Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 34 of 226
Found at i:11834402 original size:127 final size:126
Alignment explanation
Indices: 11834196--11834555 Score: 501
Period size: 126 Copynumber: 2.9 Consensus size: 126
11834186 AAAAACTTTT
* * * *
11834196 TTTTTCTACAGTAGTTTTTG-AAAAATAATTTTGAAAAAACGGTTCTA-AA-AGATAATGTAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACGGTTC-AGAACAAATAGTGTAAAA
* * *
11834258 AACGCTTAAAGCAGGATGCACTGTTAGCAAAATTACTAAAAAATAGCTCCCATGTGGATGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAA-AGCTCCCACGTGGATGCTC
* *
11834321 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGATTCAGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACGGTTCAGAACAAATAGTGTAAAAA
* *
11834386 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGATGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGATGCTC
* * * *
11834447 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTCTGAACAAATAGTGTTAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACGGTTCAGAACAAATAGTGTAAAAA
* * * * *
11834512 ACTCTTCAAGCAAGATGTACTGTCAGCAAAATTATTGAAAAAAG
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAG
11834556 TTACATAAGT
Statistics
Matches: 212, Mismatches: 20, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
125 20 0.09
126 141 0.67
127 51 0.24
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACGGTTCAGAACAAATAGTGTAAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGATGCTC
Found at i:11836060 original size:227 final size:227
Alignment explanation
Indices: 11835665--11836123 Score: 909
Period size: 227 Copynumber: 2.0 Consensus size: 227
11835655 AAAAAGTACA
11835665 AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
1 AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
11835730 TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
66 TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
11835795 TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAAGGCGGATCCAAGAACTTCAGTG
131 TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAAGGCGGATCCAAGAACTTCAGTG
11835860 TCGGTCTTAATTGCCAATATTTGTAGCCAATT
196 TCGGTCTTAATTGCCAATATTTGTAGCCAATT
11835892 AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
1 AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
11835957 TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
66 TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
*
11836022 TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAATGCGGATCCAAGAACTTCAGTG
131 TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAAGGCGGATCCAAGAACTTCAGTG
11836087 TCGGTCTTAATTGCCAATATTTGTAGCCAATT
196 TCGGTCTTAATTGCCAATATTTGTAGCCAATT
11836119 AAGGT
1 AAGGT
11836124 ACACGCATTC
Statistics
Matches: 231, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 231 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (227 bp):
AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAAGGCGGATCCAAGAACTTCAGTG
TCGGTCTTAATTGCCAATATTTGTAGCCAATT
Found at i:11837754 original size:24 final size:24
Alignment explanation
Indices: 11837698--11837754 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
11837688 AAGAACTTCT
*
11837698 ATTTTATTAAAAATATAAAAATAA
1 ATTTTATTAAAAATATAAAAACAA
*
11837722 ATTACTATT-AAAATATTAAAAACAA
1 ATT-TTATTAAAAATA-TAAAAACAA
*
11837747 CTTTTATT
1 ATTTTATT
11837755 TTATAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (24 bp):
ATTTTATTAAAAATATAAAAACAA
Found at i:11837896 original size:93 final size:92
Alignment explanation
Indices: 11837702--11837893 Score: 318
Period size: 93 Copynumber: 2.1 Consensus size: 92
11837692 ACTTCTATTT
*
11837702 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATAAATTGAA
1 TATTAAAAATATAAAAATAAATTACTAATAAAATATTAAAAACAACTTTTATTTTATAAATTGAA
*
11837767 ACAATATAAAAATAGTTTGTACAAATA
66 ACAATATAAAAATAGATTGTACAAATA
*
11837794 TATTAAAAATATAAAAAATAAATTACTAATAAAATATTAAAAGCAACTTTTATTTTATTAAA-TG
1 TATTAAAAATAT-AAAAATAAATTACTAATAAAATATTAAAAACAACTTTTATTTTA-TAAATTG
11837858 AAACAATATAAAAA-A-ATTGTACAAATA
64 AAACAATATAAAAATAGATTGTACAAATA
11837885 TATTAAAAA
1 TATTAAAAA
11837894 AATCAATGTT
Statistics
Matches: 95, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
91 20 0.21
92 13 0.14
93 58 0.61
94 4 0.04
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.34
Consensus pattern (92 bp):
TATTAAAAATATAAAAATAAATTACTAATAAAATATTAAAAACAACTTTTATTTTATAAATTGAA
ACAATATAAAAATAGATTGTACAAATA
Found at i:11839868 original size:18 final size:20
Alignment explanation
Indices: 11839845--11839884 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
11839835 AAAATTAATT
*
11839845 AAAATTACATAA-A-TGAAA
1 AAAATTAAATAATATTGAAA
11839863 AAAATTAAATAATATTGAAA
1 AAAATTAAATAATATTGAAA
11839883 AA
1 AA
11839885 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAATTAAATAATATTGAAA
Found at i:11841837 original size:10 final size:10
Alignment explanation
Indices: 11841824--11841857 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
11841814 CACACCCCCT
*
11841824 CTCTCTCTCT
1 CTCTCTCTCA
11841834 CTCTCTCTCA
1 CTCTCTCTCA
*
11841844 CTCTTTCTCA
1 CTCTCTCTCA
11841854 CTCT
1 CTCT
11841858 GGTTTAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.06, C:0.47, G:0.00, T:0.47
Consensus pattern (10 bp):
CTCTCTCTCA
Found at i:11853331 original size:190 final size:180
Alignment explanation
Indices: 11852978--11853339 Score: 458
Period size: 190 Copynumber: 2.0 Consensus size: 180
11852968 AAAATAAAAA
11852978 GTTTTTGGGGAATAAAATTTTGAGGGAAAGTAAATAGGTAAAATTTTGGAAGGAAAATATTAAAA
1 GTTTTTGGGGAATAAAATTTTGAGGGAAAGTAAATAGGTAAAATTTTGGAAGGAAAATATTAAAA
* ** *
11853043 AAAAATTGGGGGGATGGGTTTGGGGTAGATGAGGGTGGGAAAGGAGGGGAGTAAAAGTTTTAGGG
66 AAAAATTGGGGGAATGAATTTGGGGTAGATGAGGGTGGGAAAGGAGGGAAGTAAAAGTTTTAGGG
*
11853108 GGAAAGTGGGAGGGAGTAAAAATTTTGGGGAAAAATAAAAAGTTTTAAGG
131 GGAAAGTGGGAAGGAGTAAAAATTTTGGGGAAAAATAAAAAGTTTTAAGG
* ** *
11853158 GTTTTT-GGGAGTAAAATTTTGAGGGAAAGTAAATGGGAGAGTAAAATTTTTTAGGGAAAATATT
1 GTTTTTGGGGAATAAAATTTTGAGGGAAAGTAAAT---AG-GTAAAATTTTGGAAGGAAAATATT
* **
11853222 AAAAAAATATATTTGGTGGGAAATGAATTTTGGGTAGATGAGGGATTGGGATGGGAGGGAAGTAA
62 AAAAAAA-A-A-TTGG-GGG-AATGAATTTGGGGTAGATGAGGG--TGGGAAAGGAGGGAAGTAA
* * * *
11853287 AAGTTTT-GGGGGGAAGTGGGAAGGAGTTAAAGTTTTGGGGGAAAAGTAAAAAG
120 AAGTTTTAGGGGGAAAGTGGGAAGGAGTAAAAATTTT-GGGGAAAAATAAAAAG
11853340 GTCTGGGGTT
Statistics
Matches: 154, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
179 27 0.18
180 6 0.04
182 2 0.01
183 28 0.18
184 1 0.01
185 1 0.01
186 4 0.03
187 3 0.02
188 19 0.12
189 25 0.16
190 38 0.25
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.27
Consensus pattern (180 bp):
GTTTTTGGGGAATAAAATTTTGAGGGAAAGTAAATAGGTAAAATTTTGGAAGGAAAATATTAAAA
AAAAATTGGGGGAATGAATTTGGGGTAGATGAGGGTGGGAAAGGAGGGAAGTAAAAGTTTTAGGG
GGAAAGTGGGAAGGAGTAAAAATTTTGGGGAAAAATAAAAAGTTTTAAGG
Found at i:11855064 original size:39 final size:40
Alignment explanation
Indices: 11855019--11855186 Score: 211
Period size: 38 Copynumber: 4.3 Consensus size: 40
11855009 GCTCCTCGTT
* * *
11855019 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
11855059 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
11855098 CGAATGCCTTC-GGACTTAACCCGGA-TTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
11855136 CAAATGCCTTCGGG-CTTAACCCGGATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
11855174 CAAATGCCTTCGG
1 CAAATGCCTTCGG
11855187 ATCTTAGTCC
Statistics
Matches: 115, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
38 54 0.47
39 51 0.44
40 10 0.09
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:11855142 original size:38 final size:38
Alignment explanation
Indices: 11855019--11855239 Score: 194
Period size: 38 Copynumber: 5.7 Consensus size: 38
11855009 GCTCCTCGTT
* * * *
11855019 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTC-GGACTTAACCCGG-ATTAGTAACTCGCA
* **
11855059 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTC-GGACTTAACCCGGA-TTAGTAACTCGCA
* *
11855098 CGAATGCCTTCGGACTTAACCCGGATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAACCCGGATTAGTAACTCGCA
* * *
11855136 CAAATGCCTTCGGGCTTAACCCGGATTTGTATCTCGCA
1 CAAATGCCTTCGGACTTAACCCGGATTAGTAACTCGCA
** * * *
11855174 CAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAACCCGGAT-TAGTAAC-TCGCA
*
11855215 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAACCCGGA
11855240 CAGCATTCAA
Statistics
Matches: 154, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
38 58 0.38
39 56 0.36
40 29 0.19
41 11 0.07
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAACCCGGATTAGTAACTCGCA
Found at i:11855157 original size:77 final size:77
Alignment explanation
Indices: 11855019--11855192 Score: 208
Period size: 77 Copynumber: 2.2 Consensus size: 77
11855009 GCTCCTCGTT
* * *
11855019 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTC-GGACTTAACCCGGTATTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
11855084 TTTAACAACTCGCA
65 TTT-ACAACTCGCA
* * * *
11855098 CGAATGCCTTCGGACTTAACCCGG-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAACCCGGA
