220963 ATCACCCCCA
* * *
28220973 CACCCTACTAAATCATCCCACTAACTCCAT
1 CACCCCACTAAACCAT-CCACTATCTCCAT
28221003 CACCCCACTAAACCATCCACTATCTCCAT
1 CACCCCACTAAACCATCCACTATCTCCAT
28221032 CACCCCACTAAACCATCCACTATCTCCAT
1 CACCCCACTAAACCATCCACTATCTCCAT
28221061 CACCCCACT
1 CACCCCACT
28221070 TGCCTACAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
29 50 0.78
30 14 0.22
ACGTcount: A:0.31, C:0.48, G:0.00, T:0.21
Consensus pattern (29 bp):
CACCCCACTAAACCATCCACTATCTCCAT
Found at i:28221454 original size:3 final size:3
Alignment explanation
Indices: 28221431--28221613 Score: 108
Period size: 3 Copynumber: 60.7 Consensus size: 3
28221421 GGGGAGAGTG
* * *
28221431 TTA TTT TTA ATA TTG TTA TTA TTA TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * * *
28221477 TTA -TA TTA -TA CTTA TT- TTA TTA CTG TTA CTA TTA TTT TGTA TATA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA
* ** ** *
28221522 TTTA TTA TCA TTA TTGA TTTA TTA TTA TTA TTA GAA ACA -TA TTT TTA
1 -TTA TTA TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
28221569 TTT TTA TTA TTT TTA -TA TTA TTA TTT TTA TTA ATA -TA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28221614 GTCTTCTATT
Statistics
Matches: 137, Mismatches: 31, Indels: 24
0.71 0.16 0.12
Matches are distributed among these distances:
2 11 0.08
3 110 0.80
4 13 0.09
5 3 0.02
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28221462 original size:28 final size:29
Alignment explanation
Indices: 28221431--28221511 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 29
28221421 GGGGAGAGTG
*
28221431 TTATTTTTAATATTGTTATTATTATATA-
1 TTATTTTTATTATTGTTATTATTATATAC
* *
28221459 TTATTATTATTATTATTATTA-TATTATAC
1 TTATTTTTATTATTGTTATTATTA-TATAC
* *
28221488 TTA-TTTTATTACTGTTACTATTAT
1 TTATTTTTATTATTGTTATTATTAT
28221512 TTTGTATATA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 2 0.05
28 36 0.84
29 5 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (29 bp):
TTATTTTTATTATTGTTATTATTATATAC
Found at i:28221496 original size:25 final size:25
Alignment explanation
Indices: 28221432--28221613 Score: 101
Period size: 25 Copynumber: 7.3 Consensus size: 25
28221422 GGGAGAGTGT
* * *
28221432 TATTTTTAATATTGTTATTATTATA
1 TATTATTATTATTATTATTATTATA
28221457 TATTATTATTATTATTATTATTATA
1 TATTATTATTATTATTATTATTATA
* * *
28221482 T-TATACTTATT-TTATTACTGTTA-C
1 TAT-TA-TTATTATTATTATTATTATA
* *
28221506 TATTATTTTGTATATATTTATTATCAT-
1 TATTATTAT-TAT-TA-TTATTATTATA
** *
28221533 TATTGATTTATTATTATTATTAGAAACA
1 TATT-A-TTATTATTATTATTA-TTATA
* *
28221561 TATTTTTATTTTTATTATT-TT-TA
1 TATTATTATTATTATTATTATTATA
* *
28221584 TATTATTATTTTTATTAATA-TAT-
1 TATTATTATTATTATTATTATTATA
28221607 TATTATT
1 TATTATT
28221614 GTCTTCTATT
Statistics
Matches: 122, Mismatches: 21, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
23 29 0.24
24 6 0.05
25 37 0.30
26 26 0.21
27 13 0.11
28 8 0.07
29 3 0.02
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (25 bp):
TATTATTATTATTATTATTATTATA
Found at i:28221869 original size:19 final size:21
Alignment explanation
Indices: 28221832--28221870 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28221822 TTTATCTATG
*
28221832 TATATATATATATTATATTTT
1 TATATATACATATTATATTTT
28221853 TATATATACA-ATT-TATTT
1 TATATATACATATTATATTT
28221871 CTTTTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATATACATATTATATTTT
Found at i:28228231 original size:20 final size:20
Alignment explanation
Indices: 28228208--28228252 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28228198 GTAGGGTAAC
28228208 AGGCTAAAATTTACAGATCT
1 AGGCTAAAATTTACAGATCT
**
28228228 AGGCTCCAATTTACAGATCT
1 AGGCTAAAATTTACAGATCT
*
28228248 GGGCT
1 AGGCT
28228253 CACCGAGCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
AGGCTAAAATTTACAGATCT
Found at i:28228253 original size:20 final size:20
Alignment explanation
Indices: 28228215--28228253 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28228205 AACAGGCTAA
28228215 AATTTACAGATCTAGGCTCC
1 AATTTACAGATCTAGGCTCC
*
28228235 AATTTACAGATCTGGGCTC
1 AATTTACAGATCTAGGCTC
28228254 ACCGAGCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (20 bp):
AATTTACAGATCTAGGCTCC
Found at i:28228375 original size:85 final size:84
Alignment explanation
Indices: 28228235--28228586 Score: 530
Period size: 85 Copynumber: 4.2 Consensus size: 84
28228225 TCTAGGCTCC
*
28228235 AATTTACAGATCTGGGCTCACCGAGCAGTGGTGGAGCAGGTCGAAGACTCGCCTTAAACCCCTAA
1 AATTTACAGATCTGGGCTCGCCGAGCAGTGGTGGAGCAGGTCGAAGACTCGCCTT-AACCCCTAA
*
28228300 GCAATAGGGTAACAGGCTAA
65 GCAGTAGGGTAACAGGCTAA
*
28228320 AATTTACAGATCTGGGCTCGCCGAGCAGTGGTGGAGCAGGTCGAAGACTCACCTTAACCCCTTAA
1 AATTTACAGATCTGGGCTCGCCGAGCAGTGGTGGAGCAGGTCGAAGACTCGCCTTAACCCC-TAA
28228385 GCAGTAGGGTAACAGGCTAA
65 GCAGTAGGGTAACAGGCTAA
* *
28228405 AATTTACAGATCTAGGCTCGCCGAGCAGTGGTGGAGCAGGTCGAAGA-TCCGCCTTAACCACTTA
1 AATTTACAGATCTGGGCTCGCCGAGCAGTGGTGGAGCAGGTCGAAGACT-CGCCTTAACC-CCTA
28228469 AGCAGTAGGGTAACAGGCTAA
64 AGCAGTAGGGTAACAGGCTAA
* * * * *
28228490 AATTTACAGATCCT-AGCTCTCCGAGCAGTGGTGGAGTAGGTCGAAGACTCGGCTTAATCCTCTA
1 AATTTACAGAT-CTGGGCTCGCCGAGCAGTGGTGGAGCAGGTCGAAGACTCGCCTTAA-CCCCTA
28228554 AGCAGTAGGGTAACAGGCTAA
64 AGCAGTAGGGTAACAGGCTAA
*
28228575 AA-TTGCAGATCT
1 AATTTACAGATCT
28228587 CATCCCACTG
Statistics
Matches: 248, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
83 2 0.01
84 14 0.06
85 226 0.91
86 6 0.02
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.21
Consensus pattern (84 bp):
AATTTACAGATCTGGGCTCGCCGAGCAGTGGTGGAGCAGGTCGAAGACTCGCCTTAACCCCTAAG
CAGTAGGGTAACAGGCTAA
Found at i:28228667 original size:21 final size:21
Alignment explanation
Indices: 28228643--28228682 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28228633 TCTATGGCTA
28228643 AAATTTACAGATCTGGGCTGT
1 AAATTTACAGATCTGGGCTGT
*
28228664 AAATTTATAGATCTGGGCT
1 AAATTTACAGATCTGGGCT
28228683 CGCCGAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (21 bp):
AAATTTACAGATCTGGGCTGT
Found at i:28229099 original size:46 final size:47
Alignment explanation
Indices: 28229041--28229241 Score: 138
Period size: 46 Copynumber: 4.4 Consensus size: 47
28229031 AACAGGCTAA
*
28229041 AAGTAAAGCAGATCAAATTTCGA-CAGATCTTATCTTCACTGAGCAG
1 AAGTGAAGCAGATCAAATTTCGACCAGATCTTATCTTCACTGAGCAG
* * * * * *
28229087 AAGTGAAGCAGATCAAATTTTGGCAAG-TCTTATCTCCA-TGTAACGG
1 AAGTGAAGCAGATCAAATTTCGACCAGATCTTATCTTCACTG-AGCAG
* * *
28229133 AAAT--AG-AG-T-AGATTTCAGCCACCAG-CCTTATCTTCACTGAGCAG
1 AAGTGAAGCAGATCAAATTTC-G--ACCAGATCTTATCTTCACTGAGCAG
* * * **
28229177 GAGTGGAGCAG-GCTAAACAT--ACCAGATCTTATCTTCACTGAGCAG
1 AAGTGAAGCAGATC-AAATTTCGACCAGATCTTATCTTCACTGAGCAG
28229222 AAGTGAAGCAGATCAAATTT
1 AAGTGAAGCAGATCAAATTT
28229242 TGGCAAGTCT
Statistics
Matches: 114, Mismatches: 28, Indels: 27