1 CAAATGCCTTCGGACTTAACCCGGTATTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGA
** *
11855161 TTTGTATCTCGCA
65 TTTACAACTCGCA
11855174 CAAATGCCTTCGGATCTTA
1 CAAATGCCTTCGGA-CTTA
11855193 GTCCGGATAT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
76 20 0.24
77 29 0.35
78 23 0.28
79 10 0.12
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (77 bp):
CAAATGCCTTCGGACTTAACCCGGTATTAGTAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTACAACTCGCA
Found at i:11855248 original size:41 final size:41
Alignment explanation
Indices: 11855171--11855248 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
11855161 TTTGTATCTC
* * *
11855171 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
11855212 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
11855249 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:11859347 original size:36 final size:36
Alignment explanation
Indices: 11859250--11859433 Score: 134
Period size: 36 Copynumber: 4.9 Consensus size: 36
11859240 GTATGATCAT
*
11859250 TATCAC-TTGTC-CCTGATCAGATAAGT-TAGCCACAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAG-C-CAC
*
11859285 GTATTCAC-TCGT-TCTTGATCAGATAAGTGT-GCTGC-C
1 -TA-TCACTTTGTCTCTTGATCAGATAAGTGTAGC--CAC
*
11859321 TTATCACTTTGTTTC-TGATCAGATAAGTGTAGCCAC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCAC
11859357 TATCACTTTGTCTCTTGATCAGATAAGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGT-G-T--AGC---CAC
*
11859400 TTATCAC-TTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
11859434 GAAGCTATGC
Statistics
Matches: 124, Mismatches: 7, Indels: 34
0.75 0.04 0.21
Matches are distributed among these distances:
35 18 0.15
36 39 0.31
37 28 0.23
38 2 0.02
39 3 0.02
40 3 0.02
41 1 0.01
43 24 0.19
44 6 0.05
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (36 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCAC
Found at i:11859373 original size:72 final size:72
Alignment explanation
Indices: 11859249--11859384 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 72
11859239 CGTATGATCA
11859249 TTATCACTTGTCCCTGATCAGATAAGTTAGCCACACGTATTCACTCGTTCTTGATCAGATAAGTG
1 TTATCACTTGTCCCTGATCAGATAAGTTAGCCACACGTATTCACTCGTTCTTGATCAGATAAGTG
11859314 TGCTGCC
66 TGCTGCC
** *
11859321 TTATCACTTTGTTTCTGATCAGATAAGTGTAG-C-CAC-TA-TCACTTTGTCTCTTGATCAGATA
1 TTATCAC-TTGTCCCTGATCAGATAAGT-TAGCCACACGTATTCAC-TCGT-TCTTGATCAGATA
11859382 AGT
62 AGT
11859385 AGCTAAAGCT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
70 4 0.07
71 5 0.09
72 26 0.46
73 19 0.33
74 3 0.05
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (72 bp):
TTATCACTTGTCCCTGATCAGATAAGTTAGCCACACGTATTCACTCGTTCTTGATCAGATAAGTG
TGCTGCC
Found at i:11859463 original size:53 final size:52
Alignment explanation
Indices: 11859394--11859609 Score: 265
Period size: 53 Copynumber: 4.3 Consensus size: 52
11859384 TAGCTAAAGC
* *
11859394 TATCACTTATCACTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATGCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT-CACT
*
11859447 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGT-ATAGCCGAAGCTATCACT
*
11859500 TATCAC---T---TTGTCACTT-ATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
11859545 T-TCACTTTCCACTTGTCACTTGATCAGATAAGTGTAG-CTAAGC--TCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
11859593 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
11859610 ATCAAAGTAC
Statistics
Matches: 143, Mismatches: 10, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
44 4 0.03
45 17 0.12
46 11 0.08
47 9 0.06
48 5 0.03
49 7 0.05
50 21 0.15
51 14 0.10
53 42 0.29
54 13 0.09
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:11859532 original size:99 final size:97
Alignment explanation
Indices: 11859359--11859613 Score: 362
Period size: 99 Copynumber: 2.7 Consensus size: 97
11859349 GTAGCCACTA
* * *
11859359 TCACTTTGTCTCTTGATCAGATAA--GTAGCTAAAGCTATCACTTATCAC-TTGTCTCTTGATCA
1 TCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCA
11859421 GATAAGTATAGCCGAAGCTATGCACTTATCACTTT
65 GATAAGTATAGCCGAAGCTAT-CACTT-TCACTTT
*
11859456 TCACTTGTCACTTGATCAGATAAGTGTTAGCCGAAGCTATCACTTATCACTTTGTCACTT-ATCA
1 TCACTTGTCACTTGATCAGATAAGTG-TAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCA
*
11859520 GATAAGTATAGCCGAAGCTATTACTTTCACTTT
65 GATAAGTATAGCCGAAGCTATCACTTTCACTTT
* *
11859553 CCACTTGTCACTTGATCAGATAAGTGTAG-CTAAGC--TCACTTATCACTTTGTCACTTGATCA
1 TCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCA
11859614 AAGTACTCAA
Statistics
Matches: 146, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
93 21 0.14
94 4 0.03
95 5 0.03
96 21 0.14
97 36 0.25
98 5 0.03
99 46 0.32
100 8 0.05
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (97 bp):
TCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAG
ATAAGTATAGCCGAAGCTATCACTTTCACTTT
Found at i:11869859 original size:21 final size:20
Alignment explanation
Indices: 11869813--11869860 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
11869803 ATACAATTAA
*
11869813 ATATAAAAAGATATATATAG
1 ATATAAAAAAATATATATAG
* * *
11869833 ACATAAACAAAATATGTATAT
1 ATATAAA-AAAATATATATAG
11869854 ATATAAA
1 ATATAAA
11869861 TTAACAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (20 bp):
ATATAAAAAAATATATATAG
Found at i:11869866 original size:25 final size:27
Alignment explanation
Indices: 11869823--11869872 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
11869813 ATATAAAAAG
11869823 ATATATATAGACATAAACAAAATATGT
1 ATATATATAGACATAAACAAAATATGT
*
11869850 ATATATATA-A-ATTAACAAAATAT
1 ATATATATAGACATAAACAAAATAT
11869873 ATAAAGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
26 1 0.05
27 9 0.41
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (27 bp):
ATATATATAGACATAAACAAAATATGT
Found at i:11870101 original size:3 final size:3
Alignment explanation
Indices: 11870093--11870122 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
11870083 AAATAAGTAG
11870093 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11870123 GGACTAAATC
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11871221 original size:15 final size:16
Alignment explanation
Indices: 11871195--11871224 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11871185 TAGTGTTTAG
11871195 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
11871211 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
11871225 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:11874715 original size:3 final size:3
Alignment explanation
Indices: 11874702--11874734 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
11874692 AGACGACAAT
11874702 GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GA
11874735 CCTGAATCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11884640 original size:7 final size:7
Alignment explanation
Indices: 11884625--11884659 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
11884615 TTATTTTTAT
*
11884625 TTTTTAA
1 TTTTAAA
11884632 TTTTAAA
1 TTTTAAA
11884639 TTTTAAA
1 TTTTAAA
11884646 TTTTAAA
1 TTTTAAA
11884653 TTTTAAA
1 TTTTAAA
11884660 ATACTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTTAAA
Found at i:11884642 original size:14 final size:14
Alignment explanation
Indices: 11884611--11884656 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
11884601 TATATTTTTT
*
11884611 ATTTTT-ATTTTTA
1 ATTTTTAATTTTAA
*
11884624 TTTTTTAATTTTAA
1 ATTTTTAATTTTAA
*
11884638 ATTTTAAATTTTAA
1 ATTTTTAATTTTAA
11884652 ATTTT
1 ATTTT
11884657 AAAATACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTTAATTTTAA
Found at i:11889211 original size:20 final size:20
Alignment explanation
Indices: 11889186--11889225 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11889176 TTTCAAATTA
*
11889186 ATTTTACCAAATATAATATT
1 ATTTTAACAAATATAATATT
**
11889206 ATTTTAATGAATATAATATT
1 ATTTTAACAAATATAATATT
11889226 TATCTAGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTTTAACAAATATAATATT
Found at i:11893675 original size:54 final size:54
Alignment explanation
Indices: 11893568--11893713 Score: 168
Period size: 54 Copynumber: 2.7 Consensus size: 54
11893558 CTAACAGAAC
* * * * * * * *
11893568 ACGCCATACAGGCAAT-CATATAGAGTATGCCACCAAGTCGATCCATTCTGAGT
1 ACGCCACAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
* * *
11893621 ATGCCACAAAGGCAATCCATTTAAAGTGTGCCACAAAGGCGAGCCAGTCAGAGT
1 ACGCCACAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
* *
11893675 ACGCCACAAAGGCAATCCAATTAGAGTACGCCACAAAGG
1 ACGCCACAAAGGCAATCCATTTAGAGTATGCCACAAAGG
11893714 TAATCCAGTT
Statistics
Matches: 76, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
53 13 0.17
54 63 0.83
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (54 bp):
ACGCCACAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
Found at i:11893734 original size:27 final size:27
Alignment explanation
Indices: 11893588--11893734 Score: 143
Period size: 27 Copynumber: 5.4 Consensus size: 27
11893578 GGCAATCATA
* * *
11893588 TAGAGTATGCCACCAAGTCGATCCA-T
1 TAGAGTATGCCACAAAGGCAATCCAGT