0.67 0.17 0.16
Matches are distributed among these distances:
41 5 0.04
42 2 0.02
43 2 0.02
44 24 0.21
45 35 0.31
46 39 0.34
47 4 0.04
49 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (47 bp):
AAGTGAAGCAGATCAAATTTCGACCAGATCTTATCTTCACTGAGCAG
Found at i:28229317 original size:135 final size:135
Alignment explanation
Indices: 28229064--28229376 Score: 404
Period size: 135 Copynumber: 2.3 Consensus size: 135
28229054 CAAATTTCGA
28229064 CAGATCTTATCTTCACTGAGCAGAAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
1 CAGATCTTATCTTCACTGAGCAGAAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
** * ** ** *
28229129 ACGGAAATAGAGTAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
66 ACGGAAATAGAGTAGATACCAGCCACCAGCCTCATCCCCACACACCAGGAGTGGAGCAGGCTAAA
28229194 CATAC
131 CATAC
28229199 CAGATCTTATCTTCACTGAGCAGAAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
1 CAGATCTTATCTTCACTGAGCAGAAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
* * * *
28229264 ACGGAAATA-AG-A-A-ACCATCCACTA-CCTCCATCACCCCCACACCCTAAGTAGTGGAGCAGG
66 ACGGAAATAGAGTAGATACCAGCCACCAGCCT-CATC-CCCACACA-CC--AGGAGTGGAGCAGG
28229324 CTAAACATAC
126 CTAAACATAC
* *
28229334 CAGATCTTATCTTTACTGAGCA-AGAGTAAAGCAGATCAAATTT
1 CAGATCTTATCTTCACTGAGCAGA-AGTGAAGCAGATCAAATTT
28229377 CGACAGATCT
Statistics
Matches: 158, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
130 3 0.02
131 10 0.06
132 4 0.03
133 2 0.01
134 3 0.02
135 136 0.86
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (135 bp):
CAGATCTTATCTTCACTGAGCAGAAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
ACGGAAATAGAGTAGATACCAGCCACCAGCCTCATCCCCACACACCAGGAGTGGAGCAGGCTAAA
CATAC
Found at i:28229437 original size:46 final size:46
Alignment explanation
Indices: 28229334--28229422 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
28229324 CTAAACATAC
*
28229334 CAGATCTTATCTTTACTGAGCAAGAGTAAAGCAGATCAAATTTCGA
1 CAGATCTTATCTTCACTGAGCAAGAGTAAAGCAGATCAAATTTCGA
* *
28229380 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTT
1 CAGATCTTATCTTCACTGAGCAAGAGTAAAGCAGATCAAATTT
28229423 GGGCAAGTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (46 bp):
CAGATCTTATCTTCACTGAGCAAGAGTAAAGCAGATCAAATTTCGA
Found at i:28229587 original size:133 final size:136
Alignment explanation
Indices: 28229380--28229689 Score: 416
Period size: 133 Copynumber: 2.3 Consensus size: 136
28229370 CAAATTTCGA
28229380 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAA-TTTGGGCAAGTCTTATCTCCATGT
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGGCAAGTCTTATCTCCATGT
* * * *
28229444 AATGATAATGGAGTAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-A
66 AATGACAATGGAGCAGATTCCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAA
28229508 A-ATAC
131 ACATAC
* * * * *
28229513 TAGATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCAAATTTTGATG-AA-TCTTATCTCCATG
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTG-GGCAAGTCTTATCTCCATG
* * * *
28229576 T-ATCGGCAATGGAGCAGATTCCAATCATCAGTCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT
65 TAAT-GACAATGGAGCAGATTCCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT
28229640 AAACATAC
129 AAACATAC
* * *
28229648 CAGATCTTATCTTTACTGAGCATGAGTAAAGCAGATCAAATT
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATT
28229690 ACAGCAGATC
Statistics
Matches: 152, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
132 2 0.01
133 102 0.67
134 8 0.05
135 40 0.26
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (136 bp):
CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGGCAAGTCTTATCTCCATGT
AATGACAATGGAGCAGATTCCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAA
ACATAC
Found at i:28229722 original size:135 final size:133
Alignment explanation
Indices: 28229380--28229725 Score: 317
Period size: 133 Copynumber: 2.6 Consensus size: 133
28229370 CAAATTTCGA
** * * **
28229380 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATT-TG-GGCAAGTCTTATCTCCATG
1 CAGATCTTATCTTCACTGAGCAGGAGCAAAGCAGATCAAATTCAGATG-AA-TCACATCTCCATG
* * * ** * *
28229443 TAATG-A-TAATGGAGTAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGC
64 -AA-GCAGCAATGGAGCAGATTCCAATCATCAGTCTTATCTTCACTGAGCAGGAGTGGAGCAGGC
28229506 TAAATAC
127 TAAATAC
* * ** ** ** *
28229513 TAGATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCAAATTTTGATGAATCTTATCTCCATGTA
1 CAGATCTTATCTTCACTGAGCAGGAGCAAAGCAGATCAAATTCAGATGAATCACATCTCCATGAA
* *
28229578 TCGGCAATGGAGCAGATTCCAATCATCAGTCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
66 GCAGCAATGGAGCAGATTCCAATCATCAGTCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA
28229643 CATAC
130 -ATAC
* * * **
28229648 CAGATCTTATCTTTACTGAGCATGAGTAAAGCAGATCAAATTACAGCA-G-ATCACATCTCTGTG
1 CAGATCTTATCTTCACTGAGCAGGAGCAAAGCAGATCAAATT-CAG-ATGAATCACATCTCCATG
28229711 AAGCAGCAATGGAGC
64 AAGCAGCAATGGAGC
28229726 GTTTTGAAGC
Statistics
Matches: 174, Mismatches: 31, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
132 1 0.01
133 102 0.59
134 6 0.03
135 62 0.36
136 2 0.01
137 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (133 bp):
CAGATCTTATCTTCACTGAGCAGGAGCAAAGCAGATCAAATTCAGATGAATCACATCTCCATGAA
GCAGCAATGGAGCAGATTCCAATCATCAGTCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
TAC
Found at i:28230009 original size:17 final size:17
Alignment explanation
Indices: 28229987--28230043 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
28229977 ACCCTACTAA
28229987 ATCACCCCACTAACTCC
1 ATCACCCCACTAACTCC
*
28230004 ATCACCCCACTAA-ACC
1 ATCACCCCACTAACTCC
*
28230020 AT----CCACTATCTCC
1 ATCACCCCACTAACTCC
28230033 ATCACCCCACT
1 ATCACCCCACT
28230044 TGCCGACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
12 6 0.19
13 4 0.12
16 4 0.12
17 18 0.56
ACGTcount: A:0.30, C:0.51, G:0.00, T:0.19
Consensus pattern (17 bp):
ATCACCCCACTAACTCC
Found at i:28230420 original size:3 final size:3
Alignment explanation
Indices: 28230402--28230566 Score: 86
Period size: 3 Copynumber: 54.7 Consensus size: 3
28230392 GGGGAGAGTG
* * *
28230402 TTA TTT TTA ATA TTA TTA TTA ATA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
28230449 CTG TTA CTA TTA TTT TGTA TATA TTTA TTA TCA TTA TTGA TTTA TTA
1 TTA TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA TTA TT-A -TTA TTA
** ** * * * *
28230496 TTA TTA TTA GAA ACA -TA TTT TTA TTT TTA TTA TTT TTA -TA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
28230542 TTT TTA TTA ATA -TA TTT TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
28230567 GTCTTCTATT
Statistics
Matches: 119, Mismatches: 35, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
2 7 0.06
3 101 0.85
4 8 0.07
5 3 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28230531 original size:14 final size:14
Alignment explanation