* *
11893614 TCTGAGTATGCCACAAAGGCAATCCATT
1 T-AGAGTATGCCACAAAGGCAATCCAGT
* * * *
11893642 TAAAGTGTGCCACAAAGGCGAGCCAGT
1 TAGAGTATGCCACAAAGGCAATCCAGT
* * *
11893669 CAGAGTACGCCACAAAGGCAATCCAAT
1 TAGAGTATGCCACAAAGGCAATCCAGT
* *
11893696 TAGAGTACGCCACAAAGGTAATCCAGT
1 TAGAGTATGCCACAAAGGCAATCCAGT
*
11893723 TAGAGTTTGCCA
1 TAGAGTATGCCA
11893735 TGGTCATGGA
Statistics
Matches: 97, Mismatches: 22, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
26 1 0.01
27 94 0.97
28 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (27 bp):
TAGAGTATGCCACAAAGGCAATCCAGT
Found at i:11898080 original size:26 final size:26
Alignment explanation
Indices: 11898032--11898081 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
11898022 ATGAAAAAGG
**
11898032 GGTTGCTAAGTACAGATTTCCCGAGA
1 GGTTGCTAAGTACAGATGCCCCGAGA
* *
11898058 GGTTGCTAAGTGCTGATGCCCCGA
1 GGTTGCTAAGTACAGATGCCCCGA
11898082 ATTATTGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (26 bp):
GGTTGCTAAGTACAGATGCCCCGAGA
Found at i:11934677 original size:17 final size:17
Alignment explanation
Indices: 11934640--11934677 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11934630 TTTTATACCG
**
11934640 TAAAGTTCCTCTATTTT
1 TAAAGTTCCTCTATTGA
11934657 TAAAGTTCCTCTATTGA
1 TAAAGTTCCTCTATTGA
11934674 TAAA
1 TAAA
11934678 TTCAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (17 bp):
TAAAGTTCCTCTATTGA
Found at i:11935065 original size:27 final size:28
Alignment explanation
Indices: 11935035--11935099 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
11935025 CTTATCAGGT
11935035 AGGCGCCAATGAAA-GTGCCTCATAGAG
1 AGGCGCCAATGAAATGTGCCTCATAGAG
* * *
11935062 AGGCACCAA-GAAATGTGCCTCTTAGGG
1 AGGCGCCAATGAAATGTGCCTCATAGAG
11935089 AGGCGCCAATG
1 AGGCGCCAATG
11935100 GTGGCCTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.12
27 27 0.84
28 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (28 bp):
AGGCGCCAATGAAATGTGCCTCATAGAG
Found at i:11935245 original size:17 final size:17
Alignment explanation
Indices: 11935220--11935276 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
11935210 GTAGGAAAAA
*
11935220 AAAAAGAGAGAAAGGAG
1 AAAAAGAGAGAAAGAAG
*
11935237 AAGAAGAGA-AGAAGAAG
1 AAAAAGAGAGA-AAGAAG
* *
11935254 AAAAAGAAAGAAAGAAA
1 AAAAAGAGAGAAAGAAG
11935271 AAAAAG
1 AAAAAG
11935277 GTAATGTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAGAAAGAAG
Found at i:11935432 original size:19 final size:19
Alignment explanation
Indices: 11935404--11935592 Score: 114
Period size: 19 Copynumber: 9.2 Consensus size: 19
11935394 TTGGATTAGT
*
11935404 ATTTTATATGAATATTGTA
1 ATTTTGTATGAATATTGTA
11935423 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
* *
11935442 ATTATTTTAT-AATTAAATTAATA
1 ATT-TTGTATGAA-T--ATT-GTA
* * * *
11935465 TTTTTAGTTTTGGAT-TAGT-
1 ATTTT-G-TATGAATATTGTA
11935484 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
11935503 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
11935522 ATTTTTTGTATGAATGTTGTA
1 A--TTTTGTATGAATATTGTA
*
11935543 ATTTCGGGATATATTGTAATATTGTAA
1 ATTT-----TGTA-TG-AATATTGT-A
11935570 ATTTTTGTATGAATATTGTA
1 A-TTTTGTATGAATATTGTA
11935590 ATT
1 ATT
11935593 ATTTTATAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
17 5 0.04
18 4 0.03
19 52 0.39
20 9 0.07
21 27 0.20
22 7 0.05
23 7 0.05
24 6 0.05
25 3 0.02
26 7 0.05
27 2 0.02
28 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:11935470 original size:61 final size:58
Alignment explanation
Indices: 11935405--11935610 Score: 139
Period size: 61 Copynumber: 3.3 Consensus size: 58
11935395 TGGATTAGTA
*
11935405 TTTTATATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTAT-AATTAAAT-TAATAT
1 TTTTATATGAAT-TTGTAATTTTGTATGAATATTGTAATT-TTGTATGAA-T-AATGTAAT-T
* * * *
11935466 TTTTAGTTTTGGATTAGT-ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATT
1 TTTTA--TATGAATTTGTAATTTTGTATGAATATTGTAATTTTGTATGAATAATGTAATT
* * *
11935525 TTTTGTATGAATGTTGTAATTTCGGGATATATTGTAATATTGTAAATTTTTGTATGAATATTGTA
1 TTTTATATGAAT-TTGTAATTT-----TGTA-TG-AATATTGT-AA-TTTTGTATGAATAATGTA
11935590 ATT
56 ATT
*
11935593 ATTTTATAATTAATTTGT
1 -TTTTAT-ATGAATTTGT
11935611 TAGTAATTTA
Statistics
Matches: 116, Mismatches: 12, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
57 5 0.04
58 3 0.03
59 11 0.09
60 10 0.09
61 29 0.25
62 3 0.03
63 5 0.04
64 3 0.03
65 2 0.02
66 8 0.07
67 2 0.02
68 21 0.18
69 9 0.08
70 5 0.04
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (58 bp):
TTTTATATGAATTTGTAATTTTGTATGAATATTGTAATTTTGTATGAATAATGTAATT
Found at i:11935530 original size:21 final size:21
Alignment explanation
Indices: 11935485--11935546 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
11935475 TGGATTAGTA
11935485 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
11935504 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
11935525 TTTTGTATGAATGTTGTAATT
1 TTTTGTATGAATATTGTAATT
11935546 T
1 T
11935547 CGGGATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.56
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:11935655 original size:60 final size:60
Alignment explanation
Indices: 11935585--11935706 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
11935575 TGTATGAATA
* * * * *
11935585 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
11935645 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
11935705 TT
1 TT
11935707 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.11
60 49 0.89
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:11935845 original size:16 final size:15
Alignment explanation
Indices: 11935824--11935860 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
11935814 CTCATTTAAT
11935824 TTTTATATAATGTAA
1 TTTTATATAATGTAA
*
11935839 CTTTTATATAATTTAA
1 -TTTTATATAATGTAA
11935855 TTTTAT
1 TTTTAT
11935861 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
TTTTATATAATGTAA
Found at i:11940987 original size:24 final size:24
Alignment explanation
Indices: 11940935--11940987 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
11940925 ATACCTTATC
* *
11940935 CTTCTTCTTCTTTACCTTTCTTTT
1 CTTCTTCTGCCTTACCTTTCTTTT
*
11940959 TTTCTTCTGCCTT-CCTTTCTATTT
1 CTTCTTCTGCCTTACCTTTCT-TTT
11940983 CTTCT
1 CTTCT
11940988 GTTTCTCTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.64
Consensus pattern (24 bp):
CTTCTTCTGCCTTACCTTTCTTTT
Found at i:11941116 original size:27 final size:27
Alignment explanation
Indices: 11941043--11941120 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
11941033 GAAAAATCAG
*
11941043 ACCATTGGCGCCTCTTAACAT-GGCACC
1 ACCATTGGCGCCT-TTAAGATAGGCACC
* * *
11941070 ACTATTGGCGCCTCTCAGATAGGCACC
1 ACCATTGGCGCCTTTAAGATAGGCACC
*
11941097 ACCATTGGCGCCTTTGAGATAGGC
1 ACCATTGGCGCCTTTAAGATAGGC
11941121 GCCAATACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 4 0.09
27 39 0.91
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (27 bp):
ACCATTGGCGCCTTTAAGATAGGCACC
Found at i:11941352 original size:30 final size:29
Alignment explanation
Indices: 11941299--11941376 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 29
11941289 TGAAAAAAGT
* *
11941299 ACCCCATTTTGGTAAATAATTTTTCTGAC
1 ACCCCATTTTAGTAAAAAATTTTTCTGAC
* * *
11941328 ACCCCATTTTAGTACAAAAATTTTTTTTAT
1 ACCCCATTTTAGTA-AAAAATTTTTCTGAC
11941358 ACCCCATTTTAGTAAAAAA
1 ACCCCATTTTAGTAAAAAA
11941377 ACCCCTATAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 18 0.42
30 25 0.58
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (29 bp):
ACCCCATTTTAGTAAAAAATTTTTCTGAC
Found at i:11944156 original size:3 final size:3
Alignment explanation
Indices: 11944135--11944179 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
11944125 TTAAAATACT
* *
11944135 TAA TAA TCA TAA -AA AAA TAA TAA TAA -AA TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11944180 GATCTGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:11944162 original size:11 final size:11
Alignment explanation
Indices: 11944143--11944179 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
11944133 CTTAATAATC
*
11944143 ATAAAAAAATA
1 ATAATAAAATA
11944154 ATAATAAAATA
1 ATAATAAAATA
11944165 ATAATAAAATA
1 ATAATAAAATA
11944176 ATAA
1 ATAA
11944180 GATCTGACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:11944164 original size:8 final size:9
Alignment explanation
Indices: 11944135--11944179 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 9
11944125 TTAAAATACT
*
11944135 TAATAATCA
1 TAATAATAA
*
11944144 TAA-AAAAA
1 TAATAATAA
11944152 TAATAATAA
1 TAATAATAA
11944161 -AATAATAA
1 TAATAATAA
11944169 TAA-AATAA
1 TAATAATAA
11944177 TAA
1 TAA
11944180 GATCTGACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
8 22 0.71
9 9 0.29
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
TAATAATAA
Found at i:11944179 original size:14 final size:14
Alignment explanation
Indices: 11944135--11944171 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11944125 TTAAAATACT
*
11944135 TAATAATCATAAAA
1 TAATAATAATAAAA
*
11944149 AAATAATAATAAAA
1 TAATAATAATAAAA