Indices: 28230511--28230566 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
28230501 ATTAGAAACA
*
28230511 TATTTTTATTTTTAT
1 TATTTTTATTATT-T
28230526 TATTTTTA-TATTTT
1 TATTTTTATTA-TTT
* *
28230540 TATTTTTATTAATA
1 TATTTTTATTATTT
28230554 TATTTTTATTATT
1 TATTTTTATTATT
28230567 GTCTTCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TATTTTTATTATTT
Found at i:28230565 original size:23 final size:23
Alignment explanation
Indices: 28230488--28230566 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
28230478 ATCATTATTG
* * *
28230488 ATTTATTATTATTATTAGAAACAT
1 ATTT-TTATTTTTATTAGATATAT
** *
28230512 ATTTTTATTTTTATTATTTTTAT
1 ATTTTTATTTTTATTAGATATAT
28230535 ATTTTTATTTTTATTA-ATATAT
1 ATTTTTATTTTTATTAGATATAT
*
28230557 TTTTATTATT
1 ATTT-TTATT
28230567 GTCTTCTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 7 0.16
23 34 0.76
24 4 0.09
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (23 bp):
ATTTTTATTTTTATTAGATATAT
Found at i:28231397 original size:126 final size:126
Alignment explanation
Indices: 28231167--28231400 Score: 373
Period size: 126 Copynumber: 1.9 Consensus size: 126
28231157 TTCTCAATTG
* * *
28231167 TTTTTAAAATAATAGCAATGTTCAGTATTTAAAGACTTCGAAGAATCGTACCCTAACGTACTGGG
1 TTTTCAAAATAATAGCAATGATCAGTATTTAAAGAATTCGAAGAATCGTACCCTAACGTACTGGG
*
28231232 TTTCGCTTTCTTTGTTTGTCTTGAATATTCAGATATCCTCTTACCAGTTCACTCTAAAAAA
66 TTTCGCTTTCTTTCTTTGTCTTGAATATTCAGATATCCTCTTACCAGTTCACTCTAAAAAA
* *
28231293 TTTTCAAAATAA-AGGCAATGATCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGG
1 TTTTCAAAATAATA-GCAATGATCAGTATTTAAAGAATTCGAAGAATCGTACCCTAACGTACTGG
*
28231357 GTTTCGCTTTCTTTCTTTGTTTTGAATATTC-GAATATCCTCTTA
65 GTTTCGCTTTCTTTCTTTGTCTTGAATATTCAG-ATATCCTCTTA
28231401 AGGTTAAAAC
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
125 2 0.02
126 97 0.98
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (126 bp):
TTTTCAAAATAATAGCAATGATCAGTATTTAAAGAATTCGAAGAATCGTACCCTAACGTACTGGG
TTTCGCTTTCTTTCTTTGTCTTGAATATTCAGATATCCTCTTACCAGTTCACTCTAAAAAA
Found at i:28243473 original size:5 final size:5
Alignment explanation
Indices: 28243459--28243508 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
28243449 ATTTATGTTT
28243459 TATTA TATTA TATTA T-TATA TTATTA TATTA -ATCTA TTATTA TATTA
1 TATTA TATTA TATTA TAT-TA -TATTA TATTA TAT-TA -TATTA TATTA
28243506 TAT
1 TAT
28243509 ACTTAAGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
4 3 0.08
5 28 0.72
6 5 0.13
7 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:28243475 original size:8 final size:8
Alignment explanation
Indices: 28243464--28243506 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
28243454 TGTTTTATTA
28243464 TATTATAT
1 TATTATAT
28243472 TATTATAT
1 TATTATAT
28243480 TATTATAT
1 TATTATAT
* *
28243488 TAATCTAT
1 TATTATAT
28243496 TATTATAT
1 TATTATAT
28243504 TAT
1 TAT
28243507 ATACTTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:28243514 original size:24 final size:24
Alignment explanation
Indices: 28243458--28243514 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
28243448 TATTTATGTT
28243458 TTATTATATT-A--TATTATTATA
1 TTATTATATTAATCTATTATTATA
28243479 TTATTATATTAATCTATTATTATA
1 TTATTATATTAATCTATTATTATA
28243503 TTA-TATACTTAA
1 TTATTATA-TTAA
28243515 GTATTACGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.31
22 1 0.03
23 4 0.12
24 17 0.53
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTATATTAATCTATTATTATA
Found at i:28244139 original size:15 final size:15
Alignment explanation
Indices: 28244119--28244149 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28244109 CGTTGACAAC
28244119 ATCCTCAAAAAGATA
1 ATCCTCAAAAAGATA
28244134 ATCCTCAAAAAGATA
1 ATCCTCAAAAAGATA
28244149 A
1 A
28244150 GTTTCTGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
ATCCTCAAAAAGATA
Found at i:28249038 original size:18 final size:17
Alignment explanation
Indices: 28249015--28249048 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28249005 TTTTGAATTT
28249015 TATTATTTATTTAATATA
1 TATTA-TTATTTAATATA
*
28249033 TATTATTATTTTATAT
1 TATTATTATTTAATAT
28249049 TAAAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTTAATATA
Found at i:28249344 original size:17 final size:17
Alignment explanation
Indices: 28249322--28249374 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
28249312 GTTTTCATAT
28249322 TATTTTATTACATATTA
1 TATTTTATTACATATTA
* * *
28249339 TATTTTACTCCATATGA
1 TATTTTATTACATATTA
*
28249356 TATTTT-TTATATATTA
1 TATTTTATTACATATTA
28249372 TAT
1 TAT
28249375 ACATTTTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTTATTACATATTA
Found at i:28254262 original size:14 final size:14
Alignment explanation
Indices: 28254233--28254271 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
28254223 TATTATTATT
*
28254233 ATTATTTT-TTAAC
1 ATTATTTTATAAAC
28254246 ATTATTTTATAAAC
1 ATTATTTTATAAAC
28254260 ATTATTTTATAA
1 ATTATTTTATAA
28254272 GTACAACAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATTTTATAAAC
Found at i:28254326 original size:16 final size:17
Alignment explanation
Indices: 28254305--28254337 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28254295 AAACACATTA
*
28254305 TTTTAAACAT-CTTTTT
1 TTTTAAAAATACTTTTT
28254321 TTTTAAAAATACTTTTT
1 TTTTAAAAATACTTTTT
28254338 ATTCGTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAAATACTTTTT
Found at i:28255958 original size:17 final size:17
Alignment explanation
Indices: 28255936--28255972 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
28255926 TTTATGGTGA
28255936 ATTTTCAAAGTCGAACT
1 ATTTTCAAAGTCGAACT
28255953 ATTTTCAAAGTCGAACT
1 ATTTTCAAAGTCGAACT
28255970 ATT
1 ATT
28255973 GCTACTAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (17 bp):
ATTTTCAAAGTCGAACT
Found at i:28256471 original size:35 final size:35
Alignment explanation
Indices: 28256393--28256520 Score: 125
Period size: 35 Copynumber: 3.7 Consensus size: 35
28256383 TCTTCATTTA
* * *
28256393 AATACCATACCTACATTTCGCAATTC-GATATGGGA-
1 AATACCATACCTACGTTTCACAACTCAG-TAT-GGAT
* * **
28256428 AATGCCATACCTATGTTTCTTAACTCAGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* * *
28256463 AATACCATACTTACATTTCACAACTTAGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
*
28256498 GATACCATACCTACGTTTCACAA
1 AATACCATACCTACGTTTCACAA
28256521 ATTTTCCATG
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
34 3 0.04
35 71 0.95
36 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACGTTTCACAACTCAGTATGGAT
Found at i:28257620 original size:12 final size:12
Alignment explanation
Indices: 28257603--28257635 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
28257593 TGGCCCGCCC
28257603 ATATTAATTTTT
1 ATATTAATTTTT
28257615 ATATT-ATTTTT
1 ATATTAATTTTT
28257626 ATA-TAATTTT