11944163 TAATAATAA
1 TAATAATAA
11944172 AATAATAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:11946388 original size:17 final size:16
Alignment explanation
Indices: 11946366--11946426 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 16
11946356 ATAATGATTC
*
11946366 TTTAATTTTATATATTT
1 TTTAATTTT-TATAATT
11946383 TTTAATTTTTATAATT
1 TTTAATTTTTATAATT
* * *
11946399 TATAATTTATACTTATT
1 TTTAATTTTTA-TAATT
*
11946416 TTTATTTTTTA
1 TTTAATTTTTA
11946427 ATGATTATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTAATTTTTATAATT
Found at i:11946404 original size:16 final size:17
Alignment explanation
Indices: 11946368--11946406 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
11946358 AATGATTCTT
* *
11946368 TAATTTTATATATTTTT
1 TAATTTTATATAATTTA
11946385 TAATTTT-TATAATTTA
1 TAATTTTATATAATTTA
11946401 TAATTT
1 TAATTT
11946407 ATACTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTATATAATTTA
Found at i:11947982 original size:49 final size:49
Alignment explanation
Indices: 11947888--11947980 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
11947878 TTGATTTTAT
11947888 AAATAAAATATTTATTAATTAAAAATATGAATTAAAAATAAAAAATTGA
1 AAATAAAATATTTATTAATTAAAAATATGAATTAAAAATAAAAAATTGA
* * *
11947937 AAATAATATATTTATTAATTAAAAA-ATTAATTAAGAATAAAAAA
1 AAATAAAATATTTATTAATTAAAAATATGAATTAAAAATAAAAAA
11947981 ATGTTTGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 17 0.41
49 24 0.59
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (49 bp):
AAATAAAATATTTATTAATTAAAAATATGAATTAAAAATAAAAAATTGA
Found at i:11950316 original size:23 final size:23
Alignment explanation
Indices: 11950290--11950371 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
11950280 CACAACCTAT
*
11950290 CGGGACGCTCCGAAGAGCTATAA
1 CGGGATGCTCCGAAGAGCTATAA
* *
11950313 CGGGAAGCT-CGCAAGAACCATATAA
1 CGGGATGCTCCG-AAG-AGC-TATAA
*
11950338 CGGGATGCTCATG-AGAGCTAATAA
1 CGGGATGCTC-CGAAGAGCT-ATAA
11950362 CGGGATGCTC
1 CGGGATGCTC
11950372 TTTCAAGCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 2 0.04
23 12 0.25
24 18 0.38
25 15 0.31
27 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (23 bp):
CGGGATGCTCCGAAGAGCTATAA
Found at i:11956420 original size:56 final size:50
Alignment explanation
Indices: 11956352--11956544 Score: 226
Period size: 50 Copynumber: 3.7 Consensus size: 50
11956342 AGGAATGAGA
* *
11956352 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTAAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-TATGAGAGG
* * *
11956408 TCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
* **
11956458 TCCTC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
* *
11956508 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
11956545 GTACAGAAAA
Statistics
Matches: 121, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.01
50 82 0.68
51 3 0.02
55 1 0.01
56 34 0.28
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
Found at i:11956515 original size:100 final size:103
Alignment explanation
Indices: 11956357--11956544 Score: 265
Period size: 100 Copynumber: 1.8 Consensus size: 103
11956347 TGAGATCCCA
* **
11956357 TGTAAGACCATGTCTAGGACATGGCATTGGCATCATTAAGATTATGAGAGGTCCCATGTAAGACC
1 TGTAAGACCATGTCTAGGACATGGCATGGGCATC---AAGATTATGAGAACTCCCATGTAAGACC
* *
11956422 ATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGGTCCTC
63 ATATCTGGGATATGGCATTGGCACCGAGATGAGAGGTCCTC
* *
11956463 TGTAAGACCATGTCTGGGACATGGCATGGGCA-C-CGA-TATGAGAACTCCCATGTAAGACCATA
1 TGTAAGACCATGTCTAGGACATGGCATGGGCATCAAGATTATGAGAACTCCCATGTAAGACCATA
11956525 TCTGGGATATGGCATTGGCA
66 TCTGGGATATGGCATTGGCA
11956545 GTACAGAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 42 0.56
101 2 0.03
105 1 0.01
106 30 0.40
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (103 bp):
TGTAAGACCATGTCTAGGACATGGCATGGGCATCAAGATTATGAGAACTCCCATGTAAGACCATA
TCTGGGATATGGCATTGGCACCGAGATGAGAGGTCCTC
Found at i:11956810 original size:12 final size:12
Alignment explanation
Indices: 11956793--11956831 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11956783 ATGAGTTATT
11956793 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
11956805 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
11956817 TAAGTGAGTAAG
1 TAAGTAAGCAAG
11956829 TAA
1 TAA
11956832 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:11957827 original size:20 final size:19
Alignment explanation
Indices: 11957790--11957828 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
11957780 AATTTTAAAA
*
11957790 TATTTTTAAAATACTTTTT
1 TATTTTTAAAATAATTTTT
11957809 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAAT-AATTTTT
11957829 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTAAAATAATTTTT
Found at i:11959236 original size:31 final size:31
Alignment explanation
Indices: 11959198--11959260 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
11959188 TTATTCGGGA
**
11959198 TACGCAATGTCACTGTTAAGGAAGAAGTTAT
1 TACGCAATGTCACCATTAAGGAAGAAGTTAT
11959229 TACGCAATGTCACCATTAAGGAAGAAGTTAT
1 TACGCAATGTCACCATTAAGGAAGAAGTTAT
11959260 T
1 T
11959261 CACGAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (31 bp):
TACGCAATGTCACCATTAAGGAAGAAGTTAT
Found at i:11961832 original size:22 final size:18
Alignment explanation
Indices: 11961809--11961847 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
11961799 AGAAATAGAG
11961809 AAAGAAACAGAGAAGCAA
1 AAAGAAACAGAGAAGCAA
11961827 AAAGAAACAGAGAAGCAA
1 AAAGAAACAGAGAAGCAA
11961845 AAA
1 AAA
11961848 CAAAGCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGAAACAGAGAAGCAA
Found at i:11962793 original size:41 final size:39
Alignment explanation
Indices: 11962736--11962871 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 39
11962726 TGACTTCGAG
11962736 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATATAT
1 TCGATGAGACACTGGGTGTCAA-TTATTACTTCGGAT-TAT
* * * *
11962777 TCGATGAGGCACTGGGTGCCAA-T-TCACTTCGGTTTA-
1 TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTAT
* * *
11962813 GCTGATGAGACACTAGGTGTCAAATTATTACTTCGAATTAT
1 TC-GATGAGACACTGGGTGTC-AATTATTACTTCGGATTAT
* * *
11962854 CCGATGGGGCACTGGGTG
1 TCGATGAGACACTGGGTG
11962872 CCAAACTGGT
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
36 1 0.01
37 17 0.23
38 11 0.15
39 2 0.03
40 23 0.31
41 21 0.28
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTAT
Found at i:11969835 original size:13 final size:13
Alignment explanation
Indices: 11969817--11969865 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 13
11969807 CATTCTCATT
11969817 CCCTTTCCCCTAC
1 CCCTTTCCCCTAC
11969830 CCCTTTCCCCTTATCC
1 CCCTTTCCCC-TA--C
11969846 TTCCCTTTCCCCTAC
1 --CCCTTTCCCCTAC
11969861 CCCTT
1 CCCTT
11969866 CCCTTTCCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 15 0.48
14 2 0.06
15 1 0.03
16 1 0.03
17 2 0.06
18 10 0.32
ACGTcount: A:0.06, C:0.57, G:0.00, T:0.37
Consensus pattern (13 bp):
CCCTTTCCCCTAC
Found at i:11969853 original size:18 final size:18
Alignment explanation
Indices: 11969830--11969873 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
11969820 TTTCCCCTAC
*
11969830 CCCTTTCCCCTTA-TCCTT
1 CCCTTTCCCC-TACCCCTT
11969848 CCCTTTCCCCTACCCCTT
1 CCCTTTCCCCTACCCCTT
11969866 CCCTTTCC
1 CCCTTTCC
11969874 TGTTTCGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.05, C:0.57, G:0.00, T:0.39
Consensus pattern (18 bp):
CCCTTTCCCCTACCCCTT
Found at i:11969856 original size:37 final size:36
Alignment explanation
Indices: 11969790--11969873 Score: 87
Period size: 37 Copynumber: 2.3 Consensus size: 36
11969780 ACCCATTCTT
* * * * *
11969790 CTCCCCTTTCTCCTTCTCATTCTCATTCCCTTTCCC
1 CTCCCCTTTCCCCTTATCATTCCCATTCCCCTACCC
* *
11969826 CTACCCCTTTCCCCTTATCCTTCCCTTTCCCCTACCC
1 CT-CCCCTTTCCCCTTATCATTCCCATTCCCCTACCC
*
11969863 CTTCCCTTTCC
1 CTCCCCTTTCC
11969874 TGTTTCGAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 10 0.26
37 29 0.74
ACGTcount: A:0.06, C:0.54, G:0.00, T:0.40
Consensus pattern (36 bp):
CTCCCCTTTCCCCTTATCATTCCCATTCCCCTACCC
Found at i:11971208 original size:30 final size:30
Alignment explanation
Indices: 11971172--11971229 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11971162 GCATTTGTAC
* *
11971172 AAGACCATAAGTTCCAATTTACTATGACAT
1 AAGACCATAAGTACCAACTTACTATGACAT
*
11971202 AAGACCATAAGTACCAACTTGCTATGAC
1 AAGACCATAAGTACCAACTTACTATGAC
11971230 TGGAATGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (30 bp):
AAGACCATAAGTACCAACTTACTATGACAT
Found at i:11972399 original size:34 final size:35
Alignment explanation
Indices: 11972344--11972410 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
11972334 CAAACACCAG
*
11972344 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
11972379 AAAACATTTTCCTG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11972411 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11972752 original size:29 final size:30
Alignment explanation
Indices: 11972706--11972764 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
11972696 GAATTAGATC
11972706 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
11972736 AAATCAAAATTT-ATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
11972765 TTAAACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:11974986 original size:21 final size:19
Alignment explanation
Indices: 11974921--11974987 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 19
11974911 ATAATTAAAA
*
11974921 TAATAATTTTGTACAATTTT
1 TAATAATTTT-TATAATTTT
* *
11974941 T-ATAATTCTTAATCATTTT
1 TAATAATT-TTTATAATTTT
11974960 TAAATAATTTTCTATAATTATT
1 T-AATAATTTT-TATAATT-TT
11974982 TAATAA
1 TAATAA
11974988 GCTAATCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
19 13 0.35
20 5 0.14
21 16 0.43
22 3 0.08
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (19 bp):
TAATAATTTTTATAATTTT
Found at i:11975100 original size:21 final size:20
Alignment explanation
Indices: 11975075--11975120 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
11975065 TAGATGTTGA
*
11975075 TTTTAATAATTTAAAAATATT
1 TTTTAACAATTTAAAAAT-TT
* *
11975096 TTTTAACATTTTAAATATTT
1 TTTTAACAATTTAAAAATTT
11975116 TTTTA
1 TTTTA
11975121 TAAATTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAACAATTTAAAAATTT
Found at i:11984383 original size:46 final size:46
Alignment explanation
Indices: 11984313--11984401 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 46
11984303 ACAATGTTAT
11984313 AACTCAATATGGATTTCTTCACTGAAATACCATACCTACGTTCCAC
1 AACTCAATATGGATTTCTTCACTGAAATACCATACCTACGTTCCAC
* * *
11984359 AACTCAGTAT-GATTTTCTTTACTGAATTACCATACCTACGTTC
1 AACTCAATATGGA-TTTCTTCACTGAAATACCATACCTACGTTC
11984402 AACACTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 2 0.05
46 37 0.95
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAATATGGATTTCTTCACTGAAATACCATACCTACGTTCCAC
Found at i:11994245 original size:16 final size:16
Alignment explanation
Indices: 11994226--11994264 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11994216 TTTTAATAAA
11994226 ATTAAAACTAATTGTT
1 ATTAAAACTAATTGTT
**
11994242 ATTAAATTTAATTGTT
1 ATTAAAACTAATTGTT
*
11994258 AGTAAAA
1 ATTAAAA
11994265 TTATCAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (16 bp):
ATTAAAACTAATTGTT
Found at i:11994247 original size:22 final size:22
Alignment explanation
Indices: 11994198--11994252 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
11994188 CCTTTTTTTA
* * *
11994198 ATTAAAATTAAAATTATTTTTT
1 ATTAAAATTAAAACTAATTGTT
*
11994220 AATAAAATTAAAACTAATTGTT
1 ATTAAAATTAAAACTAATTGTT
*
11994242 ATTAAATTTAA
1 ATTAAAATTAA
11994253 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAAAATTAAAACTAATTGTT
Found at i:11994347 original size:59 final size:59
Alignment explanation
Indices: 11994278--11994417 Score: 271
Period size: 59 Copynumber: 2.4 Consensus size: 59
11994268 TCAAATTATT
*
11994278 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
11994337 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
11994396 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
11994418 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:11994411 original size:9 final size:9
Alignment explanation
Indices: 11994399--11994426 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11994389 TTTATCAAAT
11994399 TATTAATTG
1 TATTAATTG
11994408 TATTAATTG
1 TATTAATTG
11994417 TATTAATTG
1 TATTAATTG
11994426 T
1 T
11994427 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:11995610 original size:21 final size:22
Alignment explanation
Indices: 11995572--11995641 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 22
11995562 AACAAACAAT
*
11995572 AAATAAGCATATATATAAATATA
1 AAATAATCATA-ATATAAATATA
11995595 AAATAATCA-AATATAAATAT-
1 AAATAATCATAATATAAATATA
* * *
11995615 TAATAATTATATTATAAATA-A
1 AAATAATCATAATATAAATATA
11995636 AAATAA
1 AAATAA
11995642 ACATCCAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.17
21 24 0.60
22 1 0.03
23 8 0.20
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (22 bp):
AAATAATCATAATATAAATATA
Found at i:11996507 original size:20 final size:21
Alignment explanation
Indices: 11996463--11996515 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
11996453 AAAGACATGG
11996463 ATTATGTTTTACTTGAGATTT
1 ATTATGTTTTACTTGAGATTT
*
11996484 -TTATTTTTTACCTT-AG-TTT
1 ATTATGTTTTA-CTTGAGATTT
*
11996503 ATTAT-ATTTACTT
1 ATTATGTTTTACTT
11996516 TAAAGAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.11
19 7 0.25
20 15 0.54
21 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (21 bp):
ATTATGTTTTACTTGAGATTT
Found at i:11999056 original size:30 final size:30
Alignment explanation
Indices: 11999022--11999083 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
11999012 CTTAACTAAA
*
11999022 TTACAAAATGGTCATTAAATTATTCAAAAG
1 TTACAAAATAGTCATTAAATTATTCAAAAG
* *
11999052 TTACAAAATAGTTATTAAATTATTCTAAAG
1 TTACAAAATAGTCATTAAATTATTCAAAAG
11999082 TT
1 TT
11999084 TTTATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (30 bp):
TTACAAAATAGTCATTAAATTATTCAAAAG
Found at i:12003241 original size:19 final size:20
Alignment explanation
Indices: 12003207--12003244 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12003197 AAGCAGGCTG
*
12003207 TAAAAAATGTAGTATATAAA
1 TAAAAAATATAGTATATAAA
12003227 TAAAAAATATA-TATATAA
1 TAAAAAATATAGTATATAA
12003245 TATGATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAAAATATAGTATATAAA
Found at i:12004387 original size:20 final size:21
Alignment explanation
Indices: 12004349--12004388 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12004339 AAATCAAATG
*
12004349 AAAATAAAAATCTTGAAATTC
1 AAAATAAAAATATTGAAATTC
*
12004370 AAAATAAAATTATT-AAATT
1 AAAATAAAAATATTGAAATT
12004389 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATAAAAATATTGAAATTC
Found at i:12004778 original size:16 final size:16
Alignment explanation
Indices: 12004753--12004784 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12004743 AGATTTATAT
*
12004753 AAAAATATTAAATTTA
1 AAAAAAATTAAATTTA
12004769 AAAAAAATTAAATTTA
1 AAAAAAATTAAATTTA
12004785 TTTAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAAAATTAAATTTA
Found at i:12008283 original size:30 final size:31
Alignment explanation
Indices: 12008231--12008331 Score: 102
Period size: 30 Copynumber: 3.3 Consensus size: 31
12008221 ATATTTTATG
* *
12008231 TATCATTATATTAAATTATTTAAATATGATT
1 TATCATTATATTAAAATATTTAAATATAATT
12008262 TATCATTATA-TAAAATATTTAAATATAATT
1 TATCATTATATTAAAATATTTAAATATAATT
* * *
12008292 TCTTATTGTATTTAAAAT-TTTAAA-AT-ATT
1 TATCATTATA-TTAAAATATTTAAATATAATT
12008321 TCATCTATTAT
1 T-ATC-ATTAT
12008332 TAAATTTACA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 4 0.07
30 28 0.48
31 20 0.34
32 6 0.10
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (31 bp):
TATCATTATATTAAAATATTTAAATATAATT
Found at i:12014411 original size:21 final size:21
Alignment explanation
Indices: 12014387--12014451 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
12014377 TATTGGTTTA
*
12014387 TTGCGGATCAAGTCAAGTTAC
1 TTGCGGAACAAGTCAAGTTAC
12014408 TTGCGGAACAAGTCAAGTTAC
1 TTGCGGAACAAGTCAAGTTAC
*
12014429 TTGCGGAACAAGTCAAGTCAC
1 TTGCGGAACAAGTCAAGTTAC
12014450 TT
1 TT
12014452 TCTATAGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (21 bp):
TTGCGGAACAAGTCAAGTTAC
Found at i:12021760 original size:24 final size:24
Alignment explanation
Indices: 12021728--12021776 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
12021718 GTCTTTTACC
*
12021728 ACCCTTAAAGGGCTTTCATATACT
1 ACCCGTAAAGGGCTTTCATATACT
*
12021752 ACCCGTAAAGGTCTTTCATATACT
1 ACCCGTAAAGGGCTTTCATATACT
12021776 A
1 A
12021777 GTGTGCAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (24 bp):
ACCCGTAAAGGGCTTTCATATACT
Found at i:12031214 original size:8 final size:7
Alignment explanation
Indices: 12031179--12031220 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
12031169 TTTTTAACGC
12031179 ATATTTT
1 ATATTTT
12031186 ATATTTT
1 ATATTTT
*
12031193 ATAATTT
1 ATATTTT
*
12031200 ATA-TAT
1 ATATTTT
12031206 ATATTTAT
1 ATATTT-T
12031214 ATATTTT
1 ATATTTT
12031221 TCTTTATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.17
7 18 0.60
8 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATATTTT
Found at i:12037530 original size:44 final size:44
Alignment explanation
Indices: 12037482--12037620 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
12037472 AGTCACCCGC
12037482 CTTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGAT
* ** * * * * ** * * * *
12037526 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTCCCTG-GGTTACAGCGGAGCAGGTTAAAAATAGCAGAT
* *
12037570 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGAT
12037614 CTTGCCT
1 CTTGCCT
12037621 TCTTGCACTG
Statistics
Matches: 65, Mismatches: 28, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
43 18 0.28
44 28 0.43
45 19 0.29
ACGTcount: A:0.26, C:0.27, G:0.25, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:12037591 original size:88 final size:88
Alignment explanation
Indices: 12037433--12037988 Score: 758
Period size: 88 Copynumber: 6.3 Consensus size: 88
12037423 GTGAAGATAA
* * * *