1 ATATTAATTTT
28257636 AAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:28257876 original size:22 final size:22
Alignment explanation
Indices: 28257850--28257898 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28257840 ATATCTAAAC
28257850 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * **
28257872 CATAATAGTAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
28257894 AATAA
1 AATAA
28257899 GGAGAAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:28257897 original size:11 final size:11
Alignment explanation
Indices: 28257858--28257897 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
28257848 ACAATAACAA
28257858 CAAAATAGTAG
1 CAAAATAGTAG
* *
28257869 CAACATAATAG
1 CAAAATAGTAG
*
28257880 TAAAATAGTAG
1 CAAAATAGTAG
28257891 CAAAATA
1 CAAAATA
28257898 AGGAGAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:28258420 original size:8 final size:8
Alignment explanation
Indices: 28258398--28258435 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
28258388 AAATTATTTT
28258398 AATTCACC
1 AATTCACC
28258406 AAATTCACC
1 -AATTCACC
28258415 AATTCACC
1 AATTCACC
*
28258423 AATTCACA
1 AATTCACC
28258431 AATTC
1 AATTC
28258436 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (8 bp):
AATTCACC
Found at i:28260453 original size:17 final size:17
Alignment explanation
Indices: 28260428--28260511 Score: 68
Period size: 17 Copynumber: 4.9 Consensus size: 17
28260418 TTTAATTAAT
*
28260428 TTTTTAAAATTAAAAAA
1 TTTTAAAAATTAAAAAA
*
28260445 TTTTAAAAATT--AAAT
1 TTTTAAAAATTAAAAAA
28260460 TTTTAAAAATT-AAAAA
1 TTTTAAAAATTAAAAAA
*
28260476 TGATTAAAAGTATTAGAAAAA
1 T-TTTAAAA--ATTA-AAAAA
*
28260497 -TATAAAAATTAAAAA
1 TTTTAAAAATTAAAAA
28260512 TATATACATG
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 14 0.25
16 8 0.15
17 20 0.36
19 8 0.15
21 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
TTTTAAAAATTAAAAAA
Found at i:28260465 original size:15 final size:15
Alignment explanation
Indices: 28260421--28260473 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
28260411 AAGATCATTT
*
28260421 AATT-AATTTTTTAA
1 AATTAAATTTTTAAA
*
28260435 AATTAAAAAATTTTAAA
1 AATT--AAATTTTTAAA
28260452 AATTAAATTTTTAAA
1 AATTAAATTTTTAAA
28260467 AATTAAA
1 AATTAAA
28260474 AATGATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 4 0.12
15 17 0.52
17 12 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAAATTTTTAAA
Found at i:28260483 original size:32 final size:31
Alignment explanation
Indices: 28260421--28260484 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
28260411 AAGATCATTT
* *
28260421 AATTAATTTTTTAAAATTAAAAAATTTTAAA
1 AATTAATTTTTAAAAATTAAAAAATATTAAA
28260452 AATTAAATTTTTAAAAATT-AAAAATGATTAAA
1 AATT-AATTTTTAAAAATTAAAAAAT-ATTAAA
28260484 A
1 A
28260485 GTATTAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (31 bp):
AATTAATTTTTAAAAATTAAAAAATATTAAA
Found at i:28265929 original size:13 final size:11
Alignment explanation
Indices: 28265902--28265941 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 11
28265892 AAAAAACCAT
28265902 AAAAATTATAA
1 AAAAATTATAA
28265913 AAAAATTTATCAA
1 AAAAA-TTAT-AA
28265926 AAAAAGTTATAA
1 AAAAA-TTATAA
28265938 AAAA
1 AAAA
28265942 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 10 0.38
13 11 0.42
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (11 bp):
AAAAATTATAA
Done.