12037433 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGTCACCCGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
*
12037498 ACAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
*
12037521 CAGATCTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
12037586 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* ** * *
12037609 CAGATCTTGCCTTCTTGCACTGACAGTAAAGCAGATCGAAGACATCAGCCTTGCCTCCTTAGGTT
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
*
12037674 GCAGCGGAGCAAGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
12037697 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCACTGGGTT
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
* *
12037762 GCAGTGGAGTAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
12037785 CAGATCTTGCCTT-CTAGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGT
1 CAGATCTTGCCTTCCT-GCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGT
* *
12037849 TGCAGCGGAGCAGATTGAAAATAG
65 TGCAGCGGAGCAGGTTAAAAATAG
* * * ** * * *
12037873 CAGATATTGCCTTCATGTACTGACAATGAAGTAGATCGAA-ATCACAAAGCCTTGCCTCCTTAGG
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGA-CAC-CAGCCTTGCCTCCCTAGG
* * *
12037937 TTGCAGCGGAGCAGGTTGAAAACAC
64 TTGCAGCGGAGCAGGTTAAAAATAG
*
12037962 CAG-TCTTGCCTTCCTGTACTGACAGCG
1 CAGATCTTGCCTTCCTGCACTGACAGCG
12037989 GAGTAGACTT
Statistics
Matches: 418, Mismatches: 46, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
87 3 0.01
88 374 0.89
89 41 0.10
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:12037706 original size:44 final size:44
Alignment explanation
Indices: 12037570--12037708 Score: 104
Period size: 44 Copynumber: 3.2 Consensus size: 44
12037560 AGACACCAGC
* *
12037570 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCTTAGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
* ** *** ** * * * *
12037614 CTTGCCTTCTT-GCACTGACAGTAAAGC-AGATCGAAGACATCAG-C
1 CTTGCCTCCTTAG-GTTG-CAGCGGAGCAAG-TTAAAAATAGCAGAT
12037658 CTTGCCTCCTTAGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
1 CTTGCCTCCTTAGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
12037702 CTTGCCT
1 CTTGCCT
12037709 TCCTGCACCG
Statistics
Matches: 63, Mismatches: 26, Indels: 12
0.62 0.26 0.12
Matches are distributed among these distances:
43 15 0.24
44 33 0.52
45 15 0.24
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCTTAGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
Found at i:12038120 original size:44 final size:44
Alignment explanation
Indices: 12038056--12038386 Score: 303
Period size: 44 Copynumber: 7.6 Consensus size: 44
12038046 GAGACCAGCC
* *
12038056 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGGAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
* * * * * ** *
12038100 TATCTCCCTAAGAAGTAGTGGAGCAGATTG-AAGTCCCCA-ACCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGATCT
* * *
12038143 TATCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
* * * * * ** *
12038187 TATCTCCCTAAGCAGGAGTGGAGCA-GATCAAAGTCCCCAG-CCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGATCT
* *
12038230 TATCTCACTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
* * * * * *** *
12038274 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCA-ACCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
12038317 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
* *
12038361 TATCTCCCTAAACAGTAGTGGAGTAG
1 TATCTCCCTAAGCAGCAGTGGAGTAG
12038387 ATCGAAGATA
Statistics
Matches: 218, Mismatches: 62, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
43 97 0.44
44 121 0.56
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (44 bp):
TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
Found at i:12038244 original size:43 final size:43
Alignment explanation
Indices: 12038098--12038339 Score: 182
Period size: 43 Copynumber: 5.6 Consensus size: 43
12038088 AATTACAGAT
* * ** *
12038098 CTTATCTCCCTAAGAAGTAGTGGAGCAGATTGAAGTCCCCAAC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGTCCCCAGC
* * * * * * ** *
12038141 CTTATCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGCA-GATCAAAGTCCCCAG-C
*
12038185 CTTATCTCCCTAAGCAGGAGTGGAGCAGATCAAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGTCCCCAGC
* * * * * * ** *
12038228 CTTATCTCACTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGCA-GATCAAAGTCCCCAG-C
* * * *
12038272 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAAC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGTCCCCAGC
12038315 CTTATCTCCCTAAGCAGCAGTGGAG
1 CTTATCTCCCTAAGCAGCAGTGGAG
12038340 TAGGTTGAAA
Statistics
Matches: 146, Mismatches: 47, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
43 84 0.58
44 62 0.42
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.23
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGTCCCCAGC
Found at i:12038377 original size:87 final size:87
Alignment explanation
Indices: 12038056--12038394 Score: 536
Period size: 87 Copynumber: 3.9 Consensus size: 87
12038046 GAGACCAGCC
*
12038056 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTATCTCCCTAAGA-AGTAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAA-ACAGTAGTG
* *
12038120 GAGCAGATTGAAGTCCCCAACCT
65 GAGCAGATCGAAGACCCCAACCT
* * * *
12038143 TATCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGGAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGG
* * *
12038208 AGCAGATCAAAGTCCCCAGCCT
66 AGCAGATCGAAGACCCCAACCT
* *
12038230 TATCTCACTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGG
12038295 AGCAGATCGAAGACCCCAACCT
66 AGCAGATCGAAGACCCCAACCT
*
12038317 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGG
*
12038382 AGTAGATCGAAGA
66 AGCAGATCGAAGA
12038395 TAGCAAATCT
Statistics
Matches: 232, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
87 232 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (87 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGG
AGCAGATCGAAGACCCCAACCT
Found at i:12049931 original size:21 final size:19
Alignment explanation
Indices: 12049886--12049923 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12049876 ATCTTTATAG
12049886 TTTTTAAAGGATTAAATAA
1 TTTTTAAAGGATTAAATAA
12049905 TTTTTAAAGGATTAAATAA
1 TTTTTAAAGGATTAAATAA
12049924 AATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (19 bp):
TTTTTAAAGGATTAAATAA
Found at i:12050145 original size:68 final size:68
Alignment explanation
Indices: 12050036--12050171 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
12050026 GCACTGCCAG
* *
12050036 CTGCCAGATATGCCACTACCTGTGTGTTGAGCTTATCAGTTATATAATATTTTCCGATGCTGAAA
1 CTGCCAGATACGCCACTACCTGTGTGTTGAGCTTATAAGTTATATAATATTTTCCGATGCTGAAA
12050101 TTA
66 TTA
*
12050104 CTGCCAGATACGCCACTACCTGTGTGTTGAGCTTATAAGTTATATAATATTTTCTGATGCTGAAA
1 CTGCCAGATACGCCACTACCTGTGTGTTGAGCTTATAAGTTATATAATATTTTCCGATGCTGAAA
12050169 TTA
66 TTA
12050172 ATAGAGTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (68 bp):
CTGCCAGATACGCCACTACCTGTGTGTTGAGCTTATAAGTTATATAATATTTTCCGATGCTGAAA
TTA
Found at i:12060594 original size:7 final size:7
Alignment explanation
Indices: 12060582--12060613 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
12060572 TAACATTTTA
12060582 ATCACTC
1 ATCACTC
12060589 ATCACTC
1 ATCACTC
12060596 ATCACTC
1 ATCACTC
12060603 ATCACTC
1 ATCACTC
12060610 ATCA
1 ATCA
12060614 GCCACGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28
Consensus pattern (7 bp):
ATCACTC
Found at i:12065294 original size:19 final size:17
Alignment explanation
Indices: 12065260--12065294 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
12065250 AAAAAATAGT
12065260 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
12065277 AACAAGAATTATACAATA
1 AACAA-AATTA-ACAATA
12065295 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:12079375 original size:15 final size:15
Alignment explanation
Indices: 12079355--12079432 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
12079345 TTTATGGAAA
12079355 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
12079370 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
12079384 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
12079400 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
12079414 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
12079430 ATC
1 ATC
12079433 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:12079392 original size:30 final size:30
Alignment explanation
Indices: 12079351--12079432 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
12079341 CATATTTATG
*
12079351 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
12079381 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
12079411 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
12079433 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:12085023 original size:2 final size:2
Alignment explanation
Indices: 12085016--12085057 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
12085006 AAAGATAAAG
12085016 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12085058 GATGTTTGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12092014 original size:79 final size:79
Alignment explanation
Indices: 12091924--12092083 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
12091914 ACTAGTAGTA
12091924 AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
1 AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
12091989 GATAAGATTCTAGC
66 GATAAGATTCTAGC
12092003 AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
1 AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
12092068 GATAAGATTCTAGC
66 GATAAGATTCTAGC
12092082 AG
1 AG
12092084 AGATTATGGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (79 bp):
AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
GATAAGATTCTAGC
Found at i:12103804 original size:5 final size:5
Alignment explanation
Indices: 12103794--12103821 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12103784 CTAACTGCTA
12103794 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
12103822 GAAGTTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:12116326 original size:125 final size:125
Alignment explanation
Indices: 12116144--12116385 Score: 421
Period size: 125 Copynumber: 1.9 Consensus size: 125
12116134 GCCTCCAGTA
* *
12116144 GGATGCTATTTGAGAAGAAATTGTGAAATCGTGCCCTCGTAGACGCGATTTCGCTACAGTTGGTC
1 GGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTAGACGCGATTTCGCTACAGTTGGTC
* *
12116209 ATGTAGGAAATAATTATTTTTTGACGTTTTTAAGCAAATAGTATAAAATCGCTGATACCG
66 ATGTAGGAAATAATTATTTTTTAACGTTTCTAAGCAAATAGTATAAAATCGCTGATACCG
*
12116269 GGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTC
1 GGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTAGACGCGATTTCGCTACAGTTGGTC
* *
12116334 ATGTAGGAAATAATTATTTTTTAACGTTTCTGAGCAAATAGTATCAAATCGC
66 ATGTAGGAAATAATTATTTTTTAACGTTTCTAAGCAAATAGTATAAAATCGC
12116386 GCCCTCGTGG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 110 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (125 bp):
GGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTAGACGCGATTTCGCTACAGTTGGTC
ATGTAGGAAATAATTATTTTTTAACGTTTCTAAGCAAATAGTATAAAATCGCTGATACCG
Found at i:12119634 original size:56 final size:57
Alignment explanation
Indices: 12119544--12119653 Score: 170
Period size: 56 Copynumber: 1.9 Consensus size: 57
12119534 GTAAAACTAG
* * *
12119544 GTAAAATTATTACATCCCAAAAAATTTTGTTAATGGTTAGTAA-ACTTATCAAATTAT
1 GTAAAATTATTACAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGA-TTATCAAATTAT
12119601 GTAAAATTATTA-AGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
1 GTAAAATTATTACAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
12119654 CCGATGAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
56 36 0.73
57 13 0.27
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (57 bp):
GTAAAATTATTACAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAATTAT
Found at i:12119707 original size:23 final size:23
Alignment explanation
Indices: 12119681--12119931 Score: 322
Period size: 23 Copynumber: 10.3 Consensus size: 23
12119671 GGTTTTTACA
12119681 TTAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTT
12119704 TTAATTAAATTAGGTTAGGGTTTTT
1 TTAATTAAATTAGGTTAGGG--TTT
12119729 AATTAAATTAAATTAGGTTAGGGTTT
1 --TT-AATTAAATTAGGTTAGGGTTT
*
12119755 TAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTT
* *
12119778 TAAATTAAATTAGGTTAGGATTTTT
1 TTAATTAAATTAGGTTAGG--GTTT
12119803 AATTAAATTAAATTAGGTTAGGGTTT
1 --TT-AATTAAATTAGGTTAGGGTTT
12119829 TTAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTT
*
12119852 TAAATTAAATTAGGTTAGGGTTTTT
1 TTAATTAAATTAGGTTAGGG--TTT
12119877 AATTAAATTAAATTAGGTTAGGGTTT
1 --TT-AATTAAATTAGGTTAGGGTTT
*
12119903 TTAATTAAATTACGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTT
12119926 TTAATT
1 TTAATT
12119932 TTAATCAAAT
Statistics
Matches: 206, Mismatches: 7, Indels: 30
0.85 0.03 0.12
Matches are distributed among these distances:
23 126 0.61
24 5 0.02
25 9 0.04
26 9 0.04
27 4 0.02
28 53 0.26
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (23 bp):
TTAATTAAATTAGGTTAGGGTTT
Found at i:12119726 original size:51 final size:50
Alignment explanation
Indices: 12119666--12119931 Score: 368
Period size: 51 Copynumber: 5.3 Consensus size: 50
12119656 GATGAGTTAT
12119666 GTTAGGGTTTTTACATTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTA-ATTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
*
12119717 GTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTAAATTAAATTAG
1 GTTAGGGTTTTTAATT-AATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
*
12119768 GTTAGGG-TTTT-A--AATTAAATTAGGTTAGGATTTTTAATTAAATTAAATTAG
1 GTTAGGGTTTTTAATTAATTAAATTAGGTTAGG--GTTT--TT-AATTAAATTAG
*
12119819 GTTAGGG--TTT--TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAG
1 GTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
*
12119865 GTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAC
1 GTTAGGGTTTTTAATT-AATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
12119916 GTTAGGGTTTTTAATT
1 GTTAGGGTTTTTAATT
12119932 TTAATCAAAT
Statistics
Matches: 195, Mismatches: 7, Indels: 26
0.86 0.03 0.11
Matches are distributed among these distances:
46 35 0.18
47 1 0.01
48 6 0.03
49 4 0.02
50 13 0.07
51 136 0.70
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.47
Consensus pattern (50 bp):
GTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
Found at i:12119762 original size:74 final size:74
Alignment explanation
Indices: 12119681--12119931 Score: 457
Period size: 74 Copynumber: 3.4 Consensus size: 74
12119671 GGTTTTTACA
*
12119681 TTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
12119746 TTAGGGTTT
66 TTAGGGTTT
* *
12119755 TAAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGATTTTTAATTAAATTAAATTAGG
1 TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
12119820 TTAGGGTTT
66 TTAGGGTTT
12119829 TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
12119894 TTAGGGTTT
66 TTAGGGTTT
* *
12119903 TTAATTAAATTACGTTAGGGTTTTTAATT
1 TTAATTAAATTAGGTTAGGGTTTTAAATT
12119932 TTAATCAAAT
Statistics
Matches: 170, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 170 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (74 bp):
TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
TTAGGGTTT
Found at i:12122374 original size:30 final size:29
Alignment explanation
Indices: 12122329--12122386 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
12122319 TTGAAGGAAA
* *
12122329 TTGAGAGGATTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTGGAAGGAAATTGAGAGT
12122358 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAA-TTTGGAAGGAAATTGAGAG
12122387 AATTTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.29
Consensus pattern (29 bp):
TTGAGAGAATTTGGAAGGAAATTGAGAGT
Found at i:12122383 original size:22 final size:22
Alignment explanation
Indices: 12122358--12122420 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
12122348 ATTTGAGAGT
*
12122358 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
*
12122380 TTGAGAGAATTTTTGAAGTAAA
1 TTGAGAGAATTTTTGAAGGAAA
12122402 TTGAGAGAATTTTTGAAGG
1 TTGAGAGAATTTTTGAAGG
12122421 GTATGAGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:12123476 original size:23 final size:24
Alignment explanation
Indices: 12123441--12123486 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12123431 TTAATCTTTA
12123441 TATTTTTATTTTTAAAAATTTAAT
1 TATTTTTATTTTTAAAAATTTAAT
*
12123465 TATTTTTATTTTT-TAAATTTAA
1 TATTTTTATTTTTAAAAATTTAA
12123487 AAATTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTTTATTTTTAAAAATTTAAT
Found at i:12123504 original size:31 final size:31
Alignment explanation
Indices: 12123437--12123505 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
12123427 TAATTTAATC
** *
12123437 TTTATATTTTTATTTTTAAAAATTTAATTATT
1 TTTAT-TTTTTAAATTTAAAAATTTAATTATA
12123469 TTTATTTTTTAAATTTAAAAATTTAAGTT-TA
1 TTTATTTTTTAAATTTAAAAATTTAA-TTATA
12123500 TTTATT
1 TTTATT
12123506 AACGTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (31 bp):
TTTATTTTTTAAATTTAAAAATTTAATTATA
Found at i:12149054 original size:24 final size:24
Alignment explanation
Indices: 12149027--12149078 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12149017 TTAGTAAGTC
*
12149027 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12149051 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12149075 AAAT
1 AAAT
12149079 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12150092 original size:4 final size:4
Alignment explanation
Indices: 12150083--12150107 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12150073 TGTACGTTAA
12150083 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
12150108 CAATTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:12160401 original size:17 final size:18
Alignment explanation
Indices: 12160381--12160420 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
12160371 AATAAATTTT
12160381 AAAAAATCATT-AAAAT-
1 AAAAAATCATTAAAAATG
*
12160397 AAAAAATCCTTAAAAATG
1 AAAAAATCATTAAAAATG
12160415 AAAAAA
1 AAAAAA
12160421 AAATCCCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 6 0.29
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAAAATCATTAAAAATG
Found at i:12179583 original size:2 final size:2
Alignment explanation
Indices: 12179578--12179625 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
12179568 CAGAGATATA
12179578 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12179620 TG TG TG
1 TG TG TG
12179626 GAGGAGATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12182494 original size:13 final size:13
Alignment explanation
Indices: 12182476--12182500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12182466 GTTTATTAAG
12182476 CTAATTAACTAAA
1 CTAATTAACTAAA
12182489 CTAATTAACTAA
1 CTAATTAACTAA
12182501 TTAAACTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
CTAATTAACTAAA
Found at i:12194882 original size:27 final size:26
Alignment explanation
Indices: 12194843--12194913 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
12194833 GCAACTTGGC
* *
12194843 AAACCCAGTTCGCCACACAAACTGGG
1 AAACCCAGCTCGCCAAACAAACTGGG
*
12194869 AAACCTCAGCTCGCCAAACAATCTGGTG
1 AAACC-CAGCTCGCCAAACAAACTGG-G
* *
12194897 AACCCCTAGCTTGCCAA
1 AAACCC-AGCTCGCCAA
12194914 CACATTAGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 5 0.14
27 18 0.49
28 14 0.38
ACGTcount: A:0.32, C:0.35, G:0.17, T:0.15
Consensus pattern (26 bp):
AAACCCAGCTCGCCAAACAAACTGGG
Found at i:12197072 original size:24 final size:25
Alignment explanation
Indices: 12197002--12197073 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 25
12196992 TAAATATTTA
*
12197002 TATTATTAAAATATTCATATT-TATT
1 TATTATTAAAATATT-AAATTATATT
*
12197027 TA-T-TTATAAT-TTAAACTATATATT
1 TATTATTAAAATATTAAA-T-TATATT
12197051 TATTATTAAAATATT-AATTATAT
1 TATTATTAAAATATTAAATTATAT
12197074 AAACAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
21 2 0.05
22 3 0.08
23 7 0.18
24 12 0.32
25 4 0.11
26 8 0.21
27 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTATTAAAATATTAAATTATATT
Found at i:12197072 original size:26 final size:25
Alignment explanation
Indices: 12197002--12197074 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
12196992 TAAATATTTA
* *
12197002 TATTATTAAAATATTCATATTTATT
1 TATTATTAAAATATTAATATATATT
*
12197027 TA-T-TTATAAT-TTAAACTATATATT
1 TATTATTAAAATATT-AA-TATATATT
12197051 TATTATTAAAATATTAATTATATA
1 TATTATTAAAATATTAA-TATATA
12197075 AACAATAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 10 0.26
25 3 0.08
26 14 0.37
27 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTATTAAAATATTAATATATATT
Found at i:12199680 original size:25 final size:25
Alignment explanation
Indices: 12199618--12199682 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
12199608 TCTAAAAACT
*
12199618 AAAAATTTTAAAATTAAAAAATATAT
1 AAAAA-TTTAAAATTAAAAAATATAG
*
12199644 AAAAATTAAAAATT-AAAAATATAG
1 AAAAATTTAAAATTAAAAAATATAG
*
12199668 AAGAATTCTAAAATT
1 AAAAATT-TAAAATT
12199683 TGATGTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.44
25 14 0.41
26 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (25 bp):
AAAAATTTAAAATTAAAAAATATAG
Found at i:12199680 original size:33 final size:33
Alignment explanation
Indices: 12199606--12199680 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
12199596 CAATTGATGT
*
12199606 TATCTAAAAACTAAAAATTTTAAAATTAAAAAA
1 TATCTAAAAACTAAAAATTTAAAAATTAAAAAA
* * *
12199639 TATATAAAAATTAAAAA-TTAAAAATATAGAAGAA
1 TATCTAAAAACTAAAAATTTAAAAAT-TA-AAAAA
12199673 T-TCTAAAA
1 TATCTAAAA
12199681 TTTGATGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 7 0.20
33 23 0.66
34 5 0.14
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (33 bp):
TATCTAAAAACTAAAAATTTAAAAATTAAAAAA
Found at i:12200103 original size:16 final size:15
Alignment explanation
Indices: 12200080--12200109 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12200070 AAAAATCTTT
12200080 AAATTTTAAAAATAA
1 AAATTTTAAAAATAA
12200095 AAATGTTTAAAAATA
1 AAAT-TTTAAAAATA
12200110 TTTTAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAATTTTAAAAATAA
Found at i:12204095 original size:36 final size:36
Alignment explanation
Indices: 12204053--12204132 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
12204043 TTTTATCTTG
* *
12204053 AACCCCAAACCCATAACCTCAAACCTTTGAGCCCTA
1 AACCCCAAACCCATAACCTCAAACATTTGAACCCTA
* *** *
12204089 AGCCCCAAACTTGTAGCCTCAAACATTTGAACCCTA
1 AACCCCAAACCCATAACCTCAAACATTTGAACCCTA
12204125 AACCCCAA
1 AACCCCAA
12204133 GCTTGTAACA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.39, G:0.07, T:0.17
Consensus pattern (36 bp):
AACCCCAAACCCATAACCTCAAACATTTGAACCCTA
Found at i:12204138 original size:36 final size:36
Alignment explanation
Indices: 12204069--12204139 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
12204059 AAACCCATAA
* * *
12204069 CCTCAAACCTTTGAGCCCTAAGCCCCAAACTTGTAG
1 CCTCAAACATTTGAACCCTAAACCCCAAACTTGTAG
*
12204105 CCTCAAACATTTGAACCCTAAACCCCAAGCTTGTA
1 CCTCAAACATTTGAACCCTAAACCCCAAACTTGTA
12204140 ACATGTAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.31, C:0.35, G:0.11, T:0.23
Consensus pattern (36 bp):
CCTCAAACATTTGAACCCTAAACCCCAAACTTGTAG
Found at i:12208663 original size:15 final size:15
Alignment explanation
Indices: 12208636--12208673 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
12208626 TGCTTAATAA
12208636 TTTAATT-AATTAAT
1 TTTAATTAAATTAAT
12208650 TTTAATTAAATTAAT
1 TTTAATTAAATTAAT
*
12208665 TATAATTAA
1 TTTAATTAA
12208674 TTATGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTAAATTAAT
Found at i:12208671 original size:10 final size:10
Alignment explanation
Indices: 12208633--12208677 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
12208623 TTATGCTTAA
12208633 TAATT-TAAT
1 TAATTATAAT
*
12208642 TAATTA-ATTT
1 TAATTATA-AT
12208652 TAATTA-AAT
1 TAATTATAAT
12208661 TAATTATAAT
1 TAATTATAAT
12208671 TAATTAT
1 TAATTAT
12208678 GAATATAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 13 0.42
10 18 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TAATTATAAT
Found at i:12208673 original size:19 final size:19
Alignment explanation
Indices: 12208633--12208676 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12208623 TTATGCTTAA
* *
12208633 TAATTTAATTAATTAATTT
1 TAATTAAATTAATTAATAT
12208652 TAATTAAATTAATT-ATAAT
1 TAATTAAATTAATTAAT-AT
12208671 TAATTA
1 TAATTA
12208677 TGAATATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATTAAATTAATTAATAT
Found at i:12210945 original size:21 final size:21
Alignment explanation
Indices: 12210888--12210946 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
12210878 GGTTGAACGG
* * *
12210888 AAACTCATAAGAGCTGAATGA
1 AAACTCATATGAGTTAAATGA
12210909 AAAC-CTATTATG-GTTAAATGA
1 AAACTC-A-TATGAGTTAAATGA
12210930 AAACTCATATGAGTTAA
1 AAACTCATATGAGTTAA
12210947 CAGAAGCTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 5 0.16
21 22 0.71
22 4 0.13
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (21 bp):
AAACTCATATGAGTTAAATGA
Found at i:12211180 original size:46 final size:46
Alignment explanation
Indices: 12211110--12211205 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
12211100 TCATTTCAAT
* * * * *
12211110 TAAT-AATTTAACAATATTTTATTTTTCAATAATATGCTAAATACA
1 TAATAAATTTAACAACACTTCATTTTTCAAAAATATACTAAATACA
* *
12211155 TAATAAATTTAACAACACTTCATTTTTTAAAAATATATTAAATACA
1 TAATAAATTTAACAACACTTCATTTTTCAAAAATATACTAAATACA
12211201 TAATA
1 TAATA
12211206 TCATTCATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 4 0.09
46 39 0.91
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (46 bp):
TAATAAATTTAACAACACTTCATTTTTCAAAAATATACTAAATACA
Found at i:12212298 original size:13 final size:13
Alignment explanation
Indices: 12212280--12212319 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
12212270 CTAAACCGCA
12212280 TATATCATACATT
1 TATATCATACATT
* *
12212293 TATATCA-ACCTA
1 TATATCATACATT
12212305 TATATCATACATT
1 TATATCATACATT
12212318 TA
1 TA
12212320 GCCACACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATCATACATT
Found at i:12212310 original size:12 final size:13
Alignment explanation
Indices: 12212279--12212316 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
12212269 TCTAAACCGC
12212279 ATATATCATACAT
1 ATATATCATACAT
* *
12212292 TTATATCA-ACCT
1 ATATATCATACAT
12212304 ATATATCATACAT
1 ATATATCATACAT
12212317 TTAGCCACAC
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATATCATACAT
Found at i:12213597 original size:5 final size:5
Alignment explanation
Indices: 12213589--12213671 Score: 57
Period size: 5 Copynumber: 16.6 Consensus size: 5
12213579 TAATTTAAAA
* *
12213589 TATAT TATAT TATAT TATAT T-TACT TA-AT TA-AT AAT-T GTGTTAT
1 TATAT TATAT TATAT TATAT TATA-T TATAT TATAT TATAT -T-ATAT
* * *
12213633 TATAT TATAT GATTAT AATAT TATAT AATAT TATAT TAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TAT
12213672 TATATATATA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
4 9 0.15
5 46 0.74
6 6 0.10
7 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (5 bp):
TATAT
Done